Skip to Content

Human Microbiome Project (HMP)

Image of gut microbe
Scanning electron microscope images of B. thetaiotaomicron, a prominent human gut bacterium, and the intestine.

Photo from PLoS Biol. 2007 July; 5(7): e199. Published online 2007 June 19. doi: 10.1371/journal.pbio.0050199.

A human being can be viewed as a biological eco-system that includes distinctly human cells and tissues as well as thousands of microbial species that co-exist in various parts of the body. In fact, "within the body of a healthy adult, microbial cells are estimated to outnumber human cells by a factor of ten to one. These communities, however, remain largely unstudied, leaving almost entirely unknown their influence upon human development, physiology, immunity, and nutrition. To take advantage of recent technological advances and to develop new ones, the NIH Roadmap has initiated the Human Microbiome Project (HMP) with the mission of generating resources enabling comprehensive characterization of the human microbiota and analysis of its role in human health and disease." [http://nihroadmap.nih.gov/hmp/]

The Human Genome Sequencing Center at the Baylor College of Medicine has joined the Genome Sequencing Center at Washington University, the Broad Institute of MIT and Harvard as well as the J. Craig Venter Institute to address some early goals of this project. The HMP will rely on metagenomic sample sequencing as a key method for comparisons of microbial communities between individuals, sites, and states (e.g., disease, diet, age). Pilot projects will determine the appropriate sequencing platforms, quality controls, and annotation pipelines for (1) generating reference genomes and (2) sequencing metagenomic samples.

Reference genomes that are currently targeted for sequencing

HMP ID    GOLD IDOrganism name    Body SiteFinishing LevelGPID
0004Gi03555Achromobacter piechaudii ATCC 43553AirwaysStandard Draft46343
0015Gi02597Acinetobacter haemolyticus ATCC 19194AirwaysStandard Draft43187
0023Gi02599Acinetobacter sp. ATCC 27244SkinHigh Quality Draft30949
0027Gi03558Actinobacillus ureae ATCC 25976AirwaysHigh Quality Draft52977
9004Gi04427Actinomyces cardiffensis F0333OralStandard Draft53007
0044Gi02601Actinomyces coleocanis DSM 15436Urogenital tractHigh Quality Draft31427
9006Gi04429Actinomyces sp. F0310OralHigh Quality Draft53011
9005Gi04428Actinomyces sp. F0338OralHigh Quality Draft53009
9062Gi04929Actinomyces sp. F0400OralStandard Draft53017
0058Gi02602Actinomyces urogenitalis DSM 15434Urogenital tractHigh Quality Draft31429
0061Gi02603Aerococcus viridans ATCC 11563Urogenital tractHigh Quality Draft38729
0063Gi02604Aeromicrobium marinum DSM 15272OralNon-contiguous Finished34545
9064Gi04931Aggregatibacter segnis ATCC 33393OralHigh Quality Draft53019
0072Gi02610Anaerococcus lactolyticus ATCC 51172Urogenital tractHigh Quality Draft30951
0077Gi02612Anaerococcus tetradius ATCC 35098Urogenital tractHigh Quality Draft31433
0078Gi03600Anaerococcus vaginalis ATCC 51170SkinHigh Quality Draft38727
9401Gi05704Arcobacter butzleri JV22Gastrointestinal tractHigh Quality Draft53195
0091Gi02616Atopobium vaginae DSM 15829Urogenital tractHigh Quality Draft31435
0168Gi03612Bifidobacterium dentium ATCC 27679Urogenital tractHigh Quality Draft51373
0175Gi03513Bifidobacterium longum longum ATCC 55813Gastrointestinal tractHigh Quality Draft31437
0183Gi02663Brevibacterium mcbrellneri ATCC 49030Urogenital tractHigh Quality Draft34583
9399Gi05701Campylobacter coli JV20Gastrointestinal tractHigh Quality Draft50513
9400Gi05703Campylobacter upsaliensis JV21Gastrointestinal tractHigh Quality Draft53193
1977Gi03877Capnocytophaga ochracea F0287OralHigh Quality Draft51493
9071Gi04938Capnocytophaga sp. F0234OralHigh Quality Draft53023
0198Gi03628Cardiobacterium hominis ATCC 15826BloodHigh Quality Draft37269
9081Gi04948Centipeda periodontii DSM 2778Oral 53025
0204Gi02674Chryseobacterium gleum F93, ATCC 35910Urogenital tractFinished30953
0219Gi03537Clostridium difficile NAP07Gastrointestinal tractHigh Quality Draft31439
0220Gi03538Clostridium difficile NAP08Gastrointestinal tractHigh Quality Draft31441
0276Gi02699Corynebacterium accolens ATCC 49725AirwaysHigh Quality Draft31443
0277Gi03634Corynebacterium accolens ATCC 49726AirwaysHigh Quality Draft50523
0284Gi04425Corynebacterium aurimucosum ATCC 700975Urogenital tractHigh Quality Draft31451
0290Gi02701Corynebacterium efficiens YS-314, DSM 44549SkinHigh Quality Draft34585
0291Gi02702Corynebacterium genitalium ATCC 33030Urogenital tractNon-contiguous Finished34587
0294Gi03343Corynebacterium glucuronalyticum ATCC 51867Urogenital tractNon-contiguous Finished30957
0293Gi02708Corynebacterium glucuronolyticum ATCC 51866Urogenital tractHigh Quality Draft31549
0297Gi03721Corynebacterium jeikeium ATCC 43734Blood, Urogenital tractHigh Quality Draft31445
0298Gi02705Corynebacterium lipophiloflavum DSM 44291Urogenital tractHigh Quality Draft31447
0305Gi02707Corynebacterium pseudogenitalium ATCC 33035Urogenital tract 30955
0308Gi02710Corynebacterium striatum ATCC 6940Urogenital tract 31449
9374Gi05605Desmospora sp. 8437BloodHigh Quality Draft64725
9083Gi04950Dialister micraerophilus DSM 19965Oral, Urogenital tractHigh Quality Draft53029
9086Gi04953Enterobacter hormaechei ATCC 49162Oral 53031
9087Gi04954Enterococcus casseliflavus ATCC 12755OralHigh Quality Draft53041
0345Gi02727Enterococcus faecalis ATCC 29200Urogenital tractImproved High Quality Draft31459
0346Gi01841Enterococcus faecalis HH22Urogenital tractHigh Quality Draft31457
0348Gi01843Enterococcus faecalis TX0104Gastrointestinal tractHigh Quality Draft30623
0349Gi02728Enterococcus faecalis TX1322Gastrointestinal tractImproved High Quality Draft31461
0351Gi02729Enterococcus faecium DOBlood, Gastrointestinal tract 30627
0352Gi02730Enterococcus faecium TX1330Gastrointestinal tractFinished31463
9088Gi04955Enterococcus italicus DSM 15952OralHigh Quality Draft53039
0357Gi02731Erysipelothrix rhusiopathiae ATCC 19414SkinHigh Quality Draft31465
0358Gi03725Escherichia coli 83972Urogenital tractNon-contiguous Finished31467
0381Gi04123Eubacterium saburreum DSM 3986OralHigh Quality Draft52981
0379Gi04122Eubacterium yurii margaretiae ATCC 43715OralHigh Quality Draft50511
0391Gi02745Finegoldia magna ATCC 53516Urogenital tractNon-contiguous Finished31469
9094Gi04961Fusobacterium nucleatum animalis ATCC 51191Gastrointestinal tract 64727
0397Gi01861Fusobacterium nucleatum nucleatum ATCC 23726Urogenital tractHigh Quality Draft31471
0421Gc01640Gardnerella vaginalis 317, ATCC 14019Urogenital tractNon-contiguous Finished31473
0444Gi03858Granulicatella adiacens ATCC 49175OralHigh Quality Draft37271
9095Gi04962Haemophilus aegyptius ATCC 11116Oral, EyeHigh Quality Draft53049
9417Gi05721Haemophilus parainfluenzae ATCC 33392SkinHigh Quality Draft53197
4655Gc01648Helicobacter pylori 35AGastrointestinal tractFinished34603
0462Gc01758Helicobacter pylori 83Gastrointestinal tract 34609
9098Gi04965Kingella denitrificans ATCC 33394AirwaysHigh Quality Draft53051
0476Gi04136Kingella kingaeAirwaysHigh Quality Draft52985
0484Gi04135Klebsiella pneumoniae rhinoscleromatis ATCC 13884AirwaysHigh Quality Draft40083
0492Gi02787Lactobacillus acidophilus ATCC 4796Gastrointestinal tractHigh Quality Draft31477
0493Gi02788Lactobacillus amylolyticus DSM 11664Gastrointestinal tractHigh Quality Draft34615
0494Gi02789Lactobacillus antri DSM 16041Gastrointestinal tractHigh Quality Draft31479
0496Gi03750Lactobacillus brevis gravesensis ATCC 27305Gastrointestinal tractHigh Quality Draft31481
0497Gi03751Lactobacillus buchneri ATCC 11577Gastrointestinal tractHigh Quality Draft31483
0503Gi03827Lactobacillus coleohominis DSM 14060Urogenital tract 52987
0506Gi02792Lactobacillus crispatus JV-V01Urogenital tractHigh Quality Draft30641
5505Gi03866Lactobacillus delbrueckii lactis DSM 20072Gastrointestinal tractHigh Quality Draft53001
0511Gi03753Lactobacillus fermentum ATCC 14931Gastrointestinal tractImproved High Quality Draft31485
0514Gi02794Lactobacillus gasseri JV-V03Urogenital tractImproved High Quality Draft31487
0518Gi02795Lactobacillus helveticus DSM 20075Gastrointestinal tractHigh Quality Draf34619
0519Gi03754Lactobacillus hilgardii ATCC 8290Gastrointestinal tractImproved High Quality Draft31489
9223Gi05116Lactobacillus iners ATCC 55195Urogenital tractHigh Quality Draft53061
0520Gi02796Lactobacillus iners DSM 13335Urogenital tractHigh Quality Draft31491
0526Gi02797Lactobacillus jensenii JV-V16Urogenital tractFinished31493
0528Gi02798Lactobacillus johnsonii ATCC 33200Blood, Urogenital tractNon-contiguous Finished31495
0530Gi03755Lactobacillus paracasei ATCC 25302Gastrointestinal tractHigh Quality Draft31513
0531Gi03756Lactobacillus plantarum ATCC 14917Gastrointestinal tractImproved High Quality Draft31515
0534Gi02800Lactobacillus reuteri CF48-3AGastrointestinal tractHigh Quality Draft31553
0535Gi03770Lactobacillus reuteri MM2-3Gastrointestinal tractHigh Quality Draft34627
0536Gi01862Lactobacillus reuteri MM4-1AGastrointestinal tractNon-contiguous Finished31511
0538Gi01863Lactobacillus reuteri SD2112, ATCC 55730Gastrointestinal tractHigh Quality Draft30643
0539Gi02801Lactobacillus rhamnosus LMS2-1Gastrointestinal tractHigh Quality Draft31497
0542Gi03772Lactobacillus ruminis E 194e, ATCC 25644Gastrointestinal tractImproved High Quality Draft31499
0545Gi05082Lactobacillus salivarius HO66, ATCC 11741Gastrointestinal tract, OralHigh Quality Draft31503
0548Gi02804Lactobacillus ultunensis DSM 16047Gastrointestinal tractHigh Quality Draft31505
0549Gi03861Lactobacillus vaginalis ATCC 49540Urogenital tractHigh Quality Draft31507
0551Gi04134Lautropia mirabilis ATCC 51599OralHigh Quality Draft52989
0555Gi02808Leuconostoc mesenteroides cremoris ATCC 19254Gastrointestinal tractHigh Quality Draft34629
0556Gi02809Listeria grayi DSM 20601Gastrointestinal tractNon-contiguous Finished31517
0573Gc01434Mobiluncus curtisii ATCC 43063Urogenital tractFinished31519
0388Gi02744Mobiluncus curtisii ATCC 51333Urogenital tractHigh Quality Draft52983
0574Gi03779Mobiluncus curtisii curtisii ATCC 35241Urogenital tractHigh Quality Draft34631
0576Gi04125Mobiluncus curtisii holmesii ATCC 35242Urogenital tractHigh Quality Draft52991
0580Gi03473Mobiluncus mulieris ATCC 35239Urogenital tractHigh Quality Draft51375
0577Gi02821Mobiluncus mulieris ATCC 35243Urogenital tractHigh Quality Draft34633
0591Gi02825Mycobacterium parascrofulaceum ATCC BAA-614Urogenital tractHigh Quality Draft31521
9123Gi04987Neisseria bacilliformis ATCC BAA-1200OralHigh Quality Draft53053
9418Gi05722Neisseria macacae ATCC 33926Gastrointestinal tract 64729
0602Gi04529Neisseria meningitidis ATCC 13091AirwaysHigh Quality Draft50525
9371Gi05602Neisseria shayeganii 871Airways  
9370Gi05601Neisseria wadsworthii 9715Skin  
6123Gi03643Oribacterium sinus F0268OralHigh Quality Draft34635
0620Gi04175Parascardovia denticolens DSM 10105OralHigh Quality Draft50509
0621Gi04129Pasteurella dagmatis ATCC 43325AirwaysImproved High Quality Draft40085
0623Gi02835Pediococcus acidilactici DSM 20284Gastrointestinal tractHigh Quality Draft50527
9225Gi05118Peptoniphilus duerdenii ATCC BAA-1640Urogenital tractHigh Quality Draft50529
9129Gi04998Peptoniphilus indolicus ATCC 29427OralHigh Quality Draft64733
0645Gi02841Prevotella bergensis DSM 17361SkinHigh Quality Draft34637
6485Gi03787Prevotella buccae ATCC 33574OralHigh Quality Draft51491
9136Gi05005Prevotella dentalis ATCC 49559Oral 64735
0658Gi03795Prevotella marshii DSM 16973OralHigh Quality Draft50531
9141Gi05010Prevotella multiformis DSM 16608OralHigh Quality Draf53055
9419Gi05723Prevotella nigrescens ATCC 33563Oral 64737
0663Gi03796Prevotella oralis ATCC 33269Oral, Urogenital tractHigh Quality Draft51495
9144Gi05013Prevotella pallens ATCC 700821Oral 64739
9420Gi05724Prevotella salivae DSM 15606Gastrointestinal tractHigh Quality Draft53199
6745Gi03869Prevotella sp. F0295OralHigh Quality Draft38731
9153Gi05022Propionibacterium avidum ATCC 25577Oral 64741
0693Gi02844Proteus mirabilis ATCC 29906Urogenital tractHigh Quality Draft31523
0721Gi04127Pseudoramibacter alactolyticus ATCC 23263OralHigh Quality Draft52995
9373Gi05604Psychrobacter sp. 1501BloodHigh Quality Draft 
0724Gi02851Rhodococcus equi ATCC 33707SkinNon-contiguous Finished31525
0731Gi02855Roseomonas cervicalis ATCC 49957Urogenital tractHigh Quality Draft31527
0733Gc01662Rothia dentocariosa ATCC 17931OralFinished48447
7543Gi03870Selenomonas flueggei ATCC 43531OralHigh Quality Draft37273
7545Gi03818Selenomonas noxia ATCC 43541OralHigh Quality Draft34641
9166Gi05035Selenomonas sp. 67H29BPOralHigh Quality Draft50535
0758Gi04126Serratia odorifera DSM 4582Airways, SkinNon-contiguous Finished40087
0765Gi02866Sphingobacterium spiritivorum ATCC 33300Urogenital tractHigh Quality Draft31529
0766Gi03705Sphingobacterium spiritivorum ATCC 33861Urogenital tractImproved High Quality Draft31531
9372Gi05603Sporosarcina newyorkensis 2681Blood 64749
0782Gi04810Staphylococcus aureus aureus ATCC 51811AirwaysHigh Quality Draft48445
0783Gi04811Staphylococcus aureus aureus ATCC BAA-39AirwaysHigh Quality Draft50533
0769Gi02870Staphylococcus aureus aureus MN8Urogenital tractNon-contiguous Finishe31533
0774Gi03700Staphylococcus aureus aureus TCH130SkinHigh Quality Draft31541
0772Gc01663Staphylococcus aureus aureus TCH60SkinFinished31539
0773Gi03701Staphylococcus aureus aureus TCH70SkinImproved High Quality Draft31543
0776Gi02336Staphylococcus aureus aureus USA300_TCH959SkinHigh Quality Draft19921
0793Gi03694Staphylococcus capraeSkinHigh Quality Draft34647
0789Gi03698Staphylococcus epidermidis BCM-HMP0060SkinHigh Quality Draft31545
0794Gi02874Staphylococcus epidermidis M23864:W2(grey)SkinHigh Quality Draft34643
0791Gi03696Staphylococcus epidermidis W23144SkinHigh Quality Draft34655
0790Gi03697Staphylococcus lugdunensis M23590SkinHigh Quality Draft34653
9171Gi05040Streptococcus agalactiae ATCC 13813OralHigh Quality Draft53057
9421Gi05725Streptococcus australis ATCC 700641OralHigh Quality Draft53201
9319Gi05215Streptococcus bovis ATCC 700338Urogenital tractHigh Quality Draft50519
9422Gi05726Streptococcus cristatus ATCC 51100OralHigh Quality Draft53203
0819Gi04200Streptococcus equinus ATCC 9812Gastrointestinal tractHigh Quality Draft52999
9352Gi05399Streptococcus gallolyticus gallolyticus TX20005HeartHigh Quality Draft30645
9423Gi05727Streptococcus infantis ATCC 700779AirwaysHigh Quality Draft53205
8571Gi03871Streptococcus mitis ATCC 6249OralHigh Quality Draft50515
8579Gi03876Streptococcus oralis ATCC 35037OralImproved High Quality Draft38733
0833Gi04201Streptococcus parasanguinis ATCC 15912OralHigh Quality Draft48315
8577Gi03874Streptococcus parasanguinis ATCC 903AirwaysHigh Quality Draft53003
9180Gi05049Streptococcus peroris ATCC 700780OralHigh Quality Draft53059
0837Gc01351Streptococcus pneumoniae TCH8431/19AAirwaysFinished34659
0841Gi04202Streptococcus pyogenes ATCC 10782AirwaysHigh Quality Draft50517
8573Gi03873Streptococcus sanguinis ATCC 29667Oral 64743
8578Gi03875Streptococcus sanguinis ATCC 49296OralHigh Quality Draft53005
9378Gi05680Streptococcus sanguinis SK1HeartHigh Quality Draft53155
9393Gi05694Streptococcus sanguinis SK1056BloodHigh Quality Draft53181
9394Gi05695Streptococcus sanguinis SK1057BloodHigh Quality Draft53183
9395Gi05696Streptococcus sanguinis SK1058BloodHigh Quality Draft53185
9396Gi05697Streptococcus sanguinis SK1059BloodHigh Quality Draft53187
9397Gi05698Streptococcus sanguinis SK1087BloodHigh Quality Draft53189
9382Gi05683Streptococcus sanguinis SK115OralHigh Quality Draft53161
9383Gi05684Streptococcus sanguinis SK150OralHigh Quality Draft53163
9384Gi05685Streptococcus sanguinis SK160OralHigh Quality Draft53165
9386Gi05687Streptococcus sanguinis SK330OralHigh Quality Draft53167
9387Gi05688Streptococcus sanguinis SK340OralHigh Quality Draft53169
9388Gi05689Streptococcus sanguinis SK353OralHigh Quality Draft53171
9389Gi05690Streptococcus sanguinis SK355OralHigh Quality Draft53173
9390Gi05691Streptococcus sanguinis SK405BloodHigh Quality Draft53175
9391Gi05692Streptococcus sanguinis SK408BloodHigh Quality Draft53177
9380Gi05681Streptococcus sanguinis SK49OralHigh Quality Draft53157
9392Gi05693Streptococcus sanguinis SK678BloodHigh Quality Draft53179
9381Gi05682Streptococcus sanguinis SK72OralHigh Quality Draft53159
9398Gi05699Streptococcus sanguinis VMC66BloodHigh Quality Draft53191
9189Gi05058Streptococcus sp. 73H25APOralHigh Quality Draft50521
9425Gi05729Streptococcus vestibularis ATCC 49124OralHigh Quality Draft53209
0877Gi02881Weissella paramesenteroides ATCC 33313Gastrointestinal tractImproved High Quality Draft34661

 



about seo | page