Table of Contents: The Human Microbiome Project Collection


Image Credit: National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH)
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The healthy adult body hosts ten times as many microbial cells as human cells, including bacteria, archaea, viruses, and eukaryotic microbes resident on nearly every body surface. 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. This includes reference genomes of host-associated microbial isolates, 16S rRNA marker gene sequencing for thousands of healthy microbiomes, 3.5Tb of metagenomic sequences, assemblies, and metabolic reconstructions, and a catalogue of over 5M microbial genes. 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. All resources generated by the Human Microbiome Project are publicly available at:

The Human Microbiome Project Collection encompasses publications from consortium members generating, leveraging, and exploring these resources. Articles are presented in order of publication date and new articles will be added to the Collection as they are published. For more information on the Human Microbiome Project, please contact

Accompanying the Collection are the following freely accessible consortium articles published outside of the PLoS family of journals:

'Structure, function and diversity of the healthy human microbiome' (The Human Microbiome Project Consortium):

'A framework for human microbiome research' (The Human Microbiome Project Consortium):

'Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples' (Segata et al.):

PLoS Collections: The Human Microbiome Project Collection (2012)

NIH generated images are in the public domain. This image cannot be used to misrepresent the NIH or imply that the NIH endorses any commercial or private product, service, or activity.


Bioinformatics for the Human Microbiome Project

Dirk Gevers, Mihai Pop, Patrick D. Schloss, Curtis Huttenhower

Community Page

The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome

Dirk Gevers, Rob Knight, Joseph F. Petrosino, Katherine Huang, Amy L. McGuire, Bruce W. Birren, Karen E. Nelson, Owen White, Barbara A. Methé, Curtis Huttenhower

Research Articles

Deep Sequencing Identifies Ethnicity-Specific Bacterial Signatures in the Oral Microbiome

Matthew R. Mason, Haikady N. Nagaraja, Terry Camerlengo, Vinayak Joshi, Purnima S. Kumar

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

Omry Koren, Dan Knights, Antonio Gonzalez, Levi Waldron, Nicola Segata, Rob Knight, Curtis Huttenhower, Ruth E. Ley

Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

Patricio S. La Rosa, J. Paul Brooks, Elena Deych, Edward L. Boone, David J. Edwards, Qin Wang, Erica Sodergren, George Weinstock, William D. Shannon

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

Alison R. Erickson, Brandi L. Cantarel, Regina Lamendella, Youssef Darzi, Emmanuel F. Mongodin, Chongle Pan, Manesh Shah, Jonas Halfvarson, Curt Tysk, Bernard Henrissat, Jeroen Raes, Nathan C. Verberkmoes, Claire M. Fraser, Robert L. Hettich, Janet K. Jansson

Statistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data

Patricio S. La Rosa, Berkley Shands, Elena Deych, Yanjiao Zhou, Erica Sodergren, George Weinstock, William D. Shannon

Estimation of Distribution Overlap of Urn Models

Jerrad Hampton, Manuel E. Lladser

Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome

Margaret L. Zupancic, Brandi L. Cantarel, Zhenqiu Liu, Elliott F. Drabek, Kathleen A. Ryan, Shana Cirimotich, Cheron Jones, Rob Knight, William A. Walters, Daniel Knights, Emmanuel F. Mongodin, Richard B. Horenstein, Braxton D. Mitchell, Nanette Steinle, Soren Snitker, Alan R. Shuldiner, Claire M. Fraser

The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing

Anthony A. Fodor, Todd Z. DeSantis, Kristine M. Wylie, Jonathan H. Badger, Yuzhen Ye, Theresa Hepburn, Ping Hu, Erica Sodergren, Konstantinos Liolios, Heather Huot-Creasy, Bruce W. Birren, Ashlee M. Earl

Microbial Co-occurrence Relationships in the Human Microbiome

Karoline Faust, J. Fah Sathirapongsasuti, Jacques Izard, Nicola Segata, Dirk Gevers, Jeroen Raes, Curtis Huttenhower

IMG/M-HMP: A Metagenome Comparative Analysis System for the Human Microbiome Project

Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Biju Jacob, Anna Ratner, Konstantinos Liolios, Ioanna Pagani, Marcel Huntemann, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides

Non-Invasive Mapping of the Gastrointestinal Microbiota Identifies Children with Inflammatory Bowel Disease

Eliseo Papa, Michael Docktor, Christopher Smillie, Sarah Weber, Sarah P. Preheim, Dirk Gevers, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Jay Ingram, David B. Schauer, Doyle V. Ward, Joshua R. Korzenik, Ramnik J. Xavier, Athos Bousvaros, Eric J. Alm

Association of Fecal Microbial Diversity and Taxonomy with Selected Enzymatic Functions

Roberto Flores, Jianxin Shi, Mitchell H. Gail, Pawel Gajer, Jacques Ravel, James J. Goedert

Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria

Sujatha Srinivasan, Noah G. Hoffman, Martin T. Morgan, Frederick A. Matsen, Tina L. Fiedler, Robert W. Hall, Frederick J. Ross, Connor O. McCoy, Roger Bumgarner, Jeanne M. Marrazzo, David N. Fredricks

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Sahar Abubucker, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Mitreva, Curtis Huttenhower

Diverse CRISPRs Evolving in Human Microbiomes

Mina Rho, Yu-Wei Wu, Haixu Tang, Thomas G. Doak, Yuzhen Ye

Inflammatory Bowel Diseases Phenotype, C. difficile and NOD2 Genotype Are Associated with Shifts in Human Ileum Associated Microbial Composition

Ellen Li, Christina M. Hamm, Ajay S. Gulati, R. Balfour Sartor, Hongyan Chen, Xiao Wu, Tianyi Zhang, F. James Rohlf, Wei Zhu, Chi Gu, Charles E. Robertson, Norman R. Pace, Edgar C. Boedeker, Noam Harpaz, Jeffrey Yuan, George M. Weinstock, Erica Sodergren, Daniel N. Frank

Sequence Analysis of the Human Virome in Febrile and Afebrile Children

Kristine M. Wylie, Kathie A. Mihindukulasuriya, Erica Sodergren, George M. Weinstock, Gregory A. Storch

Complex Carbohydrate Utilization by the Healthy Human Microbiome

Brandi L. Cantarel, Vincent Lombard, Bernard Henrissat

A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP)

Johannes Goll, Mathangi Thiagarajan, Sahar Abubucker, Curtis Huttenhower, Shibu Yooseph, Barbara A. Methé

Host Genes Related to Paneth Cells and Xenobiotic Metabolism Are Associated with Shifts in Human Ileum-Associated Microbial Composition

Tianyi Zhang, Robert A. DeSimone, Xiangmin Jiao, F. James Rohlf, Wei Zhu, Qing Qing Gong, Steven R. Hunt, Themistocles Dassopoulos, Rodney D. Newberry, Erica Sodergren, George Weinstock, Charles E. Robertson, Daniel N. Frank, Ellen Li

Analyses of the Microbial Diversity across the Human Microbiome

Kelvin Li, Monika Bihan, Shibu Yooseph, Barbara A. Methé

A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters

Susan M. Huse, Yuzhen Ye, Yanjiao Zhou, Anthony A. Fodor

Novel Bacterial Taxa in the Human Microbiome

Kristine M. Wylie, Rebecca M. Truty, Thomas J. Sharpton, Kathie A. Mihindukulasuriya, Yanjiao Zhou, Hongyu Gao, Erica Sodergren, George M. Weinstock, Katherine S. Pollard

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

John Martin, Sean Sykes, Sarah Young, Karthik Kota, Ravi Sanka, Nihar Sheth, Joshua Orvis, Erica Sodergren, Zhengyuan Wang, George M. Weinstock, Makedonka Mitreva

A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy

Kjersti Aagaard, 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

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

Jumpstart Consortium Human Microbiome Project Data Generation Working Group