AU2016245213A1 - Method and apparatus for estimating the quantity of microorganisms within a taxonomic unit in a sample - Google Patents
Method and apparatus for estimating the quantity of microorganisms within a taxonomic unit in a sample Download PDFInfo
- Publication number
- AU2016245213A1 AU2016245213A1 AU2016245213A AU2016245213A AU2016245213A1 AU 2016245213 A1 AU2016245213 A1 AU 2016245213A1 AU 2016245213 A AU2016245213 A AU 2016245213A AU 2016245213 A AU2016245213 A AU 2016245213A AU 2016245213 A1 AU2016245213 A1 AU 2016245213A1
- Authority
- AU
- Australia
- Prior art keywords
- computer
- sample
- microorganisms
- reads
- taxonomic
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Abandoned
Links
- 244000005700 microbiome Species 0.000 title claims abstract description 101
- 238000000034 method Methods 0.000 title claims abstract description 66
- 241000894007 species Species 0.000 claims abstract description 44
- 238000012163 sequencing technique Methods 0.000 claims description 41
- 238000005259 measurement Methods 0.000 claims description 26
- 238000007635 classification algorithm Methods 0.000 claims description 17
- 238000004088 simulation Methods 0.000 abstract description 5
- 230000008569 process Effects 0.000 description 10
- 238000005516 engineering process Methods 0.000 description 6
- 239000011159 matrix material Substances 0.000 description 6
- NOIRDLRUNWIUMX-UHFFFAOYSA-N 2-amino-3,7-dihydropurin-6-one;6-amino-1h-pyrimidin-2-one Chemical compound NC=1C=CNC(=O)N=1.O=C1NC(N)=NC2=C1NC=N2 NOIRDLRUNWIUMX-UHFFFAOYSA-N 0.000 description 5
- 238000004458 analytical method Methods 0.000 description 5
- 108090000623 proteins and genes Proteins 0.000 description 5
- 241001386813 Kraken Species 0.000 description 4
- 230000015654 memory Effects 0.000 description 4
- 238000005457 optimization Methods 0.000 description 4
- 241000233866 Fungi Species 0.000 description 3
- 238000004590 computer program Methods 0.000 description 3
- 238000010586 diagram Methods 0.000 description 3
- 238000002474 experimental method Methods 0.000 description 3
- 230000003287 optical effect Effects 0.000 description 3
- 241000894006 Bacteria Species 0.000 description 2
- 241000700605 Viruses Species 0.000 description 2
- 230000001580 bacterial effect Effects 0.000 description 2
- 230000005540 biological transmission Effects 0.000 description 2
- 238000003745 diagnosis Methods 0.000 description 2
- 201000010099 disease Diseases 0.000 description 2
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 2
- 230000006870 function Effects 0.000 description 2
- 230000036541 health Effects 0.000 description 2
- 244000000010 microbial pathogen Species 0.000 description 2
- 238000012545 processing Methods 0.000 description 2
- 238000011160 research Methods 0.000 description 2
- 238000012360 testing method Methods 0.000 description 2
- OKTJSMMVPCPJKN-UHFFFAOYSA-N Carbon Chemical compound [C] OKTJSMMVPCPJKN-UHFFFAOYSA-N 0.000 description 1
- 208000035473 Communicable disease Diseases 0.000 description 1
- 241000588724 Escherichia coli Species 0.000 description 1
- 241000187479 Mycobacterium tuberculosis Species 0.000 description 1
- 241000588652 Neisseria gonorrhoeae Species 0.000 description 1
- 238000012300 Sequence Analysis Methods 0.000 description 1
- 241000191967 Staphylococcus aureus Species 0.000 description 1
- 230000009471 action Effects 0.000 description 1
- 239000004599 antimicrobial Substances 0.000 description 1
- 238000004422 calculation algorithm Methods 0.000 description 1
- 229910052799 carbon Inorganic materials 0.000 description 1
- 238000004891 communication Methods 0.000 description 1
- 238000012937 correction Methods 0.000 description 1
- 238000013479 data entry Methods 0.000 description 1
- 238000013461 design Methods 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 244000039328 opportunistic pathogen Species 0.000 description 1
- 244000052769 pathogen Species 0.000 description 1
- 230000001717 pathogenic effect Effects 0.000 description 1
- 238000011002 quantification Methods 0.000 description 1
- 230000002441 reversible effect Effects 0.000 description 1
- 238000012552 review Methods 0.000 description 1
- 239000007787 solid Substances 0.000 description 1
- 239000000126 substance Substances 0.000 description 1
- 230000009885 systemic effect Effects 0.000 description 1
- 230000001052 transient effect Effects 0.000 description 1
- 238000012070 whole genome sequencing analysis Methods 0.000 description 1
Classifications
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B30/10—Sequence alignment; Homology search
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
- Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
- Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
Landscapes
- Physics & Mathematics (AREA)
- Life Sciences & Earth Sciences (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Medical Informatics (AREA)
- Biophysics (AREA)
- Bioinformatics & Computational Biology (AREA)
- Biotechnology (AREA)
- Evolutionary Biology (AREA)
- General Health & Medical Sciences (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Theoretical Computer Science (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Analytical Chemistry (AREA)
- Chemical & Material Sciences (AREA)
- Databases & Information Systems (AREA)
- Genetics & Genomics (AREA)
- Molecular Biology (AREA)
- Bioethics (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
- Apparatus Associated With Microorganisms And Enzymes (AREA)
- Management, Administration, Business Operations System, And Electronic Commerce (AREA)
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| AU2021212155A AU2021212155B2 (en) | 2015-04-09 | 2021-08-06 | Method and apparatus for estimating the quantity of microorganisms within a taxonomic unit in a sample |
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201562145026P | 2015-04-09 | 2015-04-09 | |
| US62/145,026 | 2015-04-09 | ||
| PCT/EP2016/057799 WO2016162504A1 (en) | 2015-04-09 | 2016-04-08 | Method and apparatus for estimating the quantity of microorganisms within a taxonomic unit in a sample |
Related Child Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| AU2021212155A Division AU2021212155B2 (en) | 2015-04-09 | 2021-08-06 | Method and apparatus for estimating the quantity of microorganisms within a taxonomic unit in a sample |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| AU2016245213A1 true AU2016245213A1 (en) | 2017-11-23 |
Family
ID=55701971
Family Applications (2)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| AU2016245213A Abandoned AU2016245213A1 (en) | 2015-04-09 | 2016-04-08 | Method and apparatus for estimating the quantity of microorganisms within a taxonomic unit in a sample |
| AU2021212155A Ceased AU2021212155B2 (en) | 2015-04-09 | 2021-08-06 | Method and apparatus for estimating the quantity of microorganisms within a taxonomic unit in a sample |
Family Applications After (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| AU2021212155A Ceased AU2021212155B2 (en) | 2015-04-09 | 2021-08-06 | Method and apparatus for estimating the quantity of microorganisms within a taxonomic unit in a sample |
Country Status (10)
| Country | Link |
|---|---|
| US (1) | US10998083B2 (enExample) |
| EP (1) | EP3281136B1 (enExample) |
| JP (1) | JP7023711B2 (enExample) |
| CN (1) | CN107533587B (enExample) |
| AU (2) | AU2016245213A1 (enExample) |
| BR (1) | BR112017021318A2 (enExample) |
| CA (1) | CA2981913A1 (enExample) |
| MX (1) | MX391844B (enExample) |
| RU (1) | RU2751241C2 (enExample) |
| WO (1) | WO2016162504A1 (enExample) |
Families Citing this family (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CA3054487A1 (en) * | 2017-03-01 | 2018-09-07 | Bluedot Llc | Systems and methods for metagenomic analysis |
| CN110277139B (zh) * | 2019-06-18 | 2023-03-21 | 江苏省产品质量监督检验研究院 | 一种基于互联网的微生物限度检查系统及方法 |
| CN113284560B (zh) * | 2021-04-28 | 2022-05-17 | 广州微远基因科技有限公司 | 病原检测背景微生物判断方法及应用 |
| CN114334004B (zh) * | 2021-12-04 | 2024-03-15 | 江苏先声医学诊断有限公司 | 一种病原微生物快速比对鉴定方法及其应用 |
| CN115841847B (zh) * | 2022-12-12 | 2023-05-12 | 哈尔滨因极科技有限公司 | 一种微生物信息测定及提取系统和方法 |
Family Cites Families (8)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US6780602B2 (en) * | 2001-11-01 | 2004-08-24 | Microbiosystems, Limited Partnership | Taxonomic identification of pathogenic microorganisms and their toxic proteins |
| CN102089419A (zh) * | 2008-07-10 | 2011-06-08 | 塔康特精确有限公司 | 用于进行可培养细胞计数的方法、试剂盒和系统 |
| EP2390810B1 (en) | 2010-05-26 | 2019-10-16 | Tata Consultancy Services Limited | Taxonomic classification of metagenomic sequences |
| KR101347509B1 (ko) * | 2011-06-20 | 2014-01-06 | 가톨릭대학교 산학협력단 | 섬망 고위험군 예측모형 시스템 및 그 예측모형 방법, 및 그것을 이용한 섬망 고위험군 예측 시스템 |
| KR20160103175A (ko) * | 2011-07-19 | 2016-08-31 | 오비지오 이미징 시스템스 엔.브이. | 세포 샘플에서의 암 세포들의 검출 및/또는 분류를 위한 방법 및 시스템 |
| US9914979B2 (en) * | 2013-03-04 | 2018-03-13 | Fry Laboratories, LLC | Method and kit for characterizing microorganisms |
| CN104252627A (zh) * | 2013-06-28 | 2014-12-31 | 广州华多网络科技有限公司 | Svm分类器训练样本获取方法、训练方法及其系统 |
| CN103627800B (zh) * | 2013-11-14 | 2015-02-25 | 浙江天科高新技术发展有限公司 | 环境微生物快速检测方法 |
-
2016
- 2016-04-08 BR BR112017021318-4A patent/BR112017021318A2/pt not_active Application Discontinuation
- 2016-04-08 EP EP16715525.8A patent/EP3281136B1/en active Active
- 2016-04-08 CN CN201680020777.1A patent/CN107533587B/zh active Active
- 2016-04-08 MX MX2017012758A patent/MX391844B/es unknown
- 2016-04-08 JP JP2017547118A patent/JP7023711B2/ja not_active Expired - Fee Related
- 2016-04-08 AU AU2016245213A patent/AU2016245213A1/en not_active Abandoned
- 2016-04-08 CA CA2981913A patent/CA2981913A1/en not_active Abandoned
- 2016-04-08 RU RU2017138867A patent/RU2751241C2/ru active
- 2016-04-08 US US15/564,216 patent/US10998083B2/en active Active
- 2016-04-08 WO PCT/EP2016/057799 patent/WO2016162504A1/en not_active Ceased
-
2021
- 2021-08-06 AU AU2021212155A patent/AU2021212155B2/en not_active Ceased
Also Published As
| Publication number | Publication date |
|---|---|
| US10998083B2 (en) | 2021-05-04 |
| AU2021212155B2 (en) | 2023-06-29 |
| BR112017021318A2 (pt) | 2018-06-26 |
| US20180129777A1 (en) | 2018-05-10 |
| JP2018518725A (ja) | 2018-07-12 |
| RU2751241C2 (ru) | 2021-07-12 |
| CA2981913A1 (en) | 2016-10-13 |
| MX2017012758A (es) | 2018-01-30 |
| CN107533587B (zh) | 2021-10-08 |
| MX391844B (es) | 2025-03-21 |
| WO2016162504A1 (en) | 2016-10-13 |
| JP7023711B2 (ja) | 2022-02-22 |
| RU2017138867A3 (enExample) | 2020-06-26 |
| RU2017138867A (ru) | 2019-05-13 |
| EP3281136A1 (en) | 2018-02-14 |
| EP3281136B1 (en) | 2024-06-05 |
| CN107533587A (zh) | 2018-01-02 |
| AU2021212155A1 (en) | 2021-08-26 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| AU2021212155B2 (en) | Method and apparatus for estimating the quantity of microorganisms within a taxonomic unit in a sample | |
| Dilthey et al. | Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps | |
| Mohsen et al. | Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks | |
| Tierney et al. | The landscape of genetic content in the gut and oral human microbiome | |
| Almeida et al. | A new genomic blueprint of the human gut microbiota | |
| Escudié et al. | FROGS: find, rapidly, OTUs with galaxy solution | |
| Lindgreen et al. | An evaluation of the accuracy and speed of metagenome analysis tools | |
| Forster et al. | Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants | |
| Ssekagiri et al. | microbiomeSeq: an R package for analysis of microbial communities in an environmental context | |
| Bartoszewicz et al. | DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks | |
| Mande et al. | Classification of metagenomic sequences: methods and challenges | |
| Moran-Gilad et al. | Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities | |
| Anyansi et al. | QuantTB–a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data | |
| Jackson et al. | A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units | |
| US20200140925A1 (en) | Methods for validation of microbiome sequence processing and differential abundance analyses via multiple bespoke spike-in mixtures | |
| Du et al. | MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data | |
| Valverde et al. | Analysis of metagenomic data containing high biodiversity levels | |
| Baruzzo et al. | Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results | |
| US20120010823A1 (en) | System for the quantification of system-wide dynamics in complex networks | |
| Bundalovic-Torma et al. | RecPD: A Recombination-aware measure of phylogenetic diversity | |
| Yadav et al. | OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes | |
| Pongor et al. | Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification | |
| Sorbie et al. | Increasing transparency and reproducibility in stroke-microbiota research: A toolbox for microbiota analysis | |
| Sun et al. | Eliminate false positives in metagenomic profiling based on type IIB restriction sites | |
| Bartoszewicz et al. | DeePaC: Predicting pathogenic potential of novel DNA with a universal framework for reverse-complement neural networks |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| MK5 | Application lapsed section 142(2)(e) - patent request and compl. specification not accepted |