These data are the result of analyses of the metagenome of North American bats, including 18s and 16s barcode genes designed to target microorganisms of the gut. These files are Phyloseq import files created by the DADA2 program. Each barcode gene is uploaded separately as the four files required to build a phyloseq object. For each barcode gene, the files include amplicon sequence variant (ASV) sequences, sequence tables (seqtab) which connect individual samples to the ASVs, tax tables (taxtab) which identify the taxa present as determined by a Bayesian RDP classifier, and rooted phylogenetic trees for the ASVs. Additionally, we have included a "sample_data" file which is necessary for sorting of samples across all four sequence analysis data sets by study and species. Some sample information which could identify the location of endangered species has been restricted. Multiple studies are represented in the data which can be accessed using standard methods in the Phyloseq program (e.g. For a study of bats, parasites, and gut microbiome dysregulation by Bennett, Suski, and OKeefe 2024 [in prep March 2024], study specific data can be accessed using the Study variable "DYSBIOMICS." File names include reference to the primer set used to generate them (18s primer sets: G3, G4, G6; 16s primer set: 341F3_806R5).