메뉴 건너뛰기




Volumn 32, Issue 8, 2014, Pages 834-841

An integrated catalog of reference genes in the human gut microbiome

(87)  Li, Junhua a,b,c   Jia, Huijue a   Cai, Xianghang a   Zhong, Huanzi a   Feng, Qiang a,d   Sunagawa, Shinichi e   Arumugam, Manimozhiyan a,e,f   Kultima, Jens Roat e   Prifti, Edi g   Nielsen, Trine f   Juncker, Agnieszka Sierakowska h   Manichanh, Chaysavanh i   Chen, Bing a   Zhang, Wenwei a   Levenez, Florence g   Wang, Juan a   Xu, Xun a   Xiao, Liang a   Liang, Suisha a   Zhang, Dongya a   more..


Author keywords

[No Author keywords available]

Indexed keywords

POPULATION STATISTICS;

EID: 84905730165     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2942     Document Type: Article
Times cited : (1508)

References (53)
  • 1
    • 84858376593 scopus 로고    scopus 로고
    • The impact of the gut microbiota on human health: An integrative view
    • Clemente, J.C., Ursell, L.K., Parfrey, L.W. & Knight, R. The impact of the gut microbiota on human health: an integrative view. Cell 148, 1258-1270 (2012).
    • (2012) Cell , vol.148 , pp. 1258-1270
    • Clemente, J.C.1    Ursell, L.K.2    Parfrey, L.W.3    Knight, R.4
  • 2
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
    • (2010) Nature , vol.464 , pp. 59-65
    • Qin, J.1
  • 3
    • 84862286169 scopus 로고    scopus 로고
    • A framework for human microbiome research
    • The Human Microbiome Project Consortium
    • The Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486, 215-221 (2012).
    • (2012) Nature , vol.486 , pp. 215-221
  • 4
    • 84867074831 scopus 로고    scopus 로고
    • A metagenome-wide association study of gut microbiota in type 2 diabetes
    • Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55-60 (2012).
    • (2012) Nature , vol.490 , pp. 55-60
    • Qin, J.1
  • 5
    • 84878709716 scopus 로고    scopus 로고
    • Gut metagenome in European women with normal, impaired and diabetic glucose control
    • Karlsson, F.H. et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498, 99-103 (2013).
    • (2013) Nature , vol.498 , pp. 99-103
    • Karlsson, F.H.1
  • 6
    • 84883110880 scopus 로고    scopus 로고
    • Richness of human gut microbiome correlates with metabolic markers
    • Le Chatelier, E. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541-546 (2013).
    • (2013) Nature , vol.500 , pp. 541-546
    • Le Chatelier, E.1
  • 7
    • 84905730761 scopus 로고    scopus 로고
    • Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
    • doi:10.1038/nbt.2939 6 July
    • Nielsen, H.B. et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Biotechnol. doi:10.1038/nbt.2939 (6 July 2014).
    • (2014) Biotechnol
    • Nielsen, H.B.1
  • 8
    • 84860477454 scopus 로고    scopus 로고
    • Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing
    • Xiong, X. et al. Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLOS ONE 7, e36009 (2012).
    • (2012) PLOS ONE , vol.7
    • Xiong, X.1
  • 9
    • 84892828465 scopus 로고    scopus 로고
    • Diet rapidly and reproducibly alters the human gut microbiome
    • David, L.A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559-563 (2014).
    • (2014) Nature , vol.505 , pp. 559-563
    • David, L.A.1
  • 10
    • 84870322666 scopus 로고    scopus 로고
    • Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease
    • Erickson, A.R. et al. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLOS ONE 7, e49138 (2012).
    • (2012) PLOS ONE , vol.7
    • Erickson, A.R.1
  • 11
    • 84905742451 scopus 로고    scopus 로고
    • Supporting data for the paper: An integrated catalog of reference genes in the human gut microbiome
    • doi:10.5524/100064
    • Li, J. et al. Supporting data for the paper: "An integrated catalog of reference genes in the human gut microbiome." GigaScience Database doi:10.5524/100064 (2014).
    • (2014) GigaScience Database
    • Li, J.1
  • 12
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • DOI 10.1093/bioinformatics/btl158
    • Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659 (2006). (Pubitemid 43985301)
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 13
    • 84867634981 scopus 로고    scopus 로고
    • MOCAT: A metagenomics assembly and gene prediction toolkit
    • Kultima, J.R. et al. MOCAT: a metagenomics assembly and gene prediction toolkit. PLOS ONE 7, e47656 (2012).
    • (2012) PLOS ONE , vol.7
    • Kultima, J.R.1
  • 14
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • DOI 10.1128/AEM.00062-07
    • Wang, Q., Garrity, G.M., Tiedje, J.M. & Cole, J.R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267 (2007). (Pubitemid 47326658)
    • (2007) Applied and Environmental Microbiology , vol.73 , Issue.16 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 15
    • 84891820094 scopus 로고    scopus 로고
    • IMG 4 version of the integrated microbial genomes comparative analysis system
    • Markowitz, V.M. et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 42, D560-D567 (2014).
    • (2014) Nucleic Acids Res. , vol.42
    • Markowitz, V.M.1
  • 16
    • 58749112734 scopus 로고    scopus 로고
    • A core gut microbiome in obese and lean twins
    • Turnbaugh, P.J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480-484 (2009).
    • (2009) Nature , vol.457 , pp. 480-484
    • Turnbaugh, P.J.1
  • 17
    • 38449088143 scopus 로고    scopus 로고
    • Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
    • Kurokawa, K. et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14, 169-181 (2007).
    • (2007) DNA Res. , vol.14 , pp. 169-181
    • Kurokawa, K.1
  • 18
    • 0023526239 scopus 로고
    • Estimating the population size for capture-recapture data with unequal catchability
    • Chao, A. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43, 783-791 (1987).
    • (1987) Biometrics , vol.43 , pp. 783-791
    • Chao, A.1
  • 19
    • 0028562529 scopus 로고
    • Estimating population size via sample coverage for closed capture- recapture models
    • Lee, S.M. & Chao, A. Estimating population size via sample coverage for closed capture-recapture models. Biometrics 50, 88-97 (1994). (Pubitemid 24138576)
    • (1994) Biometrics , vol.50 , Issue.1 , pp. 88-97
    • Lee, S.-M.1    Chao, A.2
  • 20
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
    • (2010) Genome Res. , vol.20 , pp. 265-272
    • Li, R.1
  • 21
    • 77955902981 scopus 로고    scopus 로고
    • Ab initio gene identification in metagenomic sequences
    • Zhu, W., Lomsadze, A. & Borodovsky, M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 38, e132 (2010).
    • (2010) Nucleic Acids Res. , vol.38
    • Zhu, W.1    Lomsadze, A.2    Borodovsky, M.3
  • 22
    • 84883464181 scopus 로고    scopus 로고
    • Accurate and universal delineation of prokaryotic species
    • Mende, D.R., Sunagawa, S., Zeller, G. & Bork, P. Accurate and universal delineation of prokaryotic species. Nat. Methods 10, 881-884 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 881-884
    • Mende, D.R.1    Sunagawa, S.2    Zeller, G.3    Bork, P.4
  • 23
    • 85027927719 scopus 로고    scopus 로고
    • Enterotypes of the human gut microbiome
    • Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174-180 (2011).
    • (2011) Nature , vol.473 , pp. 174-180
    • Arumugam, M.1
  • 24
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000). (Pubitemid 30047706)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 25
    • 84861203603 scopus 로고    scopus 로고
    • EggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges
    • Powell, S. et al. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 40, D284-D289 (2012).
    • (2012) Nucleic Acids Res. , vol.40
    • Powell, S.1
  • 26
    • 57349131283 scopus 로고    scopus 로고
    • Micro-eukaryotic diversity of the human distal gut microbiota: Qualitative assessment using culture-dependent and-independent analysis of faeces
    • Scanlan, P.D. & Marchesi, J.R. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and-independent analysis of faeces. ISME J. 2, 1183-1193 (2008).
    • (2008) ISME J. , vol.2 , pp. 1183-1193
    • Scanlan, P.D.1    Marchesi, J.R.2
  • 27
    • 77954304079 scopus 로고    scopus 로고
    • Prokaryotic and eukaryotic diversity of the human gut
    • Marchesi, J.R. Prokaryotic and eukaryotic diversity of the human gut. Adv. Appl. Microbiol. 72, 43-62 (2010).
    • (2010) Adv. Appl. Microbiol. , vol.72 , pp. 43-62
    • Marchesi, J.R.1
  • 28
    • 83755222630 scopus 로고    scopus 로고
    • Microbial eukaryotes in the human microbiome: Ecology, evolution, and future directions
    • Parfrey, L.W., Walters, W.A. & Knight, R. Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Front. Microbiol. 2, 153 (2011).
    • (2011) Front. Microbiol. , vol.2 , pp. 153
    • Parfrey, L.W.1    Walters, W.A.2    Knight, R.3
  • 29
    • 84879744885 scopus 로고    scopus 로고
    • The long-term stability of the human gut microbiota
    • Faith, J.J. et al. The long-term stability of the human gut microbiota. Science 341, 1237439 (2013).
    • (2013) Science , vol.341 , pp. 1237439
    • Faith, J.J.1
  • 30
    • 84880050412 scopus 로고    scopus 로고
    • Country-specific antibiotic use practices impact the human gut resistome
    • Forslund, K. et al. Country-specific antibiotic use practices impact the human gut resistome. Genome Res. 23, 1163-1169 (2013).
    • (2013) Genome Res , vol.23 , pp. 1163-1169
    • Forslund, K.1
  • 31
    • 84880831180 scopus 로고    scopus 로고
    • Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota
    • Hu, Y. et al. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat. Commun. 4, 2151 (2013).
    • (2013) Nat. Commun. , vol.4 , Issue.2151
    • Hu, Y.1
  • 32
    • 77954627922 scopus 로고    scopus 로고
    • Viruses in the faecal microbiota of monozygotic twins and their mothers
    • Reyes, A. et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334-338 (2010).
    • (2010) Nature , vol.466 , pp. 334-338
    • Reyes, A.1
  • 33
    • 80053528043 scopus 로고    scopus 로고
    • The human gut virome: Inter-individual variation and dynamic response to diet
    • Minot, S. et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21, 1616-1625 (2011).
    • (2011) Genome Res , vol.21 , pp. 1616-1625
    • Minot, S.1
  • 34
    • 79251573217 scopus 로고    scopus 로고
    • Cryptic prophages help bacteria cope with adverse environments
    • Wang, X. et al. Cryptic prophages help bacteria cope with adverse environments. Nat. Commun. 1, 147 (2010).
    • Nat. Commun. , vol.1 , Issue.147 , pp. 2010
    • Wang, X.1
  • 35
    • 84865169911 scopus 로고    scopus 로고
    • Going viral: Next-generation sequencing applied to phage populations in the human gut
    • Reyes, A., Semenkovich, N.P., Whiteson, K., Rohwer, F. & Gordon, J.I. Going viral: next-generation sequencing applied to phage populations in the human gut. Nat. Rev. Microbiol. 10, 607-617 (2012).
    • (2012) Nat. Rev. Microbiol. , vol.10 , pp. 607-617
    • Reyes, A.1    Semenkovich, N.P.2    Whiteson, K.3    Rohwer, F.4    Gordon, J.I.5
  • 36
    • 84880509968 scopus 로고    scopus 로고
    • Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
    • Modi, S.R., Lee, H.H., Spina, C.S. & Collins, J.J. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499, 219-222 (2013).
    • (2013) Nature , vol.499 , pp. 219-222
    • Modi, S.R.1    Lee, H.H.2    Spina, C.S.3    Collins, J.J.4
  • 37
    • 65549150087 scopus 로고    scopus 로고
    • Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR
    • Furet, J.-P. et al. Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. FEMS Microbiol. Ecol. 68, 351-362 (2009).
    • (2009) FEMS Microbiol. Ecol. , vol.68 , pp. 351-362
    • Furet, J.-P.1
  • 38
    • 84872151297 scopus 로고    scopus 로고
    • A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor
    • Li, A. et al. A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. Biotechnol. Biofuels 6, 3 (2013).
    • (2013) Biotechnol. Biofuels , vol.6 , pp. 3
    • Li, A.1
  • 39
    • 84888884475 scopus 로고    scopus 로고
    • Metagenomic species profiling using universal phylogenetic marker genes
    • Sunagawa, S. et al. Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods 10, 1196-1199 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 1196-1199
    • Sunagawa, S.1
  • 41
    • 36249021315 scopus 로고    scopus 로고
    • Genome-wide experimental determination of barriers to horizontal gene transfer
    • DOI 10.1126/science.1147112
    • Sorek, R. et al. Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318, 1449-1452 (2007). (Pubitemid 350208955)
    • (2007) Science , vol.318 , Issue.5855 , pp. 1449-1452
    • Sorek, R.1    Zhu, Y.2    Creevey, C.J.3    Francino, M.P.4    Bork, P.5    Rubin, E.M.6
  • 42
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: An improved ultrafast tool for short read alignment
    • Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966-1967 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1966-1967
    • Li, R.1
  • 43
    • 84864384245 scopus 로고    scopus 로고
    • The most wanted" taxa from the human microbiome for whole genome sequencing
    • Fodor, A.A. et al. The "most wanted" taxa from the human microbiome for whole genome sequencing. PLOS ONE 7, e41294 (2012).
    • (2012) PLOS ONE , vol.7
    • Fodor, A.A.1
  • 44
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss, P.D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541 (2009).
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 7537-7541
    • Schloss, P.D.1
  • 45
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent, W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 47
    • 77953050946 scopus 로고    scopus 로고
    • A catalog of reference genomes from the human microbiome
    • Nelson, K.E. et al. A catalog of reference genomes from the human microbiome. Science 328, 994-999 (2010).
    • (2010) Science , vol.328 , pp. 994-999
    • Nelson, K.E.1
  • 48
    • 0034764307 scopus 로고    scopus 로고
    • SSAHA: A fast search method for large DNA databases
    • DOI 10.1101/gr.194201
    • Ning, Z., Cox, A.J. & Mullikin, J.C. SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725-1729 (2001). (Pubitemid 33040499)
    • (2001) Genome Research , vol.11 , Issue.10 , pp. 1725-1729
    • Ning, Z.1    Cox, A.J.2    Mullikin, J.C.3
  • 49
    • 0003200806 scopus 로고    scopus 로고
    • The Asia Pacific perspective: Redefining obesity and its treatment
    • World Health Organization Western Pacific Region & WHO/IASO/IOTF Ltd.
    • World Health Organization Western Pacific Region & WHO/IASO/IOTF. The Asia Pacific perspective: redefining obesity and its treatment. Heal. Commun. Aust. Pty. Ltd. (2000) at http://www.wpro.who.int/nutrition/documents/ Redefining-obesity/en/index.html.
    • (2000) Heal. Commun. Aust. Pty
  • 50
    • 0347992980 scopus 로고    scopus 로고
    • The New BMI Criteria for Asians by the Regional Office for the Western Pacific Region of WHO are Suitable for Screening of Overweight to Prevent Metabolic Syndrome in Elder Japanese Workers
    • DOI 10.1539/joh.45.335
    • Anuurad, E. et al. The new BMI criteria for Asians by the regional office for the western pacific region of WHO are suitable for screening of overweight to prevent metabolic syndrome in elder Japanese workers. J. Occup. Health 45, 335-343 (2003). (Pubitemid 38036188)
    • (2003) Journal of Occupational Health , vol.45 , Issue.6 , pp. 335-343
    • Anuurad, E.1    Shiwaku, K.2    Nogi, A.3    Kitajima, K.4    Enkhmaa, B.5    Shimono, K.6    Yamane, Y.7
  • 51
    • 0032702909 scopus 로고    scopus 로고
    • Prediction of hypertension, diabetes, dyslipidaemia or albuminuria using simple anthropometric indexes in Hong Kong Chinese
    • Ko, G.T., Chan, J.C., Cockram, C.S. & Woo, J. Prediction of hypertension, diabetes, dyslipidaemia or albuminuria using simple anthropometric indexes in Hong Kong Chinese. Int. J. Obes. Relat. Metab. Disord. 23, 1136-1142 (1999).
    • (1999) Int. J. Obes. Relat. Metab. Disord. , vol.23 , pp. 1136-1142
    • Ko, G.T.1    Chan, J.C.2    Cockram, C.S.3    Woo, J.4
  • 53
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genome-wide studies
    • Storey, J.D. & Tibshirani, R. Statistical significance for genome-wide studies. Proc. Natl. Acad. Sci. USA 100, 9440-9445 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.