摘要

    在微生物群落中鉴定抗生素抗性基因（ARG）是生物学中最具挑战性的任务之一。 基因组测序技术的发展和改进，再加上计算分析技术的改进，使我们能够获得有关在最异构的环境中共存和共进化的复杂多样的微生物群落的越来越详细的信息。 本章介绍如何使用特定工具（Bowtie2，用于覆盖率，G / C内容的Bedtools和映射每个开放阅读框的预计阅读数）来鉴定和定量ARG；在CARD数据库的支持下，RGI工具用于检查ARGs。 抗生素抗性基因的分布）。 一旦获得了这些信息，科学家将能够突出分析的元基因组中ARG的相对丰度，并能够了解抗生素抗性机制如何在微生物群落中进化。

    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