摘要

    肠道菌群是抗生素抗性基因（ARG）的库。然而，关于肠道菌群中ARG的存在（基因组DNA水平）和表达模式（转录组RNA水平）的信息有限。在这里，我们同时使用了宏基因组学和超转录组学方法，全面揭示了中国人，鸡和猪肠道微生物区系中ARG的丰度，多样性和表达。根据深度测序数据和ARG数据库，在18例人，鸡和猪粪便样本中共鉴定出与21种抗生素相关的330种ARG。元转录组学分析表明，分别在人，鸡和猪肠道菌群中鉴定出的ARGs分别占49.4％，66.5％和56.6％，这表明很大比例的ARGs没有转录活性。进一步的分析表明，四环素，氨基糖苷和β-内酰胺抗性基因的转录本丰度主要是由获得性ARG引起的。我们还发现，各种杀生物剂，化学和金属抗性基因均在人类和动物的肠道中被主动转录。这项研究中宏基因组学和元转录组学分析相结合，使我们能够将ARGs与它们的转录本特异性连接，从而全面了解肠道菌群中ARGs的流行和表达。综上所述，这些数据加深了我们对人，鸡和猪肠道菌群中ARG和金属抗性基因的分布，进化和传播的理解。

    Gut microbiota is a reservoir of antibiotic resistance genes (ARGs). Yet, limited information is available regarding the presence (metagenomic DNA level) and expression profiles (metatranscriptomic RNA level) of ARGs in gut microbiota. Here, we used both metagenomic and metatranscriptomic approaches to comprehensively reveal the abundance, diversity, and expression of ARGs in human, chicken, and pig gut microbiomes in China. Based on deep sequencing data and ARG databases, a total of 330 ARGs associated with 21 antibiotic classes were identified in 18 human, chicken, and pig fecal samples. Metatranscriptomic analysis revealed that 49.4, 66.5, and 56.6% of ARGs identified in human, chicken, and pig gut microbiota, respectively, were expressed, indicating that a large proportion of ARGs were not transcriptionally active. Further analysis demonstrated that transcript abundance of tetracycline, aminoglycoside, and beta-lactam resistance genes was mainly contributed by acquired ARGs. We also found that various biocide, chemical, and metal resistance genes were actively transcribed in human and animal guts. The combination of metagenomic and metatranscriptomic analysis in this study allowed us to specifically link ARGs to their transcripts, providing a comprehensive view of the prevalence and expression of ARGs in gut microbiota. Taken together, these data deepen our understanding of the distribution, evolution, and dissemination of ARGs and metal resistance genes in human, chicken, and pig gut microbiota.

    https://www.sciencedirect.com/science/article/pii/S0160412019349918