Skip to main content

Table 1 Main species constituting the microbiota in 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 (50.7%) Bacteroidia (50.7%) Bacteroidales (50.7%) Bacteroidaceae (5.7%) Bacteroides (5.7%) Bacteroides caecimuris 1796613 "SPF -core species" (91.4%)
Muribaculaceae (45%) Duncaniella (9.9%) Duncaniella sp. B8 2576606
Duncaniella sp. C9 2530392
Muribaculum (35.1%) Muribaculum intestinale 1796646
Muribaculum sp. H5 2530393
Muribaculum sp. TLL-A4 2530390
Firmicutes (16.6%) Bacilli (6.3%) Lactobacillales (6.3%) Enterococcaceae (4.3%) Enterococcus (4.3%) Enterococcus faecalis 1351
Lactobacillaceae (2%) Lactobacillus (2%) Lactobacillus johnsonii 33959
Clostridia (33.3%) Clostridiales (33.3%) Clostridiaceae (3.2%) Mordavella (3.2%) Mordavella sp. Marseille-P3756 2086584
Lachnospiraceae (13.7%) Lachnoclostridium (11.3%) [Clostridium] scindens 29347
Lachnoclostridium phocaeense 1871021
Lachnoclostridium sp. YL32 1834196
Unknown (2.4%) Lachnospiraceae bacterium GAM79 2109691
Oscillospiraceae (1%) Unknown (1%) Oscillospiraceae bacterium J115 2093857
Peptostreptococcaceae (5%) Clostridioides (5%) Clostridioides difficile 1496
Ruminococcaceae (8.6%) Faecalibacterium (5.2%) Faecalibacterium prausnitzii 853
Flavonifractor (3.3%) Flavonifractor plautii 292800
Unknown (1.8%) Unknown (1.8%) Clostridiales bacterium CCNA10 2109688
Erysipelotrichia (1.1%) Erysipelotrichales (1.1%) Erysipelotrichaceae (1.1%) Faecalitalea (1.1%) Faecalitalea cylindroides 39483
  1. List of the nineteen species with an average abundance higher than 1% ("SPF-core species"), comprising 91.4% of bacteria present in the gut of the 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)