Abstract：
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.
摘要：
蜜蜂和大黄蜂作为必不可少的传粉媒介起着至关重要的作用。社交蜜蜂的特殊肠道微生物群是决定宿主整体健康和健康的关键因素。尽管蜜蜂在属一级拥有相对简单的微生物群落，最近的研究揭示了每个细菌属内显著的遗传差异和基因含量的变异。然而,仍然缺乏针对社交蜜蜂肠道微生物组的全面和完善的基于基因组学的分类数据库。这里,我们首先概述了有关社交蜜蜂肠道细菌的分布和功能的当前知识，以及影响肠道种群动态的因素。然后，我们合并了社交蜜蜂肠道细菌的所有可用基因组，并完善了物种级分类法，通过构建最大似然核心基因组系统发育并计算全基因组成对平均核苷酸同一性。在完善的物种分类法的基础上，我们构建了一个精选的基因组参考数据库，命名为蜜蜂肠道微生物基因组序列数据库(BGM-GDb)。为了评估策划的BGM-GDb的物种剖面性能，我们检索了一系列蜜蜂肠道宏基因组数据，并使用宏基因组种内多样性分析系统（MIDAS）推断物种水平的组成，然后将结果与从预构建的MIDAS数据库中获得的结果进行比较。我们发现与默认数据库相比，BGM-GDb在对齐读数计数和细菌丰富度方面表现出色。总的来说,这个高分辨率和精确的基因组参考数据库将有助于研究了解社会蜜蜂的肠道群落结构。
