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.

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 <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 <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)

Microbial communities of wild bees and comparative phylogenetics of key bacterial taxa across the bee tree of life

Data files

Abstract

Microbial communities of wild bees and comparative phylogenetics of key bacterial taxa across the bee tree of life

Data files

Abstract

README: Microbial communities of wild bees and comparative phylogenetics of key bacterial taxa across the bee tree of life