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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)