DOI: 10.5061/dryad.gqnk98t2c
title: Microbial communities of wild bees and comparative phylogenetics of key bacterial taxa across the bee tree of life

description: Recent years have seen a rapidly growing interest in the study of
 microbiomes across many animals to understand their health and well-being.
 Within bees, much of this work has focused on managed species of
 agricultural importance, such as honey bees and bumble bees. However,
 unmanaged wild bees are also vital to both agricultural and natural
 systems, and studying their microbial associates is essential to better
 understand the impacts of microbiomes on bee health. We used metabarcoding
 based on 16S and ITS1 loci to identify the bacterial and fungal associates
 of adult bees from 16 species representing a diverse sampling of wild bees
 common to eastern North America. We measured alpha and beta diversity
 across these species which span 10 genera and five families. Additionally,
 we conducted a broad phylogenetic comparison of bacterial communities
 across bees using previously published 16S datasets, and contrasted these
 findings with functional and life history traits across the bee tree of
 life. This study provides expanded insights into the adult microbial
 associates of wild bees, as well as the broadest investigation to date
 into patterns of phylogenetic conservation in bacterial communities across
 a total of 42 species representing the five most diverse bee families.
description: # Microbial communities of wild bees and comparative phylogenetics of key
 bacterial taxa across the bee tree of life
 [https://doi.org/10.5061/dryad.gqnk98t2c](https://doi.org/10.5061/dryad.gqnk98t2c) Supplementary Data Files Sless et al. 2025, Proceedings of the Royal Society B, doi: 10.1098/rspb.2025.1823 "Microbial communities of wild bees and comparative phylogenetics of key bacterial taxa across the bee tree of life" `Sless_et_al_rspb.2025.1823_Rscript.R`: R script including phyloseq analyses of 16S and ITS1 datasets, statistical tests, and phylogenetic comparisons (R version 4.3.2) `Genbank_accessions.xlsx`: Spreadsheet of all samples with corresponding GenBank BioSample and SRA Accessions (read files are available through BioProject PRJNA1124100) `table_16S.qza`: QIIME2 feature table of 16S reads from all samples. Includes up to 3 replicates of 421 total samples (373 bees, 48 blank/control) `table_ITS1.qza`: QIIME2 feature table of ITS1 reads from all samples. Includes up to 3 replicates of 422 total samples (373 bees, 49 blank/control) `metadata_16S.txt`: Metadata file with sample variables for 16S sequence samples (again including up to 3 replicates) `metadata_ITS1.txt`: Metadata file with sample variables for ITS1 sequence samples (again including up to 3 replicates) `taxonomy_16S.txt`: Taxonomy file for all 16S ASVs based on consensus of top 10 BLAST hits supplemented by feature classification with SILVA database taxonomy_ITS1.txt: Taxonomy file for all ITS1 ASVs based on consensus of top 10 BLAST hits supplemented by feature classification with UNITE database `16S_full_ASV_table.xlsx`: Raw ASV table from 16S dataset including all samples (with replicates merged) and all 16S taxa (ASVs) `16S_filtered_ASV_table.xlsx`: ASV table from 16S dataset after taxon and sample filtering steps. Samples with &lt;1000 reads were dropped, as well as non-bacterial taxa and taxa identified as contaminants or intracellular endosymbionts `16S_genglom_ASV_table.xlsx`: As above filtered ASV table from 16S dataset, but with ASVs agglomerated by genus `ITS1_full_ASV_table.xlsx`: Raw ASV table from ITS1 dataset including all samples (with replicates merged) and all ITS1 taxa (ASVs) `ITS1_filtered_ASV_table.xlsx`: ASV table from ITS1 dataset after taxon and sample filtering steps. Samples with &lt;1000 reads were dropped, as well as non-fungal taxa and taxa identified as contaminants `ITS1_genglom_ASV_table.xlsx`: As above filtered ASV table from ITS1 dataset, but with ASVs agglomerated by genus `BEE_prunedtree.nexus`: Phylogeny of bee species used for phylogenetic comparisons, obtained from beetreeoflife.org (Henríquez-Piskulich et al. 2024) `phylogeny_bacteria_matrix.csv`: Prevalence of selected bacterial taxa for all 42 bee species in phylogeny, based on our dataset as well as previously published data covering other species (Cohen et al. 2020; Figueroa et al. 2021; Holley et al. 2022; Kwong et al. 2017; Nguyen & Rehan 2023; Ronchetti et al. 2022)