WO2024007079A1 - Probiotic bacteria isolated from phytoplankton biomass and related compositions and methods - Google Patents

Probiotic bacteria isolated from phytoplankton biomass and related compositions and methods Download PDF

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Publication number
WO2024007079A1
WO2024007079A1 PCT/CA2023/050910 CA2023050910W WO2024007079A1 WO 2024007079 A1 WO2024007079 A1 WO 2024007079A1 CA 2023050910 W CA2023050910 W CA 2023050910W WO 2024007079 A1 WO2024007079 A1 WO 2024007079A1
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probiotic bacteria
seq
disorder
condition
gastrointestinal disease
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PCT/CA2023/050910
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French (fr)
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John F. BURLET
Julie Lee
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Canbiocin Inc.
The Adored Beast Apothecary Ltd.
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Publication of WO2024007079A1 publication Critical patent/WO2024007079A1/en

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N1/00Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/20Bacteria; Culture media therefor
    • C12N1/205Bacterial isolates
    • AHUMAN NECESSITIES
    • A23FOODS OR FOODSTUFFS; TREATMENT THEREOF, NOT COVERED BY OTHER CLASSES
    • A23LFOODS, FOODSTUFFS, OR NON-ALCOHOLIC BEVERAGES, NOT COVERED BY SUBCLASSES A21D OR A23B-A23J; THEIR PREPARATION OR TREATMENT, e.g. COOKING, MODIFICATION OF NUTRITIVE QUALITIES, PHYSICAL TREATMENT; PRESERVATION OF FOODS OR FOODSTUFFS, IN GENERAL
    • A23L33/00Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof
    • A23L33/10Modifying nutritive qualities of foods; Dietetic products; Preparation or treatment thereof using additives
    • A23L33/135Bacteria or derivatives thereof, e.g. probiotics
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66Microorganisms or materials therefrom
    • A61K35/74Bacteria
    • A61K35/741Probiotics
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66Microorganisms or materials therefrom
    • A61K35/74Bacteria
    • A61K35/741Probiotics
    • A61K35/742Spore-forming bacteria, e.g. Bacillus coagulans, Bacillus subtilis, clostridium or Lactobacillus sporogenes
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/66Microorganisms or materials therefrom
    • A61K35/74Bacteria
    • A61K35/741Probiotics
    • A61K35/744Lactic acid bacteria, e.g. enterococci, pediococci, lactococci, streptococci or leuconostocs
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00Drugs for disorders of the alimentary tract or the digestive system
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/12Antidiarrhoeals
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12RINDEXING SCHEME ASSOCIATED WITH SUBCLASSES C12C - C12Q, RELATING TO MICROORGANISMS
    • C12R2001/00Microorganisms ; Processes using microorganisms
    • C12R2001/01Bacteria or Actinomycetales ; using bacteria or Actinomycetales
    • C12R2001/225Lactobacillus
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12RINDEXING SCHEME ASSOCIATED WITH SUBCLASSES C12C - C12Q, RELATING TO MICROORGANISMS
    • C12R2001/00Microorganisms ; Processes using microorganisms
    • C12R2001/01Bacteria or Actinomycetales ; using bacteria or Actinomycetales
    • C12R2001/46Streptococcus ; Enterococcus; Lactococcus

Definitions

  • the present disclosure relates to probiotics. More particularly, the present disclosure relates to probiotic bacteria isolated from phytoplankton biomass and related compositions and methods.
  • the gastrointestinal (Gl) tracts of most mammals are colonized by native micro-organisms forming a microbiota.
  • Intestinal dysbiosis refers to an imbalance of the microbiota of the intestine.
  • Dysbiosis in microbiota of the intestine may cause a shift in the balance of immunostimulatory cytokines in the Gl tract, intestinal permeability (“leaky gut”), proliferation of pathogenic bacteria, increase intestinal transit time which negatively impacts nutrient digestion and absorption, impacts on the central nervous system and other systemic health conditions.
  • This shift in immunostimulatory cytokines may in turn alter the balance of the inflammatory signals in the gut, causing enteritis and other acute and chronic Gl disorders.
  • Probiotics are intended to restore the balance of beneficial bacteria in the Gl tract in order to treat or prevent intestinal dysbiosis and Gl disorders.
  • probiotic formulations commercially available, not all commercial probiotics provide a beneficial health effect.
  • probiotic bacteria isolated from phytoplankton biomass.
  • the probiotic bacteria are of the Lactobacillaceae family or the Enterococcaceae family.
  • the probiotic bacteria are of the Lactobacillus, Limosilactobacillus, Lacticaseibacillus, Leuconostoc, Pediococcus, Lactococcus, Weissella, Enterococcus, Tetragenococcus, or Vagococcus genus.
  • the probiotic bacteria are of a species selected from Limosilactobacillus fermentum, Lacticaseibacillus casei, Levilactobacillus brevis, Enterococcus gallinarum, Enterococcus casseliflavus, Enterococcus thailandicus, Enterococcus avium, and Pediococcus acidilactici.
  • the probiotic bacteria are of a species selected from Enterococcus thailandicus, Enterococcus avium, and Limosilactobacillus fermentum.
  • the probiotic bacteria have a 16S rDNA sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO:1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NO: 10 as determined by a sequence alignment performed using BLAST (Basic Local Alignment Search Tool).
  • BLAST Basic Local Alignment Search Tool
  • the probiotic bacteria have a 16S rDNA sequence that is identical to SEQ ID NO:1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NQ:10.
  • the probiotic bacteria are of a strain selected from Limosilactobacillus fermentum FT1-1 (IDAC Accession Number 050723-01 ), Limosilactobacillus fermentum FT2-1 (IDAC Accession Number 050723-02), Lacticaseibacillus casei FT2-3 (IDAC Accession Number 050723-03), Enterococcus gallinarum FT3-1 (IDAC Accession Number 050723-04), Limosilactobacillus fermentum FT3-2 (IDAC Accession Number 050723-05), Enterococcus sp.
  • Limosilactobacillus fermentum FT1-1 IDAC Accession Number 050723-01
  • Limosilactobacillus fermentum FT2-1 IDAC Accession Number 050723-02
  • Lacticaseibacillus casei FT2-3 IDAC Accession Number 050723-03
  • Enterococcus gallinarum FT3-1 IDAC Accession Number 050723-04
  • FT3-4 (IDAC Accession Number 050723-06), Enterococcus thailandicus FT3-5 (IDAC Accession Number 050723-07), Enterococcus avium FT3-6 (IDAC Accession Number 050723-08), Levilactobacillus brevis PN-9 (IDAC Accession Number 050723-09), or Pediococcus acidilactici PN-10 (IDAC Accession Number 050723-10).
  • any embodiment of the probiotic bacteria disclosed herein for the prevention or treatment of a gastrointestinal disease, condition, or disorder is provided.
  • the gastrointestinal disease, condition, or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
  • the gastrointestinal disease, condition, or disorder is intestinal dysbiosis.
  • composition comprising any embodiment of the probiotic bacteria disclosed herein and at least one additional ingredient.
  • the at least one additional ingredient comprises a prebiotic, an additional pharmaceutical or nutritional ingredient, or a pharmaceutically or nutritionally acceptable excipient.
  • the composition is in the form of a dietary supplement.
  • the composition is in the form of a food product.
  • compositions disclosed herein for the prevention or treatment of a gastrointestinal disease, condition or disorder.
  • the gastrointestinal disease, condition or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
  • the gastrointestinal disease, condition or disorder is intestinal dysbiosis.
  • a method for preparing a composition comprising: providing at least one additional ingredient; and combining the probiotic bacteria and the at least one additional ingredient.
  • the at least one additional ingredient is an edible ingredient.
  • the probiotic bacteria are provided in the form of a powder or a liquid.
  • kits comprising any embodiment of the probiotic bacteria disclosed herein and instructions for use thereof.
  • the instructions include directions for administering the probiotic bacteria to a subject to treat or prevent a gastrointestinal disease, condition, or disorder.
  • the gastrointestinal disease, condition, or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
  • the gastrointestinal disease, condition, or disorder is intestinal dysbiosis.
  • the subject is a mammalian subject.
  • a method for treating or preventing a gastrointestinal disease, condition, or disorder in a subject comprising administering any embodiment of the probiotic bacteria disclosed herein to the subject.
  • the gastrointestinal disease, condition, or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
  • the gastrointestinal disease, condition, or disorder is intestinal dysbiosis.
  • the subject is a mammalian subject.
  • the probiotic bacteria are administered orally.
  • Figure 1 is a flowchart of a method for making an ingestible composition, according to some embodiments.
  • Figures 2A-2C are gram stain images of 32 isolated strains of bacteria from phytoplankton biomass, under 100X power with oil immersion in microscope;
  • RAPD Random Amplified Polymorphic DNA
  • PCR polymerase chain reaction
  • Figure 6A is a 16S rDNA sequence of Limosilactobacillus fermentum FT1 -1 (SEQ. ID NO: 1 );
  • Figure 6B is a 16S rDNA sequence of Limosilactobacillus fermentum FT2-1 (SEQ. ID NO: 2);
  • Figure 6C v a 16S rDNA sequence of Lacticaseibacillus casei FT2-3 (SEQ. ID NO: 3);
  • Figure 6D is a 16S rDNA sequence of Enterococcus gallinarum FT3-1 (SEQ. ID NO: 4);
  • Figure 6E is a 16S rDNA sequence of Limosilactobacillus fermentum FT3-2 (SEQ.
  • Figure 6F is a 16S rDNA sequence of Enterococcus sp. FT3-4 (SEQ. ID NO: 6);
  • Figure 6G is a 16S rDNA sequence of Enterococcus thailandicus FT3-5 (SEQ. ID NO: 7);
  • Figure 6H is a 16S rDNA sequence of Enterococcus avium FT3-6 (SEQ. ID NO: 8);
  • Figure 6I is a 16S rDNA sequence of Levilactobacillus brevis PN-9 (SEQ. ID NO:9); and
  • Figure 6J is a 16S rDNA sequence of Pediococcus acidilactici PN-10 (SEQ. ID NQ:10).
  • the present disclosure provides probiotic bacteria isolated from phytoplankton biomass for use as probiotics.
  • the probiotic bacteria are for use as probiotics in mammals, including but not limited to humans, livestock, and companion animals.
  • the probiotic bacteria may be used to treat or prevent a gastrointestinal disease, condition, or disorder in the subject. Also provided are related compositions, kits, and methods.
  • probiotic bacteria refers to bacteria that produce at least one beneficial effect on a host organism and a “probiotic” refers to a cell culture or preparation of probiotic bacteria.
  • the beneficial effects on the host organism may include, for example, a beneficial effect on the host’s digestive system, immune system, and/or brain-gut-microbiome system. Embodiments are not limited by the specific beneficial effects described herein.
  • isolated when used in reference to the probiotic bacteria disclosed herein refers to bacteria that have been separated from their natural environment.
  • phytoplankton biomass refers to biological material that includes phytoplankton cells, lysed phytoplankton cells, and/or extracellular material of phytoplankton cells and may also include other microorganisms such as other types of bacteria.
  • phytoplankton refers to microorganisms capable of photosynthesis that inhabit bodies of water, including microalgae and cyanobacteria.
  • the probiotic bacteria may be isolated from phytoplankton biomass using the methods described in the Examples below. In other embodiments, the probiotic bacteria may be isolated from phytoplankton biomass by any other suitable means. For greater clarity, it will be understood that the probiotic bacteria are not phytoplankton themselves but, rather, are other bacteria that are associated with phytoplankton biomass.
  • the probiotic bacteria are in the form of at least one isolated strain.
  • isolated strain or “isolate” refers to a culture of probiotic bacteria that has been obtained from culturing a single cell or a single colony isolated from its original source.
  • at least one isolated strain may be genotypically and/or phenotypically distinct from other strains of the same species.
  • the isolated strains may also be referred to as “primordial strains” as they represent an ancient source of nutrition for animal life.
  • at least one isolated strain is biologically pure.
  • biologically pure refers to an isolated strain that is substantially free of any other strain of organism.
  • probiotic bacteria may be described with reference to isolated strains and isolates. However, it will be understood that the probiotic bacteria of this disclosure may be in any other suitable form, including as a heterogenous mixture.
  • the probiotic bacteria are lactic acid bacteria (LAB).
  • the probiotic bacteria may be within the order Lactobacillales.
  • the probiotic bacteria are of a species of the Lactobacillaceae family including, but not limited to, a species of the Lactobacillus, Limosilactobacillus, Lacticaseibacillus, Levilactobacillus, Leuconostoc, Pediococcus, or Weissella genus or any other species of the former Lactobacillus genus (also referred to as “lactobacilli”).
  • the probiotic bacteria are of a species of the Enterococcaceae family including, for example, a species of the Enterococcus, Tetragenococcus, or Vagococcus genus.
  • the probiotic bacteria are of another species of lactic acid bacteria including, but not limited to, a species of the Lactococcus, Streptococcus, Aerococcus, Carnobacterium, Oenococcus, or Sporolactobacillus genus.
  • the probiotic bacteria are of any other genus or species of bacteria isolated from phytoplankton biomass.
  • the Limosilactobacillus species is Limosilactobacillus fermentum (formerly Lactobacillus fermentum).
  • the Lacticaseibacillus species is Lacticaseibacillus casei (formerly Lactobacillus casei).
  • the Levilactobacillus species is Levilactobacillus brevis (formerly Lactobacillus brevis).
  • the Enterococcus species is Enterococcus gallinarum, Enterococcus casseliflavus, Enterococcus thailandicus, or Enterococcus avium.
  • the Pediococcus species is Pediococcus acidilactici.
  • the probiotic bacteria are selected from the isolated strains listed in Table 1 below. Gram staining results showing the bacterial morphologies of each of the isolated strains of Table 1 are shown in Figures 2A- 20 and the 16S rDNA sequences are shown in Figures 6A to 6J.
  • the probiotic bacteria have a 16S rDNA sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to SEQ ID NO:1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8 as determined by a sequence alignment performed using BLAST (Basic Local Alignment Search Tool).
  • BLAST Basic Local Alignment Search Tool
  • the probiotic bacteria have a 16S rDNA sequence that is identical to SEQ ID NO:1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO: 9, or SEQ ID NO: 10.
  • the probiotic bacteria are a mutant strain of one of the strains listed in Table 1 .
  • a “mutant” or a “mutant strain” refers to a bacterial strain that has at least one DNA mutation compared to the parent (wild-type) strain from which it derives.
  • DNA mutations may include base substitutions including transitions and transversions, deletions, insertions, and any other type of natural or induced DNA modification.
  • the probiotic bacteria may be capable of probiotic activity in a subject.
  • probiotic activity refers to the ability of the bacteria to produce at least one beneficial effect in the subject.
  • the probiotic bacteria are capable of surviving and colonizing in the gastrointestinal tract of the subject to provide the beneficial effect to the subject.
  • the probiotic bacteria show tolerance to a pH for a period of time.
  • the pH is a low pH, such as, for example, when assayed in vitro, indicating that the bacteria may be capable of surviving passage through the acidic mammalian stomach.
  • “low pH” refers to a pH of about 6.9 or less.
  • the bacteria are able to survive at a pH of about 2.5 for at least about 6 hours when assayed in vitro.
  • the bacteria are able to survive at a pH of about 2.0 for at least about 6 hours when assayed in vitro.
  • survive means that the viable cell count of a test culture (as measured in colony forming units (CFU) per mL) is above detection limit, such as, for example, [1.7logio(CFU/mL) or 50 CFU/mL],
  • the probiotic bacteria are tolerant to the presence of bile salt, such as, for example, when assayed in vitro, indicating that the bacteria may survive the passage through the mammalian intestine.
  • the bacteria are able to survive in the presence of bile salts for a period of time, such as, for example, in the presence of about 3% bile salts for at least about 6 hours when assayed in vitro.
  • the probiotic bacteria have autoaggregation ability, such as, for example, when assayed in vitro, indicating that the bacterial cells may be able to bind host intestinal epithelial cells in the subject to facilitate colonization of the gastrointestinal tract.
  • autoaggregation or “autoaggregate” refers to the bacterial cells binding to one another to floc out of solution.
  • the bacteria have high cell surface hydrophobicity when assayed in vitro, indicating that the bacterial cells may be able to adhere to host cells in the subject to facilitate colonization of the gastrointestinal tract.
  • the probiotic bacteria have one or more additional properties when assayed in vitro, ex vivo, and/or in vivo that support their use as probiotics.
  • additional properties include: the ability to bind to mammalian cells; the ability to modulate expression of at least one antiinflammatory or pro-inflammatory cytokine by host immune cells; the ability to produce one or more inhibitory substances that inhibit the growth of pathogenic and/or spoilage microorganisms; susceptibility to at least one antibiotic; and/or stability for a suitable shelf-life period.
  • the probiotic bacteria are in a viable form. In some embodiments, the probiotic bacteria are in a lyophilized (freeze-dried) form or in the form of a liquid suspension.
  • postbiotic refers to a metabolite or other bioactive compound produced by a microorganism that confers at least one beneficial effect on a host organism.
  • the postbiotics may be produced intracellularly or extracellularly.
  • the probiotic bacteria disclosed herein are provided in combination with one or more postbiotics produced by the probiotic bacteria when grown in a suitable media.
  • the probiotic bacteria may be lysed or heat-killed and the postbiotics may be used in place of the probiotic bacteria in any of the compositions, kits, methods, and/or uses described below.
  • compositions comprising probiotic bacteria isolated from phytoplankton biomass. Any of the isolated strains described above may be used as the probiotic bacteria in the compositions described herein. In some embodiments, the composition may comprise two or more isolated strains of bacteria isolated from phytoplankton biomass. The strains may be from the same or different phytoplankton biomass.
  • the composition may comprise the probiotic bacteria and one or more additional ingredients.
  • the composition may further comprise at least one prebiotic.
  • prebiotic refers to a substance that stimulates the growth or activity of at least one beneficial micro-organism.
  • the prebiotic compound induces the growth or activity of at least one isolated strain of probiotic bacteria.
  • prebiotics include inulin, pectin, beta-glucans, fructooligosaccharides (FOS), galactooligosaccharides (GOS), xylooligosaccharides (XOS), resistant starch, and organic molecules such as humic and fulvic acid.
  • the composition may further comprise at least one additional pharmaceutical or nutritional ingredient including, for example, at least one vitamin, mineral, fiber, fatty acid, amino acid, or any other suitable pharmaceutical or nutritional ingredient.
  • the composition may further comprise at least one encapsulation material.
  • encapsulation materials include polysaccharides such as alginate, plant/microbial gums, chitosan, starch, k-carrageenan, cellulose acetate phthalate; proteins such as gelatin or milk proteins; and fats.
  • the probiotic bacteria may be encapsulated in the encapsulated material by spray drying, extrusion, gelation, droplet extrusion, emulsion, freeze- drying, or any other suitable encapsulation method. Encapsulation of the probiotic bacteria may protect the cells and extend the shelf-life of the composition.
  • the composition is an ingestible composition.
  • ingestible refers to a substance that is orally consumable by the subject.
  • the ingestible composition is in the form of a dietary supplement.
  • the dietary supplement may be in the form of a powder, a capsule, a gel capsule, a microcapsule, a bead, a tablet, a chewable tablet, a gummy, a liquid, or any other suitable form of dietary supplement.
  • the dietary supplement further comprises at least one pharmaceutically or nutritionally acceptable excipient.
  • excipients include fillers, binders, carriers, diluents, stabilizers, lubricants, glidants, coloring agents, flavoring agents, coatings, disintegrants, preservatives, sorbents, and sweeteners.
  • the dietary supplement may further comprise a suitable encapsulation material, including but not limited to, polyvinyl alcohol (PVA), polyvinylpurrolidone (PVP), alginates, gelatin, and any other suitable encapsulation material.
  • the ingestible composition is in the form of a food product.
  • the food product may be in any form suitable for a mammalian subject, such as a human, a livestock animal, companion animal, or any other mammalian subject.
  • the food product is a solid food product.
  • the solid food product may be dry, wet, semi-moist, frozen, dehydrated, freeze-dried, or in any other suitable form.
  • the food product is a liquid food product. Examples of liquid food products include, but are not limited to, beverages, broths, oil suspensions, gravies, milk-based products, and liquid or semi-solid yogurts.
  • the ingestible composition is provided in a powder form suitable to sprinkle onto the surface of a solid food product or mix into a liquid food product.
  • the ingestible composition is provided in a liquid form suitable to spray, pour, or drop onto the surface of the solid food product or mix with a liquid food product.
  • the ingestible composition is in a form suitable to be sprayed, poured, or dropped directly into the subject’s mouth.
  • the ingestible composition is in the form of a surface coating for a solid food product.
  • the surface coating may comprise a carrier to allow the bacteria to adhere to the surface of the solid food product.
  • the carrier may comprise an edible oil or any other suitable carrier.
  • the composition may be in a non- ingestible form, for example, as a suppository, or any other suitable form.
  • FIG. 1 is a flowchart of an exemplary method 100 for making a composition, according to some embodiments.
  • probiotic bacteria isolated from phytoplankton biomass are provided.
  • at block 104 at least one additional ingredient is provided.
  • the term “providing” in this context may refer to making (including isolating or culturing), receiving, buying, or otherwise obtaining the probiotic bacteria and the ingredient.
  • the probiotic bacteria are combined with the additional ingredient.
  • the probiotic bacteria are at least one of the isolated strains listed in Table 1. In some embodiments, the probiotic bacteria are in a powder form. In other embodiments, the probiotic bacteria are in a liquid form.
  • the ingredient is an edible ingredient. In some embodiments, the edible ingredient is at least one pharmaceutically or nutritionally acceptable excipient as described above for dietary supplements. In other embodiments, the edible ingredient is one of the solid or liquid food products described above or any components thereof.
  • the probiotic bacteria and the edible ingredient are combined during production of the dietary supplement, solid food product, or liquid food product.
  • the probiotic bacteria are combined with the supplement, solid food product or liquid food product postproduction.
  • the probiotic bacteria may be in powder form and the powder may be sprinkled onto a solid food product or mixed with a liquid food product or supplement.
  • the probiotic bacteria may be in liquid form (e.g., an edible oil) and the liquid may be sprayed, poured, dropped, or coated onto the solid food product or mixed with an edible liquid.
  • the probiotic bacteria may be combined with the additional ingredient using any other suitable means.
  • the probiotic bacteria, isolated strains, and compositions described herein may be used to improve and/or maintain the health of a subject.
  • the subject may be a mammalian subject, including but not limited to humans, livestock, and companion animals.
  • companion animals include domestic dogs and cats.
  • livestock include cattle, sheep, goats, and pigs.
  • the probiotic bacteria, isolated strain(s), or composition may be used to treat or prevent a gastrointestinal disease, disorder, or condition in the subject.
  • “treat” or “treatment” refers to obtaining a desired pharmacologic and/or physiologic effect.
  • the effect can be prophylactic in terms of completely or partially preventing a health condition or symptom thereof and/or can be therapeutic in terms of a partial or complete cure for the health condition and/or adverse effect attributable to the health condition.
  • the terms “treat” or “treatment” in this context are intended to include providing any beneficial physiological effect to the subject and their meaning is not limited to preventing or curing a specific disorder or health condition.
  • the gastrointestinal disease, disorder, or condition comprises intestinal dysbiosis.
  • intestinal dysbiosis refers to any imbalance of the microbial community in the gastrointestinal tract of the subject or any portion thereof.
  • the gastrointestinal disease, disorder, or condition comprises enteritis and/or diarrhea.
  • the isolated strain(s) or composition may be used in the preparation of a medicament for treatment or prevention of intestinal dysbiosis, enteritis, diarrhea, or any other suitable disease, disorder, or condition.
  • the probiotic bacteria, isolated strain(s), or composition may be used to provide any other health benefit to the subject.
  • probiotic bacteria isolated from phytoplankton are similar to ancient food sources for animals. Modern food (including commercial pet foods and livestock feed) has a significantly different nutritional profile compared to ancient food sources, which may result in alternations to the intestinal microbiome. By introducing “primordial strains” of probiotic bacteria isolated from phytoplankton, the intestinal microbiome may shift towards more of an ancestral state and thereby treat or prevent gastrointestinal conditions such as dysbiosis.
  • the probiotic bacteria, isolated strain(s), or composition may be administered to the subject in an effective amount.
  • effective amount refers to an amount that provides at least one health benefit to the subject.
  • the effective amount may vary based on a number of factors including but not limited to the specific probiotic bacteria (e.g., strain) being administered and its characteristics; the age, weight, sex, diet, and general health of the subject; the mode and time of administration; the severity of the condition being treated; the nature of any concurrent therapies or medications; and any other relevant factor.
  • the probiotic bacteria, isolated strain(s), or composition is orally administrable to the subject.
  • the probiotic bacteria, isolated strain(s), or composition may be enterally and/or rectally administrable to the subject.
  • the probiotic bacteria, isolated strain(s), or composition may be administered to the subject at any suitable interval including, for example, at least once per month, at least once per week, or at least once per day.
  • a daily serving of about 1 billion CFU, per 20 lbs of body weight of the subject may be orally administered to the subject.
  • kits comprising probiotic bacteria isolated from phytoplankton biomass in a container and instructions for use thereof.
  • the kit comprises one or more of the isolated strains of the probiotic bacteria.
  • the kit comprises a composition that comprises the probiotic bacteria, such as one or more of the isolated strains(s).
  • the isolated strain(s) and/or composition may be any embodiment of isolated strains and compositions disclosed herein.
  • the instructions may comprise directions for administering the probiotic bacteria to a mammalian subject, for example, to treat or prevent a gastrointestinal disease, disorder, or condition including, but not limited to, intestinal dysbiosis, enteritis, and/or diarrhea.
  • the instructions may include a recommended dosage and frequency for administration and may also include directions to take the probiotic bacteria with or without food, with or without other medications, etc.
  • the instructions comprise directions for combining the probiotic bacteria with a solid or liquid food product.
  • Lactic acid bacteria were isolated from three bags of freeze- dried phytoplankton products provided by Adored Beast Apothecary LtdTM.
  • the phytoplankton products were marine microalgae products obtained from Fitoplankton MarinoTM, El Puerto de Santa Maria - Cadiz, Spain.
  • Powder from each bag was dissolved with 0.1 % peptone water (PW) in a 1 in 10 ratio. The weight of the powder was 0.5 g, thus the volume of the 0.1 % PW was 4.5 mL. Dilutions were then vortexed for 1 min to make sure the solutions were thoroughly homogenized.
  • PW peptone water
  • the candidate strains were cultured in MRS broth at 37 °C overnight, and then 5 mL overnight cultures were harvested at 8,000 rpm for 5 min for the extraction.
  • the protocol was as following: cell pellets were resuspended and washed with 500 pL T 100E, twice, and then 10 pL of lysozyme stock solution (10 mg lysozyme in 0.5 mL ddF ) was added. The lysates were incubated at 37 °C for more than 3 h and centrifuged at 10,000 rpm for 5 min when the incubation was finished. The cell pellets were then homogenized with 500 pL T100E buffer.
  • the gene encoding the 16S ribosomal RNA was amplified by PCR and sequenced by Sanger Sequencing.
  • the DNA sequence encoding the 16S rRNA is referred to as the 16S rDNA sequence.
  • PCR reactions with 16S rDNA primers were conducted to amplify the conserved regions of the 16S rRNA gene.
  • the PCR was programed as follows: 95 °C for 5 min; 95 °C for 30 sec, 55 °C for 30 sec, 72 °C for 30 sec with 35 cycles in total; 72 °C for 10 min, and store at 4 °C.
  • the products from the 16S rDNA PCR reaction were purified with GeneJETTM PCR Purification Kit (Cat#: K0701 , Thermo ScientificTM, Canada) and submitted for sequencing to Molecular Biology Facility (MBSLI) (Department of Biological Sciences, University of Alberta).
  • the sequencing data were further aligned in the GenbankTM database using the basic local alignment search tool (BLAST, www.ncbi.nlm.nih.gov/BLAST) for the final identification of the LAB strains.
  • Reagents and equipment used in this study were as follows: the Taq polymerase used in this study was DreamTaqTM DNA polymerase (Cat#: EP0703, Thermo ScientificTM, Canada).
  • the PCR products were analyzed for electrophoresis and then images were visualized and captured by transillumination under UV light using AlphaimagerTM Gel Imager (ThermoFisher, Canada).
  • Figures 4A and 4B show the agarose gel electrophoresis of the 16S rDNA PCR products for 33 of the 35 isolated LAB strains.
  • Lacticaseibacillus casei 1 strain was Levilactobacillus brevis, 1 strain was Pediococcus acidilactici, and 9 strains were Enterococcus sp. Most Enterococcus sp. were isolated from Bag #3, while mostly Lacticaseibacillus casei and Limosilactobacillus fermentum were isolated from Bag #1 and Bag #2. RAPD profiling of one representative strain of Lacticaseibacillus casei and Limosilactobacillus fermentum from each bag was performed again using the M13 primer, with K9-1 (Lacticaseibacillus casei) and K9-2 (Limosilactobacillus fermentum) as positive controls, as shown in Figure 5.
  • MATH microbial adhesion to hydrocarbons
  • the testing tube was kept still for 1 hour to allow the immiscible solvent and aqueous phase to separate.
  • the aqueous layer was removed and the OD6oo (ODtest) was measured and recorded.
  • the percentage of hydrophobicity of each strain was calculated as the following formula:

Abstract

Probiotic bacteria isolated from phytoplankton biomass are provided. The probiotic bacteria may be in the form of at least one isolated strain. In some embodiments, the probiotic bacteria are for use as probiotics in mammals, including humans, livestock, and companion animals. In some embodiments, the probiotic bacteria may be used to treat or prevent a gastrointestinal disease, condition, or disorder in the subject. Also provided are related compositions comprising the probiotic bacteria and at least one additional ingredient and methods for making such compositions.

Description

PROBIOTIC BACTERIA ISOLATED FROM PHYTOPLANKTON BIOMASS AND RELATED COMPOSITIONS AND METHODS
RELATED APPLICATION:
[0001 ] The present disclosure claims priority to U.S. Provisional Patent Application No. 63/358,336, filed July 5, 2022, the entire content of which is herein incorporated by reference.
TECHNICAL FIELD:
[0002] The present disclosure relates to probiotics. More particularly, the present disclosure relates to probiotic bacteria isolated from phytoplankton biomass and related compositions and methods.
BACKGROUND:
[0003] The gastrointestinal (Gl) tracts of most mammals are colonized by native micro-organisms forming a microbiota. In a healthy mammal, there is a balance between beneficial or benign bacteria and pathogenic bacteria. Intestinal dysbiosis refers to an imbalance of the microbiota of the intestine. Dysbiosis in microbiota of the intestine may cause a shift in the balance of immunostimulatory cytokines in the Gl tract, intestinal permeability (“leaky gut”), proliferation of pathogenic bacteria, increase intestinal transit time which negatively impacts nutrient digestion and absorption, impacts on the central nervous system and other systemic health conditions. This shift in immunostimulatory cytokines may in turn alter the balance of the inflammatory signals in the gut, causing enteritis and other acute and chronic Gl disorders.
[0004] Probiotics are intended to restore the balance of beneficial bacteria in the Gl tract in order to treat or prevent intestinal dysbiosis and Gl disorders. However, while there are a number of probiotic formulations commercially available, not all commercial probiotics provide a beneficial health effect. SUMMARY:
[0005] In one aspect, there is provided probiotic bacteria isolated from phytoplankton biomass.
[0006] In some embodiments, the probiotic bacteria are of the Lactobacillaceae family or the Enterococcaceae family.
[0007] In some embodiments, the probiotic bacteria are of the Lactobacillus, Limosilactobacillus, Lacticaseibacillus, Leuconostoc, Pediococcus, Lactococcus, Weissella, Enterococcus, Tetragenococcus, or Vagococcus genus.
[0008] In some embodiments, the probiotic bacteria are of a species selected from Limosilactobacillus fermentum, Lacticaseibacillus casei, Levilactobacillus brevis, Enterococcus gallinarum, Enterococcus casseliflavus, Enterococcus thailandicus, Enterococcus avium, and Pediococcus acidilactici.
[0009] In some embodiments, the probiotic bacteria are of a species selected from Enterococcus thailandicus, Enterococcus avium, and Limosilactobacillus fermentum.
[0010] In some embodiments, the probiotic bacteria have a 16S rDNA sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO:1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NO: 10 as determined by a sequence alignment performed using BLAST (Basic Local Alignment Search Tool).
[0011 ] In some embodiments, the probiotic bacteria have a 16S rDNA sequence that is identical to SEQ ID NO:1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NQ:10. [0012] In some embodiments, wherein the probiotic bacteria are of a strain selected from Limosilactobacillus fermentum FT1-1 (IDAC Accession Number 050723-01 ), Limosilactobacillus fermentum FT2-1 (IDAC Accession Number 050723-02), Lacticaseibacillus casei FT2-3 (IDAC Accession Number 050723-03), Enterococcus gallinarum FT3-1 (IDAC Accession Number 050723-04), Limosilactobacillus fermentum FT3-2 (IDAC Accession Number 050723-05), Enterococcus sp. FT3-4 (IDAC Accession Number 050723-06), Enterococcus thailandicus FT3-5 (IDAC Accession Number 050723-07), Enterococcus avium FT3-6 (IDAC Accession Number 050723-08), Levilactobacillus brevis PN-9 (IDAC Accession Number 050723-09), or Pediococcus acidilactici PN-10 (IDAC Accession Number 050723-10).
[0013] In another aspect, there is provided any embodiment of the probiotic bacteria disclosed herein for the prevention or treatment of a gastrointestinal disease, condition, or disorder.
[0014] In some embodiments, the gastrointestinal disease, condition, or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
[0015] In some embodiments, the gastrointestinal disease, condition, or disorder is intestinal dysbiosis.
[0016] In another aspect, there is provided an isolated strain of any embodiment of the probiotic bacteria disclosed herein.
[0017] In another aspect, there is provided a biologically pure culture of any embodiment of the probiotic bacteria disclosed herein.
[0018] In another aspect, there is provided a composition comprising any embodiment of the probiotic bacteria disclosed herein and at least one additional ingredient. [0019] In some embodiments, the at least one additional ingredient comprises a prebiotic, an additional pharmaceutical or nutritional ingredient, or a pharmaceutically or nutritionally acceptable excipient.
[0020] In some embodiments, the composition is in the form of a dietary supplement.
[0021] In some embodiments, the composition is in the form of a food product.
[0022] In another aspect, there is provided any embodiment of the composition disclosed herein for the prevention or treatment of a gastrointestinal disease, condition or disorder.
[0023] In some embodiments, the gastrointestinal disease, condition or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
[0024] In some embodiments, the gastrointestinal disease, condition or disorder is intestinal dysbiosis.
[0025] In another aspect, there is provided a method for preparing a composition comprising: providing at least one additional ingredient; and combining the probiotic bacteria and the at least one additional ingredient.
[0026] In some embodiments, the at least one additional ingredient is an edible ingredient.
[0027] In some embodiments, the probiotic bacteria are provided in the form of a powder or a liquid.
[0028] In another embodiment, there is provided a kit comprising any embodiment of the probiotic bacteria disclosed herein and instructions for use thereof. [0029] In some embodiments, the instructions include directions for administering the probiotic bacteria to a subject to treat or prevent a gastrointestinal disease, condition, or disorder.
[0030] In some embodiments, the gastrointestinal disease, condition, or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
[0031] In some embodiments, the gastrointestinal disease, condition, or disorder is intestinal dysbiosis.
[0032] In some embodiments, the subject is a mammalian subject.
[0033] In another aspect, there is provided a method for treating or preventing a gastrointestinal disease, condition, or disorder in a subject, comprising administering any embodiment of the probiotic bacteria disclosed herein to the subject.
[0034] In some embodiments, the gastrointestinal disease, condition, or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
[0035] In some embodiments, the gastrointestinal disease, condition, or disorder is intestinal dysbiosis.
[0036] In some embodiments, the subject is a mammalian subject.
[0037] In some embodiments, the probiotic bacteria are administered orally.
[0038] In another aspect, there is provided a use of any embodiment of the probiotic bacteria disclosed herein for treating or preventing a gastrointestinal disease, condition, or disorder.
[0039] In another aspect, there is provided a use of any embodiment of the probiotic bacteria disclosed herein in the manufacture of a medicament for the treatment of a gastrointestinal disease, condition, or disorder. [0040] Other aspects and features of the present disclosure will become apparent, to those ordinarily skilled in the art, upon review of the following description of the specific embodiments of the disclosure.
BRIEF DESCRIPTION OF THE DRAWINGS:
[0041 ] Some aspects of the disclosure will be described in greater detail with reference to the accompanying drawings. In the drawings:
[0042] Figure 1 is a flowchart of a method for making an ingestible composition, according to some embodiments;
[0043] Figures 2A-2C are gram stain images of 32 isolated strains of bacteria from phytoplankton biomass, under 100X power with oil immersion in microscope;
[0044] Figures 3A and 3B are photos of the agarose gel electrophoresis of Random Amplified Polymorphic DNA (RAPD) polymerase chain reaction (PCR) profiling of 33 isolated strains of bacteria from phytoplankton biomass (M = marker, NC = negative control);
[0045] Figures 4A and 4B are photos of the agarose gel electrophoresis of PCR products after amplification of respective 16S rDNA sequences of the 33 isolated strains of Figures 3A-3B (M = marker, NC = negative control);
[0046] Figure 5 is a photo of the agarose gel electrophoresis of RAPD-PCR profiling of isolated strains 1 -11 (lane A), 2-1 (lane B), 3-10B (lane C), and 2-3 (lane D) in comparison to positive controls for Lacticaseibacillus casei (PC1 ) and Limosilactobacillus fermentum (PC2) (M = marker, NC = negative control); and
[0047] Figure 6A is a 16S rDNA sequence of Limosilactobacillus fermentum FT1 -1 (SEQ. ID NO: 1 ); Figure 6B is a 16S rDNA sequence of Limosilactobacillus fermentum FT2-1 (SEQ. ID NO: 2); Figure 6C v a 16S rDNA sequence of Lacticaseibacillus casei FT2-3 (SEQ. ID NO: 3); Figure 6D is a 16S rDNA sequence of Enterococcus gallinarum FT3-1 (SEQ. ID NO: 4); Figure 6E is a 16S rDNA sequence of Limosilactobacillus fermentum FT3-2 (SEQ. ID NO: 5); Figure 6F is a 16S rDNA sequence of Enterococcus sp. FT3-4 (SEQ. ID NO: 6); Figure 6G is a 16S rDNA sequence of Enterococcus thailandicus FT3-5 (SEQ. ID NO: 7); Figure 6H is a 16S rDNA sequence of Enterococcus avium FT3-6 (SEQ. ID NO: 8); Figure 6I is a 16S rDNA sequence of Levilactobacillus brevis PN-9 (SEQ. ID NO:9); and Figure 6J is a 16S rDNA sequence of Pediococcus acidilactici PN-10 (SEQ. ID NQ:10).
DETAILED DESCRIPTION OF EMBODIMENTS:
[0048] Generally, the present disclosure provides probiotic bacteria isolated from phytoplankton biomass for use as probiotics. In some embodiments, the probiotic bacteria are for use as probiotics in mammals, including but not limited to humans, livestock, and companion animals. In some embodiments, the probiotic bacteria may be used to treat or prevent a gastrointestinal disease, condition, or disorder in the subject. Also provided are related compositions, kits, and methods.
[0049] As used herein, “probiotic bacteria” refers to bacteria that produce at least one beneficial effect on a host organism and a “probiotic” refers to a cell culture or preparation of probiotic bacteria. The beneficial effects on the host organism may include, for example, a beneficial effect on the host’s digestive system, immune system, and/or brain-gut-microbiome system. Embodiments are not limited by the specific beneficial effects described herein.
[0050] As used herein, “isolated”, when used in reference to the probiotic bacteria disclosed herein refers to bacteria that have been separated from their natural environment.
[0051 ] As used herein, “phytoplankton biomass” refers to biological material that includes phytoplankton cells, lysed phytoplankton cells, and/or extracellular material of phytoplankton cells and may also include other microorganisms such as other types of bacteria. The term “phytoplankton” refers to microorganisms capable of photosynthesis that inhabit bodies of water, including microalgae and cyanobacteria.
[0052] In some embodiments, the probiotic bacteria may be isolated from phytoplankton biomass using the methods described in the Examples below. In other embodiments, the probiotic bacteria may be isolated from phytoplankton biomass by any other suitable means. For greater clarity, it will be understood that the probiotic bacteria are not phytoplankton themselves but, rather, are other bacteria that are associated with phytoplankton biomass.
[0053] In some embodiments, the probiotic bacteria are in the form of at least one isolated strain. As used herein, “isolated strain” or “isolate” refers to a culture of probiotic bacteria that has been obtained from culturing a single cell or a single colony isolated from its original source. In some embodiments, at least one isolated strain may be genotypically and/or phenotypically distinct from other strains of the same species. The isolated strains may also be referred to as “primordial strains” as they represent an ancient source of nutrition for animal life. In some embodiments, at least one isolated strain is biologically pure. As used herein, “biologically pure” refers to an isolated strain that is substantially free of any other strain of organism.
[0054] Hereafter, the probiotic bacteria may be described with reference to isolated strains and isolates. However, it will be understood that the probiotic bacteria of this disclosure may be in any other suitable form, including as a heterogenous mixture.
[0055] In some embodiments, the probiotic bacteria are lactic acid bacteria (LAB). The probiotic bacteria may be within the order Lactobacillales. In some embodiments, the probiotic bacteria are of a species of the Lactobacillaceae family including, but not limited to, a species of the Lactobacillus, Limosilactobacillus, Lacticaseibacillus, Levilactobacillus, Leuconostoc, Pediococcus, or Weissella genus or any other species of the former Lactobacillus genus (also referred to as “lactobacilli”). In some embodiments, the probiotic bacteria are of a species of the Enterococcaceae family including, for example, a species of the Enterococcus, Tetragenococcus, or Vagococcus genus. In other embodiments, the probiotic bacteria are of another species of lactic acid bacteria including, but not limited to, a species of the Lactococcus, Streptococcus, Aerococcus, Carnobacterium, Oenococcus, or Sporolactobacillus genus. In other embodiments, the probiotic bacteria are of any other genus or species of bacteria isolated from phytoplankton biomass.
[0056] In some embodiments, the Limosilactobacillus species is Limosilactobacillus fermentum (formerly Lactobacillus fermentum). In some embodiments, the Lacticaseibacillus species is Lacticaseibacillus casei (formerly Lactobacillus casei). In some embodiments, the Levilactobacillus species is Levilactobacillus brevis (formerly Lactobacillus brevis). In some embodiments, the Enterococcus species is Enterococcus gallinarum, Enterococcus casseliflavus, Enterococcus thailandicus, or Enterococcus avium. In some embodiments, the Pediococcus species is Pediococcus acidilactici. A person skilled in the art will understand that the current and former names refer to the same species and embodiments are not limited to any one specific terminology.
[0057] In some embodiments, the probiotic bacteria are selected from the isolated strains listed in Table 1 below. Gram staining results showing the bacterial morphologies of each of the isolated strains of Table 1 are shown in Figures 2A- 20 and the 16S rDNA sequences are shown in Figures 6A to 6J.
TABLE 1
Figure imgf000011_0001
Figure imgf000012_0001
[0058] In some embodiments, the probiotic bacteria have a 16S rDNA sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to SEQ ID NO:1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8 as determined by a sequence alignment performed using BLAST (Basic Local Alignment Search Tool). In some embodiments, the probiotic bacteria have a 16S rDNA sequence that is identical to SEQ ID NO:1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO: 9, or SEQ ID NO: 10.
[0059] In some embodiments, the probiotic bacteria are a mutant strain of one of the strains listed in Table 1 . As used herein, a “mutant” or a “mutant strain” refers to a bacterial strain that has at least one DNA mutation compared to the parent (wild-type) strain from which it derives. DNA mutations may include base substitutions including transitions and transversions, deletions, insertions, and any other type of natural or induced DNA modification.
[0060] A biologically pure stock of each strain in Table 1 was deposited in the International Depositary Authority of Canada (IDAC) (1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3R2) under the Budapest Treaty at the date indicated in the table below. TABLE 2
Figure imgf000013_0001
[0061] The probiotic bacteria may be capable of probiotic activity in a subject. As used herein, “probiotic activity” refers to the ability of the bacteria to produce at least one beneficial effect in the subject. In some embodiments, the probiotic bacteria are capable of surviving and colonizing in the gastrointestinal tract of the subject to provide the beneficial effect to the subject.
[0062] In some embodiments, the probiotic bacteria show tolerance to a pH for a period of time. In particular embodiments, the pH is a low pH, such as, for example, when assayed in vitro, indicating that the bacteria may be capable of surviving passage through the acidic mammalian stomach. As used herein, “low pH” refers to a pH of about 6.9 or less. In some embodiments, the bacteria are able to survive at a pH of about 2.5 for at least about 6 hours when assayed in vitro. In some embodiments, the bacteria are able to survive at a pH of about 2.0 for at least about 6 hours when assayed in vitro. As used herein, “survive” means that the viable cell count of a test culture (as measured in colony forming units (CFU) per mL) is above detection limit, such as, for example, [1.7logio(CFU/mL) or 50 CFU/mL],
[0063] In some embodiments, the probiotic bacteria are tolerant to the presence of bile salt, such as, for example, when assayed in vitro, indicating that the bacteria may survive the passage through the mammalian intestine. In some embodiments, the bacteria are able to survive in the presence of bile salts for a period of time, such as, for example, in the presence of about 3% bile salts for at least about 6 hours when assayed in vitro.
[0064] In some embodiments, the probiotic bacteria have autoaggregation ability, such as, for example, when assayed in vitro, indicating that the bacterial cells may be able to bind host intestinal epithelial cells in the subject to facilitate colonization of the gastrointestinal tract. As used herein, “autoaggregation” or “autoaggregate” refers to the bacterial cells binding to one another to floc out of solution. In some embodiments, the bacteria have high cell surface hydrophobicity when assayed in vitro, indicating that the bacterial cells may be able to adhere to host cells in the subject to facilitate colonization of the gastrointestinal tract.
[0065] In some embodiments, the probiotic bacteria have one or more additional properties when assayed in vitro, ex vivo, and/or in vivo that support their use as probiotics. Non-limiting examples of such properties include: the ability to bind to mammalian cells; the ability to modulate expression of at least one antiinflammatory or pro-inflammatory cytokine by host immune cells; the ability to produce one or more inhibitory substances that inhibit the growth of pathogenic and/or spoilage microorganisms; susceptibility to at least one antibiotic; and/or stability for a suitable shelf-life period.
[0066] In some embodiments, the probiotic bacteria are in a viable form. In some embodiments, the probiotic bacteria are in a lyophilized (freeze-dried) form or in the form of a liquid suspension.
[0067] Also provided herein are one or more postbiotics produced by the probiotic bacteria. As used herein, “postbiotic” refers to a metabolite or other bioactive compound produced by a microorganism that confers at least one beneficial effect on a host organism. The postbiotics may be produced intracellularly or extracellularly. In some embodiments, the probiotic bacteria disclosed herein are provided in combination with one or more postbiotics produced by the probiotic bacteria when grown in a suitable media. In other embodiments, the probiotic bacteria may be lysed or heat-killed and the postbiotics may be used in place of the probiotic bacteria in any of the compositions, kits, methods, and/or uses described below.
[0068] Also provided is a composition comprising probiotic bacteria isolated from phytoplankton biomass. Any of the isolated strains described above may be used as the probiotic bacteria in the compositions described herein. In some embodiments, the composition may comprise two or more isolated strains of bacteria isolated from phytoplankton biomass. The strains may be from the same or different phytoplankton biomass.
[0069] The composition may comprise the probiotic bacteria and one or more additional ingredients. In some embodiments, the composition may further comprise at least one prebiotic. As used herein, “prebiotic” refers to a substance that stimulates the growth or activity of at least one beneficial micro-organism. In some embodiments, the prebiotic compound induces the growth or activity of at least one isolated strain of probiotic bacteria. Non-limiting examples of prebiotics include inulin, pectin, beta-glucans, fructooligosaccharides (FOS), galactooligosaccharides (GOS), xylooligosaccharides (XOS), resistant starch, and organic molecules such as humic and fulvic acid.
[0070] In some embodiments, the composition may further comprise at least one additional pharmaceutical or nutritional ingredient including, for example, at least one vitamin, mineral, fiber, fatty acid, amino acid, or any other suitable pharmaceutical or nutritional ingredient.
[0071 ] In some embodiments, the composition may further comprise at least one encapsulation material. Non-limiting examples of encapsulation materials include polysaccharides such as alginate, plant/microbial gums, chitosan, starch, k-carrageenan, cellulose acetate phthalate; proteins such as gelatin or milk proteins; and fats. The probiotic bacteria may be encapsulated in the encapsulated material by spray drying, extrusion, gelation, droplet extrusion, emulsion, freeze- drying, or any other suitable encapsulation method. Encapsulation of the probiotic bacteria may protect the cells and extend the shelf-life of the composition.
[0072] In some embodiments, the composition is an ingestible composition. As used herein, “ingestible” refers to a substance that is orally consumable by the subject.
[0073] In some embodiments, the ingestible composition is in the form of a dietary supplement. The dietary supplement may be in the form of a powder, a capsule, a gel capsule, a microcapsule, a bead, a tablet, a chewable tablet, a gummy, a liquid, or any other suitable form of dietary supplement.
[0074] In some embodiments, the dietary supplement further comprises at least one pharmaceutically or nutritionally acceptable excipient. Non-limiting examples of excipients include fillers, binders, carriers, diluents, stabilizers, lubricants, glidants, coloring agents, flavoring agents, coatings, disintegrants, preservatives, sorbents, and sweeteners. In embodiments in which the dietary supplement is in the form of a capsule, the dietary supplement may further comprise a suitable encapsulation material, including but not limited to, polyvinyl alcohol (PVA), polyvinylpurrolidone (PVP), alginates, gelatin, and any other suitable encapsulation material.
[0075] In some embodiments, the ingestible composition is in the form of a food product. The food product may be in any form suitable for a mammalian subject, such as a human, a livestock animal, companion animal, or any other mammalian subject.
[0076] In some embodiments, the food product is a solid food product. The solid food product may be dry, wet, semi-moist, frozen, dehydrated, freeze-dried, or in any other suitable form. In other embodiments, the food product is a liquid food product. Examples of liquid food products include, but are not limited to, beverages, broths, oil suspensions, gravies, milk-based products, and liquid or semi-solid yogurts.
[0077] In some embodiments, the ingestible composition is provided in a powder form suitable to sprinkle onto the surface of a solid food product or mix into a liquid food product. In other embodiments, the ingestible composition is provided in a liquid form suitable to spray, pour, or drop onto the surface of the solid food product or mix with a liquid food product. Alternatively, the ingestible composition is in a form suitable to be sprayed, poured, or dropped directly into the subject’s mouth.
[0078] In other embodiments, the ingestible composition is in the form of a surface coating for a solid food product. The surface coating may comprise a carrier to allow the bacteria to adhere to the surface of the solid food product. The carrier may comprise an edible oil or any other suitable carrier.
[0079] In alternative embodiments, the composition may be in a non- ingestible form, for example, as a suppository, or any other suitable form.
[0080] Figure 1 is a flowchart of an exemplary method 100 for making a composition, according to some embodiments. At block 102, probiotic bacteria isolated from phytoplankton biomass are provided. At block 104, at least one additional ingredient is provided. The term “providing” in this context may refer to making (including isolating or culturing), receiving, buying, or otherwise obtaining the probiotic bacteria and the ingredient. At block 106, the probiotic bacteria are combined with the additional ingredient.
[0081 ] In some embodiments, the probiotic bacteria are at least one of the isolated strains listed in Table 1. In some embodiments, the probiotic bacteria are in a powder form. In other embodiments, the probiotic bacteria are in a liquid form. [0082] In some embodiments, the ingredient is an edible ingredient. In some embodiments, the edible ingredient is at least one pharmaceutically or nutritionally acceptable excipient as described above for dietary supplements. In other embodiments, the edible ingredient is one of the solid or liquid food products described above or any components thereof.
[0083] In some embodiments, the probiotic bacteria and the edible ingredient are combined during production of the dietary supplement, solid food product, or liquid food product. In other embodiments, the probiotic bacteria are combined with the supplement, solid food product or liquid food product postproduction. For example, the probiotic bacteria may be in powder form and the powder may be sprinkled onto a solid food product or mixed with a liquid food product or supplement. As another example, the probiotic bacteria may be in liquid form (e.g., an edible oil) and the liquid may be sprayed, poured, dropped, or coated onto the solid food product or mixed with an edible liquid.
[0084] In other embodiments, the probiotic bacteria may be combined with the additional ingredient using any other suitable means.
[0085] The probiotic bacteria, isolated strains, and compositions described herein may be used to improve and/or maintain the health of a subject. The subject may be a mammalian subject, including but not limited to humans, livestock, and companion animals. Non-limiting examples of companion animals include domestic dogs and cats. Non-limiting examples of livestock include cattle, sheep, goats, and pigs.
[0086] In some embodiments, the probiotic bacteria, isolated strain(s), or composition may be used to treat or prevent a gastrointestinal disease, disorder, or condition in the subject. As used herein, “treat” or “treatment” refers to obtaining a desired pharmacologic and/or physiologic effect. The effect can be prophylactic in terms of completely or partially preventing a health condition or symptom thereof and/or can be therapeutic in terms of a partial or complete cure for the health condition and/or adverse effect attributable to the health condition. For greater clarity, it will be understood that the terms “treat” or “treatment” in this context are intended to include providing any beneficial physiological effect to the subject and their meaning is not limited to preventing or curing a specific disorder or health condition.
[0087] In some embodiments, the gastrointestinal disease, disorder, or condition comprises intestinal dysbiosis. As used herein, “intestinal dysbiosis” refers to any imbalance of the microbial community in the gastrointestinal tract of the subject or any portion thereof. In some embodiments, the gastrointestinal disease, disorder, or condition comprises enteritis and/or diarrhea. In some embodiments, the isolated strain(s) or composition may be used in the preparation of a medicament for treatment or prevention of intestinal dysbiosis, enteritis, diarrhea, or any other suitable disease, disorder, or condition.
[0088] In other embodiments, the probiotic bacteria, isolated strain(s), or composition may be used to provide any other health benefit to the subject.
[0089] Without being limited by theory, it is believed that the probiotic bacteria isolated from phytoplankton are similar to ancient food sources for animals. Modern food (including commercial pet foods and livestock feed) has a significantly different nutritional profile compared to ancient food sources, which may result in alternations to the intestinal microbiome. By introducing “primordial strains” of probiotic bacteria isolated from phytoplankton, the intestinal microbiome may shift towards more of an ancestral state and thereby treat or prevent gastrointestinal conditions such as dysbiosis.
[0090] The probiotic bacteria, isolated strain(s), or composition may be administered to the subject in an effective amount. As used herein, “effective amount” refers to an amount that provides at least one health benefit to the subject. The effective amount may vary based on a number of factors including but not limited to the specific probiotic bacteria (e.g., strain) being administered and its characteristics; the age, weight, sex, diet, and general health of the subject; the mode and time of administration; the severity of the condition being treated; the nature of any concurrent therapies or medications; and any other relevant factor.
[0091] In some embodiments, the probiotic bacteria, isolated strain(s), or composition is orally administrable to the subject. In other embodiments, the probiotic bacteria, isolated strain(s), or composition may be enterally and/or rectally administrable to the subject. The probiotic bacteria, isolated strain(s), or composition may be administered to the subject at any suitable interval including, for example, at least once per month, at least once per week, or at least once per day. As one example, a daily serving of about 1 billion CFU, per 20 lbs of body weight of the subject, may be orally administered to the subject.
[0092] Also provided herein is a kit comprising probiotic bacteria isolated from phytoplankton biomass in a container and instructions for use thereof. In some embodiments, the kit comprises one or more of the isolated strains of the probiotic bacteria. In some embodiments, the kit comprises a composition that comprises the probiotic bacteria, such as one or more of the isolated strains(s). The isolated strain(s) and/or composition may be any embodiment of isolated strains and compositions disclosed herein.
[0093] The instructions may comprise directions for administering the probiotic bacteria to a mammalian subject, for example, to treat or prevent a gastrointestinal disease, disorder, or condition including, but not limited to, intestinal dysbiosis, enteritis, and/or diarrhea. The instructions may include a recommended dosage and frequency for administration and may also include directions to take the probiotic bacteria with or without food, with or without other medications, etc. In some embodiments, the instructions comprise directions for combining the probiotic bacteria with a solid or liquid food product. [0094] Without any limitation to the foregoing, the present strains, compositions, uses, and methods are further described by way of the following examples.
EXAMPLE 1 - Bacterial Isolation and Genomic DNA Extraction
[0095] Lactic acid bacteria (LAB) were isolated from three bags of freeze- dried phytoplankton products provided by Adored Beast Apothecary Ltd™. The phytoplankton products were marine microalgae products obtained from Fitoplankton Marino™, El Puerto de Santa Maria - Cadiz, Spain. Powder from each bag was dissolved with 0.1 % peptone water (PW) in a 1 in 10 ratio. The weight of the powder was 0.5 g, thus the volume of the 0.1 % PW was 4.5 mL. Dilutions were then vortexed for 1 min to make sure the solutions were thoroughly homogenized. After homogenization, 100 pL dilutions were spread on De Man, Rogosa, Sharpe (MRS) agar (Oxoid Limited™, Canada), and then incubated at 37 °C for 24-48 h under aerobic conditions. In order to obtain enough bacteria for the downstream studies, individual colonies with different morphologies were first picked up and inoculated on new MRS agar plates for 24-48 h at 37 °C under aerobic conditions, and then successfully purified strains were transferred into MRS broth and incubated for 24 h at 37 °C for overnight. The isolates were stored at -80 °C in MRS broth plus 20% glycerol (El-Soda et al., 2003).
[0096] To extract the genomic DNA (gDNA) from all isolates, the candidate strains were cultured in MRS broth at 37 °C overnight, and then 5 mL overnight cultures were harvested at 8,000 rpm for 5 min for the extraction. The protocol was as following: cell pellets were resuspended and washed with 500 pL T 100E, twice, and then 10 pL of lysozyme stock solution (10 mg lysozyme in 0.5 mL ddF ) was added. The lysates were incubated at 37 °C for more than 3 h and centrifuged at 10,000 rpm for 5 min when the incubation was finished. The cell pellets were then homogenized with 500 pL T100E buffer. 50 pL 20% SDS (sodium dodecyl sulfate) was added and the tubes were inverted 5-7 times. 300 pL of sodium acetate solution (3M, pH5.2) were added into the lysates with an immediate inverting for 5-7 times. The lysates were then incubated for 20 min at 4 °C, and pelleted with a speed of 13,000 for 10 min. The supernatants were harvested and mixed with equal volumes of ice-cold isopropanol. The gDNA was precipitated by centrifuging at 13,000 rpm for 20 min and washed with 600 pL of 70% Ethanol. The harvested gDNA products were air dried for 15 min and rehydrated with 50 pL of nuclease- free H2O.
EXAMPLE 2 - Isolate Identification
Gram Staining of Isolates
[0097] Gram staining was performed with the BD BBL™ Gram Stain Kits (Cat#: B4312539, FisherScientific™, Canada) and the images were captured with Scopelmage™ and microscope. The gram staining results are shown in Figures 2A to 2C.
[0098] Based on the typical morphological appearance, 35 LAB strains were isolated from three bags of phytoplankton products in total. All 35 strains were gram positive bacteria. Strains were assigned with a unique strain ID according to the bag they were isolated from, e.g., strain ID ‘1 -2’ means the second strain isolated from Bag #1 . A second round of isolation was performed from Bag #1 with strains assigned a unique strain ID according to the source material each strain was isolated from, e.g., strain ID PN-9 means strain 9 isolated from Phytoplankton (PN).
Molecular Identification of Isolates
[0099] The molecular identification of LAB strains was firstly conducted with M13 primer (Rossetti, L, 2005), the sequence of which is 5’-GAG GGT GGC GGT TCT -3’ (Ta (°C) = 45 °C). To obtain a fingerprint profile of the isolates, the amplification reactions were conducted with RAPD-PCR (Random Amplified Polymorphic DNA - Polymerase Chain Reaction) technique with a total volume of 25 pL, and a program of 94 °C for 5 min; 94 °C for 1 min, 45 °C for 1 min, 72 °C for 2 min with 40 cycles in total; 72 °C for 5 min, and store at 4 °C. Figures 3A and 3B show the RAPD profiles for 33 of the 35 isolated LAB strains.
[0100] To identify the isolates at the species level, the gene encoding the 16S ribosomal RNA (rRNA) was amplified by PCR and sequenced by Sanger Sequencing. The DNA sequence encoding the 16S rRNA is referred to as the 16S rDNA sequence.
[0101 ] PCR reactions with 16S rDNA primers were conducted to amplify the conserved regions of the 16S rRNA gene. The sequences of the primers are: 16S- 8F: 5’-AGA GTT TGA TCC TGG CTC AG-3’; 16S-805R: 5’-GAC TAC CAG GGT ATC TAA TCC-3’ (Ta (°C) = 55 °C). The PCR was programed as follows: 95 °C for 5 min; 95 °C for 30 sec, 55 °C for 30 sec, 72 °C for 30 sec with 35 cycles in total; 72 °C for 10 min, and store at 4 °C. The products from the 16S rDNA PCR reaction were purified with GeneJET™ PCR Purification Kit (Cat#: K0701 , Thermo Scientific™, Canada) and submitted for sequencing to Molecular Biology Facility (MBSLI) (Department of Biological Sciences, University of Alberta). The sequencing data were further aligned in the Genbank™ database using the basic local alignment search tool (BLAST, www.ncbi.nlm.nih.gov/BLAST) for the final identification of the LAB strains. Reagents and equipment used in this study were as follows: the Taq polymerase used in this study was DreamTaq™ DNA polymerase (Cat#: EP0703, Thermo Scientific™, Canada). The PCR products were analyzed for electrophoresis and then images were visualized and captured by transillumination under UV light using Alphaimager™ Gel Imager (ThermoFisher, Canada).
[0102] Figures 4A and 4B show the agarose gel electrophoresis of the 16S rDNA PCR products for 33 of the 35 isolated LAB strains.
[0103] The presumed identification of the species of each strain, based on BLAST alignment, is shown in Tables 3, 4, and 5 below. TABLE 3 - LAB isolates from Bag #1
Strain ID Presumed identification
1 -1 Limosilactobacillus fermentum
1-2B Limosilactobacillus fermentum
1 -2S Limosilactobacillus fermentum
1 -4 Limosilactobacillus fermentum
1 -5 Limosilactobacillus fermentum
1 -7 Limosilactobacillus fermentum
1 -10 Limosilactobacillus fermentum
1 -11 Limosilactobacillus fermentum
PN-9 Levilactobacillus brevis
P N-10 Pediococcus acidilactici
TABLE 4 - LAB isolates from Bag #2
Strain ID Presumed identification
2-1 Limosilactobacillus fermentum
2-2 B Limosilactobacillus fermentum
2-2S Limosilactobacillus fermentum
2-3 Lacticaseibacillus casei
2-4 Lacticaseibacillus casei
2-5 Limosilactobacillus fermentum
2-6 Limosilactobacillus fermentum
2-7 Limosilactobacillus fermentum
2-8 Limosilactobacillus fermentum
2-9 Limosilactobacillus fermentum
2-10 Limosilactobacillus fermentum
2-11 Limosilactobacillus fermentum
2-12 Limosilactobacillus fermentum TABLE 5 - LAB isolates from Bag #3
Strain ID Presumed identification
3-1 Enterococcus gallinarum
3-2 Limosilactobacillus fermentum
3-4 Enterococcus sp.
3-5 Enterococcus thailandicus
3-6 Enterococcus avium
3-7 Enterococcus gallinarum
3-8 Enterococcus thailandicus
3-9 Enterococcus thailandicus
3-10-B Limosilactobacillus fermentum
3-10-S Limosilactobacillus fermentum
3-11 Enterococcus gallinarum
3-12 Enterococcus thailandicus
[0104] 22 strains were Limosilactobacillus fermentum, 2 strains were
Lacticaseibacillus casei, 1 strain was Levilactobacillus brevis, 1 strain was Pediococcus acidilactici, and 9 strains were Enterococcus sp. Most Enterococcus sp. were isolated from Bag #3, while mostly Lacticaseibacillus casei and Limosilactobacillus fermentum were isolated from Bag #1 and Bag #2. RAPD profiling of one representative strain of Lacticaseibacillus casei and Limosilactobacillus fermentum from each bag was performed again using the M13 primer, with K9-1 (Lacticaseibacillus casei) and K9-2 (Limosilactobacillus fermentum) as positive controls, as shown in Figure 5.
[0105] The 16S rDNA sequencing results for strains FT1-1 (Limosilactobacillus fermentum), FT2-1 (Limosilactobacillus fermentum), FT2-3 (Lacticaseibacillus casei), FT3-1 (Enterococcus gallinarum), FT3-2 (Limosilactobacillus fermentum), FT3-4 (Enterococcus sp.), FT3-5 (Enterococcus thailandicus), FT3-6 (Enterococcus avium), PN-9 (Levilactobacillus brevis), and PN-10 (Pediococcus acidilactici) are shown in Figures 6A-6J. These strains were deposited in the International Depositary Authority of Canada (IDAC) (1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3R2) under the Budapest Treaty on July 5, 2023 and assigned the accession numbers listed in Table 2 above.
EXAMPLE 3 - Isolate Characterization
[0001 ] The biological activity of eight strains (FT1 -1 , FT2-1 , FT2-3, FT3-1 , FT3-2, FT3-4, FT3-5, and FT3-6) was characterized using the methods described in International PCT Application No. PCT/CA2019/051140, hereby incorporated by reference, as outlined below.
Auto-Aggregation Ability
[0106] To assess the auto-aggregation activity of the isolate, autoaggregation assays were performed. Samples of fully-grown culture was mixed thoroughly by vortexing. The initial optical density at 600 nm (ODeoo, Ao) was measured and recorded. The remaining cell suspension was kept still and undisturbed at ambient temperature for 4 hours. An aliguot of the upper suspension (the cell suspension was not vortexed) was taken to measure the ODeoonm (At). The auto-aggregation percentage was expressed as:
Figure imgf000026_0001
wherein Ao stands for ODeoo at 0 h and At stands for ODeoo at t = 4 h. The autoaggregation rates (in percentage) of the eight isolates at 4 hours are shown in Table 6 below. These results indicate that the isolates have the potential to adhere to host intestinal epithelial cell surface.
TABLE 6
Strain ID Autoaggregation FT1 -1 9%
FT2-1 10%
FT2-3 17%
FT3-1 17%
FT3-2 15%
FT3-4 23%
FT3-5 19%
FT3-6 3%
Cell Surface Hydrophobicity
[0107] To assess the hydrophobic nature of the bacterial cell surface of each isolate, microbial adhesion to hydrocarbons (MATH) assays (Otero et al., 2004) were performed to measure the hydrophobicity of the strains in terms of adhesion. A sample of fully-grown culture was harvested by centrifugation, followed by washing the cells with saline solution. The cell pellet was resuspended with saline solution and the ODeooof each cell suspension was adjusted. The actual final ODeooof each cell suspension was measured and recorded. An aliquot of the cell suspension was combined with solvent (toluene or xylene) in a testing tube and vortexing vigorously for 1 minute. The testing tube was kept still for 1 hour to allow the immiscible solvent and aqueous phase to separate. The aqueous layer was removed and the OD6oo (ODtest) was measured and recorded. The percentage of hydrophobicity of each strain was calculated as the following formula:
% hydrophobicity = (ODinitiai - ODtest)/ ODinitiai
[0108] The percentage hydrophobicities of the seven isolates are shown in Table 7 below. These results indicate that the isolates have the potential to adhere to host intestinal epithelial cell surface.
TABLE 7 Strain ID Hydrophobicity
FT1 -1 10%
FT2-1 4%
FT2-3 24%
FT3-1 13%
FT3-2 8%
FT3-4 42%
FT3-5 2%
FT3-6 7%
Low pH Tolerance Assays
[0109] To assess the tolerance of the isolates to acidic conditions, for each isolate, an aliquot of fully-grown culture was subcultured into Simulated Gastric Fluid (SGF, without pepsin) at pH = 2.0 and pH 2.5. The SGF solutions with different pH values were prepared by adjusting the pH of SGF with HCI and NaOH, followed by sterilization by filtering. Once a culture was inoculated into each SGF solution, the mixture was mixed thoroughly by vortexing and a 0 h aliquot was taken for diluting and plating. The remaining cultures were immediately incubated at 37°C under airtight conditions for 6 h, after which aliquots were taken for diluting and plating.
[0110] A serial 10-fold dilution of each culture was prepared and dilutions were plated on MRS agar plates and incubated at 37°C for 2 days. Viable cell counts were recorded and expressed as the Mean [logio(CFU/mL)] ± Standard Error of at least three independent replicates. The results of the low pH tolerance assays for the eight isolates are shown in Table 8 below, wherein 1 = the strain survives at pH 2 and pH 2.5 at 6h; 2 = the strain does not survive at pH 2 but survives at pH 2.5 at 6 h; 3 = the strain does not survive at pH 2 and pH 2.5 at 6 h. TABLE 8
Strain ID Low pH Tolerance
FT1 -1 2
FT2-1 2
FT2-3 2
FT3-1 2
FT3-2 1
FT3-4 2
FT3-5 1
FT3-6 1
[0111 ] The results indicate that all strains are capable of surviving in pH 2.5 for 6 hours and strains FT3-2, FT3-5, and FT3-6 are also capable of surviving at pH 2.0 for 6 hours.
Bile Salt Tolerance Assays
[0112] To assess the tolerance of the isolates to bile salt, for each isolate, an aliquot of fully-grown culture was subcultured into a set of Phosphate Buffered Saline (PBS, pH = 7.2) solutions with varying bile salt concentrations (0%, 3%, and 5%). The PBS solutions with different bile salt concentrations were prepared by dissolving a corresponding amount of bile salt into sterile PBS. Once a culture was inoculated into each PBS solution, the mixture was mixed thoroughly by vortexing and a 0 h aliquot was taken for diluting and plating. The remaining cultures were immediately incubated at 37°C under airtight conditions for 24 h. Aliquots were taken after 6 h and 24 h for diluting and plating.
[0113] A serial 10-fold dilution of each culture was prepared and proper dilutions were plated on MRS agar plates and incubated at 37°C for 2 days. Viable cell counts were recorded and expressed as the Mean [logio(CFU/mL)] ± Standard Error of at least three independent replicates. The results of the bile salt tolerance assays for the eight isolates are shown in Table 9 below, wherein 1 = the strain survived without bile at 0, 6 and 24hr; 2 = the strain survived 3% bile at Ohr; 3 = the strain survived 3% bile at 6hr; the strain 4 = survived 3% bile at 24 hr; 5 = the strain survived 5% bile at Ohr; 6 = the strain survived 5% bile at 6hr; 7 = the strain survived 5% bile at 24hr.
TABLE 9
Strain ID Bile Salt Tolerance
FT1-1 1
FT2-1 1
FT2-3 1
FT3-1 1
FT3-2 1
FT3-4 1
FT3-5 1 ,2,3
FT3-6 1 ,2,3
[0114] The results indicate that strains FT3-5 and FT3-6 are capable of surviving 3% bile for 6 hours.
[0115] Although particular embodiments have been shown and described, it will be appreciated by those skilled in the art that various changes and modifications might be made without departing from the scope of the disclosure. The terms and expressions used in the preceding specification have been used herein as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding equivalents of the features shown and described or portions thereof. Moreover, in interpreting the disclosure, all terms should be interpreted in the broadest possible manner consistent with the context. In particular, the terms "comprises" and "comprising" should be interpreted as referring to elements, components, or steps in a non-exclusive manner, indicating that the referenced elements, components, or steps may be present, or utilized, or combined with other elements, components, or steps that are not expressly referenced.
REFERENCES
The following references are hereby incorporated by reference in their entirety:
El Soda, M., Ahmed, N., Omran, N., Osman, G., & Morsi, A. (2003). Isolation, identification and selection of lactic acid bacteria cultures for cheesemaking. Emirates Journal of Food and Agriculture, 51-71 .
Rossetti, L., & Giraffa, G. (2005). Rapid identification of dairy lactic acid bacteria by M13-generated, RAPD-PCR fingerprint databases. Journal of microbiological methods, 63(2), 135-144.
Otero et al. (2004) “Bacterial surface characteristics applied to selection of probiotic microorganisms”, in Public Health Microbiology, pp. 435-440. Humana Press.

Claims

CLAIMS:
1 . Probiotic bacteria isolated from phytoplankton biomass.
2. The probiotic bacteria of claim 1 , wherein the probiotic bacteria comprise lactic acid bacteria.
3. The probiotic bacteria of claim 2, wherein the probiotic bacteria are of the Lactobacillaceae family or the Enterococcaceae family.
4. The probiotic bacteria of claim 3, wherein the probiotic bacteria are of the Lactobacillus, Limosilactobacillus, Lacticaseibacillus, Levilactobacillus, Leuconostoc, Pediococcus, Lactococcus, Weissella, Enterococcus, Tetragenococcus, or Vagococcus genus.
5. The probiotic bacteria of claim 4, wherein the probiotic bacteria are of a species selected from Limosilactobacillus fermentum, Lacticaseibacillus casei, Levilactobacillus brevis, Enterococcus gallinarum, Enterococcus casseliflavus, Enterococcus thailandicus, Enterococcus avium, and Pediococcus acidilactici.
6. The probiotic bacteria of claim 5, wherein the probiotic bacteria are of a species selected from Enterococcus thailandicus, Enterococcus avium, and Limosilactobacillus fermentum.
7. The probiotic bacteria of claim 1 , wherein the probiotic bacteria have a 16S rDNA sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO:1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NOT, SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NO: 10 as determined by a sequence alignment performed using BLAST (Basic Local Alignment Search Tool).
8. The probiotic bacteria of claim 7, wherein the probiotic bacteria have a 16S rDNA sequence that is identical to SEQ ID NO:1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NOT, SEQ ID NO:8, SEQ ID NO:9, or SEQ ID NO:10.
9. The probiotic bacteria of claim 1 , wherein the probiotic bacteria are of a strain selected from Limosilactobacillus fermentum FT1-1 (IDAC Accession Number 050723-01 ), Limosilactobacillus fermentum FT2-1 (IDAC Accession Number 050723-02), Lacticaseibacillus casei FT2-3 (IDAC Accession Number 050723-03), Enterococcus gallinarum FT3-1 (IDAC Accession Number 050723- 04), Limosilactobacillus fermentum FT3-2 (IDAC Accession Number 050723-05), Enterococcus sp. FT3-4 (IDAC Accession Number 050723-06), Enterococcus thailandicus FT3-5 (IDAC Accession Number 050723-07), Enterococcus avium FT3-6 (IDAC Accession Number 050723-08), Levilactobacillus brevis PN-9 (IDAC Accession Number 050723-09), or Pediococcus acidilactici PN-10 (IDAC Accession Number 050723-10).
10. The probiotic bacteria of any one of claims 1 to 9 for the prevention or treatment of a gastrointestinal disease, condition, or disorder.
11. The probiotic bacteria of claim 10, wherein the gastrointestinal disease, condition, or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
12. The probiotic bacteria of claim 11 , wherein the gastrointestinal disease, condition, or disorder is intestinal dysbiosis.
13. An isolated strain of the probiotic bacteria of any one of claims 1 to 9.
14. A biologically pure culture of the isolated strain of claim 13.
15. A composition comprising the probiotic bacteria of any one of claims 1 to 9 and at least one additional ingredient.
16. The composition of claim 15, wherein the at least one additional ingredient comprises a prebiotic, an additional pharmaceutical or nutritional ingredient, or a pharmaceutically or nutritionally acceptable excipient.
17. The composition of claim 15 or 16, wherein the composition is in the form of a dietary supplement.
18. The composition of claim 15 or 16, wherein the composition is in the form of a food product.
19. The composition of any one of claims 15 to 18 for the prevention or treatment of a gastrointestinal disease, condition or disorder.
20. The composition of claim 19, wherein the gastrointestinal disease, condition or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
21 . The composition of claim 20, wherein the gastrointestinal disease, condition or disorder is intestinal dysbiosis.
22. A method for preparing a composition comprising: providing the probiotic bacteria of any one of claims 1 to 9; providing at least one additional ingredient; and combining the probiotic bacteria and the at least one additional ingredient.
23. The method of claim 22, wherein the at least one additional ingredient is an edible ingredient.
24. The method of claim 22, wherein the probiotic bacteria are provided in the form of a powder or a liquid.
25. A kit comprising the probiotic bacteria of any one of claims 1 to 9 and instructions for use thereof.
26. The kit of claim 25, wherein the instructions include directions for administering the probiotic bacteria to a subject to treat or prevent a gastrointestinal disease, condition, or disorder.
27. The kit of claim 26, wherein the gastrointestinal disease, condition, or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
28. The kit of claim 27, wherein the gastrointestinal disease, condition, or disorder is intestinal dysbiosis.
29. The kit of any one of claims 25 to 28, wherein the subject is a mammalian subject.
30. A method for treating or preventing a gastrointestinal disease, condition, or disorder in a subject, comprising administering the probiotic bacteria of any one of claims 1 to 9 to the subject.
31 . The method of claim 30, wherein the gastrointestinal disease, condition, or disorder is selected from intestinal dysbiosis, enteritis, and diarrhea.
32. The method of claim 31 , wherein the gastrointestinal disease, condition, or disorder is intestinal dysbiosis.
33. The method of any one of claims 30 to 32, wherein the subject is a mammalian subject.
34. The method of any one of claims 30 to 33, wherein the probiotic bacteria are administered orally.
35. Use of the probiotic bacteria of any one of claims 1 to 9 for treating or preventing a gastrointestinal disease, condition, or disorder.
36. Use of the probiotic bacteria of any one of claims 1 to 9 in the manufacture of a medicament for the treatment of a gastrointestinal disease, condition, or disorder.
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Citations (2)

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