Data from: Geographically widespread honeybee-gut symbiont subgroups show locally distinct antibiotic-resistant patterns

How long-term antibiotic treatment affects host bacterial associations is still largely unknown. The honeybee-gut microbiota has a simple composition, so we used this gut community to investigate how long-term antibiotic treatment affects host-associated microbiota. We investigated the phylogenetic relatedness, genomic content (GC percentage, genome size, number of genes, and CRISPR), and antibiotic-resistant genes for strains from two abundant members of the honeybee core gut microbiota (Gilliamella apicola and Snodgrassella alvi). Domesticated honeybees are subjected to geographically different management policies, so we used two research apiaries, representing different antibiotic treatment regimens in their apiculture: Low antibiotic usage (Norway) and high antibiotic usage (Arizona, USA). We applied whole-genome shotgun sequencing on 48 G. apicola and 22 S. alvi. We identified three predominating subgroups of G. apicola in honeybees from both Norway and Arizona. For G. apicola, genetic content substantially varied between subgroups and distance-similarity calculations showed similarity discrepancy between subgroups. Functional differences between subgroups, such as pectin-degrading enzymes (G. apicola), were also identified. In addition, we identified horizontal gene transfer (HGT) of transposon- (Tn10) associated tetracycline resistance (Tet B) across the G. apicola subgroups in the Arizonan honeybees, using interspace polymorphisms in the Tet B determinant. Our results support that honeybee-gut symbiont subgroups can resist long-term antibiotic treatment and maintain functionality through acquisition of geographically distinct antibiotic-resistant genes by HGT.

长期抗生素治疗对宿主细菌共生关系的影响，目前仍不明晰。蜜蜂肠道菌群（honeybee-gut microbiota）组成相对简单，因此本研究以该肠道菌群为模型，探究长期抗生素治疗对宿主相关菌群的影响。我们针对蜜蜂核心肠道菌群（honeybee core gut microbiota）的两个优势类群——吉氏杆菌（Gilliamella apicola）与斯诺氏菌（Snodgrassella alvi）的菌株，分析了其系统发育相关性、基因组组成（GC含量、基因组大小、基因数量及成簇规律间隔短回文重复序列（CRISPR））与抗生素耐药基因。家养蜜蜂受地域差异的养殖管理政策影响，因此本研究选取两个研究蜂场，分别代表养蜂业中两类不同的抗生素治疗方案：低抗生素使用量组（挪威）与高抗生素使用量组（美国亚利桑那州）。我们对48株吉氏杆菌与22株斯诺氏菌进行了全基因组鸟枪测序（whole-genome shotgun sequencing）。我们在挪威与美国亚利桑那州的蜜蜂样本中，均鉴定出吉氏杆菌的三个优势亚群。对于吉氏杆菌而言，不同亚群间的遗传物质组成存在显著差异，距离相似性分析结果显示亚群间的相似性存在偏差。此外，亚群间还存在功能差异，例如吉氏杆菌的果胶降解酶相关功能。另外，本研究通过四环素耐药基因（Tet B）决定区的间隔多态性分析，在亚利桑那州蜜蜂的吉氏杆菌亚群中，鉴定出与转座子（transposon）Tn10相关的四环素耐药基因的水平基因转移（Horizontal Gene Transfer, HGT）事件。本研究结果表明，蜜蜂肠道共生菌亚群可通过水平基因转移获取地域特异性的抗生素耐药基因，从而耐受长期抗生素治疗并维持其原有功能。