Scripts and data for: Increased host diversity limits bacterial generalism but may promote microbe-microbe interactions

Research Overview: In this project, we compared cloacal microbiome communities from reptiles from six localities that spanned a gradient in host taxonomic diversity. We found that diversity of the bacterial communities was relatively stable across locations, but that host-specific taxa were overrepresented in high host diversity communities. ASVs in high host diversity communities were more likely to have strong interactions with other bacterial lineages across multiple hosts. Host generalist bacteria were more likely to be from a generalist phylum.

Methodology: We used a 16S rRNA metabarcoding approach to quantify bacterial community diversity. We processed the output fastq files using qiime2, and processed the output files using the qiime2R package. We performed our analyses in R. Processed input files and scripts are described below.