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Program Resources: Databases/Libraries

Databases/LibrariesThe Human Microbiome Project has transitioned from Common Fund support. For more information please visit

Please note that since the Human Microbiome Project is no longer being supported by the Common Fund, the program website is being maintained as an archive and will not be updated on a regular basis.

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


Examples of Studies That Have Used the HMP Data

Study TitleAuthorsJournalPublication DateBrief Summary
ViromeScan: a new tool for metagenomic viral community profiling.Rampelli S, Soverini M, Turroni S, Quercia S, Biagi E, Brigidi P, Candela M.BMC Genomics2016 Mar 1Used a new tool to profile viruses in the HMP data.
Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome.Grassl N, Kulak NA, Pichler G, Geyer PE, Jung J, Schubert S, Sinitcyn P, Cox J, Mann M.Genome Med2016 Apr 21HMP data was compared to the proteomics data generated in this study.
The transfer network of bacterial mobile resistome connecting animal and human microbiome.Hu Y, Yang X, Li J, Lv N, Liu F, Wu J, Lin IY, Wu N, Weimer BC, Gao GF, Liu Y, Zhu B.Appl Environ Microbiol2016 Nov 15Searched the HMP reference genomes for mobile genes.
The effects of family, dentition, and dental caries on the salivary microbiome.Foxman B, Luo T, Srinivasan U, Ramadugu K, Wen A, Goldberg D, Shedden K, Crout R, McNeil DW, Weyant R, Marazita ML.Ann Epidemiol2016 May 26HMP data used as a control for this study.
Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets.Li L, Ma ZS.Sci Rep2016 Aug 16Used the HMP data to test the theory that biological diversity arises through a random mechanism.
Probing the diversity of healthy oral microbiome with bioinformatics approaches.Moon JH, Lee JH.BMB Rep2016 Sep 29An analysis of several oral microbiome data sets including data from HMP.
Population-level analysis of gut microbiome variation.Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, et al.Science2016 Apr 29An integrated analysis of several large gut microbiome studies including HMP data.
Optimization of alignment-based methods for taxonomic binning of metagenomics reads.Jaillard M, Tournoud M, Meynier F, Veyrieras JB.Bioinformatics2016 Jun 15HMP mock community dataset used to test a new tool.
Metabolic network-guided binning of metagenomic sequence fragments.Biggs MB, Papin JA.Bioinformatics2016 Mar 15Used the HMP data to test a new tool.
Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques.Tandon D, Haque MM, Mande SS.PLoS One2016 Apr 26Used the HMP data to test a new tool.
Individuality, Stability, and Variability of the Plaque Microbiome.Utter DR, Mark Welch JL, Borisy GG.Front Microbiol2016 Apr 22Used the HMP data to test a theory on the dynamics of microbial populations.
HuMiChip2 for strain level identification and functional profiling of human microbiomes.Tu Q, Li J, Shi Z, Chen Y, Lin L, Li J, Wang H, Yan J, Zhou Q, Li X, Li L, Zhou J, He Z.Appl Microbiol Biotechnol2016 Oct 12Developed a human microbiome microarray to be used to characterize the microbiome based on HMP data.
Hessian regularization based symmetric nonnegative matrix factorization for clustering gene expression and microbiome data.Ma Y, Hu X, He T, Jiang X.Methods2016 Jun 20Used the HMP data to test a new tool.
H2 metabolism is widespread and diverse among human colonic microbes.Wolf PG, Biswas A, Morales SE, Greening C, Gaskins HR.Gut Microbes2016 May 3Explored the distribution of molecular hydrogen consuming bacteria by evaluating the HMP reference genomes.
Fecal Microbial Transplants Reduce Antibiotic-resistant Genes in Patients With Recurrent Clostridium difficile Infection.Millan B, Park H, Hotte N, Mathieu O, Burguiere P, Tompkins TA, Kao D, Madsen KL.Clin Infect Dis2016 Jun 15HMP data was used as healthy controls to compare to those with C. difficile infection.
Capturing One of the Human Gut Microbiome's Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data.Jeraldo P, Hernandez A, Nielsen HB, Chen X, White BA, Goldenfeld N, Nelson H, Alhquist D, Boardman L, Chia N.Front Microbiol2016 May 26Assembled the genome of a new bacterium from the HMP data.
Xander: employing a novel method for efficient gene-targeted metagenomic assembly.Wang Q, Fish JA, Gilman M, Sun Y, Brown CT, Tiedje JM, Cole JR.Microbiome2015 Aug 5Used the HMP data to test a new metagenome assembly tool.
Phylogenetic approaches to microbial community classification.Ning J, Beiko RG.Microbiome2015 Oct 5HMP data was used to evaluate how bacteria are classified into groups.
Microbial "social networks".Fernandez M, Riveros JD, Campos M, Mathee K, Narasimhan G.BMC Genomics2015 Nov 10Used the HMP data to evaluate microbial networks.
Large-scale contamination of microbial isolate genomes by Illumina PhiX control.Mukherjee S, Huntemann M, Ivanova N, Kyrpides NC, Pati A.Stand Genomic Sci2015 Mar 30Screened HMP reference genomes for a common sequencing contamination.
Identification of low abundance microbiome in clinical samples using whole genome sequencing.Zhang C, Cleveland K, Schnoll-Sussman F, McClure B, Bigg M, Thakkar P, Schultz N, Shah MA, Betel D.Genome Biol2015 Nov 27Used the HMP WGS data as a positive control for the method of low abundance amplification of microbiome DNA.
Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut.Lagier JC, Khelaifia S, Azhar EI, Croce O, Bibi F, Jiman-Fatani AA, Yasir M, Helaby HB, Robert C, Fournier PE, Raoult D.Stand Genomic Sci2015 Oct 29Isolated a bacteria usually found in extreme high salt environments from a human gut and added its genome to the HMP collection.
e-DNA meta-barcoding: from NGS raw data to taxonomic profiling.Bruno F, Marinella M, Santamaria M.Methods Mol Biol2014 Dec 18Used the HMP 16S data to test a new tool.
A comprehensive repertoire of prokaryotic species identified in human beings.Hugon P, Dufour JC, Colson P, Fournier PE, Sallah K, Raoult D.Lancet Infect Dis2015 Oct 15Incorporated HMP microbial reference collection into a description of all human associated prokaryotes.
CCLasso: correlation inference for compositional data through Lasso.Fang H, Huang C, Zhao H, Deng M.Bioinformatics2015 Oct. 1Used the HMP 16S data to validate a new tool.
Universality of human microbial dynamics.Bashan A, Gibson TE, Friedman J, Carey VJ, Weiss ST, Hohmann EL, Liu YY.Nature2016 Jun 8Used the HMP data to show that although each individuals' microbiome may have a unique composition, the underlying ecological dynamics are largely universal.
PanFP: pangenome-based functional profiles for microbial communities.Jun SR, Robeson MS, Hauser LJ, Schadt CW, Gorin AA.BMC Res Notes 2015 Sep 26Used 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 Ecol2015 Sep 25Used HMP data to test a mathematical law's ability to describe microbial population abundances.
The presence of Oxalobacter formigenes in the microbiome of healthy young adults.Barnett C, Nazzal L, Goldfarb DS, Blaser MJ.J Urol2015 Aug 17The 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.
Allometry of animal-microbe interactions and global census of animal-associated microbes.Kieft TL, Simmons KA.Proc Biol Sci2015 Jul 7The 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.Methods2015 Jul 15Developed 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 Res2015 JulUsed publically available human sequence to improve computational filter and used HMP metagenome sequence 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 Res2015 Jun 12Used HMP reference data in analysing bovine microbiome.
MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.Albanese D, Fontana P, De Filippo C, Cavalieri D, Donati C.Sci Rep2015 May 19Pipeline for processing targeted metagenomic datasets that efficiently combines filtering process, OTU clustering and taxonomic assignment. Used HMP data to test tool.
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 Dis2015 AprUsed HMP data as reference data to evaulate microbial composition in Crohn's disease patients.
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 Bioinformatics2015 Mar 21Used 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 Funct2015 MarPrebiotics 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.
Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans.Can I, Javan GT, Pozhitkov AE, Noble PA.J Microbiol Methods2014 NovUsed HMP microbial genome sequence data as reference
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 Microbe2014 Oct 8Showed 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 Microbe2014 Oct 8Used 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 Microbiol2014 OctUsed HMP microbial genome sequence data as reference
Molecular and evolutionary analysis of NEAr-iron Transporter (NEAT) domains.Honsa ES, Maresso AW, Highlander SK.PLoS One2014 Aug 25Iron 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.Biotechniques 2014 Feb 1Used HMP data for reference in development of computational tool for 16S classification.

This page last reviewed on April 12, 2024