3.2 α‐diversity of gut bacteria according to host information
A sample of mock community containing known concentrations of genomic DNA from 20 bacterial strains was sequenced. 19 of the 20 different strains originally included in the sample were detected. The undetected strain was present at the lowest concentration. Therefore, our protocol allowed bacterial DNA detection and identification to the genus level as long as its concentration in the DNA extract was at least 2.8 pg/μl, and provided that the sequence was included in the reference database.
After reads processing, a total read count of 624,796 was obtained for gut microbial communities in captive E-mink, with an average counts per sample of 26,033 after rarefaction to limit sequencing depth artifacts. A total number of 5703 ASVs – or phylotypes – were distinguished in the samples. The gut microbiota of the E-mink was mostly composed of theFirmicute phylum (74%), which was dominated by theClostridiaceae and Peptostreptococcaceae families, followed by Proteobacteria (14%) with Enterobacteriaceae ,Moraxellaceae and Pseudomonadaceae families (Figure 2).
Despite an overall observation of lower microbial richness in the western compared to the eastern populations, no significant results were observed in multiple microbial richness indices (Shannon index, Chao1; Figure 3). However, we did observe slightly lower Faith’s PD in western compared to eastern individuals (χ2= 2.8834, p-value = 0.0895). Western females had significantly lower microbial phylogenetic diversity compared to males (Figure 3). Despite not reaching statistical significance (R2=0.1626, F=0.5502, p-value=0.7633), linear regression models with alpha diversity measures as response variables showed negative correlations with adaptive genetic richness measures, and particularly strong estimates for MHC-I richness (Figure S4).