3.3 β‐diversity of gut bacteria between E-mink and differential abundance
Beta diversity analyses revealed that bacterial communities were significantly different in composition according to E-mink population only when considering unweighted Unifrac distances, whereas no significant differences in microbial community composition were found between host sexes nor birth locations (Models 4 and 6, Table 2). Moreover, MHC-II gene richness had a small significant influence on gut microbial composition (Model 5, Table 2). This is reflected in the results of the PCoA, which clustered individuals with differences in number of MHC-II motifs (Figure 4). Mantel tests also shown a significant positive correlation between unweighted Unifrac distance and MHC-II genetic distance (Mantel: r=0.4811, p-value=0.019), and despite not reaching statistical significance, a negative correlation with MHC-I genetic distance (Mantel: r=-0.0823, p-value=0.862) and close to zero for neutral markers’ distance (Mantel: r=0.0065, p-value=0.229).
We recovered several bacterial genera and families whose relative abundances were significantly correlated with MHC-I and MHC-II richness and divergence, while some marginally correlated with multilocus heterozygosity of neutral markers (Table 3). A majority (65%) of the Pearson correlations appeared to be negative between bacterial genera and genetic indexes. Differential abundance analysis in microbial families according to presence of MHC motifs for both genes between E-mink populations detected a significant increase in abundance for 13 families in the eastern population, for 8 in western E-mink (Figure 5).
From the differential abundance analysis, 22 phylotypes were found to be significantly different in abundance according to MHC motifs presence. MHC-I motifs explained the variation of 3 phylotypes, and only impacted the Clostridiaceae family (Clostridium sensu stricto 1). MHC-II motifs presence was attributed to the altered the abundance of 14 microbial phylotypes and those were mostly more abundant in the eastern E-mink as 13 phylotypes were more abundant in eastern E-mink against one in the western E-mink. MHC-II motifs impacted over twelve genera compared to one for MHC-I motifs. It is also worth noting that both MHC-I and MHC-II motifs presence were observed to alter taxa abundance for 5 phylotypes, mostly from the Proteobacteria phylum (Table 4). The MHC-II motifs KM371114_EU263551, EU263554_EU263552_EU263556, and Mulu:DRB*90701 respectively took part in the variation in abundance for 17, 15 and 12 phylotypes respectively. MHC-I motif Mulu:MHC-I*00008 was significantly involved in the variation for 4 phylotypes, whereas the other motifs had relatively low impact, as they took part in abundance variation of 1-2 families.