Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
Sci Total Environ. 2022 Aug 25;836:155692. doi: 10.1016/j.scitotenv.2022.155692. Epub 2022 May 4.
The increasing risks of antibiotic resistance genes (ARGs) in livestock feces have attracted global attention. However, how the rhythmic activity of ARGs changes in fecal microbiota remains largely unclear. In our study, we collected 52 fresh fecal samples every 6 h over 72 h from laying hens and characterized circadian oscillations of bacteria and ARGs using an approach based on assembled metagenome shotgun sequencing. We found that 14% of commensal bacterial taxonomic units fluctuated over 24 h. A total of 33 out of 281 ARGs and 17 of 574 mobile genetic elements (MGEs) featured rhythmic patterns in feces. lnuC and ANT(6)H-lb were the two most abundant ARGs with circadian oscillation identified from feces, and they increased during the day and decreased at night. Acetate, butyrate, propionate, and 78 out of 392 MetaCyc pathways relating to short-chain fatty acid (SCFA) metabolism featured circadian oscillations. Assessment of the above ARG-other element connections revealed that 17 ARGs presented strong correlations with 7 MGEs, and 2 SCFAs (acetate and propanoate) and bacterial species in feces. Structural equation model (SEM) analysis showed that ARGs were directly affected by microbial β-diversity and MGEs. These results showed a comprehensive map of ARGs over 24 h and revealed circadian oscillations of ARGs, which are influenced by key bacterial species, MGEs, and metabolites. Together, our findings advance comprehension of circadian oscillations of ARGs in the fecal microbiota and provide a reference for ARGs control and management.
肠道微生物中抗生素耐药基因（ARGs）的风险日益增加引起了全球关注。然而，肠道微生物中 ARGs 的节律性活动如何变化在很大程度上仍不清楚。在我们的研究中，我们从产蛋母鸡中每 6 小时收集 52 个新鲜粪便样本，持续 72 小时，并通过组装宏基因组鸟枪法测序来研究细菌和 ARGs 的昼夜节律波动。我们发现，14%的共生细菌分类单元在 24 小时内波动。在粪便中，共有 33 个 ARG 和 17 个移动遗传元件（MGE）具有节律模式。从粪便中鉴定出 lnuC 和 ANT(6)H-lb 是两种最丰富的具有昼夜节律波动的 ARG，它们在白天增加，晚上减少。乙酸盐、丁酸盐、丙酸盐和 392 个与短链脂肪酸（SCFA）代谢相关的 MetaCyc 途径中的 78 个途径具有昼夜节律波动。对上述 ARG-其他元素连接的评估表明，17 个 ARG 与 7 个 MGE 和 2 个 SCFAs（乙酸盐和丙酸盐）以及粪便中的细菌物种具有很强的相关性。结构方程模型（SEM）分析表明，ARGs 直接受到微生物β多样性和 MGE 的影响。这些结果显示了 ARGs 在 24 小时内的综合图谱，并揭示了 ARGs 的昼夜节律波动，这受关键细菌物种、MGE 和代谢物的影响。总之，我们的研究结果提高了对肠道微生物中 ARGs 昼夜节律波动的理解，并为 ARGs 的控制和管理提供了参考。
