Fig. 4

Differential abundance of cotton rat gut taxa and corresponding pathways using whole-genome metagenomic sequencing. a Hierarchical clustering (Bray-Curtis) of the top 25 most differentially abundant bacterial species between S. fulviventer vs. S. hispidus. Lactobacillus reuteri and L. gasseri were drastically more abundant in S. hispidus stool, while Akkermansia muciniphila was more abundant in S. fulviventer stool. b Distribution of MetaCyc metabolomic pathways predicted from bacterial sequences. All 418 unique pathways found were represented in S. hispidus, and 334 were shared between S. hispidus and S. fulviventer. Most pathways were classified within the Biosynthesis, Superpathway, and Degradation/Utilization/Assimilation pathway superclasses. c Distribution of pathway ontology for both S. hispidus and S. fulviventer. Of all the identified pathways, the largest group consisted of Cofactor, Prosthetic Group, Electron Carrier, and Vitamin Biosynthesis, which are often components of host biology sourced solely by commensal bacteria