AU2016206219B2 - Bifidobacterium longum - Google Patents

Abstract

The multiple embodiments described herein comprise the genome of a probiotic Bifidobacterium longum bifidobacteria strain and genes encoded by the genome. Various 5 novel Bifidobacterium longum are described. Fig 1

Description

-1- 2016206219 18Jul2016 “Bifidobacterium longum”

The present application is a divisional application from Australian patent application number 2015201431, filed on 18 March 2015, which is itself a divisional application from Australian patent application number 2009315298, filed on 11 November 2009, which claims 5 priority from United States provisional applications 61/113,513, filed 11 November 2008, and 61/149,980, filed 4 Febnrary 2009؛ which are hereby incorporated by reference in their entirety.

FffiLD OF THE INVENTION

The invention relates to the genome of a probiotic bifidobacteria strain and genes 10 encoded by the genome. Bifidobacteria are one of several predominant culturable bacteria present in human colonic microflora.

BACKGROUND OF THE INVENTION

Bifidobacteria are considered to be probiotics as they are living organisms which exert 15 healthy effects beyond basic nutrition when ingested in sufficien ingested bifidobacteria must reach their site of action in order to exert a probiotic effect. A minimum level of approximately 106-107 viable bifidobacteria per gram intestinal contents has been suggested (Bouhnik, Y., Lait 1993). There are reports in the literature which show that in vivo studies completed in adults and in infants indicate that some strains of bifidobacteria are 20 capable of surviving passage through the gastrointestinal tract. Significant differences have been observed between the abilities of different bifidobacteria strains to tolerate acid and bile salts, indicating that survival is an important criterion for the selection of potential probiotic strains.

Ingestion of bifidobacteria can improve gastrointestinal transit and may prevent or 25 assist in the treatment of illnesses which may be caused by deficient or compromised microflora such as gastrointestinal tract (GIT) infections, constipation, initable bowel syndrome (IBS), inflammatory bowel disease (IBD) - Crohn's disease and ulcerative colitis, food allergies, antibiotic-induced diarrhoea, cardiovascular disease, and certain cancers (e.g. colorectal cancer). 30 Because of their perceived health-pronroting activities, bifid years enjoyed an increased amount of scientific scrutiny, which included the fiill genomic sequencing of a number of strains (reviewed by Liu et al., 2005). These genomic sequences 2016206219 18Jul2016 -la- will provide the genetic platforms that allow the study of the molecular mechanisms by which these micro organisms interact with their human host and elicit their probiotic function.

The discussion of documents, acts, materials, devices, articles and the like is included in this specification solely for the purpose of providing a context for the present invention. It is not 5 suggested or represented that any or all of these matters formed part of the prior art base or were common general knowledge in the field relevant to the present invention as it existed before the priority date of each claim of this application.

Where the terms “comprise”, “comprises”, “comprised” or “comprising” are used in this specification (including the claims) they are to be interpreted as specifying the presence of the stated 10 features, integers, steps or components, but not precluding the presence of one or more other features, integers, steps or components, or group thereof.

SUMMARY OF THE INVENTION

The invention provides an isolated and purified Bifidobacterium longum strain, 15 excluding Bifidobacterium longum strain 35624 (NCIMB 41003), wherein the strain: a) expresses an exopolysaccharide; and .2. b) comprises at least two nucleic acid sequences selected ftom the group comprising 85% SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least and ؛sequence homology thereto c) induces an [ILIO] : [IL12] ratio of at least 10 in a peripheral blood mononuclear cell CFU/ml bacteria. ؟10 5 (PMBC) co-incubation assay at a concentration of 1 X A Bifidobacterium longum strain according to the invention may include any 2 or more ΒΙ00778,ΒΙ00795 or any three or more such as ؛ΒΙ00778, ΒΙ00794 ؛such as ΒΙ00778, ΒΙ00793 ΒΙ00796,ΒΙ00797,ΒΙ00798 or any four ؛ΒΙ00794,ΒΙ00795,ΒΙ00796 ؛ΒΙ00793,ΒΙ00794,ΒΙ00798 ؛ΒΙ00778,ΒΙ00779,ΒΙ00785,ΒΙ00786 ؛0 or more such as ΒΙ00778,ΒΙ00779,ΒΙ00780,ΒΙ00794 ΒΙ00790,ΒΙ00791,ΒΙ00794,ΒΙ00798 or any five or more such as ؛ΒΙ00780,ΒΙ00782,ΒΙ00785,ΒΙ00786,ΒΙ00790 ؛ΒΙ00783,ΒΙ00786,ΒΙ00790,ΒΙ00794,ΒΙ00798 ΒΙ00778,ΒΙ00779,ΒΙ00787,ΒΙ00789,ΒΙ00798 or any six or more such as ؛ΒΙ00778,ΒΙ00779,ΒΙ00780,ΒΙ00781,ΒΙ00782,ΒΙ00794 ؛5 ΒΙ00782,ΒΙ00784,ΒΙ00785,ΒΙ00788,ΒΙ00792,ΒΙ00797 ΒΙ00781,ΒΙ00782,ΒΙ00783,ΒΙ00791,ΒΙ00796,ΒΙ00797 or any seven or more such as ؛ΒΙ00779,ΒΙ00783,ΒΙ00784,ΒΙ00787,ΒΙ00791,ΒΙ00792,ΒΙ00797 ؛ΒΙ00780,ΒΙ00789,ΒΙ00790,ΒΙ00793,ΒΙ00794,ΒΙ00797,ΒΙ00798 ΒΙ00783,ΒΙ00784,ΒΙ00786,ΒΙ00788,ΒΙ00789,ΒΙ00793,ΒΙ00796 or any eight or more such as ؛0 ΒΙ00779,ΒΙ00782,ΒΙ00783,ΒΙ00784,ΒΙ00785,ΒΙ00794,ΒΙ00797,ΒΙ00798 ؛ΒΙ00780,ΒΙ00787,ΒΙ00788,ΒΙ00789,ΒΙ00790,ΒΙ00793,ΒΙ00794,ΒΙ00795 ΒΙ00783,ΒΙ00784,ΒΙ00785,ΒΙ00786,ΒΙ00787,ΒΙ00793,ΒΙ00795,ΒΙ00798 or any nine or more ؛such as ΒΙ00778,ΒΙ00780,ΒΙ00782,ΒΙ00784,ΒΙ00785,ΒΙ00787,ΒΙ00793,ΒΙ00795,ΒΙ00796 ؛ΒΙ00779,ΒΙ00781,ΒΙ00782,ΒΙ00784,ΒΙ00786,ΒΙ00787,ΒΙ00793,ΒΙ00795,ΒΙ00797 25 ΒΙ00782,ΒΙ00783,ΒΙ00785,ΒΙ00786,ΒΙ00787,ΒΙ00789,ΒΙ00792,ΒΙ00796,ΒΙ00797 or any ten or more such as ΒΙ00778,ΒΙ00781,ΒΙ00784,ΒΙ00785,ΒΜ ΒΙ00779,ΒΙ00781,ΒΙ00784,ΒΙ00786,ΒΙ00787,ΒΙ00788,ΒΙ0 ΒΙ00782,ΒΙ00784,ΒΙ00785,ΒΙ00786,ΒΙ00790,ΒΙ00792,ΒΙ00794,ΒΙ00796,ΒΙ00797,ΒΙ00798 or 30 any eleven or more such as ΒΙ00778,ΒΙ00781,ΒΙ00785,ΒΙ00787,ΒΙ00788,ΒΙ00790,Β ؛00798 2016206219 21Aug2017 2016206219 21Aug2017 -2a- ΒΙ00779,ΒΙ00782,ΒΙ00785,ΒΙ00786,ΒΙ00789,ΒΙ007 ؛00797 BG0781,BG0783,BG0785,BG0787,BG0788,BG0789,BG0790,BI00793,BI00794ei00795,BI 00796 or any twelve or more such as 2016206219 18Jul2016 د١ NJ ٠ tn ٠ ١ل١ ج tn ٠ ٠ ٠ ج ٥٥ ٠ m ٥٥ هح ٠ ٠ ٠ m ٠ دت١ ٠ دت١ ته ٠ sj s ل١ ٠ ل١١ S ل١٠١ ج ل ج ل- ج ج ج ج ل١ ل١١ ج لا ل١٠٠٠ ج ل١٩ ج ل١١ ج ٠ ٠ ٠ ١٥ ٠ § لا § هث ٠ ٠ ل٠١ ذ4 دق لا لا و ٠ ج ٠ لا ج“ ٥٠ ج ٠ ٥٥ ٠٠ “٥٥ لا “٥٥ ٠ ٥٥ ٠٠ “٥٥ لا “٥٥ ١٠ “٥٥ لا “٥٥ لا “٥٥ ٠ “٥٥ لا ٥٠ ة“ د ر “٥٥ ٠١ ٥٥ لا “٥٥ § § ٥٥ § ٥٥ § “٥٥ § ٥٥ ح ج ج ٠ ١٥٥ ح ٠ “٥٥ ج ج ج ٠ ج ٠ ٠ ٠ ٠ دت١ ج ٠ ح ٠ “٥٥ ٠ “٥٥ ح ج ح ج ج ج ٠ ٠ ٠ Ο ج ج لا ج ج ج ٠ ٠ ١٥ ٠ ١٥ ٠ ٠ ١٥ ١٥ ٠ ٠ ١٠ § ٠ ٠ ١٥ § ١٥ ٠ ٠ ل١١ لج ،ب ١٥ دب ح٠- ٠١ لا لا ٥٠ 03 ٠ “٥٥ لا “٥٥ ٠٠ “٥٥ لا “٠٥ لا “٥٥ K) “٥٥ ٠ “٥٥ لا “٥٥ ٠ “٥٥ ٠ “٥٥ لا “٥٠ ٠٠ “٥٥ لا “٠٥ لا ٠ لا ٠٠ ١٠ ج ٠ ج ج ٠ “٥٥ ج ٠ ثت١ ج ٠ ده١ ج ٠ ٥٥ ج ١٥ ٠ ٠ تت٢ ٠ ٥٥ § ٠ § ج ٠ “٥٥ ٠ “٥٥ ٠ “٠٥ g I ة “٥٥ “٥٥ ج ح ج ج S ج ج ج ٠ ج ٠ ح S ج ح ج ح ١٥ ٠ ٠ ١٥ ٠ ١٥ ٠ ١٥ ٠ ٠ ١٥ ١٥ ٠ ٠ ٠ ٠ ٠ ٠ دب لج دب ٠١ ٠ ٠١ ج و ٠ ٠٠ ٥٥ ٠ “٥٥ “٥٥ ٠٠ “٥٥ ٠ “٥٥ “٥٠ C» “٥٥ “٠٥ ٥٠ “٥٥ ٠٠ ٥٥ ٠ ο K) لا I ة ٠ Κ) ٥٠ ج ٠ ٥٠ ج ٠ ٠ ج ٠ “٠٥ ٠ ٠ ج ٠ “٠٥ ج ٠ “٥٥ ج ٠ ٥٥ ٠ “٥٥ ٠ “٥٥ § ج g “٥٠ “٥٥ “٥٥ “٥٥ “٥٥ “٥٥ ج ج ج ٠ ج ٠ ح sj ٠ ج ل٠١٠٠٠ ج لا ج ج ح ج ج ج ١٥ ٠ ١٥ ٠ ١٠ ٠ ١٥ ٠ ١٥ ٠ ٠ ١٥ ١٥ ٠ ١٥ ١١٥ § ٠ ٠ ٠ ٠ ٠ ٠ ء لج ٠١ لج لا د١ء بر ل١٠٠ ٠١ ٥٠ κ> “٥٠ ٠ء “٥٥ “٠٥ “٥٥ ٠٠ “٥٠ حب “٠٥ “٠٥ ٥٠ ٠ K) K) ج ج ٠٠ 3 ١٥ s ج ج “٥٥ ج “٥٥ ج “٥٥ ح ٠ “٥٥ m ج “٥٥ § “٥٥ “٥٥ دت١ ٥٥ “٥٥ ٥٥ “٥٥ ثت١ “٥٥ “٥٥ ج ج ٠ ج ى ٠ ج ج 3 ج ٠ ج ج ٠ ١٥ ٠ ١٥ ٠ ٠ ٠ ٠ ٠ ٠ ٠ ٠ C ٠ § § ٥٠ ٥٥ “٥٥ “٥٥ “٥٥ ٠ ذح 3 ٠ ج Lj' ٥٠ Κ) ء ء K) tg ة حب حب لج ٠ ج حء٠ s ٠ ٥٠ ج ج ٥٠ ج ٥٥ ج ٠ 3 “٥٥ “٥٥ ٥٥ “٥٥ ج “٥٥ ٥٥ “٥٠ “٥٥ “٥٥ “٥٥ “٠٥ ت S S ج ح ٠ ج ج ٠ ج ج ج ج V. دراً ء ٠ ٠ § § § ٠ ٠١ 3 “٥٥ ٥٥ ٠ X ٠ لا لا لا حب حب I حي حب لج ٠١ لا ٠ ق ج ٠ “٥٥ ج ٥٠ “٥٥ “٠٥ تت١ 3 “٥٥ “٥٥ “٥٥ “٥٠ “٠٥ “٥٥ “٥٥ “٥٥ “٥٠ “٥٥ “٥٥ “٥٥ ئ ب ٠ ٠ ٠ C ٠ ج ٠ ج ح ج ج ح ح ν٥ ٠ ٠ ٠ ٠ § ٠ § ٠ § ٠ <? ء ح Ο لا لا ٠١ ت3ا “٥٥ a 3 ٥٥ “٥٥ “m ة ٥٠ ٥٥ حي ٠ Λ؟ “٥٥ ٠١ ٥٥ “٥٥ ٠٠ ٠ ١٥ ٥٥ 1 “٥٥ ξ ٠ “٥٥ ٠ ٠ ٠ ٠ C ٠ ٠ ٠ ج ج ج ج ج ج 3 ٠ ο ٠ ٠ ٠ ٠ ٠ ٠ ٠ § ٠ ٠ ٠ 3- ج لا لا لا ل١ ١٥ ٠ ٠ 5؛ لا “٥٠ ٠٥ ح ح “٥٥ “٥٥ ٠ “٥٥ “٥٥ “٥٥ “٥٥ “٥٥ “٥٠ “٥٥ “٥٥ “٠٥ “٥٥ “٥٥ “٥٥ ο Η ٠ ٠ ٠ ج ج S S ج ج تت٦ ٠ ٠ ٠ ٠ ٠ ٠ ٠ § § ٠ Η 1 لا I ١٥ ١٥ لا ١٥ 3- ١٥ ٠١٥ ١٥ ٠ ٠ ٠١ ٠ ١٥ ١٥ 5؛ ؛5؛ لا لا ج ٠ “٥٥ ٠ ٠ ٥٥ ٠؟ ٥٥ ٠ تت١ ج “٥٥ ج “٥٥ “٥٥ ٥٥ “٥٥ ج٠ ٠ ٠ ٠ ٠ ٠ ج ج ٠ ج ج ٠ ٠ ٠ ٠ ٠ § ٠ ٠ لا لا ١٥ ١٥ ١٥ ١٥ لا ٠ ١٥ ٠ ٠ ٠ دا ة لا “٥٥ ٥٥ ٥٥ ٥؟ ٠؟ “٥٥ “٥٥ “٥٥ “٥٥ “٥٥ ٠٥ ٥٥ ٥٥ ٥٥ “٥٥ “٥٠ “٥٥ WO 2010/055499 PCT/IE2009/000079 -4- 2016206219 18U12016 ΒΙ00779,ΒΙ00780,ΒΙ00782,ΒΙ00783,ΒΙ00784,ΒΙ00785,ΒΙ00787,ΒΙ00788,ΒΙ00789,ΒΙ00790,ΒΙ 00791,ΒΙ00792,ΒΙ00793,ΒΙ00794,ΒΙ00795,ΒΙ00797,ΒΙ00798 or any eighteen or more such as ΒΙ00778,ΒΙ00779,ΒΙ00780,ΒΙ00781,ΒΙ00782,ΒΙ00783,ΒΙ00784,ΒΙ00785,ΒΙ00787,ΒΙ00788,ΒΙ 00789,ΒΙ00791,ΒΙ00792,ΒΙ00793,ΒΙ00794,ΒΙ00795,ΒΙ00796,ΒΙ00798; 5 ΒΙ00778,ΒΙ00779,ΒΙ00781 ,ΒΙ00782,ΒΙ00783,ΒΙ00784,ΒΙ00785,ΒΙ00786,ΒΙ00787,ΒΙ00788,ΒΙ 00789, ΒΙ00790,ΒΙ00792,ΒΙ00794,ΒΙ00795,ΒΙ00796,ΒΙ00797,ΒΙ00798؛ ΒΙ00779,ΒΙ00781,ΒΙ00782,ΒΙ00783,ΒΙ00784,ΒΙ00785,ΒΙ00786,ΒΙ00787,ΒΙ00788,ΒΙ00789,ΒΙ 00790, ΒΙ00791,ΒΙ00792,ΒΙ00793,ΒΙ00794,ΒΙ00795,ΒΙ00796,ΒΙ00797θΓ any nineteen or more such as 10 ΒΙ00778,ΒΙ00779,ΒΙ00780,ΒΙ00781 ,ΒΙ00782,ΒΙ00783,ΒΙ00784,ΒΙ00785,ΒΙ00786,ΒΙ00787,ΒΙ 00788, ΒΙ00789,ΒΙ00790,ΒΙ00791,ΒΙ00792,ΒΙ00794,ΒΙ00795,ΒΙ00796,ΒΙ00797; ΒΙ00778,ΒΙ00779,ΒΙ00780,ΒΙ00782,ΒΙ00783,ΒΙ00784,ΒΙ00785,ΒΙ00786,ΒΙ00787,ΒΙ00788,ΒΙ 00789, ΒΙ00790,ΒΙ00791,ΒΙ00792,ΒΙ00793,ΒΙ00794,ΒΙ00795,ΒΙ00796,ΒΙ00797; ΒΙ00779,ΒΙ00780,ΒΙ00781,ΒΙ00782,ΒΙ00784,ΒΙ00785,ΒΙ00786,ΒΙ00787,ΒΙ0 15 00790,ΒΙ00791,ΒΙ00792,ΒΙ00793,ΒΙ00794,ΒΙ00795,ΒΙ00796,ΒΙ00797,ΒΙ00798 or any twenty or more such as ΒΙ00778,ΒΙ00779,ΒΙ00780,ΒΙ00781,ΒΙ00782,ΒΙ00783,ΒΙ00784,ΒΙ00785,ΒΙ00786,ΒΙ00787,ΒΙ 00788, ΒΙ00789,ΒΙ00790,ΒΙ00791,ΒΙ00792,ΒΙ00793,ΒΙ00794,ΒΙ00795,ΒΙ00797,ΒΙ00798؛ ΒΙ00778,ΒΙ00779,ΒΙ00780,ΒΙ00781,ΒΙ00782,ΒΙ00783,ΒΙ00784,ΒΙ00785,ΒΙ00786,ΒΙ00787,ΒΙ 20 00789,ΒΙ00790,ΒΙ00791,ΒΙ00792,ΒΙ00793,ΒΙ00794,ΒΙ00795,ΒΙ00796,ΒΙ00797,ΒΙ00798؛ ΒΙ00778,ΒΙ00779,ΒΙ00780,ΒΙ00782,ΒΙ00783,ΒΙ00784,ΒΙ00785,ΒΙ00786,ΒΙ00787,ΒΙ00788 00789, ΒΙ00790,ΒΙ00791,ΒΙ00792,ΒΙ00793,ΒΙ00794,ΒΙ00795,ΒΙ0079 or ai twentyone of the nucleic acid sequences selected ftom the group comprising SEQ ID No. 93 to SEQ ID No. 113 or sequences homologous thereto. 25

The strain may comprise at least three nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. II3or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least four nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid 30 sequences with at least 85% sequence homology thereto. The strain may comprise at least five nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto.The strain may comprise at least six nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. The strain wo 2010/055499 PCT/IE2009/000079 -5- 2016206219 18U12016 may comprise at least seven nucleic acid sequences selected ftom the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least eight nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% 5 sequence homology thereto. The strain may comprise at least nine nucleic acid se selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least ten nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence-homology thereto. The strain may 10 comprise at least twelve nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least three nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least thirteen nucleic acid sequences 15 selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least fourteen nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least fifteen nucleic acid sequences selected from the group comprising SEQ ID NO. 20 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least sixteen nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least seventeen nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid 25 sequences with at least 85% sequence homology thereto. The strain may comprise at least eighteen nucleic acid sequences selected ftom the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least nineteen nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology 30 thereto. The strain may comprise at least twenty nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise all twenty one nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto. wo 2010/055499 PCT/IE2009/000079 -6- 2016206219 18Jul2016

The strain may not comprise the nucleic acid sequence of SEQ ID No. 112.

The strain may comprise at least one nucleic acid sequence selected from the group 5 comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto.

The strain may comprise at least two nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% 10 sequence homology thereto. The steain may comprise at least three nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least four nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may 15 comprise at least five nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least six nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least seven nucleic acid sequences selected from 20 the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least eight nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least nine nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 25 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least ten nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85٥/٥ sequence homology thereto.

The strain may comprise at least eleven nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% 30 sequence homology thereto. The strain may comprise at least twelve nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least thirteen nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain 2016206219 21Aug2017 5 0 0 25 30 .7. may comprise at least fourteen nucleic acid sequences selected ftom the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least fifteen nucleic acid sequences selected ftom the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise at least sixteen nucleic acid sequence selected ftom the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may conrprise at least seventeen nucleic acid sequences selected ftom the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may conrprise at least eighteen nucleic acid sequence selected ftom the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise all nineteen nucleic acid sequences selected ftom the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto

The strain may comprise a single nucleic acid sequence selected ftom the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least sequence homology thereto. The strain may comprise a nucleic acid sequence of SEQ ID No. 132 or a nucleic acid sequence with at least sequence homology thereto.

The strain may comprise two nucleic acid sequences selected ftom the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto. The strain may comprise the nucleic acid sequences of SEQ ID No. 131 and SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto.

The invention also provides an isolated and purified Bifidobacterium longum strain wherein the strain: a) expresses an exopolysaccharide؛ and b) comprises at least two nucleic acid sequences selected from the group compr SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto؛ and c) comprises a nucleic acid sequence of SEQ ID No. 132 or a nucleic acid sequence with at least 85% sequence homology thereto؛ or ٠ d) comprises a nucleic acid sequence of SEQ ID No. 131 ora nucleic acid sequence with at least 85% sequence homology thereto؛ and e) induces an [ILIO] : [IL12] ratio of at least 10 in a peripheral blood mononuclear cell (PMBC) co-incubation assay at a concentration of lx 10؟ CFU/ml bacteria. 5 In one embodiment, 1 X 10؟ CFU/ml of the strain may induce an [ILIO] : [IL 12] ratio of at least 10 in a peripheral blood mononuclear cell (PMBC) co-incubation assay. Fhe strain may be in the form of a bacterial broth. Fhe strain may be in the form of a freeze-dried powder. 2016206219 21 Aug 0 0

Fhe invention further provides an isolated and purified Bifidobacterium longum strain wherein the strain: a) expresses an exopolysaccharide؛ and b) comprises at least two nucleic acid sequences selected fiom the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto؛ and c) comprises a nucleic acid sequence of SEQ ID No. 132 or a nucleic acid sequence with at least 85% sequence homology thereto؛ and/or a nucleic acid sequence of SEQ ID No. 131 ora nucleic acid sequence with at least 85% sequence homology thereto؛ and d) induces an [IFIO] : [11.12] ratio of at least 10 in a peripheral blood mononuclear cell (PMBC) co-incubation assay at a concentration of 1 X 10؟ CFU/ml bacteria.

Fhe invention also provides an isolated strain of Bifidobacterium longum BL1207 (PFA- 9608). 25 Fhe invention further provides an isolated strain of Bifidobacterium longum ΑΗ121Α (NCIMB 41675).

Fhe invention further still provides an isolated strain of Bifidobacterium longum ΑΗ1714 (NCIMB 41676). 30 Fhe isolated strain may be in the form of viable cells. Fhe isolated strain may be in the form of ηοη-viable cells. 2016206219 21Aug2017 -8a-

The invention also provides a formulation comprising an isolated strain of Bifidobacterium longum as described herein. The formulation may comprise an ingestable carrier. The ingestable carrier may be a pharmaceutically acceptable carrier such as a capsule, tablet or powder. The ingestable carrier may be a food product such as acidified milk, yoghurt. wo 2010/055499 PCT/.E2009/000079 -9- 2016206219 18Jul2016 ftozen yoghurt, milk powder, milk concentrate, cheese spreads, dressings or beverages. The formulation may comprise a strain that is present at more than 10٥ cfU per gram ofingestable carrier. 5 The invention further provides a composition comprising an isolated strain of Bifidobacterium longum as described herein and a phamaceutically acceptable carrier.

The invention also provides for the use of a Bifidobacterium longum strain as described herein as a probiotic strain. 10

The invention also provides a method for identifying an exopolysaccharide expressing Bifidobacterium longum strain comprising the steps of: a) obtaining a sample comprising bacteria; b) extracting nucleic acid ftom the sample; 15 c) amplifying the extracted nucleic acid in the presence of at least two primers derived ftom a nucleic acid sequence selected ftom the group comprising: SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 10 to SEQ ID No. 12, SEQ ID No. 93 to SEQ ID No. 132 ora nucleic acid sequence with at least 85% sequence homology thereto; 20 d) identifying a bacterial strain that expresses an exopolysaccharide.

The primer may comprise at least 10 consecutive bases from a nucleic acid sequence selected from the group comprising: SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 10 to SEQ ID No. 12 and SEQ ID No. 93 to SEQ ID No. 132. 25 The primer may comprise a nucleic acid sequence selected ftom the group comprisi SEQ ID No. 10 to SEQ ID No. 12, SEQ ID No. 13 to SEQ ID No. 92 or a nucleic acid sequence with at least 85% sequence homology thereto.

The step of identifying a bacterial strain that expresses an exopolysaccharide may comprise growing the bacterial strain on a Congo red agar plate. 30 The sample is a mammalian sample. The sample may be a human derived sample. The sample may be a fecal sample. wo 2010/055499 PCT/IE2009/000079 -10- 2016206219 18Jul2016

The invention also provides for a Bifidobacterium longum strain identified by described herein. The Bifidobacterium longum strain may be in the form of viable cells. The Bifidobacterium longum strain may be in the form ofnon-viable cells.

The invention flirther provides for a formulation comprising a Bifidobacterium longum strain as 5 described herein. The formulation may comprise an ingestable carrier. The ingestable careier may be a phamaceutically acceptable carrier such as a capsule, tablet or powder. The ingestable carrier may be a food product such as acidified milk, yoghurt, ftozen yoghurt, milk powder, milk concentrate, cheese spreads, dressings or beverages. The strain may be present at more than 10٥ cfu per gram of ingestable carrier in the formulation. 10 The invention also provides a composition comprising a Bifidobacterium longum strain as described herein and a pharmaceutically acceptable carrier.

In one embodiment of the invention there is a method for identifying exopolysaccharide secreting bacterial strains comprising the steps of: 15 - obtaining a sample comprising bacteria; - extracting DNA fiom the sample; - amplifying the extracted DNA in the presence of at least one DNA primer derived from the DNA sequence ofSEQ ID No. 2 and/or SEQ ID No. 3؛ and identifying a bacterial strain that expresses an exopolysaccharide.

The extracted DNA may be amplified by real time PCR. The DNA may be amplified in the presence of at least one primer of the nucleic acid sequence ofSEQ ID No. 10, SEQ ID No. 11 or SEQ ID No. 12. 25 The sample may be a human derived sample such as a fecal sample.

In another embodiment, the invention also provides for a bacterial strain identified by the method described herein. 30 In another embodiment, the invention forther provides for the use of a bacterial strain identified by the method described herein as a probiotic bacteria.

In yet another embodiment, the invention also provides a fomiulation comprising a bacterial strain identified by the method described herein. -11In another embodiment, the invention further provides a composition comprising a bacteria] strain identified by the method described herein and a pharmaceutically acceptable carrier. 2016206219 18Jul2016 5 In another embodiment, the invention also provides an isola strain BL1207 (ΡΤΑ-9608).

In yet another embodiment, the invention further provides a formulation comprising an isolated bifidobacteria] longum strain BL1207 (ΡΤΑ-9608). 10

In anotJrer embodiment, the invention also provides a composition comprising an isolated bifidobacteria] longum strain BL1207 (ΡΤΑ-9608) and a pharmaceutically acceptable carrier. 15 In another enrbodiment, the invention further provides a DNA a least one polynucleotide derived from the nucleic acid sequence of SEQ ID NO. 1, SEQ ID No. 2, or SEQ ID No. 3.

In one embodiment, the invention also provides a computer readable medium 20 comprising a nucleic acid sequence of SEQ ID NO. 1, SEQ ID No. 2, or SEQ ID No. 3 or parts tJrereof. A Bifidobacterium longum strain in accordance with an embodiment of the invention may express or produce EPS at a yield of between about 10mg/L to about 1000mg/L of 25 bacteria] culture.

There are a number of strains of Bifidobacteria which are already deposited under the Budapest Treaty. These include the strain deposited at the NCIMB under the number 41003, the genome of which is presented herein. This strain is specifically disclaimed for the claims 30 to the strains per se. In so far as the following strains may fall within the scope of the patent claims at the relevant date(s), the following claims are also disclaimed: ATCC BAA-999, CNCM 1-1227, CNCM 1-1228, CNCM 1-2168, CNCM 1-2170, CNCM I-2618, CNCM 1-3446, CNCM 1-3853, CNCM 1-3854, CNCM 1-3855, NCIMB 41290, NttMR 41291 , NCIB 41382, NttMR 41387, NTCC 2705. 35 -12- 2016206219 18Jul2016 WO 2010/055499 PCT/IE2009/000079

Brief Description of the drawings

The invention will be more clearly understood ftom the following description thereof given by way of example only with reference to the accompanying drawings in which;-5

Fig. 1 is a Genome atlas of Bifidobacterium longum biotype infantis ucc 35624. The numbers on the genome (1, 1000001, 200001) refer to base pair position. 1 refers to the adenine nucleotide of the ATG start codon of the gene encoding the predicted replication protein. The outer circle (two strands, black and white) refers to the gene density within the chromosome. 10 The second circle (middle circle - black) refers to the GC content and the innermost circle refers to the GC skew;

Fig. 2 is a bar chart showing the induction profile of IL-lbeta in PBMCs by Bifidobacterium longum infantis strain UCC35624 (Β624), Bifidobacterium longum strain 1207 15 (BL1207), Bifidobacterium longum strain 15707 (BL15707), Bifidobacterium lactis (BL-07) and Bifidobacterium breve strain 8807 [UCC2003] (breve);

Fig. 3 is a bar chart showing the induction profile of IL-12p70 in PBMCs by Bifidobacterium longum infantis strain UCC35624 (Β624), Bifidobacterium longum strain 1207 20 (BL1207), Bifidobacterium longum strain 15707 (BL15707), Bifidobacterium lactis (BL-07) and Bifidobacterium breve strain 8807 [UCC2003] (breve);

Fig. 4 is a bar chart showing the induction profile of IL-10 in PBMCs by Bifidobacterium longum infantis strain UCC35624 (Β624), Bifidobacterium longum strain 1207 (BL1207), 25 Bifidobacterium longum strain 15707 (BL15707), Bifidobacterium lactis (BL-07) and Bifidobacterium breve strain 8807 [UCC2003] (breve);

Fig. 5 is a bar chart showing the induction profile of TNF-alpha in PBMCs by Bifidobacterium longum infantis strain UCC35624 (Β624), Bifidobacterium longum strain 1207 30 (BL1207), Bifidobacterium longum strain 15707 (BL15707), Bifidobacterium lactis (BL-07) and Bifidobacterium breve strain 8807 [UCC2003] (breve).

Fig. 6 is a photograph of B. longum 35624 grown on a Congo Red Agar plate;

Fig. 7 is a photograph of 5. longum ΑΗ121Α grown on a Congo Red Agar plate; -13- 2016206219 18Jul2016

Fig. 8 is a photograph of ع longum ΑΗ1714 grown on a Congo Red Agar plate؛ 5 WO 2010/055499 PCT/JE2009/000079

Fig. 9 is a pliotograph of 5. longum ΑΗ0119 grown on a Congo Red Agar plate؛ Fig. 10 is a photograph of 5. breve UCC2003 grown on a Congo Red Agar plate;

Fig. 11 is a photograph of 5. Rhamnosus ΑΗ308 grown on a Congo Red Agar plate؛ 10 Fig. 12 is a photograph of 5. salivarius UCCl grown on a Congo Red Agar plate؛ and

Fig. 13 is a bar chart illustrating the IL-10:IL-12p70 ratio for PBMCs stimulated with Bifidobacterium longum infantis strain 35624 (Bifidobacterium 35624), Bifidobacterium longum strain 1714 (Bifidobacterium 1714), Bifidobacterium longum strain 1207 (Bifidobacterium 15 1207), Bifidobacterium longum strain 12ΙΑ (Bifidobacterium 121Α), Bifidobacterium longum strain 0119 (Bifidobacterium 0119), Bifidobacterium longum strain 15707 (Bifidobacterium 15707), Bifidobacterium breve strain 8807 (Bifidobacterium UCC2003), Lactobacillus rhamnosus and Lactobacillus salivarius strain UCCl.

20 DETAILED DESCRIPTION OF THE INVENTION

Dislosed herein is an isolated polynucleotide of SEQ ID No. 1. The polynucleotide of SEQ ID No. 1 encodes a strain ofBifidobacterium. The Bifidobacterium encoded by the isolated polynucleotide sequence has a number of unique genes. The unique genes encoded by the polynucleotide have a unique order in the sequence of SEQ ID No. 1. As used herein, the term 25 “unique genes", mean genes that are not found in the currently available sequences of

Bifodobacterium. As used herein, the term “unique order", means that the position / sequence of the genes in the polynucleotide is not found in the currently available sequences of Bifodobacterium. The unique genes present in the isolated polynucleotide may be interspersed with nucleic acid residues that code for other (known) genes or stretches of non-coding sequence 30 but the overall order/sequence of the unique genes in the isolated polynucleotide is in itself unique compared to the order of genes found in the currently available sequences of Bifodobacterium.

The polynucleotide was isolated ftom a strain of the bacterial species Bifidobacterium longum biotype infontis with the strain designation ucc 35624. A deposit of Bifidobacterium wo 2010/055499 PCT/IE2009/000079 -14- 2016206219 18Jul2016 longum biotype infantis strain ucc 35624 was made at the National Collections of Industrial and Marine Bacteria Limited (NCIMB) Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen, ΑΒ21 9ΥΑ, Scotland, UK on January 13, 1999 and accorded the accession number NCIMB 41003. 5 A deposit of Bifidobacteria infantis strain B1.1207 was made at the American Type

Culture Collection (ATTC) 10801 University Boulevard, Manassas, Virginia 20110-2209, USA on November 14, 2008 and accorded the accession number ΡΤΑ-9608. A deposit of Bifidobacterium longum strain ΑΗ121Α was made at the National Collections of Industrial and Marine Bacteria Limited (NCIMB) Ferguson Building, Craibstone 10 Estate, Bucksburn, Aberdeen, ΑΒ21 9ΥΑ, Scotland, UK on November 5, 2009 and accorded the accession number NCIMB 41675. A deposit of Bifidobacterium longum strain ΑΗ1714 was made at the National Collections of Industrial and Marine Bacteria Limited (NCIMB) Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen, ΑΒ21 9ΥΑ, Scotland, UK on November 5, 2009 and accorded the 15 accession number NCIMB 41676.

Given the size of the isolated polynucleotide it would not be uncommon for a point mutation or some other form of mutation to be present in the sequence. As such we encompass variants ofSEQ ID No. 1 in the disclosure. As used herein, the term “variants”, means strains of Bifidobacteria that have a sequence identity of at least 99.5% or more with SEQ ID No. 1. 20 SEQ ID No. 1 contains a large number of open reading frames which represent the predicted genes. We have identified 1,836 protein coding regions or genes within this polynucleotide. As such, our disclosure encompasses ftagments of the polynucleotide ofSEQ ID No. 1. The fragments may correspond to portions of the polynucleotide sequence that encode 25 one or more proteins. Alternatively, the fragments may correspond to portions of the polynucleotide sequence that specify part of a gene or genes for example the fragment may correspond to a portion of the polynucleotide sequence that spans a part of two or more genes.

The sequence ofSEQ ID No. 1 is a DNA polynucleotide sequence, our disclosure encompasses sequences that are complementary to the DNA sequence for example 30 complementary DNA (cDNA) or RNA sequences including messenger RNA (mRNA) and transfer RNA (tRNA) or protein sequences such as amino acid sequences encoded by the polynucleotide sequence.

The polynucleotide ofSEQ ID No.1 and complementary sequences thereof may take many forms for example an isolated polynucleotide sequence; an isolated protein sequence; a wo 2010/055499 PCT/IE2009/000079 -15- 2016206219 18Jul2016 biologically pure culbire of a Bifidobacterial strain comprising the nucleic acid ofSEQ ID NO. 1 ؛ a plasmid comprising the polynucleotide of SEQ ID No. 1 ؛ and the like. All of these forms of the sequence ofSEQ ID No. 1 are encompassed in this disclosure.

As used herein, the term “expresses an exopolysaccharide”, may be interpreted to mean 5 that a bacterial strain contains a DNA sequence encoding an exopolysaccharide for example a DNA sequence that encodes at least one gene ftom SEQ ID No. 2 and/or at least one gene from SEQ ID No. 3 or a ftinctional fragment or variant thereof.

As used herein, the term “sequence homology” encompasses sequence homology at a nucleic acid and/or an amino acid (protein) level. Sequence homology is indicated as the overall 10 percentage of identity across the nucleic acid and/or amino acid sequence. The sequence homology may be determined using standard techniques known to those skilled in the art. For example sequence homology may be determined using the on-line homology algorithm “BLAST” program, publicly available at http://www.ncbi.nlm.nih.gov/BLAST/. A sequence may have at least 85% or at least 86% or at least 87% or at least 88% or at least 89% or at lest 15 90% or at least 91% or at least 92% or at least 93% or at least 94% or at least 95% or at least 96% or at least 97% or at least 98% or at least 99% sequence homology with the nucleic acid sequences described herein or the amino acid (protein) encoded thereby.

The present invention is based on the whole genome sequence of Bifidobacterium longum biotype infentis ucc 35624. The genome sequence is listed in SEQ ID No. 1 of the 20 attaclted sequence listing and comprises 2,264374 base pairs. Analysis of the genonre sequence identified 1,836 genes having the open reading frames as set out in Table 1 below.

Table 1 - Open reading frames of the genome of ucc 35624.

GenelD Start End Strand Description ΒΙ00001 1667321 1667608 CRISPR-associated protein Cas2 ΒΙ00002 1667697 1668593 CRISPR-associated protein Casl BI00002a 1668725 1669423 CRISPR-associated protein Cas4 ΒΙ00003 1669465 1670313 CRISPR-associated protein, ΤΜ1801 family ΒΙ00005 1670320 1672275 CRISPR-associated protein, CTl 133 family ΒΙ00006 1672281 1672982 CRISPR-associated protein, CTl 134 family ΒΙ00007 1672992 1675427 hypotlietical CRISPR-associated helicase Cas3 ΒΙ00008 1676109 1676426 COG3464: Transposase and inactivated derivatives ΒΙ00009 1677053 1680283 isoleucyl-tRNA synthetase ΒΙ00010 1680955 1682163 + aminotransferase, class I, putative ΒΙ00011 1682280 1683785 galactoside symporter Β100012 1684111 1687299 t beta-galactosidase, putative ΒΙ00013 1687365 1688372 sugar-binding transcriptional regulator, LacI femily, putative ΒΙ00014 1688522 1689889 Putative antibiotic resistance protein (membrane PCT/IE2009/000079 WO 2010/055499 -16- protein) ΒΙ00015 1690007 1690906 hypothetical pfkB family carbohydrate kinase ΒΙ00016 1690909 1692111 alcohol dehydrogenase, iron-containing ΒΙ00017 1692111 1692794 hypothetical haloacid dehalogenase-like hydrolase ΒΙ00018 1692921 1693901 inosine-uridine preferring nucleoside hydrolase ΒΙ00019 1693960 1694913 hypothetical pfkB femily carbohydrate kinase ΒΙ00020 1694909 1695553 hypothetical N-(5'phosphoribosyl)anthranilate isomerase Β100021 1695603 1696415 ABC transporter, ΑΤΡ-binding protein ΒΙ00022 1696415 1697242 conserved hypothetical protein ΒΙ00023 1697246 1698055 hypothetical Cobalt transport protein Β100024 1698062 1698712 conserved hypothetical protein Β100025 1698969 1700846 ا transcriptional regulator, Lacl femily/carbohydrate kinase, PfkB femily protein ΒΙ00026 1700977 1702989 ABC transporter, ATP-binding/permease protein ΒΙ00027 1702989 1704944 ABC transporter, ΑΤΡ-binding protein ΒΙ00028 1704944 1705402 transcriptional regulator, MarR family, putative ΒΙ00029 1705699 1706610 COG1472: Beta-glucosidase-related glycosidases ΒΙ00030 1706029 1706937 t COG1309: Transcriptional regulator ΒΙ00031 1707015 1708373 unnamed protein product ΒΙ00032 1708509 1710902 xylosidase/arabinosidase [importedl ΒΙ00033 1710937 1711287 hypothetical protein ΒΙ00034 1711383 1712762 glutamate-cysteine ligase, putative ΒΙ00035 1712905 1718037 t conserved domain protein ΒΙ00036 1718044 1718883 + hypothetical protein ΒΙ00037 1719052 1724187 BadF/BadG/BcrA/BcrD ATPase femily femily ΒΙ00038 1724418 1725143 anaerobic ribonucleoside-triphosphate reductase activating protein ΒΙ00039 1725294 1727699 anaerobic ribonucleoside-triphosphate reductase Β100040 1728167 1729534 + exodeoxyribonuclease VII, large subunit ΒΙ00041 1729587 1729886 + exodeoxyribonuclease VII, small subunit ΒΙ00042 1730013 1730534 t NADP(H) oxidoreductase CC0205 fimportedl ΒΙ00043 1730676 1732529 long-chain-fatty-acid--CoA ligase, putative Β100044 1732662 1732787 COG 1970: Large-conductance meclianosensitive channel ΒΙ00045 1732765 1733166 hypothetical Large-conductance mechanosensitive channel, MscL Β100046 1733337 1733762 UNKNOWN PROTEIN, putative Β100047 1733887 1734102 COG0454: Histone acetyltransferase ΗΡΑ2 and related acetyltransferases ΒΙ00048 1734587 1735696 ؛ hypothetical transmembrane protein with unknown function ΒΙ00049 1735718 1736683 exopolyphosphatase, putative ΒΙ00050 1736864 1737967 aminotransferase, class 1 Β100051 1738178 1739230 + oxidoreductase, Gfo/Idh/MocA family, putative ΒΙ00052 1739267 1739779 patch repair protein fimportedl ΒΙ00053 1739931 1740377 + acetyltransferase, GNAT family Β100054 1740356 1740841 conserved hypothetical protein ΒΙ00055 1741026 1745207 helicase, Snf2 femily Β100056 1745285 1746367 t conserved hypothetical protein Β100057 1746358 1746504 hypothetical protein Β100058 1746604 1747620 + tetrahydrodipicolinateN-succinjd transferase (dapD) 12016لال18 2016206219 2016206219 18Jul 2016 Ρ(ΙΕ2009/000079 -17- WO 2010/055499 Β.00059 1747840 1749129 citrate synthase I ΒΙ00060 1749406 1750242 methionine aminopeptidase, type I ΒΙ00061 1750378 1751355 membrane protein, putative ΒΙ00062 1751532 1753703 t belongs to peptidase family M13 ΒΙ00063 1753792 1754526 single-stranded DNA-binding protein (ssb) subfamily ΒΙ00064 1754805 1756616 prolyltRNA synthetase ΒΙ00065 1757008 1757361 + hypothetical protein ΒΙ00066 1757392 1758561 pflA Β100067 1758551 1760338 Protein of unknown function family ΒΙ00068 1760391 1761806 TPR domain protein ΒΙ00069 1761858 1762505 oligoribonuclease Β100070 1762676 1764259 inosine-5'-monophosphate dehydrogenase ΒΙ00071 1764282 1765562 undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase Β.00072 1765562 1766233 Sua5/YciO/YrdC/YwlC family protein ΒΙ00073 1766408 1767082 + maltose O-acetyltransferase ΒΙ00074 1767220 1767921 branched-chain amino acid ABC transporter, ΑΤΡ-binding protein ΒΙ00075 1767924 1768781 branched chain amino acid ABC transporter, ΑΤΡ-binding protein Β100076 1768781 1769854 branched-chain amino acid ABC transporter, permease prote.n ΒΙ00077 1769874 1770797 branched-chain amino acid ABC transporter, permease protein ΒΙ00078 1771042 1772226 branched-chain amino acid ABC transporter, amino acid-binding protein, putative ΒΙ00079 1772502 1773407 N-methylase PapM ΒΙ00080 1773473 1774492 peptide chain release factor 1 BI0٥٥03g <؟\ΊΊ4Ί\ 1774924 ribosomal protein 131 ΒΙ00081 1775256 1776482 transcription regulator ROK family VC2007 [imported], putative ΒΙ00082 1776702 1778219 t xylulokinase ΒΙ00083 1778416 1778760 + lipoprotein, putative Β100084 1778773 1779114 + hypothetical protein Β100085 1779393 \ΊΊΠΥ1 possible sugar permease Β100086 \η%% 1780930 transposase. Mutator family Β100087 1781199 1782545 xylose isomerase Β100088 1782842 1783072 drug resistance transporter, EmrB/QacA subfamily Β100089 1783095 1783409 ٠ drug resistance transporter, EmrB/QacA subfamily Β100090 1783425 1784222 conserved hypothetical protein Β100091 1785149 1785661 polypeptide deformylase Β100092 1785576 1786421 oxidoreductase, aldo/keto reductase family superfamily ΒΙ00093 1786497 1786673 COG0477: Permeases oftlie major facilitator superfamily ΒΙ00094 1786761 1787264 liypothetical COG0477: Permeases of the major facilitator superfamily ΒΙ00095 1787291 1787791 possible MarR-lype transcriptional regulator BlOOOllg 1787998 1788333 hypothetical protein Blon021361 ΒΙ00096 1788358 1789572 sugar ABC transporter, permease protein ΒΙ00097 1789575 1791125 sugar ABC transporter, ΑΤΡ-binding protein WO 2010/055499 PCT/JE2009/000079 2016206219 18Jul2016 -18- ΒΙ00098 1791229 1792383 sugar ABC transporter, periplasmic sugar-binding protein ΒΙ00099 1792462 1792608 hypothetical protein ΒΙ00100 1792854 1793801 t probable repressor protein in (NagC/XylR) family ΒΙ00101 1793842 1794705 ؛ sugar ABC transporter, ΑΤΡ-binding protein, putative ΒΙ00102 1794736 1795683 glucokinase, putative ΒΙ00103 1796537 1798192 ؛ ATP binding protein of ABC transporter Β100104 1798507 1799409 t acyl-CoA thioesterase 11 ΒΙ00105 1799511 1800035 hypothetical membrane protein with unknown function ΒΙ00106 1800213 1801622 dihydroneopterin aldolase Β100107 1801736 1802608 dihydropteroate synthase ΒΙ00108 1802699 1803295 GTP cyclohydrolase I ΒΙ00109 1803391 1805478 cell division protein FtsH ΒΙ00110 1805478 1806038 hypoxanthinephosphoribosyltransferase Β100111 1806028 1807191 COG0037:Predicted ATPase of the ΡΡ-Ιοορ superfamily implicated ΒΙ00112 1807285 1808772 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase Β100113 1808798 1810468 hypothetical transmembrane protein with unknown function ΒΙ00114 1810468 1811421 ΑΤΡ-binding protein of ABC transporter system ΒΙ00115 1811519 1812739 glycosjd transferase domain protein, putative ΒΙ00116 1812742 1814496 hypothetical integral membrane protein in upfoll8 Β100117 1814587 1815252' t probable glycosyltransferase ΒΙ00118 1815481 1816629 alcohol dehydrogenase, iron-containing Β100119 1817069 1818370 t cyclopropane-fatty-acyl-phospholipid synthase ΒΙ00120 1818383 1819687 ا hypotlietical COG0477: Permeases of the major facilitator superfemily ΒΙ0012) 1820205 1821215 UDP-glucose 4-epimerase ΒΙ00122 1821585 1822400 t methyltransferase, putative ΒΙ00123 1822698 1823195 hypothetical protein Β.00124 1823244 1823708 Orf2 ΒΙ00125 1823795 1824079 t hypothetical Helix-turn-helix ΒΙ00126 1824492 1824788 hypothetical protein ΒΙ00127 1825086 1826453 gp22 ΒΙ00128 1827148 1827699 hypothetical protein BI00170t 1827699 1828901 hypothetical Phage integrase femily ΒΙ00129 1829429 1830229 ؛ azic protein, putative ΒΙ00130 1830229 1830558 t branched-chain amino acid permease ΒΙ00131 1830743 1831258 phosphotyrosine protein phosphatase, putative ΒΙ00132 1831385 1832044 dihydrofolate reductase ΒΙ00133 1832157 1832936 thymidylate synthase ΒΙ00134 1833154 1833564 t conserved hypothetical protein ΒΙ00135 1833629 1834663 demannu, putative Β100136 1834835 1835572 Ρ60 extracellular protein, invasion associated protein lap ΒΙ00137 1835733 1836476 NLP/P60 femily domain protein Β100138 1836692 1837645 N-acetylmuramoyl-L-alanine amidase domain protein ΒΙ00139 1838255 1839178 t phosphoserine aminotransferase, putative Β100140 1839305 1839562 t conserved hypothetical protein WO 2010/055499 PCT/JE2009/000079 2016206219 18Jul 2016 -19- ΒΙ00141 1839693 1840874 sensor histidine kinase, putative ΒΙ00142 1841128 1841745 phosphate transport system regulator protein PhoU, putative ΒΙ00143 1842110 1842847 phosphoglycerate mutase ΒΙ00144 1842910 1843872 1,4-dihydroxy-2-naphthoate octaprenyltransferase Β100145 1843937 1845412 lysyl-tRNA synthetase ΒΙ00146 1846534 1847304 ا AraJ-like protein probably involved in transport ofarabinose polymers ΒΙ00147 1847394 1849754 t TPR Domain domain protein ΒΙ00148 1849833 1850462 t conserved hypothetical protein Β100149 1850618 1852216 hypothetical membrane protein possibly involved in transport ΒΙ00150 1852325 1853029 conserved hypothetical protein ΒΙ00151 1853062 1854903 conserved hypothetical protein ΒΙ00152 1854930 1856174 + possible histidine kinase sensor of two component system ΒΙ00153 1856174 1856866 ؛ transcription regulator, LuxR family ΝΜΒ1250 [imported! ΒΙ00154 1856920 1857939 UDP-glucose 4-epimerase ΒΙ00155 1858012 1859556 galactose-l -phosphate uridylyltransferase ΒΙ00156 1859606 1860682 putative desulfatase possibly for mucin ΒΙ00157 1860713 1862965 conserved hypothetical protein ΒΙ00158 1863426 1864382 sugar ABC transporter, permease protein ΒΙ00159 1864382 1865278 sugar ABC transporter, permease protein, putative ΒΙ00160 1865546 1866859 solute binding protein of ABC transporter for sugars ΒΙ00161 1867217 1867369 hypothetical protein ΒΙ00162 1867867 1868856 seiyl-tRNA synthetase ΒΙ00163 1869384 1870562 ٠ Diacylglycerol kinase catalytic domain (presumed) protein ΒΙ00164 1870573 1871409 transcription antiterminator, BglG fomily, putative ΒΙ00165 1871430 1873829 PTS system component, putative ΒΙ00166 1874293 1875843 ا major focilitator fomily transporter CC0814 [imported], putative ΒΙ00167 1875934 1877607 ٠ phosphoglucomutase, alpha-D-glucose phosphate-specific BI00222t 1878343 1879437 conserved hypothetical protein ΒΙ00168 1879668 1880087 t conserved hypothetical protein ΒΙ00169 1880224 1881837 ا oxidoreductase, pyridine nucleotide-disulfide, class I ΒΙ00170 1882002 1882151 hypothetical protein ΒΙ00171 1882305 1883360 t RNase H ΒΙ00172 1883494 1884189 t ribose 5-phosphate isomerase Β100173 1884629 1885258 conserved liypothetical protein ΒΙ00174 1885386 1886921 + DNA repair protein RadA Β100175 1886942 1888063 riboflavin biosynthesis protein RibF ΒΙ00176 1888164 1889324 tRNA pseudouridine syntliase B ΒΙ00177 1889329 1889799 ribosome-binding foctor A ΒΙ00178 1889953 1892799 translation initiation foctor lF-2 ΒΙ00179 1893150 1894214 N utilization substance protein A ΒΙ00180 1894422 1895147 t lipoprotein, putative Β100181 1895194 1896234 transcriptional regulator, LacI family, putative ΒΙ00182 1896528 1896629 hypothetical protein ΒΙ00183 1896770 1897798 - hypothetical PCT/IE2009/000079 WO 2010/055499 -20- ΒΙ00184 1897936 1898568 alpha-L-arabinosidase Β100185 1899147 1899917 Transglutaminase-like superfamily domain protein ΒΙ00186 1900154 1902331 Domain of unknown function (DUF404) family ΒΙ00187 1902473 1902586 hypothetical protein ΒΙ00188 1902727 1903515 t tRNA pseudouridine synthase A ΒΙ00189 1903603 1904142 ribosomal protein L17 ΒΙ00190 1904245 1905237 RNA polymerases L/ 13 to 16 kDa subunit ΒΙ00191 1905321 1905716 ribosomal protein Sll ΒΙ00192 1905807 1906181 ribosomal protein S13p/S18e ΒΙ00193 1906333 1906443 ribosomal protein L36 ΒΙ00194 1906470 1906685 translation initiation factor IF-1 ΒΙ00195 1906865 1907422 adenylate kinase ΒΙ00196 1907595 1908722 preprotein translocase, SecY subunit ΒΙ00197 1909207 1909656 ribosomal protein L15 ΒΙ00198 1909662 1909844 ribosomal protein L30 ΒΙ00199 1909853 1910581 ribosomal protein S5 ΒΙ00200 1910581 1910991 ribosomal protein LI 8 ΒΙ00201 1910954 1911490 ribosomal protein L6 ΒΙ00202 1911511 1911906 ribosomal protein S8 ΒΙ00203 1911999 1912181 ribosomal protein S14p/S29e ΒΙ00204 1912186 1912755 ribosomal protein L5 VC2584 rimported) ΒΙ00205 1912755 1913087 ribosomal protein L24 ΒΙ00206 1913092 1913457 ribosomal protein 114 Β100207 1913555 1913812 ribosomal protein S17 ΒΙ00208 1913818 1914066 ribosomal protein L29 ΒΙ00209 1914069 1914485 ribosomal protein L16 Β100210 1914495 1915295 ribosomal protein S3 ΒΙ0021. 1915301 1915657 ribosomal protein L22 ΒΙ00212 1915677 1915952 ribosomal protein S19 ΒΙ00213 1915971 1916798 ribosomal protein L2 ΒΙ00214 1916838 1917131 ribosomal protein L23 ΒΙ00215 1917140 1917793 ribosomal protein L4/L1 family ΒΙ00216 1917803 1918441 ribosomal protein L3 ΒΙ00217 1918461 1918766 ribosomal protein SIO Β100218 1919023 1920027 + membrane protein, putative ΒΙ00219 1920366 1923092 Unknown ΒΙ00220 1923607 1924797 ؛ probable repressor in the Rok (NagC/XylR) family ΒΙ00221 1924797 1927334 + glycogen operon protein GlgX ΒΙ00222 1927431 1927919 ribosomal protein S9 ΒΙ00223 1927945 1928391 ribosomal protein L13 ΒΙ00224 1928792 1930954 4-alpha-glucanotransferase ΒΙ00225 1931125 1931931 hypothetical Leucine rich repeat variant ΒΙ00226 1931876 1932514 conserved hypothetical protein T1GR00257 ΒΙ00227 1932579 1933592 possible 2-hydroxyacid dehydrogenase ΒΙ00228 1933669 1935009 capA protein, putative ΒΙ00229 1935547 1936608 COG0697:Permeases of the drug/metabolite transporter (DMT) superfamily Β100230 1936648 1937991 t DNA-damage-inducible protein p ΒΙ00231 1938024 1939256 aminotransferase, putative ΒΙ00232 1939374 1939691 fdxC ΒΙ00233 1939755 1941278 - possible cationic amino acid transporter 12016لال18 2016206219 WO 2010/055499 2016206219 18Jul2016 PCT/IE2009/000079 -21- ΒΙ00234 1941433 1942398 UDP-Nacetyfenolpyruvoylglucosamine reductase ΒΙ00235 1942930 1943094 ribosomal protein L33 ΒΙ00236 1943529 1944245 + possible cystathionine gamma lyase ΒΙ00237 1944924 1945214 chaperonin, lOkDa ΒΙ00238 1945390 1946604 conserved hypothetical protein ΒΙ00239 1946895 1947557 rimJ ΒΙ00240 1947644 1948360 5-formyltetrahydrofolatecyclo-ligase-related protein ΒΙ00241 1948527 1948709 + conserved hypothetical protein Β100242 1948950 1949516 + conserved hypothetical protein Β100243 1949617 1949814 hypothetical protein Β1οη021580 Β100244 1949820 1953440 conserved hypothetical protein Β100245 1953452 1954999 conserved hypothetical protein ΒΙ00246 1955200 1955577 ribosomal protein L7/L12 ΒΙ00247 1955689 1956207 ribosomal protein LIO Β100248 1956479 1957222 conserved hypothetical protein ΒΙ00249 1957561 1958952 + Unknown ΒΙ00250 1959385 1962123 polyribonucleotide nucleotidyltransferase ΒΙ00251 1962444 1962710 ribosomal protein S15 ΒΙ00252 1962882 1963562 conserved hypothetical protein ΒΙ00253 1963721 1963951 hypothetical protein ΒΙ00254 1964091 1966964 possible extracellular exo-xylanase ΒΙ00255 1967190 1969712 endo-1,4-beta-xylanase D ΒΙ00256 1970329 1971432 + 1S30 family, transposase ؛imported) ΒΙ00257 1971591 1972274 conserved hypothetical protein BI00334t 1972174 1972389 + conserved hypothetical protein ΒΙ00258 1972411 1973094 hypothetical protein Β1οη021028 ΒΙ00259 1973553 1974914 possible cell surface protein Β100260 1974994 1977351 von Willebrand factor type A domain protein Β.00261 1978150 1978326 hypothetical protein Β1οη021305 Β100262 1978353 1978820 phosphopantethiene protein transferase Β100263 1979459 1988974 MaoC like domain protein ΒΙ00264 1989016 1990635 propionyl-CoA carboxylase, beta chain Β100265 1990631 1992514 accA3 Β100266 1993105 1993701 t bioY protein Β.00267 1993739 1994710 biotin—acetyl-CoA-carboxylase ligase ΒΙ00268 1994853 1996895 t membrane protein, putative Β100269 1996904 1997731 t conserved hypothetical protein ΒΙ00270 1997829 1998524 transcriptional regulator, putative BI0035٥t 1998629 1999459 hypothetical transcriptional regulator, IclR femily Β100271 2011598 2011726 hypothetical protein ΒΙ00272 2011797 2012486 ribosomal protein LI Β100273 2012505 2012933 ribosomal protein LI 1 ΒΙ00274 2013199 2014089 transcription termination/antitermination fector NusG Β100275 2014122 2014346 preprotein translocase SecE subunit Β100276 2014593 2015795 aspartate aminotransferase ؛imported) Β100277 2015889 2016986 glutamate 5-kinase Β100278 2017023 2018711 GTP-binding protein Β100279 2018783 2019028 ribosomal protein L27 Β.00280 2019054 2019359 ribosomal protein L21 Β100281 2019502 2022534 hypothetical ribonuclease, Rne/Rng family Β100282 2022850 2024121 - succinyl-diaminopimelatedesuccinylase PCT/IE2009/000079 WO 2010/055499 -22- ΒΙ00283 2024159 2025100 + transporter, putative ΒΙ00284 2025282 2026727 permease, putative domain protein ΒΙ00285 2026727 2027818 ABC transporter, ΑΤΡ-binding protein ΒΙ00286 2027996 2029441 Maf-like protein ΒΙ00287 2029581 2030690 homoserine kinase ΒΙ00288 2030800 2032113 homoserine dehydrogenase ΒΙ00289 2032276 2033865 diaminopimelate decarboxylase ΒΙ00290 2033871 2035541 arginyl-tRNA syntlietase BI0029J 2035944 2036606 t possible TetR-type transcriptional regulator ΒΙ00292 2036606 2037880 t permease, putative Β100293 2037742 2038899 ؛ transcription regulator LysR family VC 1588 [imported], putative Β100294 2038996 2040246 t probable aminotransferase ΒΙ00295 2040298 2041521 UDPNacetylglucosamine 1-carboxyvinyltransferase Β100296 2041869 2043212 + NADH oxidase ΒΙ00297 2043424 2044548 dihydroorotate dehydrogenase family protein, putative ΒΙ00298 2044591 2046468 CAAX amino terminal protease femily protein femily ΒΙ00299 2046594 2047283 3-isopropylmalate dehydratase small subunit ΒΙ00300 2047369 2048769 3-isopropylmalate dehydratase, large subunit ΒΙ00301 2049087 2049860 + transcriptional regulator, IclR family ΒΙ00302 2050021 2051391 Ser/Thr protein phosphatase family ΒΙ00303 2051896 2054130 + polyphospliate kinase ΒΙ00304 2054291 2055487 + mutTl ΒΙ00305 2055480 2056298 ؛ hypothetical protein Blon021115 ΒΙ00306 2056564 2057871 conserved hypothetical protein ΒΙ00307 2057963 2058121 hypothetical protein ΒΙ00308 2058175 2058813 t uracil phosphoribosyltransferase ΒΙ00309 2058864 2059340 t conserved liypothetical protein T1GR00246 ΒΙ00310 2059542 2060648 possible phosphodiesterase ΒΙ00311 2060677 2061747 glutamyl-tRNA synthetase domain protein BI003J2 2061933 2064599 ATP-dependent Clp protease, ATP-binding subunit CIpB Β100313 2064821 2066371 histidine ammonia-lyase ΒΙ00314 2066617 2067489 + transcriptional regulator, IclR femily, putative ΒΙ00315 2067489 2067662 ٠ conserved hypothetical protein ΒΙ00316 2067741 2068559 possible 2-hydr0xyhepta-2,4-diene-l,7-dioate isomerase in the fumarylacetoacetate hydrolase femily Β100317 2068665 2069873 hypothetical membrane protein with unknown function ΒΙ00318 2070097 2071272 UDP-galactopyranose mutase Β100319 2071426 2072670 t dTDP-glucose 4,6-dehydratase ΒΙ00320 2072827 2074311 t conserved hypothetical protein Β.00321 2074367 2075068 + conserved hypothetical protein BI00423t 2075382 2075687 ٠ putative transposase ΒΪ00322 2075763 2076530 1S1533, Orffi ΒΙ00323 2076530 2077987 transposase (25) ΒΗ3998 [imported], putative Β100324 2078280 2078996 glycosyltransferase, putative Β100325 2079313 2079666 sialic acid-specific 9-O-acetylesterase Β100326 2080049 2081173 ٠ hypothetical Acyltransferase femily 12016لال18 2016206219 -23- 2016206219 18Jul2016 PCT^2009/000079 WO 2010/055499 ΒΙ00327 2081181 2082893 hypothetical membrane protein with unknown function ΒΙ00328 2082902 2085811 hypothetical Glycosyl transferase femily 8 ΒΙ00329 2085935 2087170 hypothetical glycosyl transferase, group 2 femily protein Β100330 2087259 2088509 polysaccharide ABC transporter, ATP-binding protein ΒΙ00331 2088515 2089351 polysaccharide ABC transporter, pemease protein, putative ΒΙ00332 2089580 2091367 ؛ hypothetical Glycosyl transferase femily 8 ΒΙ00333 2091457 2092698 UDP-glucose 6-dehydrogenase ΒΙ00334 2092974 2093636 hypothetical NAD dependent epimerase/dehydratase femily Β100335 2093654 2094844 membrane protein, putative ΒΙ00336 2094847 2097099 conserved hypothetical protein ΒΙ00337 2097441 2098844 + hypothetical membrane protein with unknown function Β100338 2098844 2099962 t possible ATP binding protein of ABC transporter Β100339 2100089 2100790 + HDIG domain protein ΒΙ00340 2100871 2101728 conserved hypothetical protein Β100341 2101825 2104335 Kup system potassium uptake protein [imported] Β100342 2104481 2105188 hydrolase, TatD femily ΒΙ00343 2105717 2106784 t Fic protein femily femily Β100344 2106816 2108621 ABC transporter, ATP-binding/permease protein Β100345 2108635 2110542 ABC transporter, ATP-binding/permease protein ΒΙ00346 2110935 2111099 hypothetical protein ΒΙ00347 2111297 2112703 possible alpha-galactosidase ΒΙ00348 2113077 2114231 t transcriptional regulator, Lacl femily, putative ΒΙ00349 2114409 2115356 probable AraC/XylS-type transcriptional regulator ΒΙ00350 2115401 2117626 conserved hypothetical protein ΒΙ00351 2117851 2119374 + aminopeptidase c ΒΙ00352 2119555 2120628 + conserved hypothetical protein ΒΙ00353 2121673 2123403 methionyl-tRNA synthetase Β100354 2123873 2124496 t conserved hypothetical protein BI00466t 2124496 2124864 t conserved hypothetical protein ΒΙ00355 2124897 2125922 conserved hypothetical protein T1GR00096 ΒΙ00356 2126487 2127902 possible symporter ΒΙ00357 2127864 2129027 + conserved hypothetical protein ΒΙ00358 2129186 2131012 ABC transporter, ATP-binding/permease protein ΒΙ00359 2131231 2133099 ABC transporter, ATP-binding/permease protein ΒΙ00360 2133289 2133684 transcriptional regulator, MarR family, putative Bl٥0475t 2134267 2134506 ؛ DNA-damage-inducible protein of Escherichia coli ΒΙ00361 2135008 2138841 LPXTG-motif cell wall anchor domain protein ΒΙ00362 2139056 2139151 hypothetical protein ΒΙ00363 2139209 2143594 secreted protein ΒΙ00364 2143901 2145394 ATP-dependent DNA helicase recG ΒΙ00365 2145737 2147257 amino acid permease Β100366 2147448 2151185 permease, putative ΒΙ00367 2151199 2151897 ABC transporter, ATP-binding protein ΒΙ00368 2152041 2152607 ؛ probable TetR-like transcriptional regulator ΒΙ00369 2152832 2154310 ؛ aromatic amino acid transport protein AroP ΒΙ00370 2154575 2155774 + putative invertase/transposase WO 2010/055499 PCT/IE2009/000079 2016206219 18Jul2016 -24- ΒΙ00371 2155961 2160952 hypothetical Glycosyl hydrolases family 43 ΒΙ00372 2161359 2164649 hypothetical ΒΙ00373 2164997 2168173 possible arabinosidase ΒΙ00374 2168529 2169131 conserved hypothetical protein ΒΙ00375 2169340 2170179 sugar ABC transporter, permease protein, putative ΒΙ00376 2170182 2171033 sugar ABC transporter, permease protein, putative ΒΙ00377 2171416 2172429 + transcription regulator, LacI family [imported], putative ΒΙ00378 2172690 2174015 possible solute binding protein of ABC transporter ΒΙ00379 2174424 2175134 phosphoglycerate mutase family protein ΒΙ00380 2175226 2175600 ٠ hypothetical COG0531: Amino acid transporters ΒΙ00381 2175612 2176550 + hypothetical nihoreductase femily protein ΒΙ00382 2176846 2179572 t pliage infectio, putotive ΒΙ00383 2179572 2181908 t pliage infection protein, putative ΒΙ00384 2188511 2189263 ٠ regulator protein, SIR2 family ΒΙ00385 2189415 2190791 threonine dehydratase ΒΙ00386 2190928 2192745 glucan 1,6-alpha-glucosidase ΒΙ00387 2192872 2194731 hypothetical Raffinose synthase or seed imbibition protein Sipl ΒΙ00388 2194766 2196433 alpha-amylase femily protein ΒΙ00389 2196537 2197358 hypothetical abc transporter permease protein yurm. [bacillus ΒΙ00390 2197364 2198383 hypotlietical Binding-protein-dependent transport systems inner membrane component ΒΙ00391 2198408 2199730 hypothetical Bacterial extracellular solute-binding protein ΒΙ00392 2199980 2201095 hypothetical protein Efae022644 ΒΙ00393 2201159 2202484 hypothetical Bacterial extracellular solute-binding protein ΒΙ00394 2202692 2203717 ا transcription regulator, Lacl family [imported], putative ΒΙ00395 2203838 2204854 ؛ transcription regulator, Lacl family [imported], putative Β100396 2204919 2205782 sugar ABC transporter, permease protein ΒΙ00397 2205804 2206730 sugar ABC transporter, permease protein ΒΙ00398 2206755 2208041 sugar ABC transporter, sugar-binding protein, putative ΒΙ00399 2208215 2209420 ا transcription regulator ROK family VC2007 [imported], putative ΒΙ00400 2209591 2211894 alpha-galactosidase ΒΙ00401 2212017 2212445 hypothetical Cytidine and deoxycytidylate deaminase zinc-binding region ΒΙ00402 2212589 2214658 ؛ Na+/H؛ antiporter ΒΙ00403 2214858 2215613 serine esterase, putative ΒΙ00404 2215613 2215714 hypothetical protein ΒΙ00405 2215735 2216592 conserved hypothetical protein ΒΙ00406 2216949 2217527 ؛ deoxycytidine triphosphate deaminase ΒΙ00407 2217593 2219320 + cell wall surface anchor family protein, putative ΒΙ00408 2219543 2222527 calcium El-E2-type ATPase ΒΙ00409 2222713 2223447 protein probably involved in xylan degradation, possible xylan esterase ΒΙ00410 2223622 2225049 liypothetical major facilitator superfamily protein ΒΙ00411 2225005 2225994 RNA methyltransferase, TrmH family, group 3 WO 2010/055499 -25- 12016لال18 2016206219 PCT/IE2009/000079 ΒΙ00412 2226107 2227516 conserved hypothetical protein Β100413 2227740 2228864 ATP binding protein of ABC transporter for sugars Β100414 2229226 2230419 glycosyl transferase domain protein ΒΙ00415 2230486 2231475 Ribonucleotide reductase, beta subunit Β.00416 2231704 2233896 ribonucleoside-diphosphate reductase, alpha subunit ΒΙ00417 2234015 2234470 nrdl protein ΒΙ00418 2234470 2234733 COG0695: Glutaredoxin and related proteins ΒΙ00419 2235324 2235767 hypothetical Helix-tum-helix ΒΙ00420 2235958 2236635 conserved hypothetical protein ΒΙ00421 2236828 2237592 ؛ ion transporter ΒΙ00422 2237788 2238891 + conserved hypothetical protein ΒΙ00423 2239035 2239349 beta-glucosidase-related glycosidase ΒΙ00424 2239828 2241951 ٠ widely conserved protein with eukatyotic protein kinase domain ΒΙ00425 2242132 2243106 t conserved hypothetical protein ΒΙ00426 2243627 2245111 t conserved hypothetical protein Β100427 2245147 2246067 ٠ dimethyladenosine transferase ΒΙ00428 2246067 2247014 t kinase, GHMP femily, group 2 ΒΙ00429 2246860 2247690 + liypothetical protein B10655 ΒΙ00430 2247781 2249193 pcnA ΒΙ00431 2249280 2250569 ٠ NUDIX domain protein ΒΙ00432 2250569 2252836 + cell wall surface anchor femily protein, putative ΒΙ00433 2252836 2254560 ٠ conserved hypothetical membrane protein in MviN femily Β100434 2254646 2256706 t conserved hypothetical protein ΒΙ00435 2256829 2257845 t thioredoxin reductase Β100436 2258158 2259516 chromosome partitioning protein ParB ΒΙ00437 2259519 2260487 Soj family protein ΒΙ00438 2260741 2261403 metliyltransferase GidB ΒΙ00439 2261558 2262088 R3H domain protein Β100440 2262215 2263219 inner membrane protein, 60 kDa ٧C0004 [imported] BI00143g 2263219 2263533 conserved hypothetical protein TIGR00278 ΒΙ005761 2263533 2264063 ribonuclease p protein component ΒΙ00441 2263925 2264056 ribosomal protein L34 ΒΙ00442 1 1500 ؛ chromosomal replication initiator protein DnaA ΒΙ00443 2239 3360 t DNA polymerase III, beta subunit ΒΙ00444 3442 4626 t recF protein ΒΙ00445 4626 5093 + conserved hypothetical protein ΒΙ00446 5229 7364 + DNA gyrase, B subunit ΒΙ00447 7534 10083 + DNA gyrase, A subunit ΒΙ00448 10156 10719 t conserved hypothetical protein ΒΙ00449 11406 12116 t hypothetical protein ΒΙ00450 12179 13699 t hypothetical Pectinesterase ΒΙ00451 14103 15446 NADP-specific glutamate dehydrogenase Β100452 15768 16199 AsnC-type transcriptional regulator Β100453 16405 \Ί1 + aspartate aminotransferase ΒΙ00454 \1is٦ 18746 hypothetical protein Β1οη021073 Β100455 19007 19600 + hypothetical protein BL0627 Β100456 19770 20462 hypothetical protein Blon٥21075 ΒΙ00457 20579 20821 ؛ Putative acrab operon repressor transcription WO 2010/055499 PCT/IE2009/000079 2016206219 18Jul2016 -26- regulator protein BI00599t 21403 21735 IS1557, transposase, putative BI00146g 21834 22397 - conserved hypothetical protein ΒΙ00458 22130 23497 hypothetical COGl 167: Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaiy/otic orthologs ΒΙ00459 24132 25454 aminotransferase, class III superfamily ΒΙ00460 25495 26397 ؛ Zinc metalloprotease ΒΙ00461 26414 26509 hypothetical protein ΒΙ00462 26487 26849 + COG3265: Gluconate kinase ΒΙ00463 27114 28424 conserved hypothetical protein ΒΙ00464 28662 29138 Dps femily protein, putative ΒΙ00465 29238 30608 CBS domain protein, putative ΒΙ00466 30841 31521 Prokaryotic-type carbonic anhydrases ΒΙ00467 31727 32287 ( alkyl hydrogen peroxide reductase Β100468 32458 34371 t thioredoxin reductase ΒΙ00469 34494 35963 oxalate:formate antiporter ΒΙ00470 35948 36094 t hypothetical protein ΒΙ00471 36333 37328 ا Laci-type transcriptional regulator ΒΙ00472 37558 40308 phosphoenolpyruvate carboxylase ΒΙ00473 40594 42471 + membrane protein, putative ΒΙ00474 42737 44344 t possible sodium/proline symporter ΒΙ00475 44680 45663 narrowly conserved hypothetical protein ΒΙ00476 45917 47533 + conserved hypothetical protein ΒΙ00477 4ΊΊ\Ί 48805 tryptophanyl-tRNA synthetase ΒΙ00478 49056 49325 t hypothetical protein ΒΙ00479 49437 49967 conserved hypothetical protein ΒΙ00480 49986 52505 t glycogen phosphotylase ΒΙ00481 52725 52940 hypothetical protein B10595 ΒΙ00482 53195 53887 t Rhomboid family protein ΒΙ00483 54562 55029 conserved liypothetical protein ΒΙ00484 55119 55907 ؛ conserved hypothetical protein ΒΙ00485 55907 57142 ؛ hypothetical transmembrane protein with unknown function Β100486 57196 57837 t pabA Β100487 58067 60136 serine/threonine protein kinase ΒΙ00488 60136 60942 serine/threonine protein kinase ΒΙ00489 61083 62546 pbpA ΒΙ00490 62546 64204 Unknown, putative Β100491 64204 65895 possible phosphoprotein phospliatase ΒΙ00492 65903 66430 FHA-domain-containing proteins ΒΙ00493 66463 67161 FHA domain protein ΒΙ00494 67349 69790 dipeptidyl peptidase IV, putative Β100495 69951 70997 t lysophospholipase L2, putative ΒΙ00496 71080 72228 ا von Willebrand factor type A domain protein ΒΙ00497 72231 72947 t conserved hypothetical protein ΒΙ00498 12941 73348 hypothetical protein Blon021556 BI00654t 73348 73497 t hypothetical protein Blon021556 ΒΙ00499 73873 74724 t tellurite resistance protein ΒΙ00500 75108 75608 t lieat shock protein, Hsp20 femily ΒΙ00501 75938 76891 ؛ Probable transmembrane protein ΒΙ00502 1 77065 1 77520 - conserved hypothetical protein PCT/IE2009/000079 WO 2010/055499 -Π - ΒΙ00503 77753 79132 ٠ COG0627: Predicted esterase ΒΙ00504 79132 81702 t COG2898:Uncharacterized BCR ΒΙ00505 82241 83212 ١ peptide methionine sulfoxide reductase ΒΙ00506 83218 83304 + hypothetical protein B10567 BI00668t 83341 83496 ٠ COG0463: Glycosyltransforases involved in cell wall biogenesis ΒΙ00507 83506 86709 helicase-related protein ΒΙ00509 86785 87195 mutator MutT protein, putative ΒΙ00510 87337 88587 t hypothetical Domain of unknown function ΒΙ00511 88678 89139 t acetyltransferase, GNAT family family ΒΙ00512 89226 90080 hypothetical ΒΙ00513 90187 90420 hypothetical protein ΒΙ00514 90480 90842 ٠ conserved hypothetical protein Β100515 91329 92639 queuine tRNA-ribosyltransferase ΒΙ00516 93056 95065 t heat shock protein HtrA ΒΙ00517 95480 97636 + cation-transporting ATPase, Ε1-Ε2 family BI00684t 97816 98862 + transcriptional regulator, LacI family ΒΙ00518 98874 99131 hypothetical mttA/Hcfl 06 family ΒΙ00519 99136 100215 Sec-independent protein translocase TatC BI00687t 100215 100730 hypothetical twin-arginine translocation protein, TatA/Ε family ΒΙ00520 101182 103581 ٠ hypothetical Tat (twin-arginine translocation) pathway signal sequence ΒΙ00521 103674 106151 t hypothetical ΒΙ00522 106547 107707 conserved hypothetical protein ΒΙ00523 107911 109359 + ferredoxin/ferredoxin-NADP reductase, putative ΒΙ00524 109452 110450 t lieat shock protein HtpX ΒΙ00525 110667 111731 fructose-bisphosphate aldolase, class 11 ΒΙ00526 111947 113230 + adenylosuccinate syntlietase ΒΙ00527 113524 114837 t chloride channel ΒΙ00528 115027 116094 + CrcB-like protein family BI00700t 116097 116489 t protein with similarity to CrcB ΒΙ00529 116581 116691 t hypothetical protein ΒΙ00530 116767 117849 ا sugar-binding transcriptional regulator, LacI family, putative ΒΙ00531 118274 119842 t Kup system potassium uptake protein fimportedl ΒΙ00532 120262 121806 ؛ alpha-L-arabinofuranosidase ΒΙ00533 121981 123012 ( transcription regulator, LacI family [imported], putative ΒΙ00534 123104 124012 glycosyl hydrolase, family 31 Β100535 124149 124370 IS861, transposase Orffi BI00711t 124604 125803 + probable integrase/recombinase BI00712t 125878 126765 t probable integrase/recombinase Β100536 5ا؛1ة1\ 127817 ؛ integrase/recombinase XerC, probable [imported], putative ΒΙ00537 127910 128956 1S3 family transposase ΒΙ00538 129291 130814 + sucrose phosphotylase Β.00539 131035 132669 ٠ liypothetical transmembrane protein with unknown function Β100540 132736 133776 sugar-binding transcriptional regulator, LacI family, putative ΒΙ00541 134407 135771 + major facilitator family transporter ΒΙ00542 135971 137020 + ketol-acid reductoisomerase 12016لال18 2016206219 WO 2010/055499 PCT/IE2009/000079 2016206219 18Jul2016 -28- ΒΙ00543 137452 138501 ٠ ketol-acid reductoisomerase ΒΙ00544 138689 140500 alpha-amylase family protein ΒΙ00545 140663 141694 transcription regulator, Lacl family [imported], putative ΒΙ00546 142008 144242 4-alpha-glucanotransferase ΒΙ00547 144506 144784 hypothetical protein Blon021648 ΒΙ00548 144856 145482 t conserved hypothetical protein ΒΙ00549 145500 146507 transcription regulator, Lacl family [imported], putative ΒΙ00550 146777 147490 t sugar ABC transporter, permease protein ΒΙ00551 147605 150139 ؛ glycosyl hydrolase, family 31 ΒΙ00552 151125 153002 t dnaK protein ΒΙ00553 153005 153658 ٠ co-chaperone GrpE ΒΙ00554 153753 154769 t DnaJ protein [imported] ΒΙ00555 154787 155371 ؛ hspR ΒΙ00556 155647 156996 + xanthine permease, putative ΒΙ00557 157036 158154 ٠ possible acyl protein synthase/acyl-CoA reductase-like protein ΒΙ00558 158144 159640 t possible acyl-CoA reductase ΒΙ00559 159715 160497 t 3-0X0acyl-acyl carrier protein reductase Β100560 160553 161281 t beta-phosphoglucomutase, putative ΒΙ00561 161435 162157 t DedA protein BI00749t 162383 163330 t conserved hypothetical protein ΒΙ00562 163340 164404 t trbB BI0٥75it 164410 165060 ٠ conserved hypothetical protein BI00752t 165060 165659 ٠ liypothetical membrane protein with unknown function ΒΙ00563 165947 166231 ؛ liypothetical protein BL0505 BI00754t 166240 166614 ؛ conserved hypothetical protein ΒΙ00564 166715 167041 + conserved hypothetical protein ΒΙ00565 167093 168220 t Bmrtl protein, putative ΒΙ00566 168424 169020 possible TetR-type transcriptional regulator ΒΙ00567 169297 172125 t DNA polymerase 111, tau/gamma subunit ΒΙ00568 172154 172753 t recombination protein RecR ΒΙ00569 Yin 173886 sortase family protein Β100570 174774 176054 ؛ conserved hypothetical protein ΒΙ00571 176649 ١٦٦١٦٩ t hypothetical Amino acid kinase family BJ00572 Yin 177801 + aspartokinase, alpha and beta subunits ΒΙ00573 177889 178980 aspartate-semialdehyde dehydrogenase BJ00574 179055 179765 ( conserved hypothetical protein Β100575 179774 181351 Ser/Thr protein phosphatase family ΒΙ00576 182040 183953 t 2-isopropylmalate syntliase ΒΙ00577 184031 186493 penicillin-binding protein, putative ΒΙ00578 186772 187959 t possible pre-pilin peptidase ΒΙ00579 188086 191169 t DNA topoisomerase I BJ0058. 191549 192067 ٠ tliymidylate kinase ΒΙ00581 192067 193215 t DNA polymerase 111, delta subunit ΒΙ00582 193337 193888 t conserved hypothetical protein TIGR00481 ΒΙ00583 194034 195632 t Unknown ΒΙ00584 195767 197281 ٠ formate—tetrahydrofolate ligase ΒΙ00585 197684 198028 conserved hypothetical protein ΒΙ00586 198149 198763 ٠ nariowly conserved hypothetical membrane protein WO 2010/055499 PCT/IE2009/000079 -29- 2016206219 18U12016 ΒΙ00587 198817 200226 hypothetical membrane protein with unknown function ΒΙ00588 200521 201177 + phosphoglycerate mutase family protein ΒΙ00589 201278 202228 t conserved hypothetical protein ΒΙ00590 202352 203224 + transglycolase, epimerase ΒΙ00591 203348 204496 extensin precursor (cell wall hydroxyproline-rich glycoprotein) ΒΙ00790Ϊ 204684 204866 t hypotlietical protein BL0470 ΒΙ00592 205053 206570 t glutamyl-tRNA synthetase ΒΙ00593 207503 207988 t hypothetical protein Blon021299 ΒΙ00594 207946 208221 hypothetical protein ΒΙΌ466 ΒΙ00595 208388 214285 ٠ cell wall surface anchor family protein, autlientic ftameshift ΒΙ00596 214390 215208 hypothetical ΒΙ00597 216652 218460 t conserved hypothetical integral membrane protein ΒΙ00598 218637 219317 ؛ membrane antigen, putative ΒΙ00599 219470 220744 t Integral membrane protein ΒΙ00600 220769 222070 ا possible permease protein of ABC transporter system ΒΙ00601 222107 223327 ا possible permease protein of ABC transporter system ΒΙ00602 223346 224140 + ABC transporter, ΑΤΡ-binding protein ΒΙ00603 224259 224819 ٠ lipoprotein, putative ΒΙ00604 224831 225427 transcriptional regulator, TetR family, putative ΒΙ00605 225545 227704 pliage infection protein, putative ΒΙ00606 227704 230250 phage infection protein, putative ΒΙ00607 230686 231969 + membrane protein, putative ΒΙ00608 232037 233602 ا 6-phosphogluconate dehydrogenase, decarboxylating ΒΙ00609 233756 234595 6-phosphogluconolactonase ΒΙ00610 234825 235847 oxppcycle protein OpcA ΒΙ00611 235847 237499 glucose-6-phosphate 1 -dehydrogenase ΒΙ00612 237652 239337 t Unknown ΒΙ00613 239417 240448 Glycosyltransferase involved in cell wall biogenesis ΒΙ00614 240475 241311 transcriptional regulator, TetR family ΒΙ00615 241407 242675 t signal recognition particle-docking protein FtsY ΒΙ00616 243046 244338 t ammonium transporter ΒΙ00617 244343 244678 t Nitrogen regulator protein Ρ-ΙΙ ΒΙ00618 244832 246613 ٠ protein-pll, uridylyltransferase ΒΙ00619 246653 248095 DNA-damage-inducible protein F, putative ΒΙ00620 248301 249827 t replicative DNA helicase BJ0062! 249830 251299 + UDP-N-acetylmuramyl tripeptide synthase Β.00622 251405 252154 t cobyric acid synthase Β100623 252306 252590 t conserved hypothetical protein ΒΙ00624 252590 254407 t ABCI family family Β100625 254428 255447 transcriptional regulator, Lacl family ΒΙ00626 255933 257255 + solute binding protein of ABC transporter system Β100627 257546 258469 + sugar ABC transporter, permease protein, putative ΒΙ00628 258493 259308 ٠ ABC transporter, permease protein, MalFG family ΒΙ00629 259473 261446 + conserved hypothetical protein ΒΙ00630 262147 267966 t hypothetical PCT/IE2009/000079 -30- WO 2010/055499 ΒΙ00631 268074 2٦\1 ؛ cell wall surface anchor family protein, putative ΒΙ00632 271911 272741 ؛ conserved hypothetical protein T.GR00044 ΒΙ00633 272825 273835 prsA Β100634 273960 274439 hypothetical COG3210: Large exoproteins involved in heme utilization or adhesion Β.00635 274604 274891 t ribosomal protein S6 Β100636 274951 275604 ٠ hypothetical single-strand binding protein ΒΙ00637 275668 275913 t ribosomal protein S18 ΒΙ00638 275936 276379 t ribosomal protein L9 ΒΙ00639 276769 277026 ؛ ptsH ΒΙ00640 277029 278705 + phosphoenolpyruvate-protein phosphotransftrase Β100641 278942 279673 ؛ glycerol uptake facilitator protein ΒΙ00642 279763 282468 copper-translocating ρ-type ATPase ΒΙ00643 282580 282858 t COG1937 family protein ΒΙ00644 283012 284325 ؛ flncharacterized BCR, YigN family, COG 1322 family ΒΙ00645 284325 284951 t conserved hypothetical protein ΒΙ00646 285048 285893 t C٥G0566:rRNA methylases ΒΙ00647 285787 286359 t glutamyl-tRNA(Gln) amidotransftrase, c subunit ΒΙ00648 286366 287904 + glutamyl-tRNA(Gln) amidotransferase, A subunit ΒΙ00649 287933 289429 t glutamyl-tRNA(Gln) amidotransferase, B subunit ΒΙ00650 289728 290789 + possible acetyltransferase ΒΙ00651 290803 291114 + conserved hypothetical protein ΒΙ00652 291501 293141 t conserved hypothetical protein ΒΙ00653 293363 294973 t BarJ ΒΙ00654 295245 297248 ؛ transcription termination fector Rho ΒΙ00655 297358 297501 t hypothetical protein ΒΙ00656 297559 297945 ٠ chorismate mutase Β100657 298070 300151 + cell wall surface anchor family protein, putative ΒΙ00658 300383 303220 valyl-tRNA synthetase, putative ΒΙ00659 303262 304686 ABC transporter, periplasmic substrate-binding protein, putative ΒΙ00660 304850 305533 endonuclease III ΒΙ00661 305595 306374 transcriptional regulator ΒΙ00662 306556 307212 membrane protein, putative ΒΙ00663 307369 307950 integral membrane protein in the up!59 Β100664 308187 308678 inorganic pyrophosphatase Β100665 308908 311145 alpha-amylase femily protein ΒΙ00666 311386 313377 ٠ conserved hypothetical protein ΒΙ00667 313988 315019 t homoserine o-succinyltransferase ΒΙ00668 315484 316293 t ATP synthase FO, A subunit ΒΙ00669 316400 316624 t ATP synthase FO, c subunit ΒΙ00670 316684 317199 t ATP synthase FO, B subunit ΒΙ00671 317237 318070 + ATP synthase FI, delta subunit ΒΙ00672 318149 319777 ؛ ATP synthase FI, alpha subunit ΒΙ00673 319784 320704 t ATP synthase FI, gamma subunit ΒΙ00674 320716 322185 t ATP synthase FI, beta subunit ΒΙ00675 322188 322478 + ATP synthase FI, epsilon subunit, putative ΒΙ00676 322539 323336 t Predicted nuclease of the RecB family ΒΙ00677 323388 324374 possible secreted peptidjd-prolyl cis-trans isomerase protein ΒΙ00678 324455 325531 t conserved hypothetical protein ΒΙ00679 325534 326538 t conserved hypothetical protein 12016لال18 2016206219 WO 2010/055499 PCT/JE2009/000079 -31- 2016206219 18U12016

ΒΙ00680 326790 327761 t thioredoxin [importedl, putative ΒΙ00681 327850 328473 Adenylate cyclase ΒΙ00682 329012 329398 t endoribonuclease L-PSP, putative ΒΙ00683 329536 330498 + Acyltransferase domain protein ΒΙ00684 330595 331593 ؛ glycerol-3-phosphate dehydrogenase, NAD-dependent ,ΒΙ00685 331783 332967 t D-ala D-ala ligase ΒΙ00686 333223 334386 ٠ ABC transporter, periplasmic substrate-binding protein ΒΙ00687 334206 335348 spermidine/putrescine ABC transporter, permease protein, putative ΒΙ00688 335348 336199 ؛ spermidine/putrescine ABC transporter, permease protein, putative ΒΙ00689 336207 337481 ؛ spermidine/putrescine ABC transporter, ATP-binding protein ΒΙ00690 337788 338828 ٠ CAAX amino terminal protease family protein family Β100691 338873 339667 Mechanosensitive ion channel family Β100692 339751 341181 aspartate ammonia-lyase ΒΙ00693 341302 342030 transcriptional regulator, TetR family domain protein ΒΙ00694 342124 343527 conserved liypothetical protein ΒΙ00695 343852 344400 methylated-DNA—protein-cysteine methyltransferase Β100696 345228 346055 t hypothetical protein with helix turn helix motif ΒΙ00697 345928 347202 MFS transporter family protein, putative ΒΙ00698 347393 348406 ribokinase [importedl BI00939t 348735 349001 t ribosomal protein L28 ΒΙ00699 349116 351944 t ATP-dependent DNA helicase RecG ΒΙ00700 352204 352782 t methyltransferase, putative ΒΙ00701 352812 353624 tRNA (guanine-N 1 )-methyltransferase Β100702 353623 355341 ؛ Unknown Β.00703 355422 356399 t conserved hypothetical protein ΒΙ00704 356482 357354 ا 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, putative ΒΙ00705 357367 358041 + pyrrolidone-carboxylate peptidase, putative ΒΙ00706 358303 359766 t IgA-specific serine endopeptidase, putative ΒΙ00707 359884 361224 t aminopeptidase c ΒΙ00708 361519 362649 t phospho-2-dehydro-3-deoxyheptonate aldolase ΒΙ00709 362781 364010 t phospho-2-dehydro-3-deoxyheptonate aldolase ΒΙ00710 364141 364845 + ΜΤΑ/SAH nucleosidase ΒΙ00711 365444 366427 + hypothetical ATPase, histidine kinase-, DNA gyrase Β-, and HSP90-like domain protein ΒΙ00712 366563 367330 t DNA-binding response regulator RegX3 ΒΙ00713 367583 368713 ٠ phosphate ABC transporter, phosphate-binding protein ΒΙ00714 368927 369877 t pstC2 ΒΙ00715 369997 370875 phospliate ABC transporter, permease protein ΒΙ00716 370931 371707 + phT ΒΙ00717 372005 372580 ؛ lemA protein ΒΙ00718 372647 374902 ٠ conserved hypotlietical protein ΒΙ00719 374971 375831 ٠ oxidoreductase, aldo/keto reductase femily ΒΙ00720 375932 376981 t inosine-uridine preferring nucleoside hydrolase Β100721 377109 377729 I6S rRNA processing protein RimM WO 2010/055499 PCT/IE2009/000079 2016206219 18U12016 -32- ΒΙ00722 ymss 377985 KH domain protein ΒΙ00723 378009 378467 ribosomal protein S16 ΒΙ00724 378703 379809 Endonuclease/Exonuclease/phosphatase family family ΒΙ00725 379889 381634 - signal recognition particle protein ΒΙ00726 381843 382748 + cation efflux family protein superfamily ΒΙ00727 382773 384488 cystcinyl-tRNA synthetase ΒΙ00728 384518 385363 t possible amidotransferase ΒΙ00729 385627 387687 + ABC transporter, ΑΤΡ-binding protein ΒΙ00730 387746 388162 plasmid stability protein StbB ΒΙ00731 388175 388450 hypothetical protein ΒΙ00732 388609 389160 acetolactate synthase, small subunit ΒΙ00733 389180 391144 acetolactate syntliase, large subunit, biosynthe-tic type ΒΙ00734 391308 392033 ribonuclease III ΒΙ00735 392189 392380 ribosomal protein L32 ΒΙ00736 392472 393098 Uncharacterized ACR, COG 1399 ΒΙ00737 393191 394078 conserved hypothetical protein ΒΙ00738 394089 394586 pantetheine-phosphate adenylyltransferase ΒΙ00739 394860 395150 conserved hypothetical protein ΒΙ00740 395198 396205 K. channel, beta subunit BI0074J 396379 396804 transcription regulator, MerR family NMB1303 [imported], putative ΒΙ00742 396910 397533 hypotlietical transmembrane protein with unknown function ΒΙ00743 397764 399083 ؛ nicotinate phosphoribosyltransferase, putative ΒΙ00744 399381 400142 + ribonuclease PH ΒΙ00745 400189 400944 + Haml family ΒΙ00746 401106 402659 t hypothetical FemAB family ΒΙ00747 402736 404043 t FemAB family protein, putative ΒΙ00748 404096 405373 + beta-lactam resistance factor, putative ΒΙ00749 405462 406460 membrane protein, putative ΒΙ00750 407182 408879 t glucose-6-phosphate isomerase ΒΙ00751 409515 409877 t ribosomal protein L19 ΒΙ00752 410047 410901 + lepB ΒΙ00753 411024 411860 t ribonuclease Hll ΒΙ00754 411990 413102 ؛ transcription regulator, Lacl family [imported] ΒΙ00755 413261 414904 ٠ probable sugar kinase ΒΙ00756 414992 415681 + sugar isomerase ΒΙ00757 416114 417430 + L-arabinose isomerase Β100758 417620 418240 trp-G type glutamine amidotransferase/dipeptidase ΒΙ00759 418178 420178 t membrane protein, putative Β100760 420330 421694 t permease, putative Β.0076. 421694 422914 t transmembrane protein ٧expl١ putative Β.00762 422930 423562 + ٧exp2 ΒΙ00763 423886 425706 long-chain-fatty-acid—CoA ligase, putative ΒΙ00764 425820 426098 + fragment ofarabinose permease BJ00765 426765 429890 ٠ hypothetical ABC transporter ΒΙ00766 430170 430436 major facilitator femily transporter CC08I4 [imported], putative ΒΙ00767 431272 432618 ا solute binding protein of ABC transporter system ΒΙ00768 432750 433799 t sugar ABC transporter, permease protein, putative WO 2010/055499 PCT/IE2009/000079 2016206219 18Jul2016 -33- ΒΙ00769 433820 434809 ؛ Unknown ΒΙ00770 435125 437128 t beta-D-galactosidase, putative ΒΙ00771 437175 438227 ؛ transcription regulator, LacI family [imported], putative ΒΙ00772 438426 441116 ا arabinogalactan endo-1,4-beta-galactosidase, putative ΒΙ00773 441755 442621 + oxidoreductose, aldo/keto reductase family ΒΙ00774 442628 443368 + conserved hypothetical protein ΒΙ00775 443378 444745 conserved hypothetical protein ΒΙ00776 445003 446367 + transport protein, NRAMP family ΒΙ00777 446472 448073 ذ drug resistance transporter, EmrB/QacA subfamily ΒΙ00778 448424 450007 t glycosyl transferase CpsE ΒΙ00779 450302 452029 + COG0840: Methyl-accepting chemotaxis protein ΒΙ00780 452064 453566 possible Etk-like tyrosine kinase involved in Eps biosynthesis ΒΙ00781 453760 454725 hypothetical glycosyl transferase, group 1 family protein ΒΙ00782 454725 456065 ؛ putative glycosyltransferase protein ΒΙ00783 456065 457126 NAD dependent epimerase/dehydratase family protein Β100784 457201 458448 + UDP-glucose 6-dehydrogenase Β100785 458489 459550 ؛ hypothetical glycosyl transferase, group 1 family protein ΒΙ00786 459581 460408 t liypothetical EpsllI Β100787 460446 460952 ؛ hypothetical Bacterial transferase hexapeptide (three repeats) ΒΙ00788 460985 461998 ٠ hypothetical Capsular polysaccliaride synthesis protein Β100789 462020 463360 + hypothetical protein Β.00790 463363 464292 t Eps9K ΒΙ00791 464362 465753 ؛ hypothetical Polysaccharide biosynthesis protein ΒΙ00792 465789 466280 + hypothetical Bacterial transferase hexapeptide (three repeats) Β100793 466366 467514 NAD-dependent epimerase/dehydratase femily protein, putative ΒΙ00794 467785 468363 transposase, degenerate Β100795 468615 468770 hypothetical COG2963: Transposase and inactivated derivatives ΒΙ00796 469189 470208 t dTDP-glucose 4,6-dehydratase ΒΙ00797 470347 471303 + dTDP-4-dehydrorhamnose3,5-epimerase ΒΙ00798 471349 472245 ؛ glucose-l -phosphate thymidylyltransferase Β.00799 472858 473046 hypothetical protein Β100800 473371 473802 conserved hypothetical protein ΒΙ00801 474083 474640 hypothetical Low molecular weight phosphotyrosine protein phosphatase ΒΙ00802 474825 475331 liypothetical protein ΒΙ00803 475655 475867 liypothetical Helix-turn-helix ΒΙ00804 475860 476042 liypothetical protein Β100805 475971 476312 t hypothetical protein ΒΙ00806 476415 477422 conserved hypothetical protein ΒΙ00807 477471 478751 t narrowly conserved hypothetical protein ΒΙ00808 477495 477866 tliioredoxin ΒΙ00809 478880 479734 t 3-oxoadipate enol-lactonase, putative WO 2010/055499 PCT/IE2009/000079 -34- 2016206219 18Jul2016 ΒΙ00810 479747 481036 ٠ MutT/nudix family protein Β100811 481065 481475 t glycine cleavage system H protein ΒΙ00812 481547 482875 + conserved hypothetical protein ΒΙ00813 482973 485453 t protease 11 ΒΙ00814 485521 486549 1 3-isopropylmalate dehydrogenase ΒΙ00815 486610 487692 + lipoate-protein ligase a ΒΙ00817 487934 488650 ا probable transcriptional regulator with cyclic nucleotide-binding domain ΒΙ00818 488757 491069 + ponA, putative ΒΙ00819 491264 492634 + NADH-dependent flavin oxidoreductase, putative ΒΙ00820 492807 493955 dihydroorotate dehydrogenase, putative ΒΙ00821 494409 495122 t glycerol-3-phosphate regulon repressor ΒΙ00822 495118 496365 ؛ galactose-l-phosphate uridylyltransferase ΒΙ00823 496241 497632 t galactokinase ΒΙ00824 497718 497987 + ACT domain protein ΒΙ00825 498201 499487 + similar to unknown proteins ΒΙ00826 499800 500516 spoil ΒΙ00827 500612 501463 + mutY ΒΙ00828 501531 502250 t conserved hypothetical protein ΒΙ00829 502633 505968 t DNA-directed RNA polymerase, beta subunit ΒΙ00830 506139 510173 ٠ DNA-directed RNA polymerase, beta-prime subunit Β100831 510338 510967 FHA domain protein Β100832 510986 511498 hypothetical protein BIon020438 Β100833 511528 512457 possible phosphoprotein phosphatase Β100834 512457 514967 membrane protein, putative ΒΙ00835 514967 516187 Protein of unknown fimction family Β100836 516215 517585 moxR2 ΒΙ00837 517599 523580 cell wall surface anchor family protein, putative ΒΙ00838 523750 525168 serine/threonine protein kinase, putative ΒΙ00839 525300 529592 ٠ hypothetical COG0210: Superfamily I DNA and RNA helicases ΒΙ00840 529427 533620 1 UvrD/REP helicase domain protein ΒΙ00841 533962 535152 + possible transport protein ΒΙ00842 535527 536243 t dihydrodipicolinate reductase ΒΙ00843 536388 537311 + dihydrodipicolinate synthase ΒΙ00844 537585 539246 t metallo-beta-lactamase superfamily protein ΒΙ00845 539291 541897 + Peptidase family Ml domain protein ΒΙ00846 542078 542971 ؛ hypothetical transmembrane protein with unknown function ΒΙ00847 543164 543502 t conserved hypothetical protein ΒΙ00848 543954 545336 t phosphoglucosamine mutase ΒΙ00849 545362 546012 + polypeptide deformylase ΒΙ00850 546072 547472 t conserved hypothetical protein ΒΙ00851 547492 547620 t hypothetical protein Β100852 547858 548979 t peptide chain release factor 2 Β.00853 548991 550121 + ftsE Β.00854 550135 551055 ؛ cell division ABC transporter, permease protein FtsX, putative ΒΙ00855 551161 552519 + autolysin, putative Β.00856 552673 553146 ٠ SsrA-binding protein Β100857 553192 554265 t amino acid ABC transporter, permease protein ΒΙ00858 554479 555420 ٠ amino acid ABC transporter, permease protein WO 2010/055499 PCT/IE2009/000079 2016206219 18Jul2016 -35- ΒΙ00859 555554 556546 ٠ amino acid ABC transporter, permease protein ΒΙ00860 556566 557393 t glutamine ABC transporter, ΑΤΡ-binding protein ΒΙ00861 557604 559493 ا glucosamine—ftuctose-6-phosphate aminotransferase, isomerizing ΒΙ00862 559699 560271 ا COG0564: Pseudouridylate synthases, 23S RNA-specific Β100863 560313 560525 hypothetical protein Blon020898 ΒΙ00864 560565 561548 transcriptional regulator, LacI family, putative ΒΙ00865 561794 562717 t sugar ABC transporter, permease protein, putative ΒΙ00866 562116 563780 t Unknown ΒΙ00867 563975 566047 t beta-D-galactosidase ΒΙ00868 566259 567185 + transcriptional regulator, LacI family, putative ΒΙ00869 567311 569008 alpha-L-arabinofuranosidase ΒΙ00870 569168 570517 t solute binding protein of ABC transporter system ΒΙ00871 570852 572192 probable solute binding protein of ABC transporter system for sugars ΒΙ00872 572449 573729 t sugar binding protein Sbp ΒΙ00873 573795 574562 transcription activator, probable Baf family ؛imported] ΒΙ00874 574688 576304 + ABC transporter, periplasmic substrate-binding protein, putative ΒΙ00875 576372 577346 ؛ membrane protein, putative ΒΙ00876 577346 578245 ؛ peptide ABC transporter, permease protein, putative ΒΙ00877 578245 579033 ؛ ABC transporter, nucleotide binding/ATPase protein ΒΙ00878 579029 579811 ٠ ABC transporter, ΑΤΡ-binding protein ΒΙ00879 580296 581360 t cystathionine beta-synthase ΒΙ00880 581455 582636 t cystathionine beta-lyase ΒΙ00881 582780 584501 ErTC/YbiS/YcfS/YnhG family ΒΙ00882 584781 586613 t ATP-dependent DNA helicase RecQ ΒΙ00883 586729 587220 t autoinducer-2 production protein LuxS BJ00884 587453 587917 + acetyltransferase, GNAT family, putative ΒΙ00885 588181 589638 hypothetical protein Blon020876 ΒΙ00886 589890 591347 amino acid permease ΒΙ00887 591542 592891 + alanine racemase Β100888 593087 594370 deoxyguanosinetriphosphatetriphosphohydrolase, putative ΒΙ00889 594546 596642 t DNA primase, putative ΒΙ00890 596961 597710 t pyridoxine biosynthesis protein ΒΙ00891 597799 598434 ؛ SNO glutamine amidotransferase femily superfamily ΒΙ00892 598495 600156 ؛ aminotransferase, class I, putative ΒΙ00893 600514 601443 + asparaginase family protein ΒΙ00894 601476 601607 t hypothetical protein Blon020867 ΒΙ00895 601574 601897 hypothetical protein ΒΙ00896 601995 603179 ٠ possible transport protein ΒΙ00897 603210 603467 hypothetical protein Blon020865 Β.00898 603634 603723 + hypothetical protein Β100899 603651 605795 similar to alpha-L-arabinofuranosidase A ΒΙ00900 605923 606921 + EF0065, putative Β100901 607014 608087 conserved hypothetical protein Β100902 608687 609373 t ABC transporter, ΑΤΡ-binding protein WO 2010/055499 PCT/IE2009/000079 2016206219 18U12016

-36- ΒΙ00903 609373 610545 + conserved hypothetical protein ΒΙ00904 610560 612116 t ABC transporter, ΑΤΡ-binding protein ΒΙ00905 612106 614304 l-deoxyxylulose-5-phosphate synthase ΒΙ00906 614478 615467 ؛ oxidoreductase, zinc-binding, putative ΒΙ00907 615572 616069 + phosphoribosylaminoimidazole carboxylase, catalytic subunit ΒΙ00908 616095 617231 + phosphoribosylaminoimidazole carboxylase, ATPase subunit ΒΙ00909 617243 617668 + furB ΒΙ00910 617709 617954 conserved hypothetical protein ΒΙ00911 618183 619103 ؛ possible solute binding protein of ABC transporter system ΒΙ00912 619367 621439 + membrane protein, putative ΒΙ00913 621563 623197 aldehyde dehydrogenase ΒΙ00914 الألآة 624842 phosphoribosylamine—glycine ligase ΒΙ00915 624872 625702 phosphoribosylformylglycinamidine cyclo-ligase ΒΙ00916 626029 6ΤΊ5Υ1 amidophosphoribosyltransferase ΒΙ00917 627944 628726 glutamine ABC transporter, ΑΤΡ-binding protein ΒΙ00918 628726 629610 amino acid ABC transporter, perjnease protein ΒΙ00919 629723 630583 amino acid ABC transporter, periplasmic amino acid-binding protein Β100920 630788 631255 conserved hypothetical protein ΒΙ00921 631328 632698 Atz/Trz family protein, putative ΒΙ00922 632741 634240 S-adenosyl-L-homocysteine hydrolase, NAD binding domain ΒΙ00923 634405 635991 ؛ structural gene for ultraviolet resistance ΒΙ00924 635991 636206 t hypothetical protein Blon020836 ΒΙ00925 636246 637220 Κ+ channel, beta subunit BJ00926 637331 638293 transcriptional regulator, HTH 1 family, putative ΒΙ00927 638512 640023 t Na+/H+ antiporter, putative ΒΙ00928 640043 640699 membrane protein, putative ΒΙ00929 640699 642066 conserved hypothetical protein ΒΙ00930 642042 643337 possible carboxylesterase or lipase ΒΙ00931 643478 647209 phosphoribosylformylglycinamidine synthase ΒΙ00932 ة4٦1٦ة 648024 phosphoribosylaminoimidazole-succinocarboxamide synthase ΒΙ00933 648113 648232 hypothetical protein ΒΙ00934 648420 649754 phosphoribosylglycinamide formyltransferase 2 VC 1228 fimportedl ΒΙ00935 649928 651085 ا type 1 capsular polysaccharide biosynthesis protein ل (capj) ΒΙ00936 651238 652260 conserved hypothetical protein ΒΙ00937 652822 653880 t transporter ΒΙ00938 654695 654967 t ribosomal protein S12 Β!00939 654976 655443 t ribosomal protein S7 Β100940 655478 657598 ؛ translation elongation factor G ΒΙ00941 1114ةة 658970 t translation elongation factor Tu Β100942 659184 659909 t conserved hypothetical protein ΒΙ00943 660169 660864 t transcriptional regulator, LysR family, putative ΒΙ00944 661085 662098 t membrane protein, putative ΒΙ00945 662161 1«٦ COG2246: Predicted membrane protein ΒΙ00946 662721 663083 CrcB protein ΒΙ00947 663086 663619 protein with similarity to CrcB WO 2010/055499 PCT/IE2009/000079 2016206219 18Jul2016 -37- ΒΙ00948 663706 663987 ٠ hypothetical protein ΒΙ00949 664023 665063 t alcohol dehydrogenase, zinc-containing ΒΙ00950 665625 t hypothetical protein ΒΙ00951 665652 667028 conserved hypothetical protein ΒΙ00952 ٦2%ةة 667462 possible MarRtype transcriptional regulator ΒΙ00953 667902 670487 ٠ excinuclease ABC, subunit A ΒΙ00954 670548 671903 + MATE efflux femily protein, putative ΒΙ00955 671914 672603 + endonuclease III, putative ΒΙ00956 672783 673076 hypothetical protein Blon020400 ΒΙ00957 673098 6ΊΎ1 t Unknown ΒΙ00958 673782 674042 hexapeptide-repeatcontaining-acetyltransferase ΒΙ00959 674207 675292 t possible integral membrane permease protein ΒΙ00960 675273 675902 ٠ hypothetical Glycosyl hydrolases family 2, TIM barrel domain ΒΙ00961 676090 677316 glutamine synthetase, type I ΒΙ00962 677846 678625 narrowly conserved hypothetical transmembrane protein ΒΙ00963 678712 680199 dihydrolipoamide dehydrogenase ΒΙ00964 680351 680971 conserved hypothetical protein ΒΙ00965 681063 682427 ٠ widely conserved protein in peptidase or deacetlylase family ΒΙ00966 682730 683326 + conserved hypothetical protein ΒΙ00967 683329 684801 t ABC transporter, ΑΤΡ-binding protein, putative Β100968 684801 685625 ٠ possible permease protein of ABC transporter for cobalt ΒΙ00969 685824 686699 + spoU rRNA methylase family protein fimported. BJ00970 686891 687820 + phenylalanyl-tRNA synthetase, alpha subunit ΒΙ00971 687831 690437 + phenylalanyl-tRNA synthetase, beta subunit ΒΙ00972 690471 691154 + conserved hypotlietical protein ΒΙ00973 691385 692347 + N-acetyl-gamma-glutamyl-phosphate reductase ΒΙ00974 692434 693519 + arginine biosynthesis bifunctional protein ArgJ BI00013g 693503 693979 hypotlietical protein Magn025872 ΒΙ00975 693809 694612 t acelylglutamate kinase ΒΙ00976 694605 695897 t acetylornithine aminotransferase ΒΙ00977 695944 696906 ؛ ornithine carbamoyltransferase ΒΙ00978 696906 697415 t arginine repressor ΒΙ00979 697501 698736 t argininosuccinate syntliase ΒΙ00980 699184 700653 t argininosuccinate lyase Bl٠!326t 701005 701196 t thiamine biosynthesis protein This Β.00981 701211 702077 t thiG protein ΒΙ00982 702157 702963 t moeB Β.00983 703023 703376 t rhodanese-like domain protein Β.00984 703541 704071 t HD domain protein ΒΙ00985 703978 704835 + hypothetical ΒΙ00986 704964 706283 t tyrosyl-tRNA syntlietase Β.00987 706314 708086 + hypotlietical protein B11050 ΒΪ00988 708098 709135 ب Predicted sugar phosphatases oftlie HAD superfamily Β100989 709395 710165 ؛ hemolysin A Β.00990 710153 710719 conserved hypotlietical protein Β100991 710729 710881 ؛ hypothetical protein Β.00992 710965 711624 similar to a bacterial K(+)-uptake system ΒΙ00993 711678 713141 Cation transport protein domain protein PCT/IE2009/000079 WO 2010/055499

.38- ΒΙ00994 713388 714407 t po٠y(P)/ATP-NAD kinase ΒΙ00995 714410 716233 ٠ DNA repair protein RecN ΒΙ00996 716266 716910 ؛ hydrolase, haloacid dehalogenase-like family, putative ΒΙ00997 717154 ة2ة1\1 ؛ transcriptional regulator, GntR family ΒΙ00998 717550 718467 + ABC transporter, ΑΤΡ-binding protein BI0135H 718477 719091 t membrane protein, putative ΒΙ00999 719985 722768 calcium-translocating Ρ-type ATPase, PMCA-type ΒΙ01000 722966 723238 t hypothetical protein ΒΙΊ037 ΒΙ01001 723291 12411% threonine synthase ΒΙ01356، 725001 725699 t serine hydroxymethyltransferase ΒΙ01002 726028 727116 + gamma-glutamyl phosphate reductase ΒΙ01003 727134 727694 ٠ conserved hypotlietical protein Β101004 727694 728476 ٠ nicotinate (nicotinamide) nucleotide adenylyltransferase ΒΙ01005 728580 729857 glycosyl hydrolase, family 3, putative Β101006 729952 733203 + Uncharacterized ACR ΒΙ01007 733340 733834 phosphinothricinacetyltransferase ΒΙ01008 734033 734629 t peptidyl-tRNA hydrolase ΒΙ01009 734622 738203 t transcription-repair coupling factor ΒΙ01010 738346 739290 + oxidoreductase, putative ΒΙ01011 739444 740739 t enolase ΒΙ01012 740809 741423 t hypothetical Septum fomation initiator ΒΙ01013 741423 741986 + conserved hypothetical protein ΒΙ01014 742052 743050 ؛ possible exopolyphosphatase-like protein Β101015 743578 744711 + IS30 family, transposase (imported] ΒΙ01016 744846 747062 ؛ L-serine dehydratase 1 ΒΙ01018 747207 747611 ؛ peptidyl-prolyl cis-trans isomerase, FKBP-type ΒΙ01019 747713 748189 ؛ transcription elongation fector GreA Β101020 748250 749191 hemolysin, putotive ΒΙ01021 749361 750086 t conserved hypothetical protein Β101022 750474 751736 t histidine kinase-like protein Β101023 751815 752090 hypothetical Transcription factor WhiB Β101024 752207 753922 diarrheal toxin Β101025 754203 755633 Transcriptional regulator B٠0١389t 755884 756180 t whiBl Β101026 756350 759319 t membrane protein, putative Β101027 759319 760857 ا LPXTG-motif cell wall anchor domain protein, putative ΒΙ01028 760966 761391 conserved hypothetical protein ΒΙ01029 761660 762283 1 conserved hypothetical protein ΒΙ01030 762332 763015 t Phosphoribosyl transferase domain protein BI00019g 762937 763509 hypotlietical Peptidase femily S24 ΒΙ01031 763391 764464 sensory box histidine kinase, putative ΒΙ01032 764464 765183 DNA-binding response regulator MtrA ΒΙ01033 765222 767432 l,4-alpha-glucan branching enzyme BIO1034 767649 768239 + possible transcriptional regulator ΒΙ0Ι035 768351 768872 ٠ 2C-methyl-D-etythritol 2,4-cyclodiphosphate synthase ΒΙ01036 768930 769760 zinc ABC transporter, pemease protein, putative ΒΙ01037 769830 770834 ABC transporter, ΑΤΡ-binding protein ΒΙ0Ι038 770893 772419 - possible solute binding protein of ABC 12016لال18 2016206219 -39- 2016206219 18Jul2016 PCT/IE2009/000079 WO 2010/055499 transporter system ΒΙ01039 772190 773062 methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase RIO1040 773185 ٦٦n t ribosomal protein SI [imported] BIO041 ا 774834 775448 + dephospho-CoA kinase ΒΙ01042 775463 + excinuclease ABC, B subunit RIO1041 777887 n t TerC family protein [imported] RIO1044 778897 780336 + pyruvate kinase ΒΙ01045 780490 781086 possible NTP pyrophosphatase in MutT family ΒΙ01046 781432 782214 + response regulator ΒΙ01047 782278 785127 + DNA polymerase 1 RIO1048 785291 786217 + conserved hypothetical protein TIGR00486 RIO1049 786266 786937 t MutT/nudix family protein, putative ΒΙ01050 787135 789132 + glycogen operon protein GlgX B٠01424t 789186 789413 t hypothetical protein with helix turn helix motif ΒΙ01051 789420 790067 + conserved hypothetical protein ΒΙ01052 790243 790794 DNA-3-methyladenine glycosylase 1 ΒΙ01053 791884 792942 hypothetical protein ΒΙ01054 793226 793780 t hypothetical protein ΒΙ01055 793761 794246 hypothetical protein BI00021g 794049 794498 + transposase B BI00020g 794300 794749 t IS1601-D ΒΙ01056 794665 794844 + transposase subunit B ΒΙ01057 794937 795989 integrase/recombinase XerC, probable [imported], putative BI01434t 795989 796876 probable integrase/recombinase ΒΙ01058 796951 798150 probable integrase/recombinase ΒΙ01059 798284 799564 IS3-Spnl, transposase ΒΙ01060 799635 800477 putative transposase subunit Β101061 800762 802579 hypothetical Protein of unknown function DUF262 Β101062 802742 803464 hypothetical protein ΒΙ01063 803748 804065 conserved hypothetical protein ΒΙ01064 804058 804405 hypothetical protein ΒΙ01065 804667 808221 ٠ DNA polymerase 111, alpha chain VC2245 [imported] ΒΙ01066 808312 808743 + conserved hypothetical protein ΒΙ01067 808952 810826 t antigen, 67 kDa ΒΙ01068 810916 811413 ؛ NH2-acetyltransferase ΒΙ01069 817553 818377 oxidoreductase, aldo/keto reductase family ΒΙ01070 818538 819956 t sugar kinase, FGGY family, putative ΒΙ0145Β 819972 820262 + Acylphosphatase Β101071 820382 821761 t histidinol dehydrogenase ΒΙ01072 821761 822918 + histidinol-phosphate aminotransferase ΒΙ01073 823007 823603 t imidazoleglycerol-phosphate dehydratase Β101074 823606 824397 + hypothetical protein Blon.20586 Β10Ι075 824435 825079 ؛ imidazole glycerol phosphate synthase, glutamine amidotransferase subunit Β101076 825152 825874 + bifunctional HisA/TrpF protein Β.01077 825984 826103 narrowly conserved hypotlietical protein BI01463t 826039 827637 conserved hypothetical protein ΒΙ01078 827738 828898 + Glutamine synthetase, catalytic domain WO 2010/055499 PCT/IE2009/000079 -40- 2016206219 18Jul2016 ΒΙ01079 829137 829604 ا transporter, putative ΒΙ01080 829657 830625 conserved hypothetical protein ΒΙ01081 830625 834758 ATP-dependent helicase HrpA ΒΙ01082 834751 835404 conserved hypothetical protein ΒΙ01083 835647 837065 t GTP-binding protein ΒΙ01084 837405 838208 t !'-lactate dehydrogenase ΒΙ01085 838356 839291 cation efflux system protein ΒΙ01086 839460 840182 LexA repressor ΒΙ01087 840333 840680 t LysM domain protein ΒΙ01088 840736 841173 ؛ conserved hypothetical protein T1GR00244 Β101089 841314 842510 D-3-phosphoglycerate dehydrogenase ΒΙ01090 842524 844800 COG3973:Superfamily I DNA and RNA helicases ΒΙ01091 845133 845651 + conserved hypothetical protein TIGR00242 ΒΙ01092 845654 846730 ؛ S-adenosyl-methyltransferase MraW ΒΙ01093 846740 847186 + hypothetical protein Blon020568 ΒΙ01094 847186 848985 t penicillin-binding protein, putative ΒΙ01095 849015 849884 + conserved hypothetical protein ΒΙ01096 849936 851384 ٠ UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate--D-alanyl-D-alanylligase ΒΙ01097 851453 852535 ؛ phospho-N-acetylmuramoyl-pentapeptide- transferase ΒΙ01098 852593 854035 ؛ UDP-N-acetylmuramoylalanine—D-glutamate ligase ΒΙ01099 854025 855239 ؛ cell division protein, FtsW/RodA/SpoVE family, putative ΒΙ01100 855258 856436 UDP-N-acetylglucosamine—N-acelylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol Ν-acetylglucosamine transferase ΒΙ01101 856651 858075 + !IDP-N-acetylmuramate—alanine ligase ΒΙ01102 858078 859139 + hypothetical Cell division protein FtsQ ΒΙ01.03 859565 860983 + hypothetical Appr-1-p processing enzyme family RIO1104 861241 861813 + unknown ΒΙ01105 861640 861885 hypothetical protein BIO!06 ا 861906 862391 ؛ D-tyrosyl-tRNA(Tyr) deacylase ΒΙΟΙ 107 862494 863735 glucose/galactose transporter, putative ΒΙΟΙ 108 863844 864230 hypothetical glyoxalase femily protein ΒΙΟΙ 109 864308 865201 frtictokinase, putative ΒΙ01110 865277 866488 transcription regulator ROK femily VC2007 [imported], putative ΒΙΟΙ11 ا 866715 867626 t glucokinase, putative ΒΙ01112 867792 868913 NagC/XylR-type transciptional regulator ΒΙΟΙ 113 869251 870060 t glucosamine-6-phosphateisomerase ΒΙΟΙ14 ا 870119 871393 + N-acetylglucosamine-6-phosphatedeacetylase ΒΙ01115 871646 873307 ؛ dipeptide ABC transporter, dipeptide-binding protein ΒΙ01116 873480 874568 ٠ oligopeptide ABC transporter, permease protein ΒΙΟΙ 117 874714 875739 t dipeptide ABC transporter, permease protein ΒΙ01118 875746 877452 + ATP binding protein of ABC transporter ΒΙΟΙ 119 877508 878026 MutT/nudix family protein ΒΙ01120 878078 879670 Xaa-Pro aminopeptidase 1 ΒΙΟΙ 121 879977 880954 conserved hypothetical protein ΒΙΟΙ 122 882044 883672 ٠ foie WO 2010/055499 PCT^2009/000079 -41- 2016206219 18Jul2016 ΒΙ01123 883736 887410 ٠ SMC family, c-terminal domain family ΒΙ01124 887535 888527 conserved hypothetical protein ΒΙ01125 888652 890202 UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase ΒΙ01126 890377 891126 t RNA polymerase sigma-70 factor, ECF subfemily ΒΙ01127 891129 891446 + conserved hypothetical protein ΒΙ01128 891719 892660 Aldose l-epimerase superfomily ΒΙ01129 892788 893741 Aldose l-epimerase superfamily ΒΙ01130 894032 895021 t hydroxymethylbutenyl pyrophosphate reductase ΒΙ01131 895067 895573 transcriptional regulator, putative ΒΙ01132 895670 896725 glyceraldehyde-3-phosphate dehydrogenase, type I ΒΙ01133 896968 897690 Thiamin pyrophosphokinase, catalytic domain family ΒΙ01134 897586 898923 t hypothetical Spermine/spermidine synthase ΒΙ01135 899364 899930 ؛ Translation initiation factor IF-3, C-terminal domain BI00041g 899764 900105 t ribosomal protein L35 ΒΙ01136 900161 900541 t ribosomal protein L20 ΒΙ01137 900605 901537 t Integrase ΒΙ01138 901668 904511 ؛ ABC transporter, ΑΤΡ-binding protein ΒΙ01139 904656 905612 t Soj family protein ΒΙ01140 905634 906545 t Uncharacterised ACR, COG1354 ΒΙ01141 906675 907274 t conserved hypothetical protein TIGR00281 ΒΙ01142 907409 908233 t MutT/nudix family protein Β101143 908296 909573 t quinolinate synthetase complex, A subunit ΒΙ01144 909668 911296 + !'-aspartate oxidase ΒΙ01145 911303 912193 t nicotinate-nucleotidepyrophosphoiylase ΒΙ01146 912292 913443 ٠ possible pyridoxal-phosphate-dependent aminotransferase ΒΙ01147 913478 914824 t major facilitator fomily transporter ΒΙ01148 915142 917070 + GTP-binding protein TypA Β101149 917197 917616 ٠ conserved hypothetical protein ΒΙ01150 917699 918673 ٠ preplienate dehydratase, putative Β101151 918670 919734 ٠ preplienate dehydrogenase ΒΙ01152 919947 920201 t conserved hypothetical protein ΒΙ01153 920239 921303 t phage integrase femily protein Rim 154 921559 923196 ٠ solute binding protein of ABC transporter system possibly for peptides ΒΙ01155 923500 924423 t dppB ΒΙ01156 924445 925446 t dppC ΒΙ01157 925505 927478 ا ABC-type transporter, duplicated ATPase component ΒΙ01158 927793 928650 exodeoxyribonuclease 1.1 ΒΙ01159 928775 929626 t conserved hypothetical protein ΒΙ01160 929645 930400 ٠ narrowly conserved hypothetical transmembrane protein ΒΙ01161 930393 931658 + RNA methyltransforase, TrmA fomily ΒΙ01162 931673 932365 t lipoprotein, putative ΒΙ01163 932483 935032 t cation-transporting ATPase, Ε1-Ε2 fomily ΒΙ01164 935156 937852 t aconitate hydratase 1 ΒΙ01Ι65 938001 938360 ٠ Ribbon-helix-helix protein, copG fomily domain protein WO 2010/055499 PCT/IE2009/000079 2016206219 18U12016 -42- ΒΙΟΙ 166 938363 938851 ٠ PIN domain, putative ΒΙΟΙ 167 938917 941019 Protein of unknown function DUF262 family ΒΙΟΙ 168 941112 %\ΊΊΊ acetyltransferase, GNAT family fomily ΒΙΟΙ 169 941793 942608 DNA-binding response regulator, putative ΒΙΟΙ 170 942553 943935 atypical histidine kinase sensor of two-component system ΒΙ01171 944117 944959 conserved hypothetical protein ΒΙΟΙ 172 945143 946039 t membrane protein, putative ΒΙ01173 946326 947195 ؛ membrane protein, putative ΒΙΟΙ 174 947234 948073 GTP pyrophosphokinase [imported] ΒΙ01175 948115 949554 ؛ tRNA-i(6)A37 thiotransferase enzyme MiaB ΒΙΟΙ 176 949568 950551 ( tRNA delta(2)-isopentenylpyrophosphate transferase ΒΙ01177 950591 951517 Fic protein family family ΒΙ01178 951663 954437 t cell division protein FtsR ΒΙ01179 954635 ء CDP-diacylglycerol—glycerol-3-phosphate3-phosphatidyltransferase ΒΙ01180 955282 955812 ؛ competence/damage-inducible protein CinA domain protein ΒΙ01181 955881 956387 ؛ possible DNA binding protein ΒΙ01182 956502 956732 t conserved hypothetical protein ΒΙ01183 957036 958226 t recA protein ΒΙΟ 1184 958232 958822 ؛ regulatory protein RecX ΒΙ01185 959702 960361 t S30AE femily protein ΒΙ01186 960556 963417 t preprotein translocase, SecA subunit BI00044g 963734 963970 COG3464: Transposase and inactivated derivatives ΒΙ01187 963974 964096 COG3464: Transposase and inactivated derivatives BI00045g 964219 964602 + hypothetical protein ΒΙ0497 ΒΙ01188 964674 965717 t anthranilate phosphoribosyltransferase ΒΙΟΙ 189 965964 966686 hypothetical transmembrane protein with unknown function ΒΙ01190 966447 967418 + hypothetical Acyltransferase ΒΙ01191 967476 969722 serine/threonine protein kinase, putative ΒΙΟΙ 192 969893 970858 idsA2 ΒΙΟΙ 193 971179 971838 ٠ conserved hypothetical protein ΒΙΟΙ 194 972002 973465 + RNA polymerase principal sigma fector, sigma 70 ΒΙΟΙ 195 973526 975799 ٠ DNA gyrase, subunit B ΒΙΟΙ 196 975969 977192 t membrane protein, putative ΒΙΟΙ 197 977269 978228 + ribokinase ΒΙΟΙ 198 978247 982977 t DEAD/DEAH box helicase domain protein ΒΙΟΙ 199 982994 983779 DNA-binding response regulator TcrA, putative ΒΙ01200 983927 986953 DNA gyrase A subunit ΒΙ01201 986925 988169 t conserved liypothetical protein ΒΙ01202 988185 989189 conserved hypothetical protein ΒΙ01203 989432 989722 + conserved hypothetical protein ΒΙ01204 989725 990198 t deoxyuridine 5triphosphate nucleotidohydrolase ΒΙ01205 990335 992656 ٠ GTP pyrophosphokinase ΒΙ01206 992780 993058 orffi ΒΙ01207 993226 994425 t probable integrase/recombinase BI01640t 994500 995387 + probable integrase/recombinase ΒΙ01208 995387 996439 t integrase/recombinase XerC, probable [imported]. 2016206219 18U12016 PCT/JE2009/000079 -43- WO 2010/055499 putative ΒΙ01209 996532 997095 COG2801: Transposase and inactivated derivatives BI00053g 997107 997619 ASOPSNART-l lOSRSI ΒΙ01210 997719 998264 possible peptidyl-prolyl cis-trans isomerase ΒΙ01211 998331 999296 COG3391: Uncharacterized conserved protein ΒΙ01212 999519 999623 hypothetical protein ΒΙ01213 999683 1000615 membrane protein, putative ΒΙ01214 1000747 1001295 t Hypothetical cytosolic protein ΒΙ01215 1001329 1002621 conserved hypothetical protein ΒΙ01216 1002648 1003532 t possible phosphoglycerate mutase ΒΙ01217 1003650 1004597 t magnesium transporter, CorA family ΒΙ01218 1004615 1005538 t glnH, putative ΒΙ01219 1005776 1008544 t leucyl-tRNA synthetase ΒΙ01220 1008708 1009484 ا competence protein ComEA helix-hairpin-helix repeat region domain protein ΒΙ01221 1009553 1011235 ؛ conserved hypothetical transmembrane protein related to ComA ΒΙ01222 1011378 1012721 possible prolidase (Χ-Pro dipeptidase) or chlorohydrolase ΒΙ01223 1012791 1013759 ؛ conserved hypothetical protein ΒΙ01224 1013783 1014346 t conserved hypothetical protein TIGR00150 ΒΙ01225 1014411 1015289 ٠ conserved hypothetical protein ΒΙ01226 1015308 1015859 ؛ ribosomal-protein-alanineacetyltransferase ΒΙ01227 1015859 1016899 ؛ O-sialoglycoprotein endopeptidase ΒΙ01228 1017438 1017539 hypothetical protein ΒΙ01229 1017569 1018501 ؛ probable integrase/recombinse ΒΙ01230 1018564 1018887 conserved hypothetical protein Β.01231 1018909 1019787 conserved liypothetical protein ΒΙ01232 1019849 1020361 conserved hypothetical protein ΒΙ01233 1020474 1021376 Fic protein femily femily ΒΙ01234 1021357 1021929 hypothetical protein B11463 ΒΙ0Ι235 1021949 1023763 conserved hypothetical protein ΒΙ01236 1023782 1024864 conserved hypothetical protein ΒΙ01237 1024893 1025600 conserved hypothetical protein ΒΙ01238 1025761 1026843 possible TraG-related protein Β101239 1026843 1027799 hypothetical protein Blon020262 BIO 1240 1027799 1028164 hypothetical protein Β1οη020261 BIO242 ا 1028379 1028669 + hypothetical protein Blon020260 ΒΙ0Ι241 1028588 1030942 t DNA topoisomerase III ΒΙΟΙ 243 1030771 1031448 t hypothetical protein Blon020258 ΒΙ0Ι244 1031753 1032193 + COG1758: DNA-directed RNA polymerase, subunit K/omega BIO1245 1032161 1032553 hypothetical protein Blon020256 BIO1246 1032621 1033400 Fic protein family family ΒΙ0Ι247 1033518 1034822 t MC38, putative ΒΙ0Ι248 1034848 1036128 PUTATIVE HIPA TRANSCRIPTION REGULATOR PROTEIN ΒΙ0Ι249 1036128 1036439 hypothetical protein Blon020251 ΒΙ0Ι250 1036545 1037675 conserved hypothetical protein ΒΙ0Ι25Ι 1038618 1040387 MC40 ΒΙ0Ι252 1040507 1041145 conserved hypothetical protein ΒΙ0Ι253 1041250 1042281 - conserved hypothetical protein PCT/JE2009/000079 WO 2010/055499 -44- ΒΙ01254 1042389 1042865 conserved hypothetical protein ΒΙ01255 1043244 1044842 ATP binding protein-like protein ΒΙ01256 1044857 1046341 conserved hypothetical protein ΒΙ01257 1046369 1048195 lipoprotein, putative ΒΙ01258 1048370 1048669 conserved hypothetical protein ΒΙ01259 1048710 1049189 MC47, putative BI01713t 1049183 1050538 liypothetical protein B 1,1487 ΒΙ01260 1049206 1050405 liypothetical protein ΒΙ01261 1050435 1051070 hypothetical protein Blon020236 ΒΙ01262 1051396 1056213 liypothetical COG2217: Cation transport ATPase Β101263 1056508 1057458 hypothetical protein Blon020231 RIO1764 1057844 1058440 hypothetical COGl 192: ATPases involved in cliromosome partitioning ΒΙ01265 1059167 1059430 COGl 192: ATPases involved in chromosome partitioning Β101266 1059569 1060042 possible WhiB-like transcription factor Β.01267 1060036 1061400 conserved hypotlietical protein BI01727t 1061400 1061597 hypothetical protein Β1οη020220 ΒΙ01268 1061748 1061894 hypothetical protein BI01730t 1061882 1062055 hypothetical protein Β1οη0202Ι7 ΒΙ0.269 1062779 1062997 conserved hypothetical protein ΒΙ0.270 1063127 1063546 ؛ Helix-turn-helix domain protein BJ01733t 1064092 1064778 t conserved hypothetical protein ΒΙ01271 1064862 1066490 lipoprotein, putative Β101272 1066742 1067959 isocitrate dehydrogenase, NADP-dependent ΒΙ01273 1068051 1069208 ؛ IMP dehydrogenase family protein Β101274 1069373 1069861 + hypothetical protein Β1οη020211 ΒΙ01275 1069955 1072039 t long-chain-fatty-acid—CoA ligase, putative ΒΙ01276 1072049 1072534 t polypeptide deformylase ΒΙ01277 1072876 1073736 ٠ ribosomal protein S2 ΒΙ01278 1073818 1074666 t translation elongation fector Ts ΒΙ01279 1074978 1075580 ٠ uridylate kinase Β101280 1075660 1076208 t ribosome recycling factor ΒΙ01281 1076309 1077217 t phosphatidate cytidylyltransferase ΒΙ01282 1077557 1078597 ٠ radical SAM enzyme, Cfr family ΒΙ01283 1078604 1079149 protease 1 ΒΙ01284 1079324 1080091 ا imidazoleglycerol phosphate synthase, cyclase subunit ΒΙ01285 1080228 1080620 t phosphoribosyl-AMP cyclohydrolase ΒΙ01286 1080704 1082257 ؛ anthranilate synthase component 1 ΒΙ01287 1082328 1082564 conserved hypothetical protein ΒΙ01288 1082576 1084174 t ATP binding protein of ABC transporter ΒΙ01289 1084221 1084925 ؛ oxidoreductase, sliort-chain dehydrogenase/reductase family, putative ΒΙ01290 1084999 1085364 + narrowly conserved protein with unknown function ΒΙ01291 1085423 1086091 conserved hypothetical protein Β101292 1086091 1087701 ABC transporter, ΑΤΡ-binding protein ΒΙ01293 1087704 1088600 possible ABC transporter permease for cobalt ΒΙ01294 1088405 1089049 narrowly conserved protein with unknown function ΒΙ01295 1089261 1090877 + conserved hypothetical protein ΒΙ01296 1090916 1091548 t conserved liypothetical protein 12016لال18 2016206219 -45- 2016206219 18U12016 PCT/IE2009/000079 WO 2010/055499 ΒΙ01297 1091551 1095093 ا hypothetical myosin-like protein with unknown function ΒΙ01298 1095170 1096351 + conserved hypothetical protein ΒΙ01299 1096680 1097084 t hypothetical protein BL0701 ΒΙ01300 1097367 1100384 + excinuclease ABC, A subunit ΒΙ01301 1100532 1102895 + excinuclease ABC, c subunit ΒΙ01302 1103007 1103975 t aroE ΒΙ01303 1103978 1104961 t Predicted Ρ-Ιοορ-containing kinase ΒΙ01304 1105247 1106110 t Uncharacterized BCR, COG1481 ΒΙ01305 1106282 1107484 t phosphoglycerate kinase ΒΙ01306 1107546 1108346 t triosephosphate isomerase ΒΙ01307 1108365 1108658 t preprotein translocase, SecG subunit ΒΙ01308 1108763 1109710 ؛ L-lactate dehydrogenase ΒΙ01309 1109710 1110558 ؛ Coffemily protein ΒΙ01310 1110672 1112225 + aminotransferase, class I ΒΙ01311 1112360 1113466 membrane protein, putative ΒΙ01312 1113642 1114943 branched-chain amino acid transport system II carrier protein ΒΙ01313 1115108 1116208 transaldolase ΒΙ01314 1116332 1118392 transketolase ΒΙ01315 1118812 1119927 + heat-inducible transcription repressor HrcA ΒΙ01316 1119986 1121128 t dnaJ protein BI0J317 1121180 1121968 - COG3001 :Uncharacterized BCR ΒΙ01318 1122113 1122994 t undecaprenol kinase, putative ΒΙ01319 1123157 1124146 conserved hypothetical protein ΒΙ01320 1124807 1126837 + threonyl-tRNA synthetase ΒΙ01321 1127061 1127561 t HIT femily protein ΒΙ01322 1127703 1128455 + conserved hypothetical protein TIGR01033 ΒΙ01323 1128464 1129045 + crossover .junction endodeoxyribonuclease RuvC BIO324 ا 1129106 1129729 t Holliday .junction DNA helicase RuvA ΒΙ01325 1129732 1130793 t Holliday junction DNA helicase RuvB ΒΙ0.326 1130876 1131292 + preprotein translocase, YajC subunit ΒΙ0Ι327 1131359 1131937 t adenine pliosphoribosyltransferase ΒΙ0Ι328 1132037 1133236 ٠ succinyl-CoA synthetase, beta subunit ΒΙ0Ι329 1133239 1134147 t succinyl-CoA synthase, alpha subunit ΒΙ01330 1133954 1135546 t membrane protein, putative ΒΙ0Ι331 1135497 1137131 ٠ phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase ΒΙ01332 1137280 1137579 + hypothetical protein ΒΙ01333 1137484 1138449 aquaporin z, putative ΒΙ0Ι334 1138645 1139412 t ribosomal large subunit pseudouridine synthase B ΒΙ0.335 1139514 1141538 + possible GTP-binding protein ΒΙ01336 1141896 1143422 + UDP-glucose pyrophosphoiydase ΒΙ01337 1143565 1145475 t conserved hypotlietical protein ΒΙ0Ι338 1145489 1145803 ٠ hypothetical protein Β1οη020144 ΒΙ0Ι339 1145819 1148407 t helY ΒΙ01340 1148524 1148868 t conserved hypothetical protein ΒΙ01341 1149001 1149717 ؛ hydrolase, haloacid dehalogenase-like family BI0I833t 1149744 1149995 + conserved hypothetical protein ΒΙ01342 1150135 1150497 hypothetical protein Β1οη020140 ΒΙ0Ι343 1150673 1151302 COG0789:Predicted transcriptional regulators ΒΙ01344 1151406 1151846 possible signal ttansduction protein ΒΙ0Ι345 1151856 1152596 conserved hypothetical protein WO 2010/055499 PCT/IE2009/000079 2016206219 18Jul2016 -46- ΒΙ01346 1152693 1153022 small basic protein ΒΙ01347 1153025 1153999 conserved hypothetical protein ΒΙ01348 1153992 1154684 CDP-diacylglycerol—glycerol-3-phosphate3-phosphatidyltransferase, putative ΒΙ01349 1154623 1155471 ATP phosphoribosyltransferase ΒΙ01350 1155486 1155746 phosphoribosyl-ATP pyrophosphohydrolase ΒΙ0Ι351 1155812 1156477 ribulose-phosphate 3-epimerase ΒΙ01352 1156556 1157500 prolipoprotein diacylglyceryl transferase ΒΙ01353 1157614 1158480 tryptophan synthase, alpha subunit ΒΙ01354 1158507 1160591 tryptophan synthase, beta subunit ΒΙ01355 1161120 1161968 endonuclease IV BI00066g 1161414 1162400 t amino acid permease ΒΙ01356 1162340 1162834 t amino acid permease ΒΙ01357 1162503 1162667 + amino acid permease BI0J358 1163206 1164216 liypothetical membrane protein with unknown function ΒΙ01359 1164333 1164536 hypothetical protein ΒΙ01360 1164570 1164860 abortive infection protein AbiGI, putative ΒΙ01361 1164981 1165262 t liypothetical protein ΒΙ01362 1165260 1165715 lin2984 ΒΙ01363 1165903 1166406 ٠ acetyltransferase, GNAT family, putative ΒΙ01364 1166567 1166746 t lin0863 ΒΙ01365 1166793 1167323 acetyltransferase, GNAT femily ΒΙ01366 1167392 1167961 acetyltransferase, GNAT family ΒΙ01367 1168315 1168992 hypothetical protein ΒΙ01368 1169017 1169823 hypothetical protein ΒΙ01369 1169832 1170527 ABC transporter, ΑΤΡ-binding protein ΒΙ01370 1170352 1171263 ٠ hypothetical Response regulator receiver domain ΒΙ01371 1171317 1172225 ؛ hypothetical protein ΒΙ01372 1172194 1172631 hypothetical Integral membrane protein ΒΙ01373 1172956 1173576 hypothetical protein ΒΙ01374 1173576 1174301 hypothetical protein BI01873t 1174309 1174962 bacteriocin ABC transporter, ATP-binding protein, putative Β101375 1175274 1176518 t 1S30 family, transposase [imported. ΒΙ01376 1176714 1177379 DNA-binding response regulator ΒΙ01377 1177379 1179001 hypothetical ATPase, histidine kinase-, DNA gyrase Β-, and HSP90-hke domain protein BI0J378 1179039 1179881 hypothetical permease, putative ΒΙ01379 1180057 1180956 ABC transporter, ΑΤΡ-binding protein ΒΙ01380 1181077 1181259 t hypothetical protein ΒΙ01381 1181154 1181684 hypothetical protein ΒΙ01382 1182016 1182315 (- ΒΙ01383 1182321 1182662 ( hypothetical protein BJ01384 1182847 1183050 hypothetical protein ΒΙ01385 1183324 1183446 ( hypothetical protein BL0771 ΒΙ01386 1183489 1183932 ( hypothetical protein Blon020116 Β101387 1183955 1184314 COG0388: Predicted amidohydrolase Β101388 1184376 1184531 hypothetical protein ΒΙ01389 1184840 1185853 inner membrane protein, 60 kDa VC0004 [imported] BJ01390 1186097 1186555 hypothetical protein ΒΙ01391 1186942 1187067 ٠ hypothetical protein WO 2010/055499 -47- 2016206219 18U12016 PCT/IE2009/000079 ΒΙ01392 1187122 1188783 t amino acid permease ΒΙ01393 1188993 1189640 Signal peptidase I BI00٥67g 1189800 1190303 ( conserved hypothetical protein ΒΙ01394 1189721 1190146 hypothetical protein Blon020104 ΒΙ01395 1190467 1191420 t lin0466 ΒΙ01396 1191479 1191799 t narrowly conserved hypothetical protein ΒΙ01397 1191887 1192165 t narrowly conserved hypothetical protein ΒΙ01398 1192540 1193727 t Unknown, putative ΒΙ01399 1193770 1195530 t Y.jeF family protein, putative BIO 1400 1195635 1196261 + possible alpha beta hydrolase ΒΙ01401 1196417 1197286 t transcriptional regulator, LysR family BIO1402 1197447 1198565 conserved hypothetical protein BIO 1403 1198783 1198932 hypothetical protein BIO1404 1199044 1199736 orotatephosphoribosyltransferase ΒΙ01405 1199748 1200716 dihydroorotate dehydrogenase ΒΙ01406 1200722 1201543 dihydroorotate dehydrogenase, electron transfer subunit ΒΙ01407 1201682 1202632 orotidine 5'-phosphate decarboxylase ΒΙ01408 1202653 1203939 dihydroorotose BI0192H 1204146 1204562 Aspartate carbamoyltransferase regulatory chain, allosteric domain ΒΙ01409 1204565 1205524 aspartate carbamoyltransferase ΒΙ01410 1205669 1208896 glutamate-ammonia ligase adenylyltransferase femily ΒΙ01411 1208955 1209905 EF0040 ΒΙ01412 1210042 1210893 5,lO-methylenetetrahydrofolate reductase ΒΙ01413 1210955 1213255 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase ΒΙ01414 1213369 1213923 phosphohistidine phosphatase SixA, putative ΒΙ01415 1214024 1215091 conserved hypothetical protein ΒΙ01416 1215168 1215803 + serine esterase, putative ΒΙ01417 1215850 1216806 oxidoreductase, aldo/keto reductase 2 femily ΒΙ01418 1217063 1217995 + lipC, putative ΒΙ01419 1218234 1219178 + hypothetical oxidoreductase, zinc-binding dehydrogenase femily ΒΙ01420 1219340 1219642 probable ATP binding protein of ABC transporter ΒΙ01421 1220459 1221484 + transposase (25) ΒΗ3998 [imported], putative BI00069g 1221277 1221948 t hypothetical protein ΒΙ01422 1221948 1222706 t Tpase2 BIO 1423 1222896 1223972 t hypothetical protein ΒΙ01424 1224236 1224811 + hypothetical protein ΒΙ01425 1224888 1225190 transcriptional regulator, HTH 3 femily ΒΙ01426 1225221 1226144 hypothetical protein ΒΙ01427 1226238 1227140 hypothetical protein BIO 1428 1227158 1228765 hypothetical protein BIO 1429 1229279 1230097 hypothetical ADP-ribosylglycohydrolase ΒΙ01430 1231271 1231726 hypothetical protein ΒΙ01431 1232085 1232906 + conserved hypothetical protein ΒΙ01432 1233000 1233539 bcp ΒΙ01433 1233681 1234511 probable amidase [imported] BIO 1434 1234511 1235365 hydrolase, haloacid dehalogenase-like femily, putative ΒΙ01435 1235520 1236365 - amino acid transport protein -48- PCT/IE2009/000079 WO 2010/055499 ΒΙ01436 1236462 1237709 possible glycosyltransferase ΒΙ01437 1237841 1238302 conserved hypothetical protein ΒΙ01438 1238382 1239917 gltD ΒΙ01439 1239922 1244265 Conserved region in glutamate synthase family ΒΙ01440 1244835 1245116 t transcription regulator, Lacl family [imported. RIO1441 1245175 1246197 conserved hypothetical protein ΒΙ01442 1246656 1246979 t conserved hypothetical protein ΒΙ01443 1247042 1247227 hypothetical protein ΒΙ01444 1247493 1248536 transcriptional regulator, Lacl femily, putative ΒΙ01445 1249246 1250073 ٠ conserved hypothetical protein ΒΙ01446 1250275 1250571 hypothetical protein BI00071g 1250541 1250888 conserved hypothetical protein ΒΙ01447 1250658 1250807 t hypothetical protein RIO1448 1251252 1252538 t MATE efflux family protein, putative ΒΙ01449 1252678 1252794 liypothetical protein ΒΙ01450 1253083 1254216 + IS30 family, transposase [imported. ΒΙ01451 1254323 1255327 glycerate kinase ΒΙ01452 1255679 1256734 ؛ transcriptional regulator, Lacl family, putative ΒΙ01453 1256820 1258094 oxygen-independent coproporpliyrinogen III oxidase, putative ΒΙ01454 1258229 1259890 GTP-binding protein LepA ΒΙ01455 1260253 1260510 ٠ ribosomal protein S20 ΒΙ01456 1260768 1261556 conserved hypothetical transmembrane protein with unknown fiinction ΒΙ01457 1261807 1262703 transcriptional regulator, MazG family ΒΙ01458 1262903 1264027 branched-chain amino acid aminotransferase BIO 1459 1264254 1264871 ribosomal 5S rRNA Ε-1οορ binding protein Ctc/L25/TL5 RI01460 1265298 1266332 + conserved hypothetical protein RI01461 1766474 1267895 NAD(P) transhydrogenase, beta subunit [imported. ΒΙ01462 1267898 1268200 NAD(P) transhydrogenase, alpha subunit RI01467 1268219 1269379 NAD(P) transhydrogenase, alpha subunit [imported. RIO1464 1269798 1271828 ؛ long-chain-fatty-acid~CoA ligase ΒΙ01465 1271887 1272948 GTP-binding protein Era R101466 1272953 1274383 CBS domain protein ΒΙ01467 1274462 1275052 conserved hypothetical protein TIGR00043 RI01468 1275000 1276172 PhoH femily protein RI01469 1776194 1276529 Hit family protein ΒΙ01470 1276581 Υ2ΊΊΥΙ5 conserved hypothetical protein TIGR00046 ΒΙ01471 1277619 1778494 t spoU rRNA methylase femily protein ΒΙ01472 1278758 12.79939 ؛ glucose-l -pliosphate adenylyltransferase ΒΙ01473 1280035 1280532 mrp protein homolog R101474 1280635 1281171 SUF system FeS assembly protein, Niffl family ΒΙ01475 1281201 1282472 aminotransferase, class-v ΒΙ01476 1787614 1283390 FeS assembly ATPase SufC ΒΙ01477 1787419 1284651 FeS assembly protein SufD ΒΙ01478 1284660 1286156 FeS assembly protein Suffl ΒΙ01479 1286383 1287849 conserved hypothetical protein ΒΙ01480 1288225 1289883 CTP synthase RI01481 1290032 1291585 dipeptidase, putative ΒΙ01482 1291684 1292127 - 3-dehydroquinate dehydratase, type 11 12016لال18 2016206219 2016206219 18Jul2016 PCT/IE2009/000079 -49- WO 2010/055499 ΒΙ01483 1292294 1293835 3-dehydroquinate synthase BIO484ا 1293999 1295132 chorismate synthase ΒΙ01485 1295247 1295717 ٠ COG0477: Permeases of the major fecilitator superfamily ΒΙ01486 1295891 1297003 Uncharacterized BCR, YceG family COG1559 BIO487ا 1297083 1297535 conserved hypothetical protein TIGR00250 ΒΙ01488 1297550 1300228 alanyl-tRNA syntlietase ΒΙ0Ι489 1300359 1300592 hypothetical protein Blon020010 ΒΙ01490 1300595 1300990 conserved hypothetical protein ΒΙ01491 1301196 1301921 phosphoglycerate mutase ΒΙ01492 1302158 1304008 + Acyltransferase family domain protein ΒΙ01493 1304105 1304728 ribosomal protein S4 ΒΙ01494 1304930 1305895 ABC transporter, ΑΤΡ-binding protein Β.01495 1305900 1307114 hypothetical transmembrane protein with unknown fimction ΒΙ01496 1307208 1307603 conserved hypothetical protein RIO1497 1307751 1310450 hypothetical UvrD/REP helicase ΒΙ01498 1310567 1311145 + xanthine phosphoribosyltransferase ΒΙ01499 1311199 1312560 + xanthine/uracil permease family protein ΒΙ01500 1312696 1312902 transcription regulator, Cro/Cl femily [imported]-related protein ΒΙ01501 1312912 1313169 hypothetical protein ΒΙ01502 1313326 1314144 hydrolase, alpha/beta fold fomily, putative ΒΙ01503 1314432 1315367 t conserved hypothetical protein ΒΙ01504 1315462 1315860 glyoxalase family protein ΒΙ01505 1316019 1316630 t isocliorismatase ΒΙ01506 1316885 1318360 t conserved hypothetical protein ΒΙ01507 1318371 1319780 membrane protein, putative ΒΙ01508 1319770 1321005 membrane protein, putative ΒΙ01509 1321109 1322089 daunorubicin resistance ΑΤΡ-binding protein ΒΙ01510 1322192 1322296 hypothetical protein ΒΙ01511 1322475 1323824 1 histidine kinase sensor of two-component system ΒΙ01512 1323917 1324477 1 DNA-binding response regulator ΒΙ01513 1324667 1325287 Protein of unknown function subfomily ΒΙ01514 1325308 1326324 phosphate transporter fomily protein ΒΙ01515 1326480 1326674 conserved hypothetical protein ΒΙ01516 1326735 1329005 carbon starvation protein A ΒΙ01517 1329406 1330668 + glycosyl hydrolase, family 13, putative ΒΙ01518 1330703 1331404 transcriptional regulator, TetR family, putative ΒΙ01519 1331486 1333669 possible ATP-dependent RNA helicase ΒΙ01520 1334052 1335338 uracil-xanthine permease ΒΙ01521 1335446 1336273 phosphoglycerate mutase fomily domain protein ΒΙ01522 1336327 1336905 conserved hypothetical protein ΒΙ01523 1337061 1337612 t conserved hypothetical protein ΒΙ01524 1337738 1338898 conserved hypothetical protein Β101525 1339275 1340816 conserved hypothetical protein ΒΙ01526 1341250 1341687 + hypotlietical COG0653: Preprotein translocase subunit SecA (ATPase, RNA helicase) ΒΙ01527 1341752 1343449 t Protein kinase domain protein ΒΙ01528 1343493 1344980 permease, putative ΒΙ01529 1345295 1347565 drug resistance transporter, EmrB/QacA subfamily ΒΙ01530 1347576 1347776 - hypothetical protein PCT/IE2009/000079 2016206219 18Jul2016 -50- WO 2010/055499 ΒΙ01531 1347947 1348309 ؛ hypothetical Domain of unknown function (DUF307) ΒΙ01532 1348405 1349910 - hypothetical protein Β101533 1349906 1351072 hypothetical protein Β101534 1351166 1351474 hypothetical protein BI02085t 1351280 1351477- + hypothetical protein Blon021394 ΒΙ01535 1351807 1352478 ؛ COG4186: Predicted pliosphoesterase or phosphohydrolase ΒΙ01536 1352565 1354004 + conserved hypothetical protein ΒΙ01537 1354044 1354253 t hypothetical protein BL0925 ΒΙ01538 1354253 1354612 ٠ hypothetical protein B10925 ΒΙ01539 1354729 1355193 t hypothetical protein ΒΙ01540 1355496 1356380 hypothetical protein BIO 1541 1356380 1357450 hypothetical Phage integrase family BIO 1542 1357650 1358675 + transposase (25) ΒΗ3998 [imported], putative BI00076g 1358468 1359139 ؛ hypothetical protein ΒΙ01543 1359139 1359897 ؛ Tpase2 ΒΙ01544 1360305 1361546 GTP-binding protein YchF ΒΙ01545 1361533 1362351 pyrroline-5-carboxylate reductase ΒΙ01546 1362416 1363891 proline iminopeptidase ΒΙ01547 1363977 1366433 + histidine kinase sensor of two-component system ΒΙ01548 1366551 1367345 t DNA-binding response regulator ΒΙ01549 1367384 1370233 possible transport protein ΒΙ01550 1370265 1371176 ABC transporter, ΑΤΡ-binding protein ΒΙ01551 1371528 1372841 O-acetylhomoserine sulfhydrylase ΒΙ01552 1373315 1374184 t pyridoxal kinase, putative ΒΙ01553 1374424 1374924 ٠ conserved hypothetical protein T1GR00252 ΒΙ01554 1374983 1376515 ٠ Mg chelatase-related protein ΒΙ01555 1376515 1378212 + DNA processing protein DprA, putative ΒΙ01556 1378272 1380134 + sdhA ΒΙ01557 1380233 1381195 t sdhB ΒΙ01558 1381277 1381954 t probable methyltransferase ΒΙ01559 1382006 1382944 conserved hypothetical protein T1GR00730 ΒΙ01560 1383180 1384595 Na+/H+ antiporter [imported] ΒΙ01561 1385070 1386485 ATP-dependent Clp protease, ATP-binding subunit ClpX ΒΙ01562 1386610 1387308 ATP-dependent Clp protease, proteolytic subunit ClpP ΒΙ01563 1387317 1387907 ATP-dependent Clp protease, proteolytic subunit ClpP ΒΙ01564 1388046 1388423 hypothetical protein Blon021418 ΒΙ01565 1388538 1390001 voltage-gated chloride channel family protein, putative ΒΙ01566 1390189 1391565 trigger factor ΒΙ01567 1391623 1392921 3-5 exonuclease domain protein ΒΙ01568 1392921 1393730 COG0477: Permeases of the major facilitator superfamily ΒΙ01569 1393622 1394500 pyruvate formate-lyase 1 activating enzyme ΒΙ01570 1394613 1396985 formate acetyltransferase Β.01571 1397254 1397475 conserved hypothetical protein ΒΙ01572 1397531 1399093 NH(3)-dependent NAD+ syntlietase ΒΙ01573 1399577 1400725 Peptidase, Μ20/Μ25/Μ40 family ΒΙ01574 1400817 1401500 ' permease protein of ABC transporter system WO 2010/055499 PCT/IE2009/000079 2016206219 18Jul2016 -51- ΒΙ01575 1401500 1402702 ABC transporter, ΑΤΡ-binding protein ΒΙ01576 1402839 1403816 lipoprotein, YaeC family ΒΙ01577 1404020 1404847 + hydrolase, haloacid dehalogenase-like family ΒΙ01578 1404975 1407449 D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase ΒΙ01579 1407895 1409454 t GMP syntliase Β101580 1409723 1410304 t COG0798: Arsenite efflux pump ACR3 and related permeases ΒΙ01581 1410343 1410720 + arsenical resistance protein/arsenate reductase ΒΙ01582 1411265 1411771 t hypothetical Transposase IS66 family BI00078g 1411579 1412214 + hypothetical protein Β1οη021471 ΒΙ01583 1412111 1413136 + transposase (25) ΒΗ3998 [imported,, putative BI00٥79g 1412929 1413600 t hypothetical protein ΒΙ01584 1413600 1414358 + Tpase2 ΒΙ01585 1414423 1414911 ٠ hypothetical COG3436: Transposase and inactivated derivatives BI02159t 1415037 1416323 COG0477: Permeases of the major facilitator superfamily ΒΙ01586 1416510 1417160 t putative ΑΤΡ-binding protein ΒΙ01587 1417164 1418444 t Uncharacterized conserved protein ΒΙ01588 1418440 1418820 ٠ hypothetical protein Blon021466 ΒΙ01589 1418965 1420548 ٠ conserved hypothetical protein ΒΙ01590 1420796 1422598 + acyltransferase, putative ΒΙ01591 1422687 1423706 t prsA ΒΙ01592 1423991 1425370 ؛ UDP-N-acetylglucosaminepyrophosphorylase ΒΙ01593 1425377 1425787 t iojap-related protein ΒΙ01594 1425942 1426637 t phosphoglycerate mutase, putative ΒΙ01595 1427363 1428961 ؛ phospliate acetyltransferase ΒΙ01596 1429099 1429695 t acetate kinase ΒΙ01597 1429811 1430326 + hypothetical COG0282: Acetate kinase ΒΙ01598 1430503 1431867 3-phosphoshikimate 1 -carboxyvinyltransferase Β101599 1431867 1433036 membrane protein, putative Β101600 1433757 1434125 hypothetical COG2217: Cation transport ATPase ΒΙ01601 1434688 1436172 galactoside symporter ΒΙ01602 1436515 1439583 ( beta-galactosidase, putative ΒΙ01603 1440389 1441246 1 hypothetical protein BIO604 ا 1441301 1441966 hypothetical protein Blon٥20709 ΒΙ0Ι605 1442167 1442559 hypothetical protein ΒΙ0Ι606 1442574 1442990 hypothetical protein ΒΙ01607 1442990 1444792 hypothetical protein ΒΙ01608 1444688 1445566 ٠ COG3757: Lyzozyme Ml (1,4-beta-N-acetylmuramidase) ΒΙ0Ι609 1445667 1445948 1 hypothetical protein ΒΙ01610 1446119 1446796 + hypothetical protein ΒΙ01611 1447212 1448801 hypothetical C-5 cytosine-specific DNA methylase ΒΙ016Ι2 1448804 1449997 liypothetical protein Psyc022392 ΒΙ016Ι3 1450130 1450393 t hypothetical protein ΒΙ0Ι614 1450514 1450891 hypothetical protein ΒΙ0Ι615 1451253 1452203 hypothetical protein ΒΙ016Ι6 1452503 1452802 TnpB ΒΙ016Ι7 1452909 1453127 t 1S861, transposase Orffl ΒΙ0Ι618 1453248 1453586 t putative transposase subunit PCT/IE2009/000079 WO 2010/055499 -52- ΒΙ01619 1455179 1455604 cell division protein FtsZ ΒΙ01620 1455752 1459864 hypothetical UvrD/REP helicase ΒΙ01621 1459861 1463163 COG3857: ATP-dependent nuclease, subunit B ΒΙ01622 1463295 1465877 hypothetical DNA polymerase III, alplia subunit ΒΙ01623 1466017 1467055 t conserved hypothetical protein ΒΙ01624 1467089 1467886 narrowly conserved hypothetical membrane protein ΒΙ01625 1468160 1468507 hypothetical protein B10124 ΒΙ01626 1468949 1469908 Pseudouridylate synthases, 23S RNA-specific ΒΙ01627 1469911 1470456 lipoprotein signal peptidase ΒΙ01628 1470481 1471857 conserved hypothetical protein ΒΙ01629 1472000 1472299 COG0762:Predicted integral membrane protein BIO630 ا 1477474 1472900 conserved hypothetical protein ΒΙ0163Ι 1472916 1473830 hypothetical Tubulin/FtsZ family, c-terminal domain ΒΙ01632 1474239 1475480 ΤΙΜ-barrel protein, NitR3 femily ΒΙ01633 1475628 1476938 glycyl-tRNA synthetase ΒΙ01634 1477533 1478474 ٠ hydroxyethylthiazole kinase ΒΙ01635 1478743 1481310 ٠ thiamine biosynthesis protein ThiC ΒΙ01636 1481353 1481679 hypothetical protein ΒΙ01637 1481870 1482626 t phosphomethylpyrimidine kinase ΒΙ01638 1482680 1483054 ٠ COGOOl 1 :Uncharacterized ACR ΒΙ01639 1483563 1484939 1 permease, putative BI02235t 1485571 1485978 t conserved hypothetical protein ΒΙ01640 1486039 1487433 ٠ Serpin (serine protease inhibitor) superfemily BIO 1641 1487717 1488517 t transcriptional regulator, LacI family, putative ΒΙ01642 1488728 1490068 t sucrose transport protein ΒΙ01643 1490082 1491635 t sucrose-6-phosphate hydrolase, putative RIO 1644 1491833 1492612 ؛ ABC transporter, permease protein, cysTW family, putative ΒΙ01645 1492927 1493943 ؛ pyrimidine precursor biosynthesis enzyme, putative BI02246t 1494070 1495254 + inosine-uridine preferring nucleoside hydrolase BIO 1646 1495416 1496207 undecaprenyl diphosphate synthase ΒΙ01647 1496207 1496923 DNA repair protein RecO RI01648 1496975 1498684 conserved hypothetical protein ΒΙ01649 1498808 1500028 1 -hydroxy-2-methyl-2-(£)-butenyl 4-diphosphate synthase ΒΙ01650 1500028 1501215 l-deoxy-D-xylulose 5-phosphate reductoisomerase ΒΙ0165Ι 1501215 1502915 conserved hypotlietical protein ΒΙ01652 1503387 1503809 conserved hypothetical protein ΒΙ01653 1503919 1504797 PDZ domain family protein ΒΙ0Ι654 1505129 1506760 t conserved hypotlietical protein ΒΙ01655 1506836 1508407 ATP-dependent DNA helicase PcrA ΒΙ01656 1508553 1510205 + conserved hypothetical protein ΒΙ01657 1510357 1510578 + putative ΑΤΡ-binding protein ΒΙ01658 1510645 1511535 PHP domain N-terminal region femily ΒΙ01659 1511673 1512407 ٠ narrowly conserved hypothetical transmembrane protein RIO1660 1512419 1513309 diaminopimelate epimerase RIO1661 1513417 1514208 1 glutamate racemase ΒΙ01662 1514340 1515182 ٠ Patatin femily 12016لال18 2016206219 WO 2010/055499 PCT/IE2009/000079 2016206219 18U12016 -53- ΒΙ01663 1515255 1516151 Unknown ΒΙ01664 1516314 1516580 trans-sulfuration enzyme BI00087g 1516749 1517024 ABC transporter, ΑΤΡ-binding protein, putative ΒΙ00086Κ 1517139 1517573 ٠ conserved hypothetical protein in upl74 ΒΙ01665 1517692 1517940 conserved hypothetical protein ΒΙ01666 1518187 1519422 cystathionine beta-lyase ΒΙ01667 1519661 1520560 glutamine ABC transporter, periplasmic glutamine-binding protein (glnH) ΒΙ01668 1520629 1521417 amino acid ABC transporter, ΑΤΡ-binding protein ΒΙ01669 1521413 1521952 amino acid ABC transporter, pemease protein SP0710 [imported] ΒΙ01670 1522074 1522730 amino acid ABC transporter, permease protein ΒΙ01671 1522793 1523605 t hypothetical Phospholipase/Carboxylesterase ΒΙ01672 1523620 1525872 Tn916, tetracycline resistance protein, putative ΒΙ01673 1526091 1526723 ؛ DNA polymerase III, epsilon subunit BIO 1674 1526731 1527318 guanylate kinase ΒΙ01675 1527501 1528418 orotidine 5'-phosphate decarboxylase, putative BIO 1676 1528421 1531801 carbamoyl-phosphate synthase, large subunit ΒΙ01677 1531806 1533176 carbamoyl-phosphate synthase, small subunit ΒΙ01678 1533219 1533788 transcription antitermination factor NusB ΒΙ01679 1533846 1534154 Elongation factor p (EF-P) ΒΙ01680 1534514 1535248 t Unknown, putative ΒΙ01681 1535248 1536033 t conserved hypothetical protein T.GR00245 ΒΙ01682 1536066 1536770 Unknown ΒΙ01683 1536878 1539436 hypothetical EAL domain ΒΙ01684 1539444 1540751 Probable hydrolase transmembrane protein ΒΙ01685 1541332 1543257 ا glycosyltransferase ΒΙ01686 1543387 1543551 hypothetical protein Β101687 1543710 1544600 3-hydroxyacyl-CoA dehydrogenase ΒΙ01688 1544959 1546782 alpha-xylosidase ΒΙ01689 1546897 1547199 hypothetical COG1653: ABC-type sugar transport system, periplasmic component ΒΙ01690 1547359 1549491 possible beta-hexosaminidase A ΒΙ01691 1549605 1550417 ABC transporter, permease protein, MalFG family BIO 1692 1551035 1551862 t conserved hypothetical protein ΒΙ01693 1552142 1553254 mrp ΒΙ01694 1553434 1556193 DNA ligase, NAD-dependent ΒΙ01695 1556261 1559881 conserved hypothetical protein ΒΙ01696 1560102 1562237 t membrane protein, putative ΒΙ01697 1562555 1564141 + hypothetical protein Blon021196 ΒΙ01698 1564204 1564977 ABC transporter, ΑΤΡ-binding protein, putative ΒΙ01699 1565037 1566299 aminotransferase, class I, putative ΒΙ01700 1566573 1567337 ROK femily protein ΒΙ01701 1567583 1568365 + Nitroreductase femily protein ΒΙ01702 1568413 1569423 probable glycosyltransferase ΒΙ01703 1569675 1570325 t conserved hypothetical protein ΒΙ01704 1570459 1572888 + ABC transporter, ΑΤΡ-binding protein, putative ΒΙ01705 1572963 1573265 ؛ Predicted RNA-binding protein containing KH domain ΒΙ0Ι706 1573370 1573732 conserved hypothetical protein ΒΙ01707 1573842 1574456 + hypothetical ΤΜ2 domain ΒΙ01708 1574885 1575301 t liypothetical protein Blon021592 WO 2010/055499 PCT/IE2009/000079 2016206219 18U12016 -54- ΒΙ01709 1575432 1576415 D-isomer specific 2-hydroxyacid dehydrogenase femily protein ΒΙ01710 1576714 1578168 drug resistance transporter, EmrB/QacA family, putative ΒΙ01711 1578399 1579418 ribose ABC transporter, permease protein VCA0129 ؛imported!, putative ΒΙ01712 1579418 1580485 ribose ABC transporter, perjnease protein VCA0129 [imported], putative ΒΙ01713 1580490 1582028 ATP binding protein of ABC transporter ΒΙ01714 1582172 1583152 ribose ABC transporter, periplasmic D-ribose-binding protein ΒΙ01715 1583472 1585199 lipoprotein, putative ΒΙ01716 1585199 1586752 sensor histidine kinase MtrB ΒΙ01717 1586893 1587837 hypothetical Response regulator receiver domain ΒΙ01718 1587674 1589005 conserved ATP/GTP binding protein ΒΙ01719 1589136 1591535 COG0513 :Superfamily II DNA and RNA helicases ΒΙ01720 1591837 1592907 Domain of unknown function (DUF344) family BI02350t 1592976 1593215 conserved hypothetical protein ΒΙ01721 1593208 1593801 COG0737: 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases ΒΙ01722 1593841 1595364 hypothetical secreted protein with probable acid phosphatase domain ΒΙ01723 1595471 1596568 glutamine ABC transporter, glutamine-binding protein/permease protein, putative ΒΙ01724 1596577 1597251 glutamine ABC transporter, permease protein ΒΙ01725 1597254 1598090 amino acid ABC transporter, amino acid-binding protein, putative ΒΙ01726 1598125 1598964 amino acid ABC transporter, ΑΤΡ-binding protein BI0J727 1599401 1600468 ؛ conserved hypothetical protein ΒΙ01728 1600932 1602728 aspartyltRNA synthetase BI0J729 1602767 1604107 histidyltRNA synthetase ΒΙ0Ι730 1604264 1605721 t conserved hypothetical protein BIOا73 ا 1605933 1607723 5'-nuc٠eot؛dase family protein, putative ΒΙ0Ι732 1607898 1608653 creatinine amidohydrolase, creatininase ΒΙ0Ι733 1608742 1610115 proline/betaine transporter ΒΙ0Ι734 1610158 1610328 t hypothetical protein ΒΙ0Ι735 1610308 1611378 hypothetical protein weakly similar to putative transcriptional regulator from Streptomyces ΒΙ01736 1611950 1613266 ؛ N-acyl-D-amino-acid deacylase family protein, putative ΒΙ01737 1613452 1616058 ATP-dependent Clp protease, ATP-binding subunit CIpC ΒΙ01738 1616208 1617170 + demannu, putative ΒΙ01739 1617288 1618208 hypothetical protein Β1οη021510 BIO 1740 1618484 1618870 cspB ΒΙ01741 1618943 1620931 sensor histidine kinase ΒΙ01742 1620965 1621738 DNA-binding response regulator BIO 1743 1621689 1622492 conserved hypothetical protein ΒΙ01744 1622567 1622854 t conserved hypothetical protein ΒΙ01745 1622957 1624579 cliaperone ΒΙ01746 1624820 1625056 cold-shock domain family protein RIO 1747 1625289 1625870 hypothetical protein Blon020592 ΒΙ01748 1626163 1626771 + uracil-DNA glycosylase 2016206219 18U12016 PCT/IE2009/000079 WO 2010/055499 -55 BIO1749 1626814 1627890 t ATPase, MoxR family ΒΙ01750 1628022 1628837 ٠ Protein of unknown function family ΒΙ01751 1628840 1629388 ٠ conserved hypothetical protein ΒΙ01752 1629388 1630443 ا conserved hypothetical protein ΒΙ01753 1630443 1631471 + conserved hypothetical protein ΒΙ01754 1631444 1632070 t platelet binding protein GspB, putative ΒΙ01755 1632316 1632660 t conserved hypothetical protein ΒΙ01756 1632660 1634261 t conserved hypothetical protein ΒΙ01757 1634531 1634893 t conserved hypothetical protein ΒΙ01758 1635034 1635672 hypothetical membrane protein with unknown fimction ΒΙ01759 1635805 1637238 t adenylosuccinate lyase VCl 126 [imported. ΒΙ01760 1637373 1639931 ؛ narrowly conserved hypothetical membrane protein ΒΙ01761 1640080 1640358 t DNA-binding protein HU ΒΙ01762 1640480 1641937 possible DNA-binding protein ΒΙ01763 1641940 1642203 liypothetical Protein of unknown function (DUF797) Β101764 1642234 1643133 possible inositol monophosphatase ΒΙ01765 1643139 1644803 hypothetical proteasome-associated protein ΒΙ01766 1644828 1646390 cell division control protein 48, AAA family ΒΙ01767 1646454 1647149 DedA family protein ΒΙ01768 1647410 1647919 t phosphoserine phosphatase SerB ΒΙ01769 1648166 1650271 t primosomal protein N ΒΙ01770 1650333 1651034 t possible alpha beta hydrolase ΒΙ01771 1651061 1652044 + methionyl-tRNA formyltransferase ΒΙ01772 1652142 1653908 dihydroxy-acid dehydratase ΒΙ01773 1654203 1654484 t DNA-directed RNA polymerase, omega subunit ΒΙ01774 1654765 1655982 t S-adenosylmethionine synthetase BI02420t 1656352 1657425 t hypothetical protein CV1232

The Open reading ftames (ORF) listed in Table 1 are defined by their position in the genomic sequence of SEQ ID No. 1. For example ΒΙ00001 is defined by the nucleotide sequence ofbase numbers 1667321 and 1667608 (inclusive) of SEQ ID No. 1. 5

Examples

The following examples further describe and demonstrate embodiments within the scope of the invention. The examples are given solely for the purpose of illustration and are not to be construed as limitations of the present invention, as many variations thereof are possible without 10 departing from the spirit and scope ofthe invention.

Example 1 - Isolation of biotype infantis ucc 35624

Appendices and sections ofthe large and small intestine ofthe human G.I.T., obtained during reconstructive surgery, were screened for probiotic bacterial strains. All samples were 15 stored immediately after surgery at -80.C in sterile containers. Frozen tissues were thawed. wo 2010/055499 PCT/IE2009/000079 -56- 2016206219 18Jul2016 weighed and placed in cysteinated (0.05%) one quarter strength Ringers’ solution. Each sample was gently shaken to remove loosely adhering microorganisms. Following transfer to a second volume of Ringers’ solution, the sample was vortexed for 7 min to remove tightly adhering bacteria. In order to isolate tissue embedded bacteria, samples were also homogenised in a 5 Braun blender. The solutions were serially diluted and spread-plated (100μ1) on to the following agar media: RCM (reinforced clostridial media) and RCM adjusted to pH 5.5 using acetic acid; TPY (trypticase, peptone and yeast extract), Chevalier, p. et al. (1990). MRS (deMann, Rogosa and Sharpe)؛ ROG (acetate medium (SL) of Rogosa)؛ LLA (Liver-lactose agar of Lapiere)؛ BHI (brain heart infosion agar)؛ LBS ( Lactobacillus selective agar) and TSAYE (tryptone soya agar 10 supplemented with 0.6% yeast extract). All agar media was supplied by Oxoid Chemicals with the exception of TPY agar. Plates were incubated in anaerobic jars (BBL, Oxoid) using CO2 generating kits (Anaerocult A, Merck) for 2-5 days at 37.C.

Gram positive, catalase negative rod-shaped or bifurcated/pleomorphic bacteria isolates were streaked for purity on to complex non-selective media (TPY). Isolates were routinely 15 cultivated in TPY medium unless otherwise stated at 37.C under anaerobic conditions. Presumptive Bifidobacteria species were stocked in 40./. glycerol and stored at -20. and -80.C.

Approxintately fifteen hundred catalase negative bacterial isolates from different samples were chosen and characterised in terms of their Gram reaction, cell size and morphology, growth at I5٥c and 45.C and fermentation end-products from glucose. Greater than sixty percent of the 20 isolates tested were Gram positive, homofermentative cocci arranged either in tetrads, chains or bunches. Eighteen percent of the isolates were Gram negative rods and heterofermentative coccobacilli.

The remaining isolates (twenty-two percent) were predominantly homofermentative coccobacilli. Thirty eight strains were characterised in more detail. All thirty eight isolates 25 tested negative both for nitrate reduction and production of indole from tryptophan.

Bifidobacterium longum biotype infentis strain 35624 was chosen for foil genome sequencing from this group of strains due to its proven anti-inflammatory activity in murine models of colitis (McCarthy et.al., 2004) and its immunomodulatory effects following oral consumption by Irritable Bowel Syndrome (IBS) patients (O’Mahony et al, 2005). 30

Example 2- Sequencing the genome of Bifidobacterium lomum infantis 35624

The Bifidobacterium longum biotype infantis strain 35624 genome sequence was detemiined using a whole shotgun approach. For this purpose two libraries were constructed: a small insert library (insert size ranging between 2 and 4 kb) employing pGEM-Τ easy vector wo 2010/055499 PCT/IE2009/000079 -SI- 2016206219 18U12016 (Promega) and a large insert (insert size ranging between 40 and 45 kb) cosmid library (Epicentre Technologies). Sequence sampling from these banks generated just over 26,828,618 base pairs of useable sequence data, which represented about 11.9-fold coverage of the Bifidobacterium longum biotype infantis strain 35624 genome (performed by MWG-Biotech, 5 Ebersberg, Germany). Sequence reads were assembled using Phrap (Green) into 11 contigs. Gap closure and quality improvement of the initial sequence assembly was achieved by additional primer-directed sequencing using pre-identified clones from the libraries resulting in a single contig, which represented a circular chromosome of 2,264,374 bp long. Based on the final consensus quality scores, we estimate an overall error rate of <1 per 4xl٥5 bases 10

Example 3 - Analysing the genome of Bifidobacterium lonsum biotype infantis 35624

Protein-encoding open reading frames (ORFs) were predicted using a combination of the methods Glimmer (Delcher et al., 1999b; Salzberg et al., 1998) and GeneBuilder (Internally developed software), as well as comparative analysis involving BLASTX (Altschul et al., 1997) 15 Results from the gene finder programs were manually combined, and preliminary identification of ORFs was made on the basis ofBIASTP (Altschul et al., 1997) analysis against a non- redundant protein database provided by the National Centre for Biotechnology Information (Wheeler et al., 2005). Artemis (Rutherford et al., 2000), was used to inspect the identified ORFs and its associated BLASTP results. A manual inspection was perforjned in order 20 to verify or, if necessary, redefine the start and stop of each predicted coding region. Annotation made use of the GC frame plot feature of Artemis, ribosome-binding site information obtained from RBSfinder (Suzek et al., 2001), alignments with similar ORFs from other organisms and G+C content analysis. 25 Example 4- Identifying unique genes in the genome of Bifidobacterium lonsum infantis 35624

Assignment of protein function to predicted coding regions of the Bifidobacterium longum biotype infantis strain 35624 genome was performed using internally developed software and manual inspection. Primary frrnctional classification of the Bifidobacterium longum biotype infantis strain 35624 gene products was performed according to the Riley rules (Riley, 1998a; 30 Riley, 1993). The COG assignment was performed using XUGNITOR (Tatusov,). HMMER (Eddy,) was used to assign PFAM (Bateman et al., 2002) classification to the predicted proteins. TMHMM (Krogh et al., 2001) was used to predict transmembrane sequences, and SignalP (Bendtsen et al, 2004) was used for the prediction of signal peptides. Ribosomal RNA genes were detected on the basis ofBLASTN searches and annotated manually. Transfer RNA genes PCT^2009/000079 WO 2010/055499 2016206219 18U12016 -58- were identified using tRNAscan-SE (Lowe and Eddy, 1997). Miscellaneous-coding RNAs were identified using the Rfam database (Griffiths-Jones et al., 2005) utilizing the INFERNAL software package (Eddy, 2002). Insertion sequence elements were identified using Repeatfinder (Volfovsky et al., 2001), Reputer (Kurtz &amp; Schleiermcher, 1999) and BLAST (Altschul et al., 5 1990) and annotated manually. IS families were assigned using ISFinder (http://www٠ is.biotoul.fi/is.html). Carbohydrate-active enzymes were identified based on similarity to the carbohydrate-active enzyme (CAZy) database entries (Coutinho &amp; Henrissat, 1999), and COG and PFAM classes annotated with carbohydrate enzyme activity. Transporter classification was performed according to the TC-DB scheme (Busch &amp; Saier, 2002). 10 We identified a region fiom base numbers 44824 to 472245 (inclusive) of SEQ ID No. 1 that we designated exopolysaccharide (EPS) region 1 (SEQ ID No. 2). The EPS region 1 encodes the following genes:

Table 2 - Open reading frames of EPS region 1 of the UCC 35624 genome

Gene ID Strand Description DNA sequence Protein sequence ΒΙ00778 t glycosyl transferase CpsE SEQ. ID No. 93 SEQ. ID No. 133 ΒΙ00779 t COG0840: Methyl-accepting chemotaxis protein SEQ. ID No. 94 SEQ. ID No. 134 ΒΙ00780 + possible Etk-like tyrosine kinase involved in Eps biosynthesis SEQ. ID No. 95 SEQ. ID No. 135 ΒΙ00781 ٠ hypothetical glycosyl transferase, group 1 family protein SEQ. ID No. 96 SEQ. ID No. 136 ΒΙ00782 t putative glycosyltransferase protein SEQ. ID No. 97 SEQ. ID No. 137 ΒΙ00783 + NAD dependent epimerase/dehydratase family protein SEQ. ID No. 98 SEQ. ID No. 138 ΒΙ00784 t UDP-glucose 6-dehydrogenase SEQ. ID No. 99 SEQ. ID No. 139 ΒΙ00785 t hypothetical glycosyl transferase, group 1 family protein SEQ. ID No. 100 SEQ. ID No. 140 ΒΙ00786 ٠ hypothetical EpsllI SEQ. ID No. 101 SEQ. ID No. 141 ΒΙ00787 ب hypothetical Bacterial transferase hexapeptide (three repeats) SEQ. ID No. 102 SEQ. ID No. 142 ΒΙ00788 + hypothetical Capsular polysaccharide synthesis protein SEQ. ID No. 103 SEQ. ID No. 143 ΒΙ00789 t hypothetical protein SEQ. ID No. 104 SEQ. ID No. 144 ΒΙ00790 t Eps9K SEQ. ID No. 105 SEQ. ID No. 145 ΒΙ00791 t hypothetical Polysaccharide biosynthesis protein SEQ. ID No. 106 SEQ. ID No. 146 ΒΙ00792 ( hypothetical Bacterial transferase hexapeptide (three repeats) SEQ. ID No. 107 SEQ. ID No. 147 ΒΙ00793 NAD-dependent epimerase/dehydratase family protein, putative SEQ. ID No. 108 SEQ. ID No. 148 PCT/IE2009/000079 -59- ΒΙ00794 transposase, degenerate SEQ. ID No. 109 SEQ. ID No. 149 ΒΙ00795 hypothetical COG2963: Transposase and inactivated derivatives SEQ. ID No. 110 SEQ. ID No. 150 ΒΙ00796 ٠ dTDP-glucose 4,6-dehydratase SEQ. ID No. Ill SEQ. ID No. 151 ΒΙ00797 t dTDP-4-dehydrorhamnose3,5-epimerase SEQ. ID No. 112 SEQ. ID No. 152 ΒΙ00798 t glucose-l-phosphate thymidylyltransferase SEQ. ID No. 113 SEQ. ID No. 153 WO 2010/055499 2016206219 18Jul2016

We also identified a region from base numbers 2071426 to 2097099 (inclusive) of SEQ ID No. 1 that we designated EPS region 2 (SEQ ID No. 3). The EPS region 2 encodes the following genes:

Table 3 - Open reading frames of EPS region 2 of the ucc 35624 genome

Gene ID Strand Description DNA sequence Protein sequence ΒΙ00319 t dTDP-glucose 4,6-dehydratase SEQ. ID No. 114 SEQ. ID No. 154 ΒΙ00320 ؛ conserved hypothetical protein SEQ. ID No. 115 SEQ. ID No. 155 ΒΙ00321 ؛ conserved hypothetical protein SEQ. ID No. 116 SEQ. ID No. 156 BI00423t + conserved putative transposase SEQ. ID No. 117 SEQ. ID No. 157 ΒΙ00322 IS1533, Orffi SEQ. ID No. 118 SEQ. ID No. 158 ΒΙ00323 transposase (25) ΒΗ3998 [imported], putative SEQ. ID No. 119 SEQ. ID No. 159 ΒΙ00324 - glycosyltransferase, putative SEQ. ID No. 120 SEQ. ID No. 160 ΒΙ00325 conserved sialic acid-specific 9-0-acetylesterase SEQ. ID No. 121 SEQ. ID No. 161 ΒΙ00326 + hypothetical Acyltransferase family SEQ. ID No. 122 SEQ. ID No. 162 ΒΙ00327 conserved> hypothetical membrane protein with unknown function SEQ. ID No. 123 SEQ. ID No. 163 ΒΙ00328 - hypothetical Glycosyl transferase family 8 SEQ. ID No. 124 SEQ. ID No. 164 ΒΙ00329 hypothetical glycosyl transferase, group 2 family protein SEQ. ID No. 125 SEQ. ID No. 165 ΒΙ00330 polysaccharide ABC transporter, ATP-binding protein SEQ. ID No. 126 SEQ. ID No. 166 ΒΙ00331 polysaccharide ABC transporter, permease protein, putative SEQ. ID No. 127 SEQ. ID No. 167 ΒΙ00332 + hypothetical Glycosyl transferase family 8 SEQ. ID No. 128 SEQ. ID No. 168 ΒΙ00333 UDP-glucose 6-dehydrogenase SEQ. ID No. 129 SEQ. ID No. 169 ΒΙ00334 + hypothetical NAD dependent epimerase/dehydratase family SEQ. ID No. 130 SEQ. ID No. 170 ΒΙ00335 membrane protein, putative SEQ. ID No. 131 SEQ. ID No. 171 ΒΙ00336 - conserved hypothetical protein SEQ. ID No. 132 SEQ. ID No. 172

Example 5 - Isolation and screening of EPS-producing Bifidobacterial strain from fecal samples 1¾ Fecal Sample Preparation WO 2010/055499 PCT/IE2009/000079 -60-

Fecal samples were collected by the subjects using a Kendall precision commode specimen collection system. The collected samples were stored chilled in a cold pack prior to sample processing. Only samples that are less than twenty four hours old were used in the evaluations. A 10.0 gm sample of mixed fecal material was placed into a plastic stomaching bag containing 90 ml of saline. The suspension was stomached for 2 minutes. The suspension was filtered through a gauze pad contained within a disposable funnel. Following the filtration, 45 ml of the filtered fecal homogenate was transferred to a 50 ml disposable centrifilge tube. This fecal suspension was forther used for DNA extraction or for bacterial isolation.

Screening Fecal Samples Using Three TaqMan Real-Time PCR Assays.

Fecal Sample DNA Preparation. A 2.0 ml aliquot of the fecal homogenate was pelleted using a microcentrifilge. The pellets were resuspended in 20 mg/ml lysozyme, for 2 hours at 37.C. DNA was extracted using a QIAamp DNA Stool Mini Kit (Qiagen). The DNA concentration was measured by Pico Green assay (Molecular Probes). Once the DNA concentration was measured, the DNA was stored at 4٥c.

TaqMan Real-Time PCR Reactions. The test samples were diluted to a concentration of DNA of 2 ng/ul so that 5 μΐ contained a total oflOng DNA. Samples were assayed by a total of three separate assays.

The following reaction mix was made:

Water 15.75μ1 10 μΜ forward primer 1.5μ1 (300 ηΜ final concentration) 10 μΜ reverse primer 1.5μ1 (300 ηΜ final concentration) 10 μΜ TaqMan probe Ιμΐ (200 ηΜ final concentration) BSA (20 mg/ml) 0.25μ1 (0.1ug/ml final concentration) TaqMan Universal Master Mix 25μ1 A bulk mix was made for the number of samples to be assayed. A 45μ1 aliquot was dispensed into each well of a 96 well microtitre plate, then 5μ1 DNA was added to each well. The plate was spun briefly, and placed into the tliermocycler (ABI 7900 HT). The standard TaqMan thermocycling protocol was used. Ρσ/ΙΕ2009/000079 WO 2010/055499 2016206219 18Jul2016 -61-

TaaMan RT-PCR Program. The standard TaqMan quantitative PCR thermocycling protocol is as follows: 5 Step 1: 95.C for 10 minutes (to activate the AmpliTaq Gold polymerase)

Step 2: 95.C for 15 seconds (the denaturation step)

Step 3: 60.C for 60 seconds (the priming/polymerization step)

Steps 2 and 3 are repeated 40 times. Fluorescent data is collected at step 3. 10 Primers and Probes for Three TaqMan RT-PCR assays. The fecal sample DNAs were screened using a EPS gene-specific assay and two B. infantis 35624 Unknown gene-specific assays (Unknown genes UNKl and 112). The specific genes used and their TaqMan primer sets are shown in Table 4 below.

15 Table 4 - ucc 35624 Primer set for TaqMan PCR

Target Gene Name Sequence 5'-3’ Genome start Genome end TaqMan Probe label ΒΙ01615 (UNK-1) UNKl- CCATGAGCGGTTTCACGAA (SEQ ID No. 4) 1451446 1451428 FAM 3' NFQ- MG UNKl- Rl TTGGACGGTGCCTGTGATTA (SEQ IDNo. 5) 1451393 1451412 MGBl CGGGCAATCAAC (SEQ ID No. 6) 1451426 1451415 BI02420t (UNK-2) UNK2- FI ACTTGACGTACCGTTTTGAGATTTC (SEQ ID No. 7) 1656479 1656503 5' 6-FAM 3' NFQ-MGB UNK2- Rl CTAAGCATGGCAAGGCTGATAGT (SEQ ID No. 8) 1656562 1656540 UNK2- MGBl TGCGACCAACACGC (SEQ ID No. 9) 1656525 1656538 ΒΙ00783 (EPS) EPS-F1 GGGTCCAATAAGAAGGTTCCATATT (SEQ ID No. 10) 456491 456515 5' 6-FAM 3' TAMR EPS-R1 GCATGTGCCAACAGCTCATC (SEQ ID No. 11) 456591 456572 EPS- TAMRA CGGATGACAAGGTAGATAATCCAGTGAGCCTATAC (SEQ ID No. 12) 456519 456553 wo 2010/055499 PCT/IE2009/000079 -62- 2016206219 18U12016

The fecal samples which showed high DNA concentration by the 5. infantis 35624 EPS gene-specific assay, but negative reactions by using B. infantis 35624 Unknown gene-specific assays, were firrther used for the isolation of potential EPS-producing bacteria.

Example 6 - Isolation and Characterization of 5Τ7207 from Fecal Samples.

One milliliter of bacterial suspension (see Example 5 above) was transferred to 9.0 ml of sterile phosphate-buffered saline which constituted the 10"' dilution. One milliliter of this 10"' dilution was transferred to 9.0 ml of sterile phosphate-buffered saline which was the 10"2 dilution. This process was continued until the 10"'٥ dilution was prepared. Then, 0.1 ml of each dilution was plated onto the surfaces of Reinforced Clostridial Agar (RCA) plates (BD or equivalent) and Lactobacillus Man-Rogosa Sharpe agar (MRSA) plates (BD or equivalent). The plates were incubated under anaerobic condition (COY anaerobic Chamber) at 33.C ± 2٥c for 48-72 hours.

Following incubation, single colonies (a total of approximately 100 colonies) were picked ftom RCA and MRSA plates and further streaked on new plates for isolate purification. The plates with the streaked colonies were incubated under anaerobic conditions (COY anaerobic Chamber) at 33.C ± 2٥c for 48 to 72 hours. After incubation, the pure colonies observed on plates were then submitted for DNA extraction.

Screening fecal isolates using three TaqMan Real-Time PCR assays

The bacterial DNA was extracted using the Preman™ Ultra Sample Preparation Reagent and Protocol (Applied Biosystems). The DNA was firrther analyzed using three TaqMan RT-PCR assays (EPS gene-specific assay [EPS-1] and two 5. infantis 35624 Unknown gene-specific assays [UNKl and UNK2] as described above in Example 5. Only one isolate showed 5. infantis 35624 EPS gene-specific assay positive, but 5. infantis 35624 Unknown gene-specific assays-negative. This isolate was further identified using 16S rDNA sequencing.

Identification of potential EPS-producing strain by 16S rDNA sequencing.

The 16S rRNA gene fragment was amplified and sequenced using ABI Full Gene PCR kit (Applied Biosystems, Foster City, CA). (1). 16S rRNA Gene amplification: PCR amplification was carried out on a GeneAmp PCR System 9700 thermal cycler with the following program: wo 2010/055499 PCT/IE2009/000079 -63- 2016206219 18Jul2016

Initial Hold: 95G for 10 minutes 30Cycles: 5 95.C for 30 seconds (Denaturing) 60 ٠c for 30 seconds (Annealing) 72.C for 45 seconds (Extension)

Final Extension: 72 ٠c for 10 minutes 10 (2). 16S IA Gene sequencing:

Sequencing was ftirther performed on the thermal cycler using the following program: 25 Cycles: 96 ٥c for 10 seconds (Denaturing) 50 ٠c for 5 seconds (Annealing) 15 60 ٥c for 4 minutes (Extension)

Final step Hold at 4.C

The sequencing PCR product was further purified using DyeEX TM 2.0 spin kit and 20 sequenced using 3130xl Genetic Analyzer (Applied Biosystems, Foster City, CA). (31 Sequence data analysis:

Comparison of the consensus sequences with GenBank sequences was done by using Basic Local Alignment Search Tool (BLAST). The GenBank search indicated that the B infantis 25 35624 EPS gene-specific positive, but B. infantis 35624 Unknown gene-specific negative strain is Bifidobacterium longum. This strain is designated Β1Τ207.

Example 7 - Isolation and screening of EPS-expressing Bifidobacterial longum strains Isolation of bacterial strains 30 Bacteria were isolated ftom bowel tissue and/or fecal samples using the methodology described in Example 1 above. In particular. Bifidobacterium longum strain AH121a was isolated ftom feline bowel tissue and Bifidobacterium longum strain ΑΗ1714 was isolated ftom colonic biopsy tissue from healthy human subjects. wo 2010/055499 PCT/IE2009/000079 -64- 2016206219 18Jul2016 EPS gene cluster screen

Bacterial strains were screened for the presence of genes from EPS cluster 1 (Table 2 above) and EPS cluster 2 (Table 3 above) using the primers listed in Tables 5 and 6 below. Briefly, the following methodology was used for the PCR EPS cluster gene screen: 10ml Modified Rogosa broth media (t 0.05% cysteine) was inoculated aseptically with a freshly grown colony of the bacterial strain and incubatd anaerobically at 37.C until turbid (about 16 to about 24 hours). The broth cultures were centrifuged and DNA was isolated ftom the resultant pellet using a Sigma™ extraction procedure. A nanodrop was used to ascertain the concentration of DNA in the sample and samples were diluted using DEPC water to a final concentration of 50ng/pl DNA per sample. The template DNA samples were used in individual PCR reactions with the primer sets listed in Tables 5 and 6 below under the following conditions:

Step Temp (٥C) Time (اح) 1 95 240 2 95 45 3 60 45 4 72 45 repeat steps 2 to 4, 25 times 5 4 hold

The primers were specifically designed to amplify a PCR product of approximately 500 base pair for the 40 genes of EPS clusters 1 and 2. PCR products were visualised following agarose gel electrophoresis with an appropriate DNA ladder for reference sizing. The presence (YES) or absence (NO) of a 500 bp PCR product is indicated in Tables 7 and 8 below.

Table 5 - Primers for screening bacterial strains for the presence of genes from EPS cluster

Gene ID Primer name LRFR Sequence SEQ ID NO. ΒΙ00778 1.01 L tat gtt gcc ggc att tat ca SEQ ID No. 13 ΒΙ00778 1.01 R tgc gcg ttc atg tea ata at SEQ ID No. 14 ΒΙ00779 1.02 L ggc gta gca agt tea agg ag SEQ ID No. 15 ΒΙ00779 1.02 R aat aac ege tgc agg aac ac SEQ ID No. 16 ΒΙ00780 1.03 L gtg cag gac ggt aat gga gt SEQ ID No. 17 ΒΙ00780 1.03 R get teg ggt ctg gat cat ta SEQ ID No. 18 ΒΙ00781 1.04 L tgc tga caa gtg gag tet gg SEQ ID No. 19 ΒΙ00781 1.04 R cca cgt eta ega gca act ca SEQ ID No. 20 WO 2010/055499 PCT/IE2009/000079 2016206219 18Jul2016 65- ΒΙ00782 1.05 L gaa age gaa gag tgg tet gg SEQ ID No. 21 ΒΙ00782 1.05 R ccg get gat ttg atg aga tt SEQ ID No. 22 ΒΙ00783 1.06 L tgc ege tgt act ggt cac SEQ ID No. 23 ΒΙ00783 1.06 R gca tgt gee aac age tea SEQ ID No. 24 ΒΙ00784 1.07 L cca aca cgt ate tgg cac tg SEQ ID No. 25 ΒΙ00784 1.07 R teg gag cca aag aag gta ga SEQ ID No. 26 ΒΙ00785 1.08 L ata ccg cgt atg ett tgg ac SEQ ID No. 27 ΒΙ00785 1.08 R aaa egg taa cca etc get tg SEQ ID No. 28 ΒΙ00786 1.09 L atg gga teg atg cat gaa at SEQ ID No. 29 ΒΙ00786 1.09 R ttc teg gca ata aac cgt tc SEQ ID No. 30 ΒΙ00787 1.10 L cca geg gtt att teg ttg tt SEQ ID No. 31 ΒΙ00787 1.10 R ggt ggc atg ate ett atg ct SEQ ID No. 32 ΒΙ00788 1.11 L get ate ttc acc gca ttg gt SEQ ID No. 33 ΒΙ00788 1.11 R cca gtc agg gaa ggt cac at SEQ ID No. 34 ΒΙ00789 1.12 L tga aat aca ege aac ccg ta SEQ ID No. 35 ΒΙ00789 1.12 R aatgcgtcaaaaccgatacc SEQ ID No. 36 ΒΙ00790 1.13 L gga aag caa tga gga age tg SEQ ID No. 37 ΒΙ00790 1.13 R gat ttg atg caa age aag ca SEQ ID No. 38 ΒΙ00791 1.14 L gtg agt acc gtt tee gca at SEQ ID No. 39 ΒΙ00791 1.14 R ttc ett ggt tee cgt gat ag SEQ ID No. 40 ΒΙ00792 1.15 L get gggattttg gaa gtg aa SEQ ID No. 41 ΒΙ00792 1.15 R tgt tac ccc egg cat aat aa SEQ ID No. 42 ΒΙ00793 1.16 L acc ggt aac gtt cag att gc SEQ ID No. 43 ΒΙ00793 1.16 R gca ata ccg cct tga cct ta SEQ ID No. 44 ΒΙ00794 1.17 L ttg tac cac cac aeg tac eg SEQ ID No. 45 ΒΙ00794 1.17 R ege gag ttc aat ggc tat g SEQ ID No. 46 ΒΙ00795 1.18 L aca teg acc tee ate tee ag SEQ ID No. 47 ΒΙ00795 1.18 R ata cgt aac age ggc tee ac SEQ ID No. 48 ΒΙ00796 1.19 L aag tac gat gtg ege tac ca SEQ ID No. 49 ΒΙ00796 1.19 R cat cac ggt cag gat gtc ac SEQ ID No. 50 ΒΙ00797 1.20 L ega ata cac gga cat caa eg SEQ ID No. 51 ΒΙ00797 1.20 R gag aat ega gca get gga ac SEQ ID No. 52 ΒΙ00798 1.21 L tgg gag agg agt tea teg ac SEQ ID No. 53 ΒΙ00798 1.21 R gta tee age cat geg taa cc SEQ ID No. 54

Table 6 - Primers for screening bacteria, strains for the presence of genes from EPS cluster 2 Gene ID Primer name LRFR Sequence SEQ ID NO. ΒΙ00319 2.01 L aeg gac tea aaa cca cca tc SEQ ID No. 55 ΒΙ00319 2.01 R acc ctg ett ccg gta ett tt SEQ ID No. 56 ΒΙ00320 2.02 T. gee tac gca aga cct tat gc SEQ ID No. 57 ΒΙ00320 2.02 R cgt tat aeg cgt get tga ga SEQ ID No. 58 ΒΙ00321 2.03 L tgg aac gca ata ttc aac ga SEQ ID No. 59 ΒΙ00321 2.03 R cca agt atg get cca ega at SEQ ID No. 60 BI00423t 2.04 L aeg cct gtc tat ggt tgg aa SEQ ID No. 61 BI00423t 2.04 R egg tag gac teg ttc teg tc SEQ ID No. 62 ΒΙ00322 2.05 L teg agg ttc gag gtg aag at SEQ ID No. 63 2016206219 18Jul2016 PCT/IE2009/000079 -66- wo 2010/055499 ΒΙ00322 2.05 R cct gtt cga gaa gga gaa eg SEQ ID No. 64 ΒΙ00323 2.06 L atg gaa gca tgt ggt cct tc SEQ ID No. 65 ΒΙ00323 2.06 R atttcc tgg tgg tgtcgttc SEQ ID No. 66 ΒΙ00324 2.07 L atg geg aaa ctg ttg gac tc SEQ ID No. 67 ΒΙ00324 2.07 R get acc gtg cct tet cat tc SEQ ID No. 68 ΒΙ00325 2.08 L gee gaa teg ett ttg aaa ta SEQ ID No. 69 ΒΙ00325 2.08 R aaa tee tea teg ggg aaa ac SEQ ID No. 70 ΒΙ00326 2.09 L gtt tat ttt ege cgt gee ta SEQ ID No. 71 ΒΙ00326 2.09 R aat tee aat ggc ttt tgc tg SEQ ID No. 72 ΒΙ00327 2.10 L atg tgc gaa tee gac ata ca SEQ ID No. 73 ΒΙ00327 2.10 R tgc tta tet cgt ccc cat tc SEQ ID No. 74 ΒΙ00328 2.11 L gca aaa tgc ttg get tet tc SEQ ID No. 75 ΒΙ00328 2.11 R ctg gat tee gat gat get tt SEQ ID No. 76 ΒΙ00329 2.12 L ctg cac gta teg gga ttt tt SEQ ID No. 77 ΒΙ00329 2.12 R etc ggc aga gga cag gat ag SEQ ID No. 78 ΒΙ00330 2.13 L gat cat cga cac gca atg ac SEQ ID No. 79 ΒΙ00330 2.13 R taa ggc cat cct cat caa gg SEQ ID No. 80 ΒΙ00331 2.14 L tet ggg gaa age agg tta tg SEQ ID No. 81 ΒΙ00331 2.14 R ctg tgc ggt acc tgt ttg tg SEQ ID No. 82 ΒΙ00332 2.15 L aat tac gtc ccg atg etc ac SEQ ID No. 83 ΒΙ00332 2.15 R caa tac acc ggc ttg gaa gt SEQ ID No. 84 ΒΙ00333 2.16 L tgt aga cct tgt ege tea eg SEQ ID No. 85 ΒΙ00333 2.16 R gca teg gtg aeg get ata at SEQ ID No. 86 ΒΙ00334 2.17 L gtg etc gac aag ctg aeg ta SEQ ID No. 87 ΒΙ00334 2.17 R gtg ttc ege ata cca ate g SEQ ID No. 88 ΒΙ00335 2.18 L ggc gag tgc acc aaa taa at SEQ ID No. 89 ΒΙ00335 2.18 R cga ttc cgt eta ttg gtt eg SEQ ID No. 90 ΒΙ00336 2.19 L ata agt ccg gtg gca ate ag SEQ ID No. 91 ΒΙ00336 2.19 R caa tgg atg ata egg tgc tg SEQ ID No. 92

TabJe 7 - ResuJts of EPS cluster 1 gene screen Gene ID Primer set B. longum 35624 B. longum 1207 B. longum ΑΗ121Α B. longum 1714 ΒΙ00778 1.01 YES YES NO YES ΒΙ00779 1.02 YES YES NO YES ΒΙ00780 1.03 YES YES NO YES ΒΙ00781 1.04 YES YES YES YES ΒΙ00782 1.05 YES YES YES YES ΒΙ00783 1.06 YES YES YES YES ΒΙ00784 1.07 YES YES YES YES ΒΙ00785 1.08 YES YES YES YES ΒΙ00786 1.09 YES YES YES YES ΒΙ00787 1.10 YES YES YES YES ΒΙ00788 1.11 YES YES YES NO ΒΙ00789 1.12 YES YES YES YES ΒΙ00790 1.13 YES YES YES YES ΒΙ00791 1.14 YES YES YES YES 2016206219 18Jul2016 -67- ΒΙ00792 1.15 YES YES YES YES ΒΙ00793 1.16 YES YES NO YES ΒΙ00794 1.17 YES YES NO YES ΒΙ00795 1.18 YES YES NO YES ΒΙ00796 1.19 YES YES YES YES ΒΙ00797 1.20 YES NO NO NO ΒΙ00798 1.21 YES YES YES YES In which YES indicates the presence and NO indicates the absence of a 500 bp PCR product.

Table 8 - Results of EPS cluster 2 gene screen Gene ID Primer set B. longum 35624 B. longum 1207 B. longum ΑΗ121Α B. longum 1714 ΒΙ00319 2.01 YES NO NO NO ΒΙ00320 2.02 YES NO NO NO ΒΙ00321 2.03 YES NO NO NO BI00423t 2.04 YES NO NO NO ΒΙ00322 2.05 YES NO NO NO ΒΙ00323 2.06 YES NO NO NO ΒΙ00324 2.07 YES NO NO NO ΒΙ00325 2.08 YES NO NO NO ΒΙ00326 2.09 YES NO NO NO ΒΙ00327 2.10 YES NO NO NO ΒΙ00328 2.11 YES NO NO NO ΒΙ00329 2.12 YES NO NO NO ΒΙ00330 2.13 YES NO NO NO ΒΙ00331 2.14 YES NO NO NO ΒΙ00332 2.15 YES NO NO NO ΒΙ00333 2.16 YES NO NO NO ΒΙ00334 2.17 YES NO NO NO ΒΙ00335 2.18 YES YES NO YES ΒΙ00336 2.19 YES YES YES YES In which YES indicates the presence and NO indicates the absence of a 500 bp PCR product.

Congo red agar screen 5 A Congo red agar screen was used to phenotypically screen for EPS expressing bacterial strains. Briefly, lOml Modified Rogosa broth media (t 0.05% cysteine) was inoculated aseptically with a freshly grown colony of the bacterial strain and incubated anaerobically at 37.C until turbid (about 16 to about 24 hours). The broth cultures were aseptically streaked onto Congo Red Agar plates and incubated anaerobically at 37.C for 48 hours. It is believed 10 that EPS produced as a by-product of the growth and/or metabolism of certain strains prevents the uptake of the Congo red stain resulting in a cream/white colony morphology. Stains that produce less EPS take up the Congo red stain easily, resulting ئ a pink/red colony morphology. Strains that do not produce an EPS stain red and look almost transparent in the red agar background. wo 2010/055499 PCT/IE2009/000079 -68- 2016206219 18Jul2016

Referring to Figs. 6 to 12, the following colony morphologies were observed:

Table 9 - Colony morphologies from Congo red agar screen

Bacterial Strain Colonv mornholo^ B. longum 35624 (Fig. 6) Convex, mucoid, bright white colonies B. longum ΑΗ121Α (Fig. 7) Convex, mucoid, bright white colonies B. logum ΑΗ1714 (Fig. 8) Convex, mucoid, bright white colonies B. longum AH0119(Fig. 9) Convex, mucoid, pale pink / off white colonies B. breve UCC2003 (Fig. 10) Convex, mucoid, pale pink / off white colonies L. rhamnosus ΑΗ308 (Fig. 11) Flat, semi-mucoid, pale pink / off white colonies L. salivarius UCCl (Fig. 12) Flat, non-mucoid, clear/transparent colonies

Example 8 - B. infantis 35624 and BL1207 Induce Nearly Identical Cytokine Profiles in PBMCs.

Peripheral blood mononuclear cells (PBMCs) were isolated from fresh human peripheral blood using BD Vacutainer CPT tubes (BD catalog 362761), as per the manufacturer’s instructions. PBMCs were washed and resuspended in Dulbecco's MEM (Gibco catalog 10569-10 010) plus 25 mM HEPES, 10% fetal bovine serum (Sigma catalog F4135), and 1% penicillin/streptomycin (Sigma catalog Ρ0781). 2 X 10و PBMCs (in 200 μΐ of DMEM) were plated into each well of a 96-well culture plate.

Bacteria were grown in Difco MRS media and harvested just after entering into stationary phase. All cells were grown under anaerobic conditions at 37٥c. Growth curves (OD 15 vs # of live cells) were constructed for each growth condition, and washed cells were normalized by cell number before addition to the PBMCs.

Bacteria (20 μΐ in phosphate buffered saline (PBS)) were added to each well of PBMCs to give the total number of bacteria as indicated for each experiment. Three different amounts of bacteria were tested: 1.25Ε+07, 6.25Ε+06, and 3.13Ε+06 were added to separate wells of 20 PBMCs. A no-bacteria control also was run. All assays were done in triplicate. After a 2-day incubation at 37٥c, the plates were spun at 300 X g, and the supernatants were removed and stored frozen at -80.C until analj/sis.

Cytokines in the culture supernatants were assayed using a 96-well assay kit from Meso Scale Discovery (Gaithersburg, MD؛ catalog Κ15008Β-1). Human Interleukin-l beta (11-lb), 25 Interleukin 10 (11-10), Interleukin 12ρ70 (Ι112ρ70), and Tumor Necrosis Factor alpha (TNFa) were quantitated and reported as picograms per milliliter. Each sample was assayed in duplicate. wo 2010/055499 PCT/IE2009/000079 -69- 2016206219 18Jul2016

Figs 2 to 5 show the results of a representative experiment. For each cytokine shown, B. infantis 35624 and BL1207 induce nearly identical levels of cytokines. These levels are very different than the levels induced by the three other Bifidobacterial strains that they were compared to. 5

Example 9 - Bifidobacteria with similar EPS genes and high EPS production induce a significantly elevated IL-10:IL-12 ratio compared to strains lacking these genes.

Peripheral blood mononuclear cells (PBMCs) were isolated from healthy human peripheral blood using BD Vacutainer CPT tubes (BD catalog 362761), as per the manufacturer’s 10 instructions. PBMCs were washed and resuspended in Dulbecco's Modified Eagle Medium-Glutamax ™ (Glutamax (Glutamine substitute) t pyruvate t 4.5 g/1 glucose (Gibco catalog 10569-010) 10% fetal bovine serum (Sigma catalog F4135), and 1% penicillin/streptomycin (Sigma catalog Ρ0781). PBMCs were incubated (2x0 cells per well) in flat-bottomed 96-well plates and 20pL of a bacterial suspension (at a concentration of lx 10؟ CFU/mL ) was added. 15 PBMCs were co-incubated with bacteria for 48 hours at 37.C / 5% CO2 in an incubator. After the 2 day incubation period, the plates were centrifuged at 300 X g, and the supernatants were removed and stored frozen at -80.C until analysis. Interleukin-lO (IL-10) and Interleukin-12ρ70 ١ levels in the culture supernatants were quantified using a 96-well assay kit from

Meso Scale Discovery (Gaithersburg, MD; catalog Κ15008Β-1) 20 Bacteria were prepared for co-culture experiments in two formats, (a) Freshly grown bacteria were grown in Difco MRS media and harvested just after entering into stationary phase. All cells were grown under anaerobic conditions at 37٥c. (b) Bacteria were grown imder anaerobic conditions at 37.C in Difco MRS media and harvested just after entering into stationary phase. Freeze dried powders were generated for each of these bacteria and stored at -25 80.C in pre-aliquoted lOOmg vials. Immediately prior to their use, one aliquot of each strain was removed from the freezer and allowed to reach room temperature. Each strain was washed 3 times in 10ml ringers followed by centrifogation. A fresh vial was used on each occasion. Growth curves (OD vs number of live cells) were constructed for each growth condition, and washed cells were normalized by cell number before addition to the PBMCs. A no-bacteria 30 control was also included in all experiments. All assays were done in triplicate.

The Bifidobacteria which contained many of the EPS genes exhibited a similar effect on IL-10:IL-12 induction while bacterial strains which do not contain the EPS genes induced a significantly lower IL-10:IL-12 ratio (Fig.13). Both freshly grown and freeze-dried cultures wo 2010/055499 PCT/IE2009/000079 -70- 2016206219 18Jul2016 exhibited a similar effect in that the strains containing similar EPS genes induced a higher IL-10:IL-12 ratio than those strains that did not contain these genes.

The control of inflammatory diseases is exerted at a number of levels. The controlling fectors include horjnones, prostaglandins, reactive oxygen and nitrogen intermediates, 5 leukotrienes and cytokines. Cytokines are low molecular weight biologically active proteins that are involved in the generation and control of immunological and inflammatory responses. A number of cell types produce these cytokines, with neutrophils, monocytes and lymphocytes being the major sources during inflammatory reactions due to their large numbers at the injured site. 10 Multiple mechanisms exist by which cytokines generated at inflanimatory sites i the inflammatory response. Chemotaxis stimulates homing of inflammatory cells to the injured site, whilst certain cytokines promote infiltration of cells into tissue. Cjrtokines released within the injured tissue result in activation of the inflammatory infiltrate. Most cytokines are pleiotropic and express multiple biologically overlapping activities. As uncontrolled 15 inflammatory responses can result in diseases such as IBD, it is reasonable to expect that cytokine production has gone astray in individuals affected with these diseases.

Interleukin-10 (IL-10) is an anti-inflammatory cytokine which is produced by many cell types including monocytes, macrophages, dendritic cells, mast cells and lymphocytes (in particular T regulatory cells). IL-10 down-regulates the expression of pro-inflammatory Thl 20 cytokines, MHC class II antigens, and co-stimulatory molecules on antigen presenting cells. It also enhances B cell survival, proliferation, and antibody production. This cytokine can block NF-κΒ activity, and is involved in the regulation of the JAK-STAT signaling pathway. Murine knock-out studies have demonstrated the essential role for IL-10 in immunoregulation as IL-10ΚΟ mice develop severe colitis. In addition, bacteria which are potent inducers ofIL-10 have 25 been shown to promote T regulatory cell differentiation in vivo thus contributing to immunological homeostasis (O’Mahony et al., AJP 2006؛ O’Mahony et al., PLoS Pathogens 2008).

Interleukin-12 (IL-12) is a pro-inflammatory cytokine associated with polarisation of Thl effector T cell responses and stimulates the production of other pro-inflammatory Thl cytokines, 30 such as interferon-gamma (IFN-γ) and tumor necrosis fector-alpha (TNF-α), from T and natural killer (1) cells. High levels of IL-12 expression is associated with autoimmunity. Administration of IL-12 to people suffering ftom autoimmune diseases was shown to worsen wo 2010/055499 PCT/IE2009/000079 -71- 2016206219 18Jul2016 disease symptoms. In contrast, IL-12 knock-out mice or treatment of mice with IL-12 neutralising antibodies ameliorated the disease.

Cjrtokine cascades and networks control the inflammatory response, rather than the action of a particular cytokine on a particular cell type. The relative levels of expression, or 5 balance, oftwo cytokines (such as IL-10 and IL-12) is more informative than the expression of a single cjdokine. In these studies, we stimulated human PBMCs -with a range of different bacterial strains. All strains induced IL-10 and all strains induced IL-12. However, examination of the ratio between IL-10 and IL-12 induction revealed that some bacterial strains induced a higher ratio (i.e. more IL-10 with less IL-12) compared to other strains. This is a meaningfirl 10 observation as it is the balance between each of these opposing signals that ultimately determines the immunological outcome. It is anticipated that a high IL-10:IL-12 ratio would promote an anti-inflammatory response associated with appropriate immunoregulatory activity while a low IL-10:IL-12 ratio would contribute to Thl polarisation of the immrme response. Thus, the PBMC IL-10:IL-12 ratio is a important selection criterion for identification of bacterial strains 15 with immunoregulatory properties.

The dimensions and values disclosed herein are not to be understood as being strictly limited to the exact numerical values recited. Instead, unless otherwise specified, each such dimension is intended to mean both the recited value and a firnctionally equivalent range 20 surrounding that value. For example, a dimension disclosed as “40 mm” is intended to mean “about 40 mm.”

All documents cited in the Detailed Description of the Invention are, in relevant part, incorporated herein by reference; the citation of any document is not to be construed as an admission that it is prior art with respect to the present invention. To the extent that any meaning 25 or definition of a term in this document conflicts with any meaning or definition of the same term in a document incorporated by reference, the meaning or definition assigned to that term in this document shall govern.

While particular embodiments of the present invention have been illustrated and described, it would be obvious to those skilled in the art that various other changes and 30 modifications can be made without departing from the spirit and scope of the invention. It is therefore intended to cover in the appended claims all such changes and modifications that are within the scope of this invention. wo 2010/055499 PCT/.E2009/000079 2016206219 18Jul2016

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Claims (19)

1. The claims defining the invention are as follows:

   1. An isolated and purified Bifidobacterium longum strain, excluding Bifidobacterium longum strain 35624 (NCIMB 41003), wherein the strain: a) expresses an exopolysaccharide; and b) comprises at least two nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto; and c) induces an [IL10] : [IL12] ratio of at least 10 in a peripheral blood mononuclear cell (PMBC) co-incubation assay at a concentration of 1 x 107 CFU/ml bacteria.
2. 2. A Bifidobacterium longum strain as claimed in claim 1 wherein the strain does not comprise the nucleic acid sequence of SEQ ID No. 112.
3. 3. A Bifidobacterium longum strain as claimed in claim 1 or claim 2 wherein the strain further comprises at least one nucleic acid sequence selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto.
4. 4. A Bifidobacterium longum strain as claimed in claim 1 or claim 2 wherein the strain further comprises a single nucleic acid sequence selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto.
5. 5. A Bifidobacterium longum strain as claimed in claim 4 wherein the strain comprises a nucleic acid sequence of SEQ ID No. 132 or a nucleic acid sequence with at least 85% sequence homology thereto.
6. 6. A Bifidobacterium longum strain as claimed in claim 1 or claim 2 wherein the strain further comprises two nucleic acid sequences selected from the group comprising SEQ ID No. 114 to SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto.
7. 7. A Bifidobacterium longum strain as claimed in claim 6 wherein the strain comprises the nucleic acid sequences of SEQ ID No. 131 and SEQ ID No. 132 or nucleic acid sequences with at least 85% sequence homology thereto.
8. 8. An isolated and purified Bifidobacterium longum strain wherein the strain: a) expresses an exopolysaccharide; and b) comprises at least two nucleic acid sequences selected from the group comprising SEQ ID NO. 93 to SEQ ID No. 113 or nucleic acid sequences with at least 85% sequence homology thereto; and c) comprises a nucleic acid sequence of SEQ ID No. 132 or a nucleic acid sequence with at least 85% sequence homology thereto; or d) comprises a nucleic acid sequence of SEQ ID No. 131 or a nucleic acid sequence with at least 85% sequence homology thereto; and e) induces an [IL10] : [IL12] ratio of at least 10 in a peripheral blood mononuclear cell (PMBC) co-incubation assay at a concentration of 1 x 107 CFU/ml bacteria.
9. 9. An isolated and purified Bifidobacterium longum strain as claimed in any one of claims 1 to 8 wherein the strain is in the form of a bacterial broth.
10. 10. An isolated and purified Bifidobacterium longum strain as claimed in any one of claims 1 to 8 wherein the strain is in the form of a freeze-dried powder.
11. 11. An isolated strain as claimed in any one of claims 1 to 10 in the form of viable cells.
12. 12. An isolated strain as claimed in any one of claims 1 to 10 in the form of non-viable cells.
13. 13. A formulation comprising an isolated strain of Bifidobacterium longum as claimed in any one of claims 1 to 12.
14. 14. A formulation as claimed in claim 13 which comprises an ingestable carrier.
15. 15. A formulation as claimed in claim 14 wherein the ingestable carrier is a pharmaceutically acceptable carrier such as a capsule, tablet or powder.
16. 16. A formulation as claimed in claim 14 wherein the ingestable carrier is a food product such as acidified milk, yoghurt, frozen yoghurt, milk powder, milk concentrate, cheese spreads, dressings or beverages.
17. 17. A formulation as claimed in any one of claims 14 to 16 wherein the strain is present at more than 106 cfu per gram of ingestable carrier.
18. 18. A composition comprising an isolated strain of Bifidobacterium longum as claimed in any one of claims 1 to 12 and a pharmaceutically acceptable carrier.
19. 19. Use of a Bifidobacterium longum strain as claimed in any one of claims 1 to 12 as a probiotic strain.