Goal I: 1,000 reference genomes

One of the goals of the Human Microbiome Project is to sequence 1,000 microbial genomes. Although the number of microbial species associated with the human body is predicted to be many times this number, these genome sequences will establish a valuable benchmark for understanding microbial communities and will enable more complex metagenomic studies.

These genome sequences represent five broad environments of the human body:

  • The gastrointestinal and urogenital tracts
  • The skin
  • The mouth
  • The airways (nasal, pharyngeal, and lung)
  • The vagina

Within each body environment, microbial strains are selected based on phylogenetic diversity, clinical importance, abundance within the body site, and significance for understanding genetic diversity within a species.

The Human Microbiome Project seeks to provide a valuable resource to the scientific community and is actively seeking input on the selection of important strains for whole genome sequencing.

The organisms currently being sequenced at the Broad Institute are listed below.

Gastrointestinal and Urogenital Tracts
Genus Species Strain
Bacteroides sp. 3_2_5, 4_3_47FAA, 9_1_42FAA, D1, D2, D4, 2_1_7, D22
Bifidobacterium bifidum NCIMB 41171
Bifidobacterium longum infantis strain 52484
Helicobacter canadensis MIT 98-5491 (LCDC 16143, ATCC 700968)
Helicobacter cinaedi CCUG 18818 (NCTC 12423)
Helicobacter pullorum MIT 98-5489 (LCDC 15115)
Helicobacter rappini taxon 8 (ATCC 49309)
Helicobacter winghamensis (ATCC BAA-430)
Clostridiales bacterium 1_7_47FAA
Clostridium sp. 7_2_43FAA
Fusobacterium sp. 12_1B
Ruminococcus sp. 5_1_39B FAA
Lactobacillus paracasei 8700_2
Oxalobacter formigenes HOxBLS
Oxalobacter formigenes OXCC13
Escherichia sp. 1_1_43
Citrobacter sp. 30_2
Clostridium sp. D5
Fusobacterium sp. D12
Coprobacillus sp. D6
Mollicutes bacterium D7
Proprionibacterium sp. D11
Shigella sp. D8, D9
Fusobacterium mortiferum ATCC 9817
Fusobacterium varium ATCC 27725
Fusobacterium ulcerans ATCC 49185
Fusobacterium sp. 1_1_41FAA, 2_1_31
Escherichia sp. 4_1_40B
Genus Species Strain
Lactobacillus crispatus MV-3A-Osel, SJ-3C-Osel, MV-1A-Osel
Lactobacillus jensenii SJ-7A-Osel, 27-2-Osel, 115-3-CHN
Lactobacillus coleohominis 101-4-CHN
Lactobacillus fermentum 28-3-CHN
Genus Species Strain
Fusobacterium periodontium Oral Taxon 201 D10
Paenibacillus sp. Oral Taxon 786 D14
Prevotella sp. Oral Taxon 313 D3
Prevotella buccae Oral Taxon 560 D17
Prevotella melaninogenica Oral Taxon 469 D18
Bacteroidetes bacterium Oral Taxon 274 F0058
Filifactor alocis ATCC 35896
Lachnospiraceae bacterium Oral Taxon 107 F0167
Peptoniphilus sp. Oral Taxon 386 F0131
Prevotella sp. Oral Taxon 317 F0108
Prevotella sp. Oral Taxon 299 F0039
Veillonella atypica Oral Taxon 524 D15
Eikenella corrodens ATCC 23834
Leptotrichia sp. Oral Taxon 219 D22
Genus Species Strain
Acinetobacter baumannii 19606
Acinetobacter calcoaceticus RUH2202
Acinetobacter genomic species 13TU RUH2624
Acinetobacter genomic species 3 SH024
Acinetobacter johnsonii SH046
Acinetobacter junii SH205
Acinetobacter lwoffii SH145
Acinetobacter radioresistens SH164