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Table 2 Main species constituting the microbiota in non-SPF animals

From: A comprehensive approach for microbiota and health monitoring in mouse colonies using metagenomic shotgun sequencing

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
  1. *Pathogens
  2. 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)