Table 1:
Numbers of genomes and BGCs in all datasets included for the large-scale diversity analysis.
| Dataset Name | Study | Counts (genomes, BGCs) | |||||
|---|---|---|---|---|---|---|---|
| Bacterial | Fungal | Others | |||||
| RefSeq complete bacteria | 19,169 (19,166) | 101,531 | 0 (0) | 0 | 0 (3) | 0 | |
| RefSeq draft bacteria | 162,352 (162,297) | 959,061 | 0 (0) | 0 | 0 (55) | 346 | |
| GenBank fungi | 0 (0) | 0 | 5,939 (5,905) | 123,816 | 0 (34) | 123 | |
| GenBank archaea | 0 (1) | 2 | 0 (0) | 0 | 1,162 (1,161) | 2,109 | |
| Parks et al. 2017 (uncultivated bacteria and archaea MAGs) | [62] | 7,280 (7,280) | 15,829 | 0 (0) | 0 | 623 (623) | 756 |
| Tully et al. 2018 (Tara Ocean MAGs) | [63] | 2,283 (2,326) | 4,829 | 0 (0) | 0 | 344 (301) | 518 |
| Almeida et al. 2019 (unified human gut MAGs) | [64] | 4,616 (4,616) | 4,766 | 0 (0) | 0 | 28 (28) | 25 |
| Stewart et al. 2019 (cow's rumen MAGs) | [65] | 4,815 (4,815) | 8,380 | 0 (0) | 0 | 126 (126) | 589 |
| Glendinning et al. 2020 (chicken's caecum MAGs) | [66] | 469 (469) | 481 | 0 (0) | 0 | 0 (0) | 0 |
| MIBiG v2.0 | [78] | 0 (0) | 15,94 | 0 (0) | 276 | 0 (0) | 40 |
| Total | 200,984 (200,970) | 10,964,073 | 5,939 (5,905) | 124,092 | 2,283 (2,331) | 4,506 | |
Numbers inside parentheses indicate the total number of genomes assigned to each kingdom based on the subsequent taxonomy analysis. The “Others” category includes the kingdom of Archaea, Viridiplantae (from MIBiG dataset), and unassigned taxa. A complete list of all genome accessions and their BGC counts can be seen in Supplementary Table S3.