Table 4.
MS Microbial Candidate List Derived from the Deep Sequencing Data.
| Phyluma | Familya | Genusa | MS Mapped Readsb | Control Mapped Readsb | MS Specimens Increasedc | Pathogend | Ecologye |
|---|---|---|---|---|---|---|---|
| Proteobacteria | Nitrosomonadaceae | Nitrosospira | 5262 | 0 | 2 | no | Soil bacterium |
| Actinobacteria | Coriobacteriaceae | Atopobium | 3562 | 90 | 2 | no | Vaginal anaerobic bacterium |
| Fusobacteria | Fusobacteriaceae | Fusobacterium | 3230 | 56 | 2 | yes | Oral anaerobic bacterium |
| Basidiomycota | Ustilaginaceae | Ustilago | 1668 | 6 | 4 | no | Corn smut fungus |
| Proteobacteria | Pasteurellaceae | Aggregatibacter | 1166 | 214 | 1 | yes | Oral anaerobic bacterium |
| Gemmatimonadetes | Gemmatimonadaceae | Gemmatimonas | 848 | 30 | 2 | no | Soil bacterium |
| Bacteroidetes | Bacteroidaceae | Bacteroides | 834 | 2 | 5 | yes | Gut anaerobe |
| Proteobacteria | Nitrosomonadaceae | Nitrosomonas | 700 | 10 | 2 | no | Soil and water bacterium |
| Fusobacteria | Leptotrichiaceae | Leptotrichia | 650 | 38 | 2 | yes | Oral anaerobic bacterium |
| Viruses | Podoviridae | Luz24likevirus | 590 | 0 | 2 | no | Bacteriophage (virus) |
| Verrucomicrobia | Akkermansiaceae | Akkermansia | 508 | 0 | 1 | no | Gut anaerobic bacterium |
| Firmicutes | Streptococcaceae | Lactococcus | 488 | 6 | 4 | no | Anaerobic fermenting bacterium |
| Nitrospirae | Nitrospiraceae | Nitrospira | 406 | 4 | 2 | no | Waterborne bacterium |
| Bacteroidetes | Flavobacteriaceae | Capnocytophaga | 358 | 12 | 4 | yes | Oral anaerobic bacterium |
| Actinobacteria | Rubrobacteraceae | Rubrobacter | 346 | 2 | 5 | no | Thermophilic bacterium |
| Actinobacteria | Bifidobacteriaceae | Bifidobacterium | 318 | 52 | 1 | no | Vaginal and gut anaerobic bacterium |
| Firmicutes | Leuconostocaceae | Leuconostoc | 314 | 30 | 1 | yes | Anaerobic bacterium |
| Proteobacteria | Moraxellaceae | Psychrobacter | 308 | 50 | 1 | yes | Aerobic bacterium |
| Firmicutes | Lactobacillaceae | Pediococcus | 270 | 0 | 1 | no | Anaerobic fermenting bacterium |
| Proteobacteria | Aeromonadaceae | Aeromonas | 246 | 26 | 2 | yes | Waterborne anaerobic bacterium |
| Proteobacteria | Moraxellaceae | Moraxella | 244 | 18 | 2 | yes | Oral aerobic bacterium |
| Actinobacteria | Acidothermaceae | Acidothermus | 214 | 36 | 3 | no | Thermophilic bacterium |
| Proteobacteria | Hyphomicrobiaceae | Hyphomicrobium | 196 | 10 | 2 | no | Soil and water anaerobic bacterium |
| Proteobacteria | Ectothiorhodospiraceae | Thioalkalivibrio | 162 | 2 | 4 | no | Extremophile bacterium |
| Firmicutes | Aerococcaceae | Aerococcus | 128 | 2 | 4 | yes | Facultatitive Anaerobic bacterium |
| Plantomycetes | Planctomycetaceae | Rhodopirellula | 120 | 22 | 1 | no | Marine bacterium |
| Proteobacteria | Aeromonadaceae | Tolumonas | 112 | 4 | 3 | no | Anaerobic soil bacterium |
| Firmicutes | Staphylococcaceae | Macrococcus | 102 | 10 | 2 | no | Skin bacterium |
| Proteobacteria | Rhodospirillaceae | Azospirillum | 100 | 22 | 1 | no | Plant bacterium |
In order to qualify as an MS Candidate Microbe at the genus level, at least one specimen from the MS group had read-pair mappings to this taxa significantly increased (q < 0.05) over the control group with MAPQ values ≥ 10 (84 separate genera). The MS microbial genus candidates shown had at least 100 mapped reads among all the specimens in the MS group (29 genera).
aAs classified in NCBI Taxonomy. Phyla are listed for bacterial and fungal candidates, but not viruses.
bTotal number of the mapped reads to the taxa derived from the entire MS (N = 12) or Control group (N = 15).
cNumber of MS specimens (out of 12) where read mappings to this taxa were significantly increased (q < 0.05) compared to the control group (N = 15).
dCommonly recognized as a human pathogen.
eAs described by MicrobeWiki (https://microbewiki.kenyon.edu/index.php/MicrobeWiki), List of Prokaryotic names with Standing in Nomenclature (LPSN, http://www.bacterio.net), UniProt (https://www.uniprot.org), and other online sources.