TABLE 3.
Prophage abundance in NTM species that carry prophages
| Species a | # genomes b | # genomes ≥1 prophage c | # prophage d | Mean # prophages e | Unique # prophages f |
|---|---|---|---|---|---|
| M. immunogenum | 17 | 17 | 61 | 3.588 | 52 |
| M. mucogenicum | 5 | 3 | 8 | 1.6 | 6 |
| M. chelonae | 54 | 41 | 85 | 1.574 | 71 |
| M. abscessus | 1,831 | 1,380 | 2,594 | 1.417 | 1,529 |
| M. franklinii | 12 | 6 | 13 | 1.083 | 9 |
| M. conceptionense | 6 | 6 | 6 | 1 | 5 |
| M. hassiacum | 3 | 3 | 3 | 1 | 1 |
| M. senegalense | 3 | 2 | 3 | 1 | 2 |
| M. branderi | 2 | 2 | 2 | 1 | 2 |
| M. heraklionensis | 2 | 1 | 2 | 1 | 2 |
| M. aichiense | 2 | 2 | 2 | 1 | 2 |
| M. fluoranthenivorans | 2 | 1 | 2 | 1 | 2 |
| M. sphagni | 2 | 1 | 2 | 1 | 2 |
| M. botniense | 1 | 1 | 1 | 1 | 1 |
| M. stephanolepidis | 1 | 1 | 1 | 1 | 1 |
| M. algericus | 1 | 1 | 1 | 1 | 1 |
| M. brisbanense | 1 | 1 | 1 | 1 | 1 |
| M. insubricum | 1 | 1 | 1 | 1 | 1 |
| M. pulveris | 1 | 1 | 1 | 1 | 1 |
| M. nivoides | 1 | 1 | 1 | 1 | 1 |
| M. persicum | 1 | 1 | 1 | 1 | 0 |
| M. litorale | 4 | 2 | 3 | 0.75 | 3 |
| M. peregrinum | 6 | 4 | 4 | 0.667 | 4 |
| M. saopaulense | 3 | 2 | 2 | 0.667 | 1 |
| M. thermoresistibile | 3 | 2 | 2 | 0.667 | 2 |
| M. xenopi | 5 | 3 | 3 | 0.6 | 2 |
| M. marinum | 12 | 1 | 7 | 0.583 | 6 |
| M. salmoniphilum | 10 | 4 | 5 | 0.5 | 4 |
| M. fortuitum | 8 | 4 | 4 | 0.5 | 4 |
| M. boenickei | 4 | 1 | 2 | 0.5 | 2 |
| Hoyosella altamirensis | 2 | 1 | 1 | 0.5 | 1 |
| M. europaeum | 2 | 1 | 1 | 0.5 | 1 |
| M. vulneris | 2 | 1 | 1 | 0.5 | 1 |
| M. dioxanotrophicus | 5 | 1 | 2 | 0.4 | 2 |
| M. celatum | 3 | 1 | 1 | 0.333 | 1 |
| M. shimoidei | 3 | 1 | 1 | 0.333 | 1 |
| M. austroafricanum | 3 | 1 | 1 | 0.333 | 1 |
| M. cosmeticum | 3 | 1 | 1 | 0.333 | 1 |
| M. septicum | 3 | 1 | 1 | 0.333 | 1 |
| M. avium | 68 | 13 | 16 | 0.235 | 9 |
| M. phlei | 5 | 1 | 1 | 0.2 | 0 |
| M. paragordonae | 5 | 1 | 1 | 0.2 | 1 |
| M. kansasii | 28 | 3 | 3 | 0.107 | 1 |
| M. intracellulare | 68 | 5 | 5 | 0.074 | 5 |
| Other Mycobacterium g | 44 | 40 | 49 | 1.114 | 40 |
| Subtotal | 2,248 | 1,572 | 2,908 | 1.294 | 1,787 |
| Total h | 2,611 | 1,572 | 2,908 | 1.114 | 1,787 |
Species in the genus Mycobacterium and the closely related strain Hoyosella altamirensis for which at least one genome entry contains at least one prophage, sorted by the mean number of prophages found among the species.
The total numbers of genomes from each species analyzed with DEPhT and SPLICE.
The total numbers of genomes from each species with one or more prophages identified using DEPhT and SPLICE.
The total numbers of intact prophages identified using DEPhT and SPLICE for each bacterial species.
The average numbers of prophages for each species are shown.
The total numbers of prophages with unique sequences identified using DEPhT.
Strains in the genus Mycobacterium which are not speciated as labeled at PATRIC.
The total numbers of genomes, prophages, and unique prophages in nontuberculous bacteria. The total number of strains includes some which do not have species designations. Strains from species which have no predicted prophages are excluded from the subtotals.