Rumen Microbiota Distribution Analyzed by High-Throughput Sequencing after Oral Doxycycline Administration in Beef Cattle

The beef cattle rumen is a heterogenous microbial ecosystem that is necessary for the host to digest food and support growth. The importance of the rumen microbiota (RM) is also widely recognized for its critical roles in metabolism and immunity. The level of health is indicated by a dynamic RM distribution. We performed high-throughput sequencing of the bacterial 16S rRNA gene to compare microbial populations between rumens in beef cattle with or without doxycycline treatment to assess dynamic microbiotic shifts following antibiotic administration. The results of the operational taxonomic unit analysis and alpha and beta diversity calculations showed that doxycycline-treated beef cattle had lower species richness and bacterial diversity than those without doxycycline. Bacteroidetes was the predominant phylum in rumen samples without doxycycline, while Proteobacteria was the governing phylum in the presence of doxycycline. On the family level, the top three predominant populations in group qlqlwy (not treated with doxycycline) were Prevotellaceae, Lachnospiraceae, and Ruminococcaceae, compared to Xanthomonadaceae, Prevotellaceae, and Rikenellaceae in group qlhlwy (treated with doxycycline). At the genus level, the top predominant population in group qlqlwy was unidentified_Prevotellaceae. However, in group qlhlwy, the top predominant population was Stenotrophomonas. The results revealed significant RM differences in beef cattle with or without doxycycline. Oral doxycycline may induce RM composition differences, and bacterial richness may also influence corresponding changes that could guide antibiotic use in adult ruminants. This study is the first to assess microbiota distribution in beef cattle rumen after doxycycline administration.

肉牛瘤胃是一类异质性微生物生态系统，是宿主消化食物、维持生长发育的必需环境。瘤胃微生物群（Rumen Microbiota, RM）在宿主代谢与免疫调控中发挥核心作用，其重要性已获得学界广泛认可。瘤胃微生物群的动态分布状态可反映宿主健康水平。本研究通过细菌16S rRNA基因高通量测序技术，对比了经多西环素处理与未处理的肉牛瘤胃微生物种群，以评估抗生素给药后微生物组的动态变化。操作分类单元（Operational Taxonomic Unit, OTU）分析以及α、β多样性计算结果显示，经多西环素处理的肉牛，其物种丰富度与细菌多样性均低于未处理组。未使用多西环素的肉牛瘤胃样本中，拟杆菌门（Bacteroidetes）为优势菌门；而经多西环素处理组的优势菌门则为变形菌门（Proteobacteria）。在科分类水平上，qlqlwy组（未接受多西环素处理）的前三大优势菌群依次为普雷沃氏菌科（Prevotellaceae）、毛螺菌科（Lachnospiraceae）与瘤胃球菌科（Ruminococcaceae）；而qlhlwy组（接受多西环素处理）的前三大优势菌群则为黄单胞菌科（Xanthomonadaceae）、普雷沃氏菌科与理研菌科（Rikenellaceae）。在属分类水平上，qlqlwy组的优势菌群为未分类普雷沃氏菌科（unidentified_Prevotellaceae）；而qlhlwy组的优势菌群则为寡养单胞菌属（Stenotrophomonas）。研究结果表明，经多西环素处理与未处理的肉牛，其瘤胃微生物群存在显著差异。口服多西环素可能会改变瘤胃微生物群的组成，而细菌丰富度也可能参与介导相应的菌群变化，该结果可为成年反刍动物的抗生素使用提供参考依据。本研究首次评估了多西环素给药后肉牛瘤胃微生物群的分布特征。