Biology & Life Sciences

The Human Microbiome Project

Published May 24, 2018 Partnered Collections, Special Issues

The healthy adult body hosts ten times as many microbial cells as human cells.The metagenome carried collectively by these microbial communities dwarfs the human genome in size, and their influences on normal development, diet and obesity, immunity, and disease are under active research. Funded by the National Institutes of Health Common Fund, the Human Microbiome Project (HMP) was established to provide a comprehensive baseline of the microbial diversity at 18 different human body sites.These data join resources generated by computational tool development for analysis of the microbiome, research on the ethical, legal, and social implications of the microbiota, technology development for investigating these microbial communities, and a range of disease-focused microbiome demonstration projects.

Image Credit: National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH)

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From the Blogs

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National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH)

EveryONE Announcing the Human Microbiome Project Collection
June 13, 2012 Jen Laloup

Community Page

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10.1371/journal.pbio.1001377

PLOS Biology The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome
August 14, 2012 Dirk Gevers, Rob Knight, Joseph Petrosino, Katherine Huang, Amy McGuire, Bruce Birren, Karen Nelson, Owen White, Barbara Methé, Curtis Huttenhower

Perspective

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10.1371/journal.pcbi.1002779

PLOS Computational Biology Bioinformatics for the Human Microbiome Project
November 29, 2012 Dirk Gevers, Mihai Pop, Patrick Schloss, Curtis Huttenhower

Research Articles

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10.1371/journal.pone.0027310

PLOS ONE Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
December 14, 2011 Patrick Schloss, Dirk Gevers, Sarah Westcott
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10.1371/journal.pone.0029044

PLOS ONE A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP)
June 13, 2012 Johannes Goll, Mathangi Thiagarajan, Sahar Abubucker, Curtis Huttenhower, Shibu Yooseph, Barbara Methé
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10.1371/journal.pone.0027735

PLOS ONE Sequence Analysis of the Human Virome in Febrile and Afebrile Children
June 13, 2012 Kristine Wylie, Kathie Mihindukulasuriya, Erica Sodergren, George Weinstock, Gregory Storch
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10.1371/journal.pcbi.1002687

PLOS Computational Biology Inferring Correlation Networks from Genomic Survey Data
September 20, 2012 Jonathan Friedman, Eric Alm
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10.1371/journal.pone.0036466

PLOS ONE A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy
June 13, 2012 Kjersti Aagaard-Tillery, Kevin Riehle, Jun Ma, Nicola Segata, Toni-Ann Mistretta, Cristian Coarfa, Sabeen Raza, Sean Rosenbaum, Ignatia Van den Veyver, Aleksandar Milosavljevic, Dirk Gevers, Curtis Huttenhower, Joseph Petrosino, James Versalovic
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10.1371/journal.pone.0039315

PLOS ONE Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research
June 13, 2012 Doyle Ward
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10.1371/journal.pone.0034242

PLOS ONE A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters
June 13, 2012 Susan Huse, Yuzhen Ye, Yanjiao Zhou, Anthony Fodor
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10.1371/journal.pone.0036427

PLOS ONE Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities
June 13, 2012 John Martin, Sean Sykes, Sarah Young, Karthik Kota, Ravi Sanka, Nihar Sheth, Joshua Orvis, Erica Sodergren, Zhengyuan Wang, George Weinstock, Makedonka Mitreva
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10.1371/journal.pone.0035294

PLOS ONE Novel Bacterial Taxa in the Human Microbiome
June 13, 2012 Kristine Wylie, Rebecca Truty, Thomas Sharpton, Kathie Mihindukulasuriya, Yanjiao Zhou, Hongyu Gao, Erica Sodergren, George Weinstock, Katherine Pollard
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10.1371/journal.pone.0037818

PLOS ONE Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria
June 18, 2012 Sujatha Srinivasan, Noah Hoffman, Martin Morgan, Frederick Matsen, Tina Fiedler, Robert Hall, Frederick Ross, Connor McCoy, Roger Bumgarner, Jeanne Marrazzo, David Fredricks
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10.1371/journal.pone.0032118

PLOS ONE Analyses of the Microbial Diversity across the Human Microbiome
June 13, 2012 Kelvin Li, Monika Bihan, Shibu Yooseph, Barbara Methé
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10.1371/journal.pone.0042368

PLOS ONE Estimation of Distribution Overlap of Urn Models
November 6, 2012 Jerrad Hampton, Manuel Lladser
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10.1371/journal.pone.0049138

PLOS ONE Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn’s Disease
November 28, 2012 Alison Erickson, Brandi Cantarel, Regina Lamendella, Youssef Darzi, Emmanuel Mongodin, Chongle Pan, Manesh Shah, Jonas Halfvarson, Curt Tysk, Bernard Henrissat, Jeroen Raes, Nathan Verberkmoes, Claire Fraser, Robert Hettich, Janet Jansson
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10.1371/journal.pone.0030044

PLOS ONE Host Genes Related to Paneth Cells and Xenobiotic Metabolism Are Associated with Shifts in Human Ileum-Associated Microbial Composition
June 13, 2012 Tianyi Zhang, Robert DeSimone, Xiangmin Jiao, F. Rohlf, Wei Zhu, Qing Qing Gong, Steven Hunt, Themistocles Dassopoulos, Rodney Newberry, Erica Sodergren, George Weinstock, Charles Robertson, Daniel Frank, Ellen Li
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10.1371/journal.pone.0039242

PLOS ONE Non-Invasive Mapping of the Gastrointestinal Microbiota Identifies Children with Inflammatory Bowel Disease
June 29, 2012 Eliseo Papa, Michael Docktor, Christopher Smillie, Sarah Weber, Sarah Preheim, Dirk Gevers, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Jay Ingram, David Schauer, Doyle Ward, Joshua Korzenik, Ramnik Xavier, Athos Bousvaros, Eric Alm
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10.1371/journal.pone.0040151

PLOS ONE IMG/M-HMP: A Metagenome Comparative Analysis System for the Human Microbiome Project
July 5, 2012 Victor Markowitz, I-Min Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Biju Jacob, Anna Ratner, Konstantinos Liolios, Ioanna Pagani, Marcel Huntemann, Konstantinos Mavromatis, Natalia Ivanova, Nikos Kyrpides
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10.1371/journal.pone.0028742

PLOS ONE Complex Carbohydrate Utilization by the Healthy Human Microbiome
June 13, 2012 Brandi Cantarel, Vincent Lombard, Bernard Henrissat
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10.1371/journal.pone.0026284

PLOS ONE Inflammatory Bowel Diseases Phenotype, C. difficile and NOD2 Genotype Are Associated with Shifts in Human Ileum Associated Microbial Composition
June 13, 2012 Ellen Li, Christina Hamm, Ajay Gulati, R. Sartor, Hongyan Chen, Xiao Wu, Tianyi Zhang, F. Rohlf, Wei Zhu, Chi Gu, Charles Robertson, Norman Pace, Edgar Boedeker, Noam Harpaz, Jeffrey Yuan, George Weinstock, Erica Sodergren, Daniel Frank
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10.1371/journal.pgen.1002441

PLOS Genetics Diverse CRISPRs Evolving in Human Microbiomes
June 13, 2012 Mina Rho, Yu-Wei Wu, Haixu Tang, Thomas Doak, Yuzhen Ye
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10.1371/journal.pcbi.1002606

PLOS Computational Biology Microbial Co-occurrence Relationships in the Human Microbiome
July 12, 2012 Karoline Faust, J. Sathirapongsasuti, Jacques Izard, Nicola Segata, Dirk Gevers, Jeroen Raes, Curtis Huttenhower
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10.1371/journal.pone.0041294

PLOS ONE The "Most Wanted" Taxa from the Human Microbiome for Whole Genome Sequencing
July 26, 2012 Anthony Fodor, Todd DeSantis, Kristine Wylie, Jonathan Badger, Yuzhen Ye, Theresa Hepburn, Ping Hu, Erica Sodergren, Konstantinos Liolios, Heather Huot-Creasy, Bruce Birren, Ashlee Earl
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10.1371/journal.pone.0043052

PLOS ONE Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome
August 15, 2012 Margaret Zupancic, Brandi Cantarel, Zhenqiu Liu, Elliott Drabek, Shana Cirimotich, Cheron Jones, Rob Knight, Emmanuel Mongodin, William Walters, Daniel Knights, Kathleen Ryan, Richard Horenstein, Braxton Mitchell, Nanette Steinle, Soren Snitker, Alan Shuldiner, Claire Fraser-Liggett
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10.1371/journal.pone.0047075

PLOS ONE Species-Level Analysis of DNA Sequence Data from the NIH Human Microbiome Project
October 10, 2012 Sean Conlan, Heidi Kong, Julia Segre
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10.1371/journal.pone.0048996

PLOS ONE Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data
November 9, 2012 Patricio La Rosa, Berkley Shands, Elena Deych, Yanjiao Zhou, Erica Sodergren, George Weinstock, William Shannon
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10.1371/journal.pcbi.1002358

PLOS Computational Biology Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
June 13, 2012 Sahar Abubucker, Nicola Segata, Johannes Goll, Alyxandria Schubert, Jacques Izard, Brandi Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott Kelley, Barbara Methé, Patrick Schloss, Dirk Gevers, Makedonka Mitreva, Curtis Huttenhower
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10.1371/journal.pone.0052078

PLOS ONE Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data
December 20, 2012 Patricio La Rosa, J. Brooks, Elena Deych, Edward Boone, David Edwards, Qin Wang, Erica Sodergren, George Weinstock, William Shannon
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10.1371/journal.pcbi.1002863

PLOS Computational Biology A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets
January 10, 2013 Omry Koren, Dan Knights, Antonio Gonzalez, Levi Waldron, Nicola Segata, Rob Knight, Curtis Huttenhower, Ruth Ley
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10.1371/journal.pone.0077287

PLOS ONE Deep Sequencing Identifies Ethnicity-Specific Bacterial Signatures in the Oral Microbiome
October 23, 2013 Matthew Mason, Haikady Nagaraja, Vinayak Joshi, Terry Camerlengo, Purnima Kumar
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10.1371/journal.pone.0039745

PLOS ONE Association of Fecal Microbial Diversity and Taxonomy with Selected Enzymatic Functions
June 28, 2012 Roberto Flores, Jianxin Shi, Mitchell Gail, Pawel Gajer, Jacques Ravel, James Goedert

Articles published outside of PLOS as part of this collection

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The Human Microbiome Project Consortium

Nature Structure, function and diversity of the healthy human microbiome
June 13, 2012 The Human Microbiome Project Consortium
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National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH)

Nature Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples
June 13, 2012 The Human Microbiome Project Consortium
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National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH)

Nature A framework for human microbiome research
June 13, 2012 The Human Microbiome Project Consortium

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Further Information on HMP

For more information, please contact: HMPinformation@mail.nih.gov.

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