摘要
      水生微生物群落是抗生素抗性基因（ARGs）的重要库。然而，不同ARG类别在具有不同生态策略的环境微生物中的分布和多样性尚未得到很好的研究。尽管里海南部可能暴露于抗生素的释放，但人们对其天然耐药性状况知之甚少。我们结合隐马尔可夫模型（HMM）、同源比对和深度学习方法，以基因组分辨率全面筛选里海宏基因组中ARGs的多样性和分布。检测到的ARGs被分为五类抗生素耐药性，包括阻止进入靶点（44%）、修饰/保护靶点（30%）、直接修饰抗生素（22%）、应激耐药性（3%）和金属耐药性（1%）。检测到的102个里海含有ARG的宏基因组组装基因组主要由酸性微生物、γ-变形菌和放线菌类的代表组成。比较分析显示，酸性微生物和放线菌的高度丰富、寡营养和基因组流线型代表通过突变修饰抗生素靶标，产生抗生素耐药性，而不是携带额外的耐药性基因。我们的研究结果有助于理解每个基因组的编码抗性类别如何与其生态策略相一致。
Abstract
Aquatic microbial communities are an important reservoir of antibiotic resistance genes (ARGs). However, distribution and diversity of different ARG categories in environmental microbes with different ecological strategies is not yet well studied. Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile. We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes at genome resolution. Detected ARGs were classified into five antibiotic resistance categories including prevention of access to target (44%), modification/protection of targets (30%), direct modification of antibiotics (22%), stress resistance (3%), and metal resistance (1%). The 102 detected ARG containing metagenome-assembled genomes of the Caspian Sea were dominated by representatives of Acidimicrobiia, Gammaproteobacteria, and Actinobacteria classes. Comparative analysis revealed that the highly abundant, oligotrophic, and genome streamlined representatives of taxa Acidimicrobiia and Actinobacteria modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes. Our results help with understanding how the encoded resistance categories of each genome are aligned with its ecological strategies.

https://www.nature.com/articles/s41598-022-25026-3