Table 2. Contingency table of the viral families identified in the feces and saliva samples of D. rotundus and M. molossus.
| Order | Viral family | Genome | Desmodus rotundus | Molossus molossus | Overall total | |||||||||||
| Cave F | Cave M | Urban | Forest | |||||||||||||
| Saliva | Feces | Total | Saliva | Feces | Total | Saliva | Feces | Total | Saliva | Feces | Total | |||||
| Insect virus | Nidovirales | Mesoniviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 0 | 0 | 0 | 2 | |
| Picronavirales | Dicistroviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 394 | 394 | 0 | 77 | 77 | 471 | ||
| Picornavirales | Iflaviviridae | ssRNA(+) | 2 | 2 | 0 | 2 | 2 | 0 | 32 | 32 | 0 | 10 | 10 | 46 | ||
| Unassigned | Alphatetraviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 20 | 20 | 0 | 1 | 1 | 21 | ||
| Unassigned | Baculoviridae | dsDNA | 0 | 0 | 2 | 1 | 3 | 0 | 1 | 1 | 4 | 0 | 4 | 8 | ||
| Unassigned | Carmotetraviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | ||
| Unassigned | Iridoviridae | dsDNA | 1 | 1 | 0 | 3 | 3 | 0 | 57 | 57 | 4 | 0 | 4 | 65 | ||
| Unassigned | Nimaviridae | dsDNA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 4 | 4 | ||
| Unassigned | Nodaviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 105 | 105 | 0 | 62 | 62 | 167 | ||
| Unassigned | Nudiviridae | dsDNA | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 2 | ||
| Unassigned | Parvoviridae | ssDNA(+/-) | 0 | 0 | 0 | 0 | 0 | 0 | 28 | 28 | 17 | 122 | 139 | 167 | ||
| Unassigned | Permutotetraviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 0 | 0 | 0 | 2 | ||
| Unassigned | Polydnaviridae | dsDNA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 4 | 6 | 6 | ||
| Unassigned | Poxviridae | dsDNA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 3 | 3 | ||
| Unassigned | Unclassified viruses | - | 0 | 0 | 0 | 0 | 0 | 0 | 23 | 23 | 0 | 11 | 11 | 34 | ||
| Phage | Caudovirales | Myoviridae | dsDNA | 279 | 279 | 1 | 617 | 618 | 2 | 1 | 3 | 19 | 42 | 61 | 961 | |
| Caudovirales | Podoviridae | dsDNA | 435 | 435 | 0 | 767 | 767 | 0 | 15 | 15 | 8 | 361 | 369 | 1586 | ||
| Caudovirales | Siphoviridae | dsDNA | 285 | 285 | 2 | 173 | 175 | 0 | 5 | 5 | 16 | 56 | 72 | 537 | ||
| Ligmaenvirales | Lipothrixviridae | dsDNA | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | ||
| Unassigned | Inoviridae | ssDNA(+) | 39 | 39 | 0 | 1 | 1 | 0 | 1 | 1 | 0 | 3 | 3 | 44 | ||
| Unassigned | Lavidaviridae | dsDNA | 4 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | ||
| Unassigned | Leviviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 3 | 0 | 0 | 0 | 3 | ||
| Unassigned | Microviridae | ssDNA(+) | 132 | 132 | 0 | 196 | 196 | 0 | 1 402 | 1 402 | 7 | 1 465 | 1 472 | 3202 | ||
| Unassigned | Tectiviridae | dsDNA | 7 | 7 | 0 | 3 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 10 | ||
| Unassigned | Unclassified Caudovirales | dsDNA | 14 | 14 | 0 | 2 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 16 | ||
| Unassigned | Unclassified dsDNA phages | dsDNA | 13 | 13 | 0 | 20 | 20 | 0 | 0 | 0 | 2 | 0 | 2 | 35 | ||
| Plant and protozoan virus | Mononegavirales | Rhabdoviridae | ssRNA(-) | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 0 | 2 | 2 | 4 | |
| Picornavirales | Secoviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 0 | 0 | 0 | 2 | ||
| Tymovirales | Tymoviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 7 | 7 | 8 | ||
| Unassigned | Bromoviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 5 | 0 | 0 | 0 | 5 | ||
| Unassigned | Closteroviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | ||
| Unassigned | Geminiviridae | ssDNA(+/-) | 9 | 9 | 0 | 10 | 10 | 0 | 7 | 7 | 0 | 27 | 27 | 53 | ||
| Unassigned | Luteoviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 9 | 9 | 0 | 2 | 2 | 11 | ||
| Unassigned | Marseilleviridae | dsDNA | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | ||
| Order | Viral family | Genome | Desmodus rotundus | Molossus molossus | Overall total | |||||||||||
| Cave F | Cave M | Urban | Forest | |||||||||||||
| Saliva | Feces | Total | Saliva | Feces | Total | Saliva | Feces | Total | Saliva | Feces | Total | |||||
| Plant and protozoan virus | Unassigned | Mimiviridae | dsDNA | 1 | 1 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | |
| Unassigned | Nanoviridae | ssDNA(+) | 3 | 3 | 0 | 1 | 1 | 0 | 2 | 2 | 0 | 7 | 7 | 13 | ||
| Unassigned | Partitiviridae | dsRNA | 0 | 0 | 0 | 0 | 0 | 0 | 17 | 17 | 0 | 4 | 4 | 21 | ||
| Unassigned | Phycodnaviridae | dsDNA | 6 | 6 | 0 | 2 | 2 | 0 | 7 | 7 | 0 | 9 | 9 | 24 | ||
| Unassigned | Potyviridae | ssRNA(+) | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 2 | ||
| Unassigned | Tombusviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 2 | ||
| Unassigned | Totiviridae | dsRNA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 2 | 2 | ||
| Unassigned | Virgaviridae | ssRNA(+) | 0 | 0 | 2 | 0 | 2 | 0 | 5 | 5 | 0 | 0 | 0 | 7 | ||
| Unassigned | Unassigned | - | 0 | 0 | 0 | 0 | 0 | 0 | 32 | 32 | 0 | 17 | 17 | 49 | ||
| Vertebrate virus | Bunyavirales | Nairoviridae | ssRNA(-) | 2 | 2 | 0 | 0 | 0 | 0 | 4 | 4 | 0 | 0 | 0 | 6 | |
| Herpesvirales | Herpesviridae | dsDNA | 4 | 4 | 3 | 3 | 6 | 0 | 2 | 2 | 450 | 5 | 455 | 467 | ||
| Picornavirales | Picornaviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 8 | 8 | 0 | 1 | 1 | 9 | ||
| Unassigned | Adenoviridae | dsDNA | 78 | 78 | 0 | 35 | 35 | 0 | 0 | 0 | 18 | 0 | 18 | 131 | ||
| Unassigned | Anelloviridae | ssDNA(-) | 272 | 272 | 6 | 348 | 354 | 1 | 56 | 57 | 12 | 9 | 21 | 704 | ||
| Unassigned | Astroviridae | ssRNA(+) | 2 | 2 | 0 | 0 | 0 | 0 | 2 | 2 | 0 | 3 | 3 | 7 | ||
| Unassigned | Circoviridae | ssDNA(+/-) | 117 | 117 | 7 | 65 | 72 | 0 | 160 | 160 | 1 | 195 | 196 | 545 | ||
| Unassigned | Genomoviridae | ssDNA(+/-) | 10 | 10 | 0 | 20 | 20 | 0 | 5 | 5 | 1 | 42 | 43 | 78 | ||
| Unassigned | Hepeviridae | ssRNA(+) | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | ||
| Unassigned | Papillomaviridae | dsDNA | 0 | 0 | 0 | 0 | 0 | 1 | 17 | 18 | 93 | 124 | 217 | 235 | ||
| Unassigned | Parvoviridae | ssDNA(+/-) | 111 | 111 | 10 | 187 | 197 | 0 | 3 | 3 | 2 | 6 | 25 | 319 | ||
| Unassigned | Polyomaviridae | dsDNA | 2 | 2 | 4 | 5 | 9 | 0 | 6 | 6 | 0 | 3 | 3 | 20 | ||
| Unassigned | Poxviridae | dsDNA | 0 | 0 | 0 | 6 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | ||
| Unassigned | Retroviridae | ssRNA-RT | 1 | 1 | 1 | 8 | 9 | 2 | 0 | 2 | 69 | 2 | 71 | 83 | ||
| ND | Unassigned | Environmental samples | - | 55 | 55 | 0 | 49 | 49 | 2 | 166 | 168 | 0 | 235 | 235 | 507 | |
| Unassigned | Unclassified ssDNA viruses | ssDNA | 45 | 45 | 0 | 15 | 15 | 0 | 78 | 78 | 4 | 106 | 110 | 248 | ||
| Unassigned | Unclassified viruses | - | 0 | 0 | 0 | 12 | 12 | 0 | 3 | 3 | 0 | 5 | 5 | 20 | ||
| Total | 1 930 | 1 930 | 39 | 2 554 | 2 593 | 8 | 2 692 | 2 700 | 729 | 3 039 | 3 768 | 10 991 | ||||
The number of viral-associated contig sequences is given for each sample (saliva and feces), overall, as well as for each habitat (caves F and M for D. rotundus, urban and forest for M. molossus). The total number of contigs detected for each collecting site is given in bold.