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

生物 基因组 基因组 微生物群 基因组学 进化生物学 系统发育学 生态学 动物 数据库 遗传学 基因 计算机科学
作者
Chengfeng Yang,Jiawei Hu,Qinzhi Su,Zijing Zhang,Yating Du,Jieni Wang,Huihui Sun,Benfeng Han,Junbo Tang,Lizhen Guo,Hu Li,Wanzhi Cai,Hao Zheng,Xin Zhou,Xue Zhang
出处
期刊:Insect Science [Wiley]
被引量:5
标识
DOI:10.1111/1744-7917.13365
摘要

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.
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