摘要

       微生物群落中抗生素抗性基因 (ARG) 的鉴定是生物学中最具挑战性的任务之一。 基因组测序技术的进化和改进，加上计算分析技术的改进，使我们能够获得关于在最异质环境中共存和共同进化的复杂多样的微生物群落的越来越详细的信息。 本章描述了如何识别和量化 ARG，使用特定工具（Bowtie2、Bedtools for coverage、G/C 内容和映射每个开放阅读框的估计读数数；RGI 工具，在 CARD 数据库的支持下，检查 抗生素抗性基因的分布）。 一旦获得这些信息，科学家们将能够突出分析宏基因组中 ARG 的相对丰度，并能够了解微生物群落中抗生素耐药机制的演变。

       The identification of antibiotic resistance genes (ARGs) in microbial communities is one of the most challenging tasks in biology. The evolution and improvement of genome sequencing techniques, combined with the improvement of computational analysis techniques, have allowed us to acquire increasingly detailed information on the complex and varied microbial community that coexists and coevolves in the most heterogeneous environment. This chapter describes how to identify and quantify ARGs, using specific tools (Bowtie2, Bedtools for coverage, G/C content, and the estimated number of reads mapping each open reading frame; RGI tool, with the support of CARD database, to inspect the distribution of antibiotic resistance genes). Once this information is obtained, scientists would be able to highlight the relative abundance of ARGs in the metagenome analyzed and be able to understand how antibiotic resistance mechanisms evolve in microbial communities.

https://link.springer.com/protocol/10.1007%2F978-1-0716-1099-2_11