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Databases/LibrariesThe Human Microbiome Project Data Analysis and Coordinating Center (DACC) Data Portal provides access to all publicly available HMP data sets. This curated portal is a comprehensive collection of databases and libraries, serving as a useful gateway for access to microbiome data.

URL: http://www.hmpdacc.org/resources/data_browser.php

The NIH also houses HMP databases through NCBI including:
This website is the major NIH portal for accessing HMP data

This site gives access to the genomes of HMP reference strains in GenBank



Examples of Studies That Have Used the HMP Data

Study Title Authors Journal Publication Date Brief Summary

Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine.

Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MA. Cell Host Microbe 2014 Oct 8 Showed that some bacteria can actually synthesize a certain neurotransmitter. Though uncommon in many other environments, using HMP data this study estimated that about 10% of humans appear to have at least one bacterium in their gut which can produce this neurotransmitter.

Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen.

Pham TA, Clare S, Goulding D, Arasteh JM, Stares MD, Browne HP, Keane JA, Page AJ, Kumasaka N, Kane L, Mottram L, Harcourt K, Hale C, Arends MJ, Gaffney DJ; Sanger Mouse Genetics Project, Dougan G, Lawley TD.

Cell Host Microbe

2014 Oct 8

Used HMP microbial genome and metagenome sequence data as reference

Veillonella seminalis sp. nov., a novel anaerobic Gram-stain-negative coccus from human clinical samples, and emended description of the genus Veillonella. Aujoulat F, Bouvet P, Jumas-Bilak E, Jean-Pierre H, Marchandin H. Int J Syst Evol Microbiol 2014 Oct Used HMP microbial genome sequence data as reference

Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans.

Can I, Javan GT, Pozhitkov AE, Noble PA.

J Microbiol Methods

2014 Nov

Used HMP microbial genome sequence data as reference

Molecular and evolutionary analysis of NEAr-iron Transporter (NEAT) domains.

Honsa ES, Maresso AW, Highlander SK.

PLoS One

2014 Aug 25

Iron scavenging from blood has been shown to be an adaptive strategy for pathogenic bacteria but little is known about the iron acquisition mechanisms of other members of the microbiome. Used the HMP datasets to demonstrate that iron acquisition strategies are common across all bacterial types and not limited to pathogenic bacteria.

TUIT, a BLAST-based tool for taxonomic classification of nucleotide sequences.

Tuzhikov A, Panchin A, Shestopalov VI.


 2014 Feb 1

Used HMP data for reference in development of computational tool for 16S classification.

DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.

Wang T, Mori H, Zhang C, Kurokawa K, Xing XH, Yamada T.

BMC Bioinformatics

2015 Mar 21

Used HMP data to test tool for computational predictions of catalytic function.

In vitro fermentation of fructooligosaccharides with human gut bacteria.

Mao B, Li D, Zhao J, Liu X, Gu Z, Chen YQ, Zhang H, Chen W.

Food Funct

2015 Mar

Prebiotics are dietary compounds which promote growth of beneficial microbes. Used the HMP data to help show that one such prebiotic (found in foods such as bananas, onions, garlic and asparagus) promotes the growth of about half of the bacteria in the gut microbiome including some pathogenic bacteria, thereby suggesting that not all prebiotics support only beneficial microbes.

Determinants of intestinal permeability in healthy first-degree relatives of individuals with Crohn's disease.

Kevans D, Turpin W, Madsen K, Meddings J, Shestopaloff K, Xu W, Moreno-Hagelsieb G, Griffiths A, Silverberg MS, Paterson A, Croitoru K; GEM Project. Inflamm Bowel Dis 2015 Apr

Used HMP data as reference data to evaulate microbial composition in Crohn's disease patients.

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

Albanese D, Fontana P, De Filippo C, Cavalieri D, Donati C.

Sci Rep

2015 May 19

Pipeline for processing targeted metagenomic datasets that efficiently combines filtering process, OTU clustering and taxonomic assignment. Used HMP data to test tool.

Qualitative analysis of the vaginal microbiota of healthy cattle and cattle with genital-tract disease.

Rodrigues NF, Kästle J, Coutinho TJ, Amorim AT, Campos GB, Santos VM, Marques LM, Timenetsky J, de Farias ST.

Genet Mol Res

2015 Jun 12

Used HMP reference data in analysing bovine microbiome.

Allometry of animal-microbe interactions and global census of animal-associated microbes.

Kieft TL, Simmons KA.

Proc Biol Sci

2015 Jul 7

The HMP datasets were used to estimate the contribution of the human microbiome to the diversity of bacterial species that exist on our planet.  It was found that humans support a surprisingly high diversity (approx. 3%) of all animal-associated microbes and livestock support 14-20% of all animal-associated microbes despite the lower abundance of these large animals compared to smaller animals such as insects.

Personalized microbial network inference via co-regularized spectral clustering. Imangaliyev S, Keijser B, Crielaard W, Tsivtsivadze E. Methods 2015 Jul 15 Developed tool for network analysis of microbial communities. Used HMP data to test tool.
Using populations of human and microbial genomes for organism detection in metagenomes. Ames SK, Gardner SN, Marti JM, Slezak TR, Gokhale MB, Allen JE. Genome Res 2015 Jul Used publically available human sequence to improve computational filter and used HMP metagenome sequence to test tool.
The presence of Oxalobacter formigenes in the microbiome of healthy young adults. Barnett C, Nazzal L, Goldfarb DS, Blaser MJ. J Urol 2015 Aug 17 The gut microbiome provides many protective functions including a particular bacterium protecting against kidney stone formation. This study used the HMP data to show that about 31% of the healthy adults carried this bacterium at relatively high levels and that this carriage was stable over time.
PanFP: pangenome-based functional profiles for microbial communities. Jun SR, Robeson MS, Hauser LJ, Schadt CW, Gorin AA. BMC Res Notes  2015 Sep 26 Used both HMP 16s and metagenomic data to test tool for inferring functional profiles from 16S rRNA data.
Power Law Analysis of the Human Microbiome. Ma ZS. Mol Ecol 2015 Sep 25 Used HMP data to test a mathematical law's ability to describe microbial population abundances.
Universality of human microbial dynamics. Bashan A, Gibson TE, Friedman J, Carey VJ, Weiss ST, Hohmann EL, Liu YY. Nature 2016 Jun 8 Used the HMP data to show that although each individuals' microbiome may have a unique composition, the underlying ecological dynamics are largely universal.

Mobile genes in the human microbiome are structured from global to individual scales.

Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, Naisilisili W, Tamminen M, Smillie CS, Wortman JR, Birren BW, Xavier RJ, Blainey PC, Singh AK,Gevers D, Alm EJ. Nature 2016 Jul 21

Bacteria often contain a small subset of mobile genes that can be transferred from one bacteria to another. This study compared the HMP datasets to the Fiji Community Microbiome Project to support the idea that this mobile gene pool within the human microbiome is shaped by human activities and behaviors.


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