摘要
      牲畜粪便中抗生素耐药性基因（ARGs）的风险越来越大，这引起了全球的关注。然而，粪便微生物群中ARGs的节律性活动是如何变化的，这在很大程度上仍不清楚。在我们的研究中，我们在72小时内每6小时从蛋鸡身上收集52份新鲜粪便样本，并使用基于组装宏基因组鸟枪测序的方法来表征细菌和ARGs的昼夜节律振荡。我们发现，14%的共生细菌分类单元在24小时内波动。281个ARGs中有33个和574个移动遗传元件（MGE）中有17个在粪便中具有节律模式。lnuC和ANT（6）H-lb是从粪便中鉴定出的具有昼夜节律振荡的两种最丰富的ARG，它们在白天增加，在晚上减少。与短链脂肪酸（SCFA）代谢相关的392条MetaCyc途径中的乙酸盐、丁酸盐、丙酸盐和78条具有昼夜节律振荡。对上述ARG-其他元素连接的评估显示，17个ARG与粪便中的7个MGE、2个SCFA（乙酸盐和丙酸盐）和细菌物种表现出强烈的相关性。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24小时内ARG的综合图谱，并揭示了ARG的昼夜节律振荡，这受到关键细菌物种、MGE和代谢产物的影响。总之，我们的发现促进了对粪便微生物群中ARGs昼夜节律振荡的理解，并为ARGs的控制和管理提供了参考。
Abstract
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.

https://www.sciencedirect.com/science/article/abs/pii/S0048969722027887