Supplementary Figure 1: Taxonomic annotation of the mouse catalogue.

(a) Taxonomic annotation of the 2.6M mouse catalogue to the superkingdom, phylum, genus and species levels. 60.31 % of the genes in the catalogue were annotated to the phylum level, whereas only 9.84% of these genes could be annotated to the genus level, and further only 1.40% of these could be annotated at the species level. (b) Taxonomic annotation of bacterial genus profiles of the mouse catalogue based on alignments against the NR and HMP databases, respectively. The mice from different providers exhibit significantly different taxonomic structures, especially prominent for mice from Taconic Denmark (TDK). Of note significantly more genes in the microbiomes of mice from TDK (unit 1-9) map to the HMP database, contrasting the microbiomes of mice from other providers (units 10-25). See supplementary table S1 for further information on the units. (c) The taxonomical distribution of the top 6 phyla and genera in the mouse catalogue compared with the 4.3M human catalogue. The percentage of the genes assigned to the Firmicutes phylum is about 20% higher in the mouse microbiome compared with the human microbiome, whereas the percentage of genes assigned to the Bacteroidetes in mouse microbiome is almost 50% lower than in the human microbiome. Thus, the ratio of Firmicutes to Bacteroidetes is markedly different in mice and humans.