{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T05:18:04Z","timestamp":1792300684978,"version":"4.4.0"},"reference-count":172,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2012,12,27]],"date-time":"2012-12-27T00:00:00Z","timestamp":1356566400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002808","type":"journal-article","created":{"date-parts":[[2012,12,27]],"date-time":"2012-12-27T21:10:12Z","timestamp":1356642612000},"page":"e1002808","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":453,"title":["Chapter 12: Human Microbiome Analysis"],"prefix":"10.1371","volume":"8","author":[{"given":"Xochitl C.","family":"Morgan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Curtis","family":"Huttenhower","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2012,12,27]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature08821","article-title":"A human gut microbial gene catalogue established by metagenomic sequencing","volume":"464","author":"J Qin","year":"2010","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","journal-title":"Nature"},{"key":"ref3","first-page":"185","article-title":"\u00dcber die isolierte F\u00e4rbung der Schizomyceten in Schnitt- und Trockenpr\u00e4paraten","volume":"2","author":"HC Gram","year":"1884","journal-title":"Fortschritte der Medizin"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4757-0611-6_1","article-title":"The analysis of natural microbial populations by ribosomal RNA sequences","volume":"9","author":"NR Pace","year":"1986","journal-title":"Advances in Microbial Ecology"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1128\/MMBR.59.1.143-169.1995","article-title":"Phylogenetic identification and in situ detection of individual microbial cells without cultivation","volume":"59","author":"RI Amann","year":"1995","journal-title":"Microbiol Rev"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1128\/MMBR.68.4.669-685.2004","article-title":"Metagenomics: application of genomics to uncultured microorganisms","volume":"68","author":"J Handelsman","year":"2004","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1016\/0022-2836(75)90213-2","article-title":"A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase","volume":"94","author":"F Sanger","year":"1975","journal-title":"Journal of molecular biology"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"5463","DOI":"10.1073\/pnas.74.12.5463","article-title":"DNA sequencing with chain-terminating inhibitors","volume":"74","author":"F Sanger","year":"1977","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1038\/nature05874","article-title":"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project","volume":"447","author":"E Birney","year":"2007","journal-title":"Nature"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1007\/BF00173160","article-title":"Arrangement and nucleotide sequence of the gene (fus) encoding elongation factor G (EF-G) from the hyperthermophilic bacterium Aquifex pyrophilus: phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the EF-G\/fus sequences","volume":"41","author":"M Bocchetta","year":"1995","journal-title":"J Mol Evol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"6955","DOI":"10.1073\/pnas.82.20.6955","article-title":"Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses","volume":"82","author":"DJ Lane","year":"1985","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/j.mib.2008.09.011","article-title":"A renaissance for the pioneering 16S rRNA gene","volume":"11","author":"SG Tringe","year":"2008","journal-title":"Curr Opin Microbiol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"JG Caporaso","year":"2010","journal-title":"Nat Methods"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"5069","DOI":"10.1128\/AEM.03006-05","article-title":"Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB","volume":"72","author":"TZ DeSantis","year":"2006","journal-title":"Appl Environ Microbiol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkn879","article-title":"The Ribosomal Database Project: improved alignments and new tools for rRNA analysis","volume":"37","author":"JR Cole","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"7188","DOI":"10.1093\/nar\/gkm864","article-title":"SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB","volume":"35","author":"E Pruesse","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/nrmicro1872","article-title":"Microbial diversity and the genetic nature of microbial species","volume":"6","author":"M Achtman","year":"2008","journal-title":"Nat Rev Microbiol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"e1000844","DOI":"10.1371\/journal.pcbi.1000844","article-title":"The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies","volume":"6","author":"PD Schloss","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"PD Schloss","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1038\/ismej.2009.97","article-title":"Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data","volume":"4","author":"M Hamady","year":"2010","journal-title":"ISME J"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Q Wang","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1101\/gr.085464.108","article-title":"Microbial community profiling for human microbiome projects: Tools, techniques, and challenges","volume":"19","author":"M Hamady","year":"2009","journal-title":"Genome Res"},{"key":"ref23","doi-asserted-by":"crossref","unstructured":"Johnson RA, Wichern DW (2007) Applied Multivariate Statistical Analysis: Prentice Hall.","DOI":"10.1002\/0471667196.ess6094"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: a new phylogenetic method for comparing microbial communities","volume":"71","author":"C Lozupone","year":"2005","journal-title":"Appl Environ Microbiol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1374","DOI":"10.1073\/pnas.0808022106","article-title":"Quantifying environmental adaptation of metabolic pathways in metagenomics","volume":"106","author":"TA Gianoulis","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1007\/s10295-003-0074-9","article-title":"Harmful algal blooms: causes, impacts and detection","volume":"30","author":"KG Sellner","year":"2003","journal-title":"J Ind Microbiol Biotechnol"},{"key":"ref27","first-page":"643","article-title":"The Birthday Problem","volume":"100","author":"MV Hildebrand","year":"1993","journal-title":"American Mathematical Monthly"},{"key":"ref28","first-page":"265","article-title":"Nonparametric estimation of the number of classes in a population","volume":"11","author":"A Chao","year":"1984","journal-title":"Scandinavian Journal of Statistics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1093\/biomet\/80.1.193","article-title":"Stopping rules and estimation for recapture debugging with unequal failure rates","volume":"80","author":"A Chao","year":"1993","journal-title":"Biometrika"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2307\/2530802","article-title":"Estimating species richness using the jackknife procedure","volume":"39","author":"JF Heltshe","year":"1983","journal-title":"Biometrics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1098\/rstb.1994.0091","article-title":"Estimating terrestrial biodiversity through extrapolation","volume":"345","author":"RK Colwell","year":"1994","journal-title":"Phil Trans R Soc London B"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"A mathematical theory of communication","volume":"27","author":"CE Shannon","year":"1948","journal-title":"Bell System Technical Journal"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/163688a0","article-title":"Measurement of diversity","volume":"163","author":"EH Simpson","year":"1949","journal-title":"Nature"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"325","DOI":"10.2307\/1942268","article-title":"An ordination of upland forest communities of southern Wisconsin","volume":"27","author":"JR Bray","year":"1957","journal-title":"Ecological Monographs"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"2317","DOI":"10.1093\/bioinformatics\/bth226","article-title":"Bellerophon: a program to detect chimeric sequences in multiple sequence alignments","volume":"20","author":"T Huber","year":"2004","journal-title":"Bioinformatics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"6288","DOI":"10.1128\/AEM.00246-06","article-title":"Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation","volume":"72","author":"EL Brodie","year":"2006","journal-title":"Appl Environ Microbiol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"5636","DOI":"10.1128\/AEM.00303-10","article-title":"Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray","volume":"76","author":"MC Schatz","year":"2010","journal-title":"Appl Environ Microbiol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1146\/annurev.genet.38.072902.091216","article-title":"Metagenomics: genomic analysis of microbial communities","volume":"38","author":"CS Riesenfeld","year":"2004","journal-title":"Annu Rev Genet"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1371\/journal.pcbi.0010024","article-title":"Bioinformatics for whole-genome shotgun sequencing of microbial communities","volume":"1","author":"K Chen","year":"2005","journal-title":"PLoS Comput Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e3042","DOI":"10.1371\/journal.pone.0003042","article-title":"Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities","volume":"3","author":"JA Gilbert","year":"2008","journal-title":"PLoS One"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"5533","DOI":"10.1128\/AEM.00502-10","article-title":"Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed","volume":"76","author":"CC Booijink","year":"2010","journal-title":"Appl Environ Microbiol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/ismej.2008.108","article-title":"Shotgun metaproteomics of the human distal gut microbiota","volume":"3","author":"NC Verberkmoes","year":"2009","journal-title":"ISME J"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"e26542","DOI":"10.1371\/journal.pone.0026542","article-title":"A metaproteomic approach to study human-microbial ecosystems at the mucosal luminal interface","volume":"6","author":"X Li","year":"2011","journal-title":"PLoS One"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1016\/j.cell.2008.08.025","article-title":"An invitation to the marriage of metagenomics and metabolomics","volume":"134","author":"PJ Turnbaugh","year":"2008","journal-title":"Cell"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"3698","DOI":"10.1073\/pnas.0812874106","article-title":"Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites","volume":"106","author":"WR Wikoff","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.tim.2005.12.006","article-title":"Metaproteomics: studying functional gene expression in microbial ecosystems","volume":"14","author":"P Wilmes","year":"2006","journal-title":"Trends Microbiol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.1111\/j.1462-2920.2008.01863.x","article-title":"Comparative day\/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre","volume":"11","author":"RS Poretsky","year":"2009","journal-title":"Environ Microbiol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/nature08055","article-title":"Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column","volume":"459","author":"Y Shi","year":"2009","journal-title":"Nature"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"R23","DOI":"10.1186\/gb-2012-13-3-r23","article-title":"Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes","volume":"13","author":"G Giannoukos","year":"2012","journal-title":"Genome biology"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"ES Lander","year":"2001","journal-title":"Nature"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1126\/science.1058040","article-title":"The sequence of the human genome","volume":"291","author":"JC Venter","year":"2001","journal-title":"Science"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nature11209","article-title":"A framework for human microbiome research","volume":"486","journal-title":"Nature"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1038\/nature02340","article-title":"Community structure and metabolism through reconstruction of microbial genomes from the environment","volume":"428","author":"GW Tyson","year":"2004","journal-title":"Nature"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1126\/science.1093857","article-title":"Environmental genome shotgun sequencing of the Sargasso Sea","volume":"304","author":"JC Venter","year":"2004","journal-title":"Science"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/455481a","article-title":"Microbiology: metagenomics","volume":"455","author":"P Hugenholtz","year":"2008","journal-title":"Nature"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1128\/MMBR.00009-08","article-title":"A bioinformatician's guide to metagenomics","volume":"72","author":"V Kunin","year":"2008","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"12115","DOI":"10.1073\/pnas.0605127103","article-title":"Microbial diversity in the deep sea and the underexplored \u201crare biosphere\u201d","volume":"103","author":"ML Sogin","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nmeth1043","article-title":"Use of simulated data sets to evaluate the fidelity of metagenomic processing methods","volume":"4","author":"K Mavromatis","year":"2007","journal-title":"Nat Methods"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nature07540","article-title":"A core gut microbiome in obese and lean twins","volume":"457","author":"PJ Turnbaugh","year":"2009","journal-title":"Nature"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"e1002358","DOI":"10.1371\/journal.pcbi.1002358","article-title":"Metabolic reconstruction for metagenomic data and its application to the human microbiome","volume":"8","author":"S Abubucker","year":"2012","journal-title":"PLoS computational biology"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"W101","DOI":"10.1093\/nar\/gkp327","article-title":"Orphelia: predicting genes in metagenomic sequencing reads","volume":"37","author":"KJ Hoff","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref62","article-title":"FragGeneScan: predicting genes in short and error-prone reads","author":"M Rho","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"e75","DOI":"10.1371\/journal.pbio.0050075","article-title":"CAMERA: a community resource for metagenomics","volume":"5","author":"R Seshadri","year":"2007","journal-title":"PLoS Biol"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1186\/1471-2164-11-242","article-title":"Finishing genomes with limited resources: lessons from an ensemble of microbial genomes","volume":"11","author":"N Nagarajan","year":"2010","journal-title":"BMC Genomics"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1093\/bib\/bbp026","article-title":"Genome assembly reborn: recent computational challenges","volume":"10","author":"M Pop","year":"2009","journal-title":"Brief Bioinform"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1111\/j.1462-2920.2004.00624.x","article-title":"Application of tetranucleotide frequencies for the assignment of genomic fragments","volume":"6","author":"H Teeling","year":"2004","journal-title":"Environ Microbiol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/nmeth976","article-title":"Accurate phylogenetic classification of variable-length DNA fragments","volume":"4","author":"AC McHardy","year":"2007","journal-title":"Nat Methods"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1038\/nmeth.1358","article-title":"Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models","volume":"6","author":"A Brady","year":"2009","journal-title":"Nat Methods"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1006\/geno.1999.5854","article-title":"Interpolated Markov models for eukaryotic gene finding","volume":"59","author":"SL Salzberg","year":"1999","journal-title":"Genomics"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"SR Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1093\/nar\/gkg128","article-title":"The TIGRFAMs database of protein families","volume":"31","author":"DH Haft","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"D281","DOI":"10.1093\/nar\/gkm960","article-title":"The Pfam protein families database","volume":"36","author":"RD Finn","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref74","article-title":"Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes","author":"P Veiga","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"D534","DOI":"10.1093\/nar\/gkm869","article-title":"IMG\/M: a data management and analysis system for metagenomes","volume":"36","author":"VM Markowitz","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1186\/1471-2105-9-386","article-title":"The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes","volume":"9","author":"F Meyer","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref77","article-title":"METAREP: JCVI Metagenomics Reports - an open source tool for high-performance comparative metagenomics","author":"J Goll","year":"2010","journal-title":"Bioinformatics"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"e82","DOI":"10.1371\/journal.pbio.0050082","article-title":"Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes","volume":"5","author":"JA Eisen","year":"2007","journal-title":"PLoS Biol"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"B Langmead","year":"2009","journal-title":"Genome Biol"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"H Li","year":"2010","journal-title":"Bioinformatics"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1186\/1471-2105-7-162","article-title":"An application of statistics to comparative metagenomics","volume":"7","author":"B Rodriguez-Brito","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"e77","DOI":"10.1371\/journal.pbio.0050077","article-title":"The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific","volume":"5","author":"DB Rusch","year":"2007","journal-title":"PLoS Biol"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"D355","DOI":"10.1093\/nar\/gkp896","article-title":"KEGG for representation and analysis of molecular networks involving diseases and drugs","volume":"38","author":"M Kanehisa","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1046\/j.1432-1327.1999.nomen.x","article-title":"Nomenclature committee of the international union of biochemistry and molecular biology (NC-IUBMB), Enzyme Supplement 5 (1999)","volume":"264","year":"1999","journal-title":"Eur J Biochem"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"D274","DOI":"10.1093\/nar\/gkl925","article-title":"TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels","volume":"35","author":"Q Ren","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1038\/nprot.2007.131","article-title":"Locating proteins in the cell using TargetP, SignalP and related tools","volume":"2","author":"O Emanuelsson","year":"2007","journal-title":"Nat Protoc"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"D5","DOI":"10.1093\/nar\/gkp967","article-title":"Database resources of the National Center for Biotechnology Information","volume":"38","author":"EW Sayers","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes","volume":"4","author":"RL Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"D190","DOI":"10.1093\/nar\/gkp951","article-title":"eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations","volume":"38","author":"J Muller","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"D473","DOI":"10.1093\/nar\/gkp875","article-title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway\/genome databases","volume":"38","author":"R Caspi","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1126\/science.1183605","article-title":"A catalog of reference genomes from the human microbiome","volume":"328","author":"KE Nelson","year":"2010","journal-title":"Science"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1146\/annurev.arplant.55.031903.141619","article-title":"Phosphoenolpyruvate carboxylase: a new era of structural biology","volume":"55","author":"K Izui","year":"2004","journal-title":"Annu Rev Plant Biol"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"W182","DOI":"10.1093\/nar\/gkm321","article-title":"KAAS: an automatic genome annotation and pathway reconstruction server","volume":"35","author":"Y Moriya","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"e1000465","DOI":"10.1371\/journal.pcbi.1000465","article-title":"A parsimony approach to biological pathway reconstruction\/inference for genomes and metagenomes","volume":"5","author":"Y Ye","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"17480","DOI":"10.1073\/pnas.0603364103","article-title":"Systems approach to refining genome annotation","volume":"103","author":"JL Reed","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1186\/1471-2105-8-212","article-title":"Optimization based automated curation of metabolic reconstructions","volume":"8","author":"V Satish Kumar","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1186\/1471-2105-5-76","article-title":"A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases","volume":"5","author":"ML Green","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1111\/j.1574-6976.2008.00146.x","article-title":"Genome-scale models of bacterial metabolism: reconstruction and applications","volume":"33","author":"M Durot","year":"2009","journal-title":"FEMS Microbiol Rev"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.ygeno.2008.07.006","article-title":"\u201cOmics\u201d data and levels of evidence for biomarker discovery","volume":"93","author":"D Ghosh","year":"2009","journal-title":"Genomics"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/nrg1521","article-title":"Genome-wide association studies for common diseases and complex traits","volume":"6","author":"JN Hirschhorn","year":"2005","journal-title":"Nat Rev Genet"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"R61","DOI":"10.1186\/gb-2009-10-6-r61","article-title":"Metabolic-network-driven analysis of bacterial ecological strategies","volume":"10","author":"S Freilich","year":"2009","journal-title":"Genome Biol"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1093\/bioinformatics\/btp704","article-title":"Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways","volume":"26","author":"N Tepper","year":"2010","journal-title":"Bioinformatics"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/msb4100131","article-title":"Metabolic modeling of a mutualistic microbial community","volume":"3","author":"S Stolyar","year":"2007","journal-title":"Mol Syst Biol"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1038\/nprot.2009.203","article-title":"A protocol for generating a high-quality genome-scale metabolic reconstruction","volume":"5","author":"I Thiele","year":"2010","journal-title":"Nat Protoc"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1038\/nrmicro1161","article-title":"Metagenomics and industrial applications","volume":"3","author":"P Lorenz","year":"2005","journal-title":"Nat Rev Microbiol"},{"key":"ref107","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/msb.2010.16","article-title":"A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion","volume":"6","author":"MO Sommer","year":"2010","journal-title":"Mol Syst Biol"},{"key":"ref108","doi-asserted-by":"crossref","first-page":"e1002606","DOI":"10.1371\/journal.pcbi.1002606","article-title":"Microbial Co-occurrence Relationships in the Human Microbiome","volume":"8","author":"K Faust","year":"2012","journal-title":"PLoS computational biology"},{"key":"ref109","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1146\/annurev.micro.030608.101423","article-title":"Rules of engagement: interspecies interactions that regulate microbial communities","volume":"62","author":"AE Little","year":"2008","journal-title":"Annu Rev Microbiol"},{"key":"ref110","first-page":"1","article-title":"Strategies for culture of \u2018unculturable\u2019 bacteria","volume":"309","author":"SR Vartoukian","year":"2010","journal-title":"FEMS Microbiol Lett"},{"key":"ref111","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1093\/gbe\/evp057","article-title":"Comparative metagenomics and population dynamics of the gut microbiota in mother and infant","volume":"2010","author":"PA Vaishampayan","year":"2010","journal-title":"Genome Biol Evol"},{"key":"ref112","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1038\/ismej.2009.96","article-title":"Convergent temporal dynamics of the human infant gut microbiota","volume":"4","author":"P Trosvik","year":"2010","journal-title":"ISME J"},{"key":"ref113","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/nrd2505","article-title":"Gut microbiota: a potential new territory for drug targeting","volume":"7","author":"W Jia","year":"2008","journal-title":"Nat Rev Drug Discov"},{"key":"ref114","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nri2515","article-title":"The gut microbiota shapes intestinal immune responses during health and disease","volume":"9","author":"JL Round","year":"2009","journal-title":"Nat Rev Immunol"},{"key":"ref115","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1126\/science.1171700","article-title":"Topographical and temporal diversity of the human skin microbiome","volume":"324","author":"EA Grice","year":"2009","journal-title":"Science"},{"key":"ref116","doi-asserted-by":"crossref","first-page":"e10598","DOI":"10.1371\/journal.pone.0010598","article-title":"The human nasal microbiota and Staphylococcus aureus carriage","volume":"5","author":"DN Frank","year":"2010","journal-title":"PLoS One"},{"key":"ref117","doi-asserted-by":"crossref","first-page":"R42","DOI":"10.1186\/gb-2012-13-6-r42","article-title":"Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples","volume":"13","author":"N Segata","year":"2012","journal-title":"Genome biology"},{"key":"ref118","article-title":"The Human Oral Microbiome","author":"FE Dewhirst","year":"2010","journal-title":"J Bacteriol"},{"key":"ref119","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1016\/S0140-6736(03)12489-0","article-title":"Gut flora in health and disease","volume":"361","author":"F Guarner","year":"2003","journal-title":"Lancet"},{"key":"ref120","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1038\/nrmicro2245","article-title":"What are the consequences of the disappearing human microbiota?","volume":"7","author":"MJ Blaser","year":"2009","journal-title":"Nat Rev Microbiol"},{"key":"ref121","doi-asserted-by":"crossref","first-page":"11971","DOI":"10.1073\/pnas.1002601107","article-title":"Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns","volume":"107","author":"MG Dominguez-Bello","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref122","doi-asserted-by":"crossref","first-page":"e1000476","DOI":"10.1371\/journal.ppat.1000476","article-title":"Pneumococcal capsular polysaccharide structure predicts serotype prevalence","volume":"5","author":"DM Weinberger","year":"2009","journal-title":"PLoS Pathog"},{"key":"ref123","doi-asserted-by":"crossref","first-page":"e11044","DOI":"10.1371\/journal.pone.0011044","article-title":"Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients","volume":"5","author":"MJ Cox","year":"2010","journal-title":"PLoS One"},{"key":"ref124","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/nrmicro1152","article-title":"Gut microorganisms, mammalian metabolism and personalized health care","volume":"3","author":"JK Nicholson","year":"2005","journal-title":"Nat Rev Microbiol"},{"key":"ref125","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1016\/j.cell.2010.01.023","article-title":"Homeostasis and inflammation in the intestine","volume":"140","author":"WS Garrett","year":"2010","journal-title":"Cell"},{"key":"ref126","article-title":"Microbes and Health Sackler Colloquium: Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation","author":"L Dethlefsen","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref127","doi-asserted-by":"crossref","first-page":"e280","DOI":"10.1371\/journal.pbio.0060280","article-title":"The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing","volume":"6","author":"L Dethlefsen","year":"2008","journal-title":"PLoS Biol"},{"key":"ref128","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography","volume":"486","author":"T Yatsunenko","year":"2012","journal-title":"Nature"},{"key":"ref129","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1093\/dnares\/dsm018","article-title":"Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes","volume":"14","author":"K Kurokawa","year":"2007","journal-title":"DNA Res"},{"key":"ref130","article-title":"Microbes and Health Sackler Colloquium: Succession of microbial consortia in the developing infant gut microbiome","author":"JE Koenig","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref131","article-title":"Microbes and Health Sackler Colloquium: Composition, variability, and temporal stability of the intestinal microbiota of the elderly","author":"MJ Claesson","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref132","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1038\/nature11319","article-title":"Gut microbiota composition correlates with diet and health in the elderly","volume":"488","author":"MJ Claesson","year":"2012","journal-title":"Nature"},{"key":"ref133","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1126\/science.1208344","article-title":"Linking long-term dietary patterns with gut microbial enterotypes","volume":"334","author":"GD Wu","year":"2011","journal-title":"Science"},{"key":"ref134","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1053\/j.gastro.2010.11.049","article-title":"Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency","volume":"140","author":"MD Spencer","year":"2011","journal-title":"Gastroenterology"},{"key":"ref135","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1038\/ismej.2009.112","article-title":"Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice","volume":"4","author":"C Zhang","year":"2010","journal-title":"ISME J"},{"key":"ref136","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1038\/nature06245","article-title":"An ecological and evolutionary perspective on human-microbe mutualism and disease","volume":"449","author":"L Dethlefsen","year":"2007","journal-title":"Nature"},{"key":"ref137","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1126\/science.1198719","article-title":"Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans","volume":"332","author":"BD Muegge","year":"2011","journal-title":"Science"},{"key":"ref138","doi-asserted-by":"crossref","first-page":"1022","DOI":"10.1038\/4441022a","article-title":"Microbial ecology: human gut microbes associated with obesity","volume":"444","author":"RE Ley","year":"2006","journal-title":"Nature"},{"key":"ref139","doi-asserted-by":"crossref","first-page":"11070","DOI":"10.1073\/pnas.0504978102","article-title":"Obesity alters gut microbial ecology","volume":"102","author":"RE Ley","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref140","doi-asserted-by":"crossref","first-page":"10011","DOI":"10.1073\/pnas.0602187103","article-title":"A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism","volume":"103","author":"BS Samuel","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref141","doi-asserted-by":"crossref","first-page":"4596","DOI":"10.1073\/pnas.0400706101","article-title":"Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota","volume":"101","author":"JF Rawls","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref142","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/j.cell.2006.08.043","article-title":"Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection","volume":"127","author":"JF Rawls","year":"2006","journal-title":"Cell"},{"key":"ref143","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/j.cell.2009.09.033","article-title":"Induction of intestinal Th17 cells by segmented filamentous bacteria","volume":"139","author":"Ivanov II","year":"2009","journal-title":"Cell"},{"key":"ref144","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/mi.2010.3","article-title":"Segmented filamentous bacteria take the stage","volume":"3","author":"DR Ivanov, II, Littman","year":"2010","journal-title":"Mucosal Immunol"},{"key":"ref145","doi-asserted-by":"crossref","first-page":"6ra14","DOI":"10.1126\/scitranslmed.3000322","article-title":"The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice","volume":"1","author":"PJ Turnbaugh","year":"2009","journal-title":"Sci Transl Med"},{"key":"ref146","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1097\/MOG.0b013e328333d751","article-title":"Obesity and the human microbiome","volume":"26","author":"RE Ley","year":"2010","journal-title":"Curr Opin Gastroenterol"},{"key":"ref147","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1038\/nature05414","article-title":"An obesity-associated gut microbiome with increased capacity for energy harvest","volume":"444","author":"PJ Turnbaugh","year":"2006","journal-title":"Nature"},{"key":"ref148","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.chom.2008.02.015","article-title":"Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome","volume":"3","author":"PJ Turnbaugh","year":"2008","journal-title":"Cell Host Microbe"},{"key":"ref149","doi-asserted-by":"crossref","first-page":"S14","DOI":"10.1186\/1472-6831-6-S1-S14","article-title":"Dental plaque as a biofilm and a microbial community - implications for health and disease","volume":"6","author":"PD Marsh","year":"2006","journal-title":"BMC Oral Health"},{"key":"ref150","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1101\/gr.084616.108","article-title":"Global diversity in the human salivary microbiome","volume":"19","author":"I Nasidze","year":"2009","journal-title":"Genome Res"},{"key":"ref151","doi-asserted-by":"crossref","first-page":"e9321","DOI":"10.1371\/journal.pone.0009321","article-title":"Oral biofilm architecture on natural teeth","volume":"5","author":"V Zijnge","year":"2010","journal-title":"PLoS One"},{"key":"ref152","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.1128\/AEM.67.3.1343-1350.2001","article-title":"Spatial arrangements and associative behavior of species in an in vitro oral biofilm model","volume":"67","author":"M Guggenheim","year":"2001","journal-title":"Appl Environ Microbiol"},{"key":"ref153","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1186\/1472-6831-6-S1-S12","article-title":"Streptococcal receptor polysaccharides: recognition molecules for oral biofilm formation","volume":"6","author":"Y Yoshida","year":"2006","journal-title":"BMC Oral Health"},{"key":"ref154","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1016\/j.tim.2005.09.006","article-title":"Oral microbial communities in sickness and in health","volume":"13","author":"HF Jenkinson","year":"2005","journal-title":"Trends Microbiol"},{"key":"ref155","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1126\/science.1155725","article-title":"Evolution of mammals and their gut microbes","volume":"320","author":"RE Ley","year":"2008","journal-title":"Science"},{"key":"ref156","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1038\/nature08937","article-title":"Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota","volume":"464","author":"JH Hehemann","year":"2010","journal-title":"Nature"},{"key":"ref157","doi-asserted-by":"crossref","first-page":"4159","DOI":"10.1113\/jphysiol.2009.172742","article-title":"The role of the intestinal microbiota in enteric infection","volume":"587","author":"I Sekirov","year":"2009","journal-title":"J Physiol"},{"key":"ref158","doi-asserted-by":"crossref","first-page":"9274","DOI":"10.1073\/pnas.0603024103","article-title":"The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution","volume":"103","author":"M van de Guchte","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref159","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1038\/msb4100190","article-title":"Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model","volume":"4","author":"FP Martin","year":"2008","journal-title":"Mol Syst Biol"},{"key":"ref160","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/sj.embor.7400731","article-title":"The gut flora as a forgotten organ","volume":"7","author":"AM O'Hara","year":"2006","journal-title":"EMBO Rep"},{"key":"ref161","unstructured":"Zimmer C (2010) How Microbes Defend and Define Us. The New York Times. New York, NY."},{"key":"ref162","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1097\/MCG.0b013e3181c87e02","article-title":"Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea","volume":"44","author":"A Khoruts","year":"2010","journal-title":"J Clin Gastroenterol"},{"key":"ref163","first-page":"3028","article-title":"\u201cFlora Power\u201d\u2013 fecal bacteria cure chronic C. difficile diarrhea","volume":"95","author":"TJ Borody","year":"2000","journal-title":"Am J Gastroenterol"},{"key":"ref164","article-title":"Illumina-based analysis of microbial community diversity","author":"PH Degnan","year":"2011","journal-title":"The ISME journal"},{"key":"ref165","doi-asserted-by":"crossref","first-page":"e1000667","DOI":"10.1371\/journal.pcbi.1000667","article-title":"A primer on metagenomics","volume":"6","author":"JC Wooley","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref166","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1093\/bioinformatics\/btp341","article-title":"Visual and statistical comparison of metagenomes","volume":"25","author":"S Mitra","year":"2009","journal-title":"Bioinformatics"},{"key":"ref167","article-title":"Microbial Ecology: Fundamentals and Applications: Benjamin Cummings","author":"RM Atlas","year":"1997"},{"key":"ref168","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1126\/science.276.5313.734","article-title":"A molecular view of microbial diversity and the biosphere","volume":"276","author":"NR Pace","year":"1997","journal-title":"Science"},{"key":"ref169","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1038\/nrmicro1935","article-title":"Molecular eco-systems biology: towards an understanding of community function","volume":"6","author":"J Raes","year":"2008","journal-title":"Nat Rev Microbiol"},{"key":"ref170","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkm882","article-title":"KEGG for linking genomes to life and the environment","volume":"36","author":"M Kanehisa","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref171","doi-asserted-by":"crossref","first-page":"5691","DOI":"10.1093\/nar\/gki866","article-title":"The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes","volume":"33","author":"R Overbeek","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref172","doi-asserted-by":"crossref","unstructured":"Morgan XC, Segata N, Huttenhower C (in press) Biodiversity and functional genomics in the human microbiome. Trends Genet. doi:10.1016\/j.tig.2012.09.005. Epub ahead of print 7 November 2012.","DOI":"10.1016\/j.tig.2012.09.005"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002808","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,4]],"date-time":"2022-02-04T19:04:06Z","timestamp":1644001446000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002808"}},"subtitle":[],"editor":[{"given":"Fran","family":"Lewitter","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]},{"given":"Maricel","family":"Kann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2012,12,27]]},"references-count":172,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2012,12,27]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002808","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,12,27]]}}}