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Fig. 3 | Animal Microbiome

Fig. 3

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

Fig. 3

Comparison of mouse gut microbiome in SPF and non-SPF facilities. a Phylum level. Graph represents phyla (average greater than 100 ppm in at least one of the two groups of samples) in SPF and non-SPF samples: there are no differences relating to the abundance of Bacteroidetes (53% in both SPF and non-SPF mice), while Firmicutes represent 45% and 19% in SPF and non-SPF mice, respectively. Proteobacteria represent 0.4% of phyla in the SPF mice, while they constitute the most abundant phylum (24%) in the non-SPF mice. Verrucomicrobia and Actinobacteria are significantly more abundant in the non-SPF mice (2% and 1%, respectively) than in the SPF mice (0.04% and 0.4%, respectively). The less abundant Phyla represent 0.5% (in SPF mice) and 0.3% (in non-SPF mice) of the total. b Family level. Graph represents families, with average above 100 ppm in both groups of samples, except for Helicobacteraceae which are absent in the SPF mice, but are the second largest family (20%) in the non-SPF mice. Muribaculaceae is confirmed as the most abundant family in both groups (46% in the SPF and 42% in the non-SPF). Bacteroidaceae represents 8% and 9% and Lactobacillaceae 3% and 9% of families in the SPF and non-SPF mice, respectively. Lachnospiraceae family is reduced in the non-SPF (5%) compared to SPF (16%) mice. c Phylogenic tree of microbiome species. Images represent bacterial composition of gut microbiome in the non-SPF and SPF samples. Branches represent taxonomic classification and nodes represent transition to the subsequent taxonomy level, from super kingdom to species level. Thickness and color of branches represent abundance difference. With respect to the SPF samples, in the non-SPF ones there is a noticeable increase of Proteobacteria and to a lesser extent of Verrucomicrobia, and a decrease of Firmicutes. A greater number of species is also appreciable in the non-SPF samples compared to the SPF ones

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