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 |
| Vaginal | ||
| 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 |
| Oral | ||
| 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 |
| Skin | ||
| 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 |
