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." [https://commonfund.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 ID Organism name     Body Site Finishing Level GPID
0004 Gi03555 Achromobacter piechaudii ATCC 43553 Airways Standard Draft 46343
0015 Gi02597 Acinetobacter haemolyticus ATCC 19194 Airways Standard Draft 43187
0023 Gi02599 Acinetobacter sp. ATCC 27244 Skin High Quality Draft 30949
0027 Gi03558 Actinobacillus ureae ATCC 25976 Airways High Quality Draft 52977
9004 Gi04427 Actinomyces cardiffensis F0333 Oral Standard Draft 53007
0044 Gi02601 Actinomyces coleocanis DSM 15436 Urogenital tract High Quality Draft 31427
9006 Gi04429 Actinomyces sp. F0310 Oral High Quality Draft 53011
9005 Gi04428 Actinomyces sp. F0338 Oral High Quality Draft 53009
9062 Gi04929 Actinomyces sp. F0400 Oral Standard Draft 53017
0058 Gi02602 Actinomyces urogenitalis DSM 15434 Urogenital tract High Quality Draft 31429
0061 Gi02603 Aerococcus viridans ATCC 11563 Urogenital tract High Quality Draft 38729
0063 Gi02604 Aeromicrobium marinum DSM 15272 Oral Non-contiguous Finished 34545
9064 Gi04931 Aggregatibacter segnis ATCC 33393 Oral High Quality Draft 53019
0072 Gi02610 Anaerococcus lactolyticus ATCC 51172 Urogenital tract High Quality Draft 30951
0077 Gi02612 Anaerococcus tetradius ATCC 35098 Urogenital tract High Quality Draft 31433
0078 Gi03600 Anaerococcus vaginalis ATCC 51170 Skin High Quality Draft 38727
9401 Gi05704 Arcobacter butzleri JV22 Gastrointestinal tract High Quality Draft 53195
0091 Gi02616 Atopobium vaginae DSM 15829 Urogenital tract High Quality Draft 31435
0168 Gi03612 Bifidobacterium dentium ATCC 27679 Urogenital tract High Quality Draft 51373
0175 Gi03513 Bifidobacterium longum longum ATCC 55813 Gastrointestinal tract High Quality Draft 31437
0183 Gi02663 Brevibacterium mcbrellneri ATCC 49030 Urogenital tract High Quality Draft 34583
9399 Gi05701 Campylobacter coli JV20 Gastrointestinal tract High Quality Draft 50513
9400 Gi05703 Campylobacter upsaliensis JV21 Gastrointestinal tract High Quality Draft 53193
1977 Gi03877 Capnocytophaga ochracea F0287 Oral High Quality Draft 51493
9071 Gi04938 Capnocytophaga sp. F0234 Oral High Quality Draft 53023
0198 Gi03628 Cardiobacterium hominis ATCC 15826 Blood High Quality Draft 37269
9081 Gi04948 Centipeda periodontii DSM 2778 Oral   53025
0204 Gi02674 Chryseobacterium gleum F93, ATCC 35910 Urogenital tract Finished 30953
0219 Gi03537 Clostridium difficile NAP07 Gastrointestinal tract High Quality Draft 31439
0220 Gi03538 Clostridium difficile NAP08 Gastrointestinal tract High Quality Draft 31441
0276 Gi02699 Corynebacterium accolens ATCC 49725 Airways High Quality Draft 31443
0277 Gi03634 Corynebacterium accolens ATCC 49726 Airways High Quality Draft 50523
0284 Gi04425 Corynebacterium aurimucosum ATCC 700975 Urogenital tract High Quality Draft 31451
0290 Gi02701 Corynebacterium efficiens YS-314, DSM 44549 Skin High Quality Draft 34585
0291 Gi02702 Corynebacterium genitalium ATCC 33030 Urogenital tract Non-contiguous Finished 34587
0294 Gi03343 Corynebacterium glucuronalyticum ATCC 51867 Urogenital tract Non-contiguous Finished 30957
0293 Gi02708 Corynebacterium glucuronolyticum ATCC 51866 Urogenital tract High Quality Draft 31549
0297 Gi03721 Corynebacterium jeikeium ATCC 43734 Blood, Urogenital tract High Quality Draft 31445
0298 Gi02705 Corynebacterium lipophiloflavum DSM 44291 Urogenital tract High Quality Draft 31447
0305 Gi02707 Corynebacterium pseudogenitalium ATCC 33035 Urogenital tract   30955
0308 Gi02710 Corynebacterium striatum ATCC 6940 Urogenital tract   31449
9374 Gi05605 Desmospora sp. 8437 Blood High Quality Draft 64725
9083 Gi04950 Dialister micraerophilus DSM 19965 Oral, Urogenital tract High Quality Draft 53029
9086 Gi04953 Enterobacter hormaechei ATCC 49162 Oral   53031
9087 Gi04954 Enterococcus casseliflavus ATCC 12755 Oral High Quality Draft 53041
0345 Gi02727 Enterococcus faecalis ATCC 29200 Urogenital tract Improved High Quality Draft 31459
0346 Gi01841 Enterococcus faecalis HH22 Urogenital tract High Quality Draft 31457
0348 Gi01843 Enterococcus faecalis TX0104 Gastrointestinal tract High Quality Draft 30623
0349 Gi02728 Enterococcus faecalis TX1322 Gastrointestinal tract Improved High Quality Draft 31461
0351 Gi02729 Enterococcus faecium DO Blood, Gastrointestinal tract   30627
0352 Gi02730 Enterococcus faecium TX1330 Gastrointestinal tract Finished 31463
9088 Gi04955 Enterococcus italicus DSM 15952 Oral High Quality Draft 53039
0357 Gi02731 Erysipelothrix rhusiopathiae ATCC 19414 Skin High Quality Draft 31465
0358 Gi03725 Escherichia coli 83972 Urogenital tract Non-contiguous Finished 31467
0381 Gi04123 Eubacterium saburreum DSM 3986 Oral High Quality Draft 52981
0379 Gi04122 Eubacterium yurii margaretiae ATCC 43715 Oral High Quality Draft 50511
0391 Gi02745 Finegoldia magna ATCC 53516 Urogenital tract Non-contiguous Finished 31469
9094 Gi04961 Fusobacterium nucleatum animalis ATCC 51191 Gastrointestinal tract   64727
0397 Gi01861 Fusobacterium nucleatum nucleatum ATCC 23726 Urogenital tract High Quality Draft 31471
0421 Gc01640 Gardnerella vaginalis 317, ATCC 14019 Urogenital tract Non-contiguous Finished 31473
0444 Gi03858 Granulicatella adiacens ATCC 49175 Oral High Quality Draft 37271
9095 Gi04962 Haemophilus aegyptius ATCC 11116 Oral, Eye High Quality Draft 53049
9417 Gi05721 Haemophilus parainfluenzae ATCC 33392 Skin High Quality Draft 53197
4655 Gc01648 Helicobacter pylori 35A Gastrointestinal tract Finished 34603
0462 Gc01758 Helicobacter pylori 83 Gastrointestinal tract   34609
9098 Gi04965 Kingella denitrificans ATCC 33394 Airways High Quality Draft 53051
0476 Gi04136 Kingella kingae Airways High Quality Draft 52985
0484 Gi04135 Klebsiella pneumoniae rhinoscleromatis ATCC 13884 Airways High Quality Draft 40083
0492 Gi02787 Lactobacillus acidophilus ATCC 4796 Gastrointestinal tract High Quality Draft 31477
0493 Gi02788 Lactobacillus amylolyticus DSM 11664 Gastrointestinal tract High Quality Draft 34615
0494 Gi02789 Lactobacillus antri DSM 16041 Gastrointestinal tract High Quality Draft 31479
0496 Gi03750 Lactobacillus brevis gravesensis ATCC 27305 Gastrointestinal tract High Quality Draft 31481
0497 Gi03751 Lactobacillus buchneri ATCC 11577 Gastrointestinal tract High Quality Draft 31483
0503 Gi03827 Lactobacillus coleohominis DSM 14060 Urogenital tract   52987
0506 Gi02792 Lactobacillus crispatus JV-V01 Urogenital tract High Quality Draft 30641
5505 Gi03866 Lactobacillus delbrueckii lactis DSM 20072 Gastrointestinal tract High Quality Draft 53001
0511 Gi03753 Lactobacillus fermentum ATCC 14931 Gastrointestinal tract Improved High Quality Draft 31485
0514 Gi02794 Lactobacillus gasseri JV-V03 Urogenital tract Improved High Quality Draft 31487
0518 Gi02795 Lactobacillus helveticus DSM 20075 Gastrointestinal tract High Quality Draf 34619
0519 Gi03754 Lactobacillus hilgardii ATCC 8290 Gastrointestinal tract Improved High Quality Draft 31489
9223 Gi05116 Lactobacillus iners ATCC 55195 Urogenital tract High Quality Draft 53061
0520 Gi02796 Lactobacillus iners DSM 13335 Urogenital tract High Quality Draft 31491
0526 Gi02797 Lactobacillus jensenii JV-V16 Urogenital tract Finished 31493
0528 Gi02798 Lactobacillus johnsonii ATCC 33200 Blood, Urogenital tract Non-contiguous Finished 31495
0530 Gi03755 Lactobacillus paracasei ATCC 25302 Gastrointestinal tract High Quality Draft 31513
0531 Gi03756 Lactobacillus plantarum ATCC 14917 Gastrointestinal tract Improved High Quality Draft 31515
0534 Gi02800 Lactobacillus reuteri CF48-3A Gastrointestinal tract High Quality Draft 31553
0535 Gi03770 Lactobacillus reuteri MM2-3 Gastrointestinal tract High Quality Draft 34627
0536 Gi01862 Lactobacillus reuteri MM4-1A Gastrointestinal tract Non-contiguous Finished 31511
0538 Gi01863 Lactobacillus reuteri SD2112, ATCC 55730 Gastrointestinal tract High Quality Draft 30643
0539 Gi02801 Lactobacillus rhamnosus LMS2-1 Gastrointestinal tract High Quality Draft 31497
0542 Gi03772 Lactobacillus ruminis E 194e, ATCC 25644 Gastrointestinal tract Improved High Quality Draft 31499
0545 Gi05082 Lactobacillus salivarius HO66, ATCC 11741 Gastrointestinal tract, Oral High Quality Draft 31503
0548 Gi02804 Lactobacillus ultunensis DSM 16047 Gastrointestinal tract High Quality Draft 31505
0549 Gi03861 Lactobacillus vaginalis ATCC 49540 Urogenital tract High Quality Draft 31507
0551 Gi04134 Lautropia mirabilis ATCC 51599 Oral High Quality Draft 52989
0555 Gi02808 Leuconostoc mesenteroides cremoris ATCC 19254 Gastrointestinal tract High Quality Draft 34629
0556 Gi02809 Listeria grayi DSM 20601 Gastrointestinal tract Non-contiguous Finished 31517
0573 Gc01434 Mobiluncus curtisii ATCC 43063 Urogenital tract Finished 31519
0388 Gi02744 Mobiluncus curtisii ATCC 51333 Urogenital tract High Quality Draft 52983
0574 Gi03779 Mobiluncus curtisii curtisii ATCC 35241 Urogenital tract High Quality Draft 34631
0576 Gi04125 Mobiluncus curtisii holmesii ATCC 35242 Urogenital tract High Quality Draft 52991
0580 Gi03473 Mobiluncus mulieris ATCC 35239 Urogenital tract High Quality Draft 51375
0577 Gi02821 Mobiluncus mulieris ATCC 35243 Urogenital tract High Quality Draft 34633
0591 Gi02825 Mycobacterium parascrofulaceum ATCC BAA-614 Urogenital tract High Quality Draft 31521
9123 Gi04987 Neisseria bacilliformis ATCC BAA-1200 Oral High Quality Draft 53053
9418 Gi05722 Neisseria macacae ATCC 33926 Gastrointestinal tract   64729
0602 Gi04529 Neisseria meningitidis ATCC 13091 Airways High Quality Draft 50525
9371 Gi05602 Neisseria shayeganii 871 Airways    
9370 Gi05601 Neisseria wadsworthii 9715 Skin    
6123 Gi03643 Oribacterium sinus F0268 Oral High Quality Draft 34635
0620 Gi04175 Parascardovia denticolens DSM 10105 Oral High Quality Draft 50509
0621 Gi04129 Pasteurella dagmatis ATCC 43325 Airways Improved High Quality Draft 40085
0623 Gi02835 Pediococcus acidilactici DSM 20284 Gastrointestinal tract High Quality Draft 50527
9225 Gi05118 Peptoniphilus duerdenii ATCC BAA-1640 Urogenital tract High Quality Draft 50529
9129 Gi04998 Peptoniphilus indolicus ATCC 29427 Oral High Quality Draft 64733
0645 Gi02841 Prevotella bergensis DSM 17361 Skin High Quality Draft 34637
6485 Gi03787 Prevotella buccae ATCC 33574 Oral High Quality Draft 51491
9136 Gi05005 Prevotella dentalis ATCC 49559 Oral   64735
0658 Gi03795 Prevotella marshii DSM 16973 Oral High Quality Draft 50531
9141 Gi05010 Prevotella multiformis DSM 16608 Oral High Quality Draf 53055
9419 Gi05723 Prevotella nigrescens ATCC 33563 Oral   64737
0663 Gi03796 Prevotella oralis ATCC 33269 Oral, Urogenital tract High Quality Draft 51495
9144 Gi05013 Prevotella pallens ATCC 700821 Oral   64739
9420 Gi05724 Prevotella salivae DSM 15606 Gastrointestinal tract High Quality Draft 53199
6745 Gi03869 Prevotella sp. F0295 Oral High Quality Draft 38731
9153 Gi05022 Propionibacterium avidum ATCC 25577 Oral   64741
0693 Gi02844 Proteus mirabilis ATCC 29906 Urogenital tract High Quality Draft 31523
0721 Gi04127 Pseudoramibacter alactolyticus ATCC 23263 Oral High Quality Draft 52995
9373 Gi05604 Psychrobacter sp. 1501 Blood High Quality Draft  
0724 Gi02851 Rhodococcus equi ATCC 33707 Skin Non-contiguous Finished 31525
0731 Gi02855 Roseomonas cervicalis ATCC 49957 Urogenital tract High Quality Draft 31527
0733 Gc01662 Rothia dentocariosa ATCC 17931 Oral Finished 48447
7543 Gi03870 Selenomonas flueggei ATCC 43531 Oral High Quality Draft 37273
7545 Gi03818 Selenomonas noxia ATCC 43541 Oral High Quality Draft 34641
9166 Gi05035 Selenomonas sp. 67H29BP Oral High Quality Draft 50535
0758 Gi04126 Serratia odorifera DSM 4582 Airways, Skin Non-contiguous Finished 40087
0765 Gi02866 Sphingobacterium spiritivorum ATCC 33300 Urogenital tract High Quality Draft 31529
0766 Gi03705 Sphingobacterium spiritivorum ATCC 33861 Urogenital tract Improved High Quality Draft 31531
9372 Gi05603 Sporosarcina newyorkensis 2681 Blood   64749
0782 Gi04810 Staphylococcus aureus aureus ATCC 51811 Airways High Quality Draft 48445
0783 Gi04811 Staphylococcus aureus aureus ATCC BAA-39 Airways High Quality Draft 50533
0769 Gi02870 Staphylococcus aureus aureus MN8 Urogenital tract Non-contiguous Finishe 31533
0774 Gi03700 Staphylococcus aureus aureus TCH130 Skin High Quality Draft 31541
0772 Gc01663 Staphylococcus aureus aureus TCH60 Skin Finished 31539
0773 Gi03701 Staphylococcus aureus aureus TCH70 Skin Improved High Quality Draft 31543
0776 Gi02336 Staphylococcus aureus aureus USA300_TCH959 Skin High Quality Draft 19921
0793 Gi03694 Staphylococcus caprae Skin High Quality Draft 34647
0789 Gi03698 Staphylococcus epidermidis BCM-HMP0060 Skin High Quality Draft 31545
0794 Gi02874 Staphylococcus epidermidis M23864:W2(grey) Skin High Quality Draft 34643
0791 Gi03696 Staphylococcus epidermidis W23144 Skin High Quality Draft 34655
0790 Gi03697 Staphylococcus lugdunensis M23590 Skin High Quality Draft 34653
9171 Gi05040 Streptococcus agalactiae ATCC 13813 Oral High Quality Draft 53057
9421 Gi05725 Streptococcus australis ATCC 700641 Oral High Quality Draft 53201
9319 Gi05215 Streptococcus bovis ATCC 700338 Urogenital tract High Quality Draft 50519
9422 Gi05726 Streptococcus cristatus ATCC 51100 Oral High Quality Draft 53203
0819 Gi04200 Streptococcus equinus ATCC 9812 Gastrointestinal tract High Quality Draft 52999
9352 Gi05399 Streptococcus gallolyticus gallolyticus TX20005 Heart High Quality Draft 30645
9423 Gi05727 Streptococcus infantis ATCC 700779 Airways High Quality Draft 53205
8571 Gi03871 Streptococcus mitis ATCC 6249 Oral High Quality Draft 50515
8579 Gi03876 Streptococcus oralis ATCC 35037 Oral Improved High Quality Draft 38733
0833 Gi04201 Streptococcus parasanguinis ATCC 15912 Oral High Quality Draft 48315
8577 Gi03874 Streptococcus parasanguinis ATCC 903 Airways High Quality Draft 53003
9180 Gi05049 Streptococcus peroris ATCC 700780 Oral High Quality Draft 53059
0837 Gc01351 Streptococcus pneumoniae TCH8431/19A Airways Finished 34659
0841 Gi04202 Streptococcus pyogenes ATCC 10782 Airways High Quality Draft 50517
8573 Gi03873 Streptococcus sanguinis ATCC 29667 Oral   64743
8578 Gi03875 Streptococcus sanguinis ATCC 49296 Oral High Quality Draft 53005
9378 Gi05680 Streptococcus sanguinis SK1 Heart High Quality Draft 53155
9393 Gi05694 Streptococcus sanguinis SK1056 Blood High Quality Draft 53181
9394 Gi05695 Streptococcus sanguinis SK1057 Blood High Quality Draft 53183
9395 Gi05696 Streptococcus sanguinis SK1058 Blood High Quality Draft 53185
9396 Gi05697 Streptococcus sanguinis SK1059 Blood High Quality Draft 53187
9397 Gi05698 Streptococcus sanguinis SK1087 Blood High Quality Draft 53189
9382 Gi05683 Streptococcus sanguinis SK115 Oral High Quality Draft 53161
9383 Gi05684 Streptococcus sanguinis SK150 Oral High Quality Draft 53163
9384 Gi05685 Streptococcus sanguinis SK160 Oral High Quality Draft 53165
9386 Gi05687 Streptococcus sanguinis SK330 Oral High Quality Draft 53167
9387 Gi05688 Streptococcus sanguinis SK340 Oral High Quality Draft 53169
9388 Gi05689 Streptococcus sanguinis SK353 Oral High Quality Draft 53171
9389 Gi05690 Streptococcus sanguinis SK355 Oral High Quality Draft 53173
9390 Gi05691 Streptococcus sanguinis SK405 Blood High Quality Draft 53175
9391 Gi05692 Streptococcus sanguinis SK408 Blood High Quality Draft 53177
9380 Gi05681 Streptococcus sanguinis SK49 Oral High Quality Draft 53157
9392 Gi05693 Streptococcus sanguinis SK678 Blood High Quality Draft 53179
9381 Gi05682 Streptococcus sanguinis SK72 Oral High Quality Draft 53159
9398 Gi05699 Streptococcus sanguinis VMC66 Blood High Quality Draft 53191
9189 Gi05058 Streptococcus sp. 73H25AP Oral High Quality Draft 50521
9425 Gi05729 Streptococcus vestibularis ATCC 49124 Oral High Quality Draft 53209
0877 Gi02881 Weissella paramesenteroides ATCC 33313 Gastrointestinal tract Improved High Quality Draft 34661