A review on recent taxonomic updates of gut bacteria associated with social bees, with a curated genomic reference database

Honeybees and bumblebees play a crucial role as essential pollinators. The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host. Although bees harbor relatively simple microbial communities at the genus level, recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus. However, a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking. Here, we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria, as well as the factors that influence the gut population dynamics. We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy, by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity. On the basis of the refined species taxonomy, we constructed a curated genomic reference database, named the bee gut microbe genome sequence database (BGM-GDb). To evaluate the species-profiling performance of the curated BGM-GDb, we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system (MIDAS), and then compared the results with those obtained from a prebuilt MIDAS database. We found that compared with the default database, the BGM-GDb excelled in aligned read counts and bacterial richness. Overall, this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees. Social corbiculate bees harbor relatively simple microbial communities at the phylotypes level, however, genetic diversification is prevalent below phylotypes, i.e. at the species or strain level. Additionally, the genetic diversity and gene repertoires of bacterial isolates vary substantial between host species. This diverse gut microbiota exerts multifaceted effects on the host, such as diet digestion, nutrient provision, pathogen resistance, immune modulation, endocrine signaling, among others. In particular, the gut microbiota is primarily responsible for the digestion and fermentation of dietary carbohydrates, including sugars toxic to the bee host, as well as defense against various bee pathogens. To deeply understand the diversity and functions of bee gut microbiota, an accurate species-level taxonomy is fundamental and necessary. For each phylotype, the species-level taxonomy is refined by constructing a maximum-likelihood core genome phylogeny and by calculating genome-wide pairwise average nucleotide identity. The curated genomic taxonomy will greatly facilitate research on the gut community structure of social bees. image