Phylogenetic analysis: core taxa ASVs display a high degree of host specificity
Phylogenetic and strain-level analysis suggests that the majority of the ASVs comprising core gut bacteria are host-specific (Figure 3, Figure 4). In contrast only a few ASVs span host species and locations, including the most abundant Lactobacillus sequence (ASV9). Moreover, while some ASVs are found at multiple geographic sampling locations, some are highly location-specific, particularly inBombilactobacillus and Bombiscordovia.
Bombilactobacillus bombi ASVs grouped into two clades (Figure 3b). One contained a known B. bombi isolated from bumble bees andB. mellis , isolated from honey bees while the other clade was phylogenetically distinct, detected only in X. sonorina , and found at all locations (Figure 3b). Lactobacillus bxid5692 ASVs formed a clade that was distinct from previous L. apis and aside from the most abundant ASV, was found primarily in X. sonorina(Figure 3c). The Bifidobacteriaceae genus Bombiscardovia coagulans also grouped into two clades, one of which contained a knownB. coagulans isolated from bumble bees; the other more closely related to the newly described B. xylocopae . We detected extensive strain-level diversity within Bombiscordovia (Figure 4). Sequence variants were exclusively restricted to a single species and were often location-specific.