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Databases/Libraries

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:
http://www.ncbi.nlm.nih.gov/bioproject/43021
This website is the major NIH portal for accessing HMP data

http://www.ncbi.nlm.nih.gov/bioproject/28331
This site gives access to the genomes of HMP reference strains in GenBank

iHMP Data Coordinating Center:
http://ihmpdcc.org/

 

 

Examples of Studies That Have Used the HMP Data

Study Title Authors Journal Publication Date Brief 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 Genomics 2016 Mar 1 Used 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 Med 2016 Apr 21 HMP 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 Microbiol 2016 Nov 15 Searched 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 Epidemiol 2016 May 26 HMP data used as a control for this study.
Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets. Li L, Ma ZS. Sci Rep 2016 Aug 16 Used 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 Rep 2016 Sep 29 An 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. Science 2016 Apr 29 An 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. Bioinformatics 2016 Jun 15 HMP mock community dataset used to test a new tool.
Metabolic network-guided binning of metagenomic sequence fragments. Biggs MB, Papin JA. Bioinformatics 2016 Mar 15 Used 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 One 2016 Apr 26 Used the HMP data to test a new tool.
Individuality, Stability, and Variability of the Plaque Microbiome. Utter DR, Mark Welch JL, Borisy GG. Front Microbiol 2016 Apr 22 Used 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 Biotechnol 2016 Oct 12 Developed 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. Methods 2016 Jun 20 Used 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 Microbes 2016 May 3 Explored 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 Dis 2016 Jun 15 HMP 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 Microbiol 2016 May 26 Assembled 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. Microbiome 2015 Aug 5 Used the HMP data to test a new metagenome assembly tool.
Phylogenetic approaches to microbial community classification. Ning J, Beiko RG. Microbiome 2015 Oct 5 HMP 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 Genomics 2015 Nov 10 Used 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 Sci 2015 Mar 30 Screened 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 Biol 2015 Nov 27 Used 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 Sci 2015 Oct 29 Isolated 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 Biol 2014 Dec 18 Used 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 Dis 2015 Oct 15 Incorporated 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. Bioinformatics 2015 Oct. 1 Used 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. 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.
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.
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.

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.

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.

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.

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.

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.

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

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

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.

Biotechniques

 2014 Feb 1

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

 

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