Supplementary Tables.pdf

Bumble bees are key pollinators with gut microbiotas that support host health. After bumble bee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumble bee queen gut microbiota community structure and metabolic potential shift during and after diapause, and if post-diapause recovery is affected by pesticide exposure. We euthanized commercial <i>Bombus impatiens</i> queens before and during diapause. Additionally, we allowed some queens to recover from diapause for one week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut phylotypes dominated communities before, during, and after diapause, but that two phylotypes, <i>Schmidhempelia </i>and <i>Snodgrassella</i>, ceased to be detected in queen microbiotas during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Also, glyphosate exposure did not affect post-diapause microbiota recovery. However, we also found that metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways varied with microbial abundance. Our study offers new insights into how bumble bee queen gut microbiotas change taxonomically and functionally during a key life stage, and provides guidance for future microbiota studies in diapausing bumble bees.

熊蜂是支撑宿主健康的关键传粉昆虫。在春季蜂群建立前经历越冬滞育的熊蜂蜂王，其肠道微生物群会发生紊乱，但目前学界对滞育过程中微生物群落的动态变化仍知之甚少。蜂王肠道微生物群还可作为工蜂肠道微生物群的定植接种源，因此滞育后恢复至典型群落结构至关重要，而农药暴露可能会阻碍这一恢复过程。
本研究旨在探究熊蜂蜂王肠道微生物群的群落结构与代谢潜能在滞育期间及滞育后的变化规律，以及滞育后的微生物群恢复是否会受到农药暴露的影响。研究人员对商业化养殖的*Bombus impatiens*蜂王在滞育前及滞育期间进行了安乐处死。此外，部分蜂王在滞育结束后恢复饲养一周再行处死，其中一半个体暴露于常见除草剂草甘膦。
通过全群落鸟枪宏基因组测序技术，研究团队发现：在滞育前、滞育期间及滞育后，核心熊蜂肠道系统型在群落中占据主导地位，但两类系统型——*Schmidhempelia*与*Snodgrassella*——在滞育后期及恢复阶段的蜂王微生物群中未再被检测到。尽管分类群落结构存在波动，但代谢潜能在整个滞育及恢复阶段均保持稳定。同时，草甘膦暴露并未对滞育后的微生物群恢复产生影响。
但研究同时发现，宏基因组组装质量以及我们检测微生物类群与代谢通路的能力，会随微生物丰度的变化而发生改变。本研究为熊蜂蜂王肠道微生物群在这一关键生命阶段的分类学与功能学变化提供了全新视角，并为未来针对滞育熊蜂的肠道微生物群研究提供了参考指导。