Assessing bacteria that distinguish bee species and are core to Xylocopa
To identify bacterial taxa that differ between host species and tissue type, we compared relative abundance of ASVs between bee species and tissues using DESeq2 (Love et al. 2013), with a false discovery rate FDR <0.05.
To identify if a core bacterial community was shared between the guts ofX. sonorina and X. tabaninformis bees, individual ASVs were first collapsed at the genus_species level usingtax_glom(). The function eulerr::core_members() was then used to identify genus_species bins present at ≥ 0.01% relative abundance in at least 95% of gut samples and heatmaps constructed to visualize the number of shared core taxa.