Table 2.
Main species constituting the microbiota in non-SPF animals
| Phylum | Class | Order | Family | Genus | Species | Species ID | |
|---|---|---|---|---|---|---|---|
| Bacteroidetes (49.6%) | Bacteroidia (49.6%) | Bacteroidales (49.6%) | Bacteroidaceae (7.7%) | Bacteroides (7.7%) | Bacteroides caecimuris | 1796613 | "Non-SPF—core species" (90.3%) |
| Muribaculaceae (41.9% | Duncaniella (8.7%) | Duncaniella sp. B8 | 2576606 | ||||
| Duncaniella sp. C9 | 2530392 | ||||||
| Muribaculum (33.2%) | Muribaculum sp. H5 | 2530393 | |||||
| Muribaculum sp. TLL-A4 | 2530390 | ||||||
| Muribaculum intestinale | 1796646 | ||||||
| Firmicutes (16.6%) | Bacilli (9.5%) | Lactobacillales (9.5%) | Enterococcaceae (0.3%) | Enterococcus (0.3%) | Enterococcus faecalis | 1351 | |
| Lactobacillaceae (9.2%) | Lactobacillus (9.2%) | Lactobacillus johnsonii | 33959 | ||||
| Lactobacillus murinus | 1622 | ||||||
| Lactobacillus reuteri | 1598 | ||||||
| Clostridia (7.1%) | Clostridiales (7.1%) | Clostridiaceae (0.3%) | Mordavella (0.3%) | Mordavella sp. Marseille-P3756 | 2086584 | ||
| Lachnospiraceae (3.8%) | Lachnoclostridium (3.3%) | [Clostridium] scindens | 29347 | ||||
| Lachnoclostridium phocaeense | 1871021 | ||||||
| Lachnoclostridium sp. YL32 | 1834196 | ||||||
| Unknown (0.5%) | Lachnospiraceae bacterium GAM79 | 2109691 | |||||
| Oscillospiraceae (0.1%) | Unknown (0.1%) | Oscillospiraceae bacterium J115 | 2093857 | ||||
| Peptostreptococcaceae (1.6%) | Clostridioides (1.6%) | Clostridioides difficile | 1496 | ||||
| Ruminococcaceae (0.9%) | Faecalibacterium (0.7%) | Faecalibacterium prausnitzii | 853 | ||||
| Flavonifractor (0.2%) | Flavonifractor plautii | 292800 | |||||
| Unknown (0.4%) | Unknown (0.4%) | Clostridiales bacterium CCNA10 | 2109688 | ||||
| Proteobacteria (20.3%) | Epsilonproteobacteria (20.3%) | Campylobacterales (20.3%) | Helicobacteraceae (20.3%) | Helicobacter (20.3%) | Helicobacter typhlonius* | 76936 | |
| Helicobacter hepaticus* | 32025 | ||||||
| Actinobacteria (1.3%) | Actinobacteria (1.3%) | Bifidobacteriales (1.3%) | Bifidobacteriaceae (1.3%) | Bifidobacterium (1.3%) | Bifidobacterium pseudolongum | 1694 | |
| Verrucomicrobia (2.4%) | Verrucomicrobiae (2.4%) | Verrucomicrobiales (2.4%) | Akkermansiaceae (2.4%) | Akkermansia (2.4%) | Akkermansia muciniphila | 239935 |
*Pathogens
List of the twenty-four species with an average abundance higher than 1% ("Conventional-core species"), constituting 90.3% of bacteria present in the gut of non-SPF mice. Taxonomy from phylum to specie level is shown. The different lines represent the species included in the list. For each species there are columns that describe the taxonomy (phylum, class, order, family, genus, species, Species ID)