| ProjectID | Metagenomic Dataset | Source of Data | Accession Numbers |
| 13699 | Waseca County Farm Soil Metagenome | soil | AAFX00000000 |
| 19733 | Global Ocean Sampling Expedition Metagenome | marine | AACY000000000 |
| 17663 | US EBPR Sludge Metagenome | sludge | AATO00000000 |
| 17663 | OZ EBPR Sludge Metagenome | sludge | AATN00000000 |
| 20823 | UBA Acid Mine Drainage Biofilm Metagenome | mine drainage | AAWO00000000 |
| 20823 | Combined UBA/UBA BS Acid Mine Drainage Biofilm Metagenome | mine drainage | ABOZ00000000 |
| 16729 | Human Distal Gut Biome | human gut | AAQK00000000, AAQL00000000 |
| 28117 | Human Gut Metagenome (healthy human sample F1-S, Adult, Male) | human gut | BAAU00000000 |
| 28117 | Human Gut Metagenome (healthy human sample F1-T, Adult, Female) | human gut | BAAV00000000 |
| 28117 | Human Gut Metagenome (healthy human sample F1-U, Infant, Female) | human gut | BAAW00000000 |
| 28117 | Human Gut Metagenome (healthy human sample F2-V, Adult, Male) | human gut | BAAX00000000 |
| 28117 | Human Gut Metagenome (healthy human sample F2-W, Adult, Female) | human gut | BAAY00000000 |
| 28117 | Human Gut Metagenome (healthy human sample F2-X, Child, Male) | human gut | BAAZ00000000 |
| 28117 | Human Gut Metagenome (healthy human sample In-A, Adult, Male) | human gut | BABB00000000 |
| 28117 | Human Gut Metagenome (healthy human sample In-B, Infant, Male) | human gut | BABC00000000 |
| 28117 | Human Gut Metagenome (healthy human sample In-D, Adult, Male) | human gut | BABD00000000 |
| 28117 | Human Gut Metagenome (healthy human sample In-E, Infant, Male) | human gut | BABE00000000 |
| 28117 | Human Gut Metagenome (healthy human sample In-M, Infant, Female) | human gut | BABF00000000 |
| 28117 | Human Gut Metagenome (healthy human sample In-R, Adult, Female) | human gut | BABG00000000 |
| 28117 | Human Gut Metagenome (healthy human sample F2-Y, Child, Female) | human gut | BABA00000000 |
| 17401 | Lean Mouse 1 Gut Metagenome | mouse gut | AATA00000000 |
| 17401 | Lean Mouse 2 Gut Metagenome | mouse gut | AATB00000000 |
| 17401 | Lean Mouse 3 Gut Metagenome | mouse gut | AATC00000000 |
| 17401 | Obese Mouse 1 Gut Metagenome | mouse gut | AATD00000000 |
| 17401 | Obese Mouse 2 Gut Metagenome | mouse gut | AATE00000000 |
| 17401 | Combined Gut Metagenome from Obese and Lean Mice | mouse gut | AATF00000000 |
| 19107 | Termite Gut Metagenome | termite gut | ABDH00000000 |
| 13700 | Whale Fall Metagenome - Microbial Mat Isolate | whale fall | AAFZ00000000 |
| 13700 | Whale Fall Metagenome - Rib Bone Isolate | whale fall | AAFY00000000 |
| 13700 | Whale Fall Metagenome - Bone Isolate | whale fall | AAGA00000000 |
| 29795 | Guerrero Negro Hypersaline Microbial Mat 01 Metagenome | microbial mat | ABPP00000000 |
| 29795 | Guerrero Negro Hypersaline Microbial Mat 02 Metagenome | microbial mat | ABPQ00000000 |
| 29795 | Guerrero Negro Hypersaline Microbial Mat 03 Metagenome | microbial mat | ABPR00000000 |
| 29795 | Guerrero Negro Hypersaline Microbial Mat 04 Metagenome | microbial mat | ABPS00000000 |
| 29795 | Guerrero Negro Hypersaline Microbial Mat 05 Metagenome | microbial mat | ABPT00000000 |
| 29795 | Guerrero Negro Hypersaline Microbial Mat 06 Metagenome | microbial mat | ABPU00000000 |
| 29795 | Guerrero Negro Hypersaline Microbial Mat 07 Metagenome | microbial mat | ABPV00000000 |
| 29795 | Guerrero Negro Hypersaline Microbial Mat 08 Metagenome | microbial mat | ABPW00000000 |
| 29795 | Guerrero Negro Hypersaline Microbial Mat 09 Metagenome | microbial mat | ABPX00000000 |
| 29795 | Guerrero Negro Hypersaline Microbial Mat 10 Metagenome | microbial mat | ABPY00000000 |
| - | Uncultured Human Fecal Virus Metagenome | human gut | AAMG00000000, AAMH00000000, AAMI00000000 |
| - | Rice Paddy Soil Viral Metagenome | soil | ABQX00000000 |
| 29433 | Coral-Associated Viral Communities: Bleaching Coral | coral | ABVT00000000 |
| 29433 | Coral-Associated Viral Communities: Healthy Coral | coral | ABVU00000000 |
