Structure, function and diversity of the healthy human microbiome
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implic...
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| Published in: | Nature (London) Vol. 486; no. 7402; pp. 207 - 214 |
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| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
London
Nature Publishing Group UK
14.06.2012
Nature Publishing Group |
| Subjects: | |
| ISSN: | 0028-0836, 1476-4687, 1476-4687 |
| Online Access: | Get full text |
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| Abstract | Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.
The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.
The human genome
The Human Microbiome Project (HMP), supported by the National Institutes of Health Common Fund, has the goal of characterizing the microbial communities that inhabit and interact with the human body in sickness and in health. In two Articles in this issue of
Nature
, the HMP Consortium presents the first population-scale details of the organismal and functional composition of the microbiota across five areas of the body. An associated News & Views discusses the initial results — which, along with those of a series of co-publications, already constitute the most extensive catalogue of organisms and genes related to the human microbiome yet published — and highlights some of the major questions that the project will tackle in the next few years. |
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| AbstractList | Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.
The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.
The human genome
The Human Microbiome Project (HMP), supported by the National Institutes of Health Common Fund, has the goal of characterizing the microbial communities that inhabit and interact with the human body in sickness and in health. In two Articles in this issue of
Nature
, the HMP Consortium presents the first population-scale details of the organismal and functional composition of the microbiota across five areas of the body. An associated News & Views discusses the initial results — which, along with those of a series of co-publications, already constitute the most extensive catalogue of organisms and genes related to the human microbiome yet published — and highlights some of the major questions that the project will tackle in the next few years. Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome. Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome. Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin, and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics, and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analyzed the largest cohort and set of distinct, clinically relevant body habitats to date. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families, and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology, and translational applications of the human microbiome. Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome. [PUBLICATION ABSTRACT] |
| Audience | Academic |
| Author | Zeng, Qiandong Wortman, Jennifer R Muzny, Donna M Knight, Rob Busam, Dana A Bonazzi, Vivien Bloom, Toby Chinwalla, Asif T Baker, Carl C Fulton, Robert S FitzGerald, Michael G Young, Sarah K Abolude, Olukemi O Giglio, Michelle G Abubucker, Sahar Buhay, Christian J Hallsworth-Pepin, Kymberlie Bihan, Monika Wollam, Aye M Martin, John C Madupu, Ramana Worley, Kim C Mitreva, Makedonka Blaser, Martin J Gevers, Dirk Begg, Lisa Creasy, Heather H Allen-Vercoe, Emma Arze, Cesar A Sodergren, Erica J Badger, Jonathan H Versalovic, James Bhonagiri, Veena Andersen, Gary L Huttenhower, Curtis Alvarado, Lucia Buck, Gregory A Armitage, Gary et. al Lobos, Elizabeth A Alm, Eric J Magrini, Vincent Paul Brooks, J Anderson, Scott Ayvaz, Tulin Aagaard, Kjersti M Appelbaum, Elizabeth Earl, Ashlee M Belachew, Tsegahiwot Arachchi, Harindra M Campbell, Joseph L |
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| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=25955577$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/22699609$$D View this record in MEDLINE/PubMed https://www.osti.gov/biblio/1153605$$D View this record in Osti.gov |
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| ContentType | Journal Article |
| Contributor | Wortman, Jennifer R Knight, Rob Bonazzi, Vivien Bloom, Toby Chinwalla, Asif T Di Francesco, Valentina Baker, Carl C Cutting, Mary A Chhibba, Shaila Young, Sarah K Conlan, Sean Farmer, Candace N Giglio, Michelle G Clemente, Jose C Buhay, Christian J Chu, Ken Hallsworth-Pepin, Kymberlie Chen, I-Min A Giannoukos, Georgia Garcia, Nathalia Wollam, Aye M Martin, John C Madupu, Ramana Fisher, Sheila Felix, Victor M Blaser, Martin J Ding, Yan Cantarel, Brandi L Begg, Lisa Friedrich, Dennis C Arze, Cesar A Goll, Johannes Sodergren, Erica J Dewhirst, Floyd E Badger, Jonathan H Versalovic, James Andersen, Gary L Buck, Gregory A Canon, Shane R Crabtree, Jonathan Magrini, Vincent Aagaard, Kjersti M Appelbaum, Elizabeth Belachew, Tsegahiwot Campbell, Joseph L Clifton, Sandra W Davis, Catherine C Goldberg, Jonathan M Brooks, J Paul Zeng, Qiandong Griggs, Allison Muzny, Donna M Fodor, Anthony A Busam, Dana A Forney, Larry J Fulton, Robert S FitzGerald, Michael G Feldgarden, Michael Abolude, Olukemi O Fulton, Lucinda L Friedman, Jonathan Chen, Lei Faust, Karoline |
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| Copyright | The Author(s) 2012 2015 INIST-CNRS COPYRIGHT 2012 Nature Publishing Group Copyright Nature Publishing Group Jun 14, 2012 |
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| Keywords | Human Digestive system Gut Vagina Microflora Metabolic pathway Biodiversity Epidemiology Structure function relationship Phenotype Bacteria Skin Microbiome |
| Language | English |
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Med.2005353189919111:CAS:528:DC%2BD2MXhtF2rsL%2FL10.1056/NEJMoa043802 GiannoukosGEfficient and robust RNA-seq process for cultured bacteria and complex community transcriptomesGenome Biol.201213R231:CAS:528:DC%2BC38Xpt1ajt7Y%3D10.1186/gb-2012-13-3-r23 Segata, N. et al. Efficient metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methodshttp://dx.doi.org/10.1038/nmeth.2066 (2012) Wylie, K. M. et al. Novel bacterial taxa in the human microbiome. PLoS ONEhttp://dx.doi.org/10.1371/journal.pone.003529 (14 June 2012) KanehisaMGotoSFurumichiMTanabeMHirakawaMKEGG for representation and analysis of molecular networks involving diseases and drugsNucleic Acids Res.201038D355D3601:CAS:528:DC%2BC3cXktlygtg%3D%3D10.1093/nar/gkp896 RavelJVaginal microbiome of reproductive-age womenProc. Natl Acad. Sci. USA2011108468046872011PNAS..108.4680R1:CAS:528:DC%2BC3MXjvVCrs7g%3D10.1073/pnas.1002611107 GriceEATopographical and temporal diversity of the human skin microbiomeScience2009324119011922009Sci...324.1190G1:CAS:528:DC%2BD1MXmsVGis7c%3D10.1126/science.1171700 SharptonTJPhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic dataPLoS Comput. Biol.20117e10010611:CAS:528:DC%2BC3MXhtlyjs7g%3D10.1371/journal.pcbi.1001061 KuehnertMJPrevalence of Staphylococcus aureus nasal colonization in the United States, 2001–2002J. Infect. Dis.20061931721791:CAS:528:DC%2BD28XhtVygu74%3D10.1086/499632 TurnbaughPJA core gut microbiome in obese and lean twinsNature20094574804842009Natur.457..480T1:CAS:528:DC%2BD1MXotlOlsw%3D%3D10.1038/nature07540 CaporasoJGQIIME allows analysis of high-throughput community sequencing dataNature Methods201073353361:CAS:528:DC%2BC3cXksFalurg%3D10.1038/nmeth.f.303 Faust, K. et al. 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A framework for human microbiome research. Naturehttp://dx.doi.org/10.1038/nature11209 (this issue) GillespieJJPATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic speciesInfect. Immun.201179428642981:CAS:528:DC%2BC3MXhtl2nsb3I10.1128/IAI.00207-11 SokolHFaecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patientsProc. Natl Acad. Sci. USA200810516731167362008PNAS..10516731S1:CAS:528:DC%2BD1cXhtleks7%2FI10.1073/pnas.0804812105 CostelloEKBacterial community variation in human body habitats across space and timeScience2009326169416972009Sci...326.1694C1:CAS:528:DC%2BD1MXhsFGmsL7K10.1126/science.1177486 Li, K., Bihan, M., Yooseph, S. & Methe, B. A. Analyses of the microbial diversity across the human microbiome. PLoS ONEhttp://dx.doi.org/10.1371/journal.pone.0032118 (14 June 2012) LangilleMGBrinkmanFSIslandViewer: an integrated interface for computational identification and visualization of genomic islandsBioinformatics2009256646651:CAS:528:DC%2BD1MXisFeksr4%3D10.1093/bioinformatics/btp030 J Qin (BFnature11234_CR3) 2010; 464 PJ Turnbaugh (BFnature11234_CR2) 2009; 457 H Sokol (BFnature11234_CR15) 2008; 105 MJ Kuehnert (BFnature11234_CR20) 2006; 193 H Li (BFnature11234_CR25) 2010; 26 BFnature11234_CR21 BFnature11234_CR6 BFnature11234_CR7 BFnature11234_CR22 G Giannoukos (BFnature11234_CR26) 2012; 13 BFnature11234_CR1 N Segata (BFnature11234_CR10) 2012; 13 EA Grice (BFnature11234_CR8) 2009; 324 TJ Sharpton (BFnature11234_CR13) 2011; 7 M Kanehisa (BFnature11234_CR24) 2010; 38 MG Langille (BFnature11234_CR27) 2009; 25 BFnature11234_CR14 AL Goodman (BFnature11234_CR19) 2009; 6 JA Aas (BFnature11234_CR16) 2005; 43 JG Caporaso (BFnature11234_CR23) 2010; 7 BFnature11234_CR11 DN Fredricks (BFnature11234_CR4) 2005; 353 JJ Gillespie (BFnature11234_CR12) 2011; 79 SK Mazmanian (BFnature11234_CR18) 2008; 453 D Medini (BFnature11234_CR17) 2008; 6 EK Costello (BFnature11234_CR5) 2009; 326 J Ravel (BFnature11234_CR9) 2011; 108 35705822 - Nature. 2022 Jun;606(7914):435. doi: 10.1038/d41586-022-01610-5. 22699602 - Nature. 2012 Jun 13;486(7402):194-5. doi: 10.1038/486194a. |
| References_xml | – reference: KuehnertMJPrevalence of Staphylococcus aureus nasal colonization in the United States, 2001–2002J. Infect. Dis.20061931721791:CAS:528:DC%2BD28XhtVygu74%3D10.1086/499632 – reference: Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput. Biol. (in the press) – reference: Li, K., Bihan, M., Yooseph, S. & Methe, B. A. Analyses of the microbial diversity across the human microbiome. PLoS ONEhttp://dx.doi.org/10.1371/journal.pone.0032118 (14 June 2012) – reference: GiannoukosGEfficient and robust RNA-seq process for cultured bacteria and complex community transcriptomesGenome Biol.201213R231:CAS:528:DC%2BC38Xpt1ajt7Y%3D10.1186/gb-2012-13-3-r23 – reference: SegataNComposition of the adult digestive tract microbiome based on seven mouth surfaces, tonsils, throat and stool samplesGenome Biol.201213R421:CAS:528:DC%2BC38XpvVWksL4%3D10.1186/gb-2012-13-6-r42 – reference: CostelloEKBacterial community variation in human body habitats across space and timeScience2009326169416972009Sci...326.1694C1:CAS:528:DC%2BD1MXhsFGmsL7K10.1126/science.1177486 – reference: KanehisaMGotoSFurumichiMTanabeMHirakawaMKEGG for representation and analysis of molecular networks involving diseases and drugsNucleic Acids Res.201038D355D3601:CAS:528:DC%2BC3cXktlygtg%3D%3D10.1093/nar/gkp896 – reference: Huse, S., Ye, Y., Zhou, Y. & Fodor, A. A core human microbiome as viewed through 16s rRNA sequences clusters. PLoS ONEhttp://dx.doi.org/10.1371/journal.pone.0034242 (14 June 2012) – reference: GriceEATopographical and temporal diversity of the human skin microbiomeScience2009324119011922009Sci...324.1190G1:CAS:528:DC%2BD1MXmsVGis7c%3D10.1126/science.1171700 – reference: GillespieJJPATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic speciesInfect. Immun.201179428642981:CAS:528:DC%2BC3MXhtl2nsb3I10.1128/IAI.00207-11 – reference: TurnbaughPJA core gut microbiome in obese and lean twinsNature20094574804842009Natur.457..480T1:CAS:528:DC%2BD1MXotlOlsw%3D%3D10.1038/nature07540 – reference: FredricksDNFiedlerTLMarrazzoJMMolecular identification of bacteria associated with bacterial vaginosisN. Engl. J. Med.2005353189919111:CAS:528:DC%2BD2MXhtF2rsL%2FL10.1056/NEJMoa043802 – reference: MazmanianSKRoundJLKasperDLA microbial symbiosis factor prevents intestinal inflammatory diseaseNature20084536206252008Natur.453..620M1:CAS:528:DC%2BD1cXmsVKqurw%3D10.1038/nature07008 – reference: SharptonTJPhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic dataPLoS Comput. Biol.20117e10010611:CAS:528:DC%2BC3MXhtlyjs7g%3D10.1371/journal.pcbi.1001061 – reference: SokolHFaecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patientsProc. Natl Acad. Sci. USA200810516731167362008PNAS..10516731S1:CAS:528:DC%2BD1cXhtleks7%2FI10.1073/pnas.0804812105 – reference: MediniDMicrobiology in the post-genomic eraNature Rev. Microbiol.200864194301:CAS:528:DC%2BD1cXlvFSisbo%3D10.1038/nrmicro1901 – reference: RavelJVaginal microbiome of reproductive-age womenProc. Natl Acad. Sci. USA2011108468046872011PNAS..108.4680R1:CAS:528:DC%2BC3MXjvVCrs7g%3D10.1073/pnas.1002611107 – reference: Segata, N. et al. Efficient metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methodshttp://dx.doi.org/10.1038/nmeth.2066 (2012) – reference: GoodmanALIdentifying genetic determinants needed to establish a human gut symbiont in its habitatCell Host Microbe200962792891:CAS:528:DC%2BD1MXhsVChs7fL10.1016/j.chom.2009.08.003 – reference: QinJA human gut microbial gene catalogue established by metagenomic sequencingNature201046459651:CAS:528:DC%2BC3cXislahsLc%3D10.1038/nature08821 – reference: LiHDurbinRFast and accurate long-read alignment with Burrows–Wheeler transformBioinformatics20102658959510.1093/bioinformatics/btp698 – reference: Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. 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| Snippet | Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and... Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin, and... |
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| SubjectTerms | 631/158/670 631/208/212/2142 631/326/2565/2134 Adolescent Adult Bacteria - classification Bacteria - genetics Bacteriology Biodiversity Biological and medical sciences Biological diversity Community structure Data processing Disease Ecosystem Epidemiology Female Fundamental and applied biological sciences. Psychology Genetics Genomes Habitats Health Humanities and Social Sciences Humans Life sciences Male Metabolic Networks and Pathways - physiology Metagenome Metagenomics Microbial activity Microbiology Microbiota (Symbiotic organisms) Morphology, structure, chemical composition multidisciplinary Phenotype RNA, Ribosomal, 16S - genetics Science Science (multidisciplinary) Skin Taxonomy Young Adult |
| Title | Structure, function and diversity of the healthy human microbiome |
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