Shotgun metagenomics and isolate sequencing for environmental microbial communities

In this pilot study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to help establish optimum protocols and approaches for sample processing. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced these samples with shotgun metagenomics at high depth (~200 million reads per sample). Alongside this, we cultured multiple single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data.

本预实验采用霰弹枪宏基因组学（shotgun metagenomics）结合同批次样本培养分离株测序，旨在确立样本处理的最优方案与方法。本研究采集了三类潜在的环境抗微生物药物耐药性（Antimicrobial Resistance, AMR）基因储库：猪盲肠、河流沉积物与出水样本，并对其开展高深度霰弹枪宏基因组测序，单样本测序数据量约为2亿条reads。与此同时，我们从上述同批次样本中分离培养了多株肠杆菌科（Enterobacteriaceae）单菌落分离株，并采用混合测序（hybrid sequencing，即短读长与长读长测序结合）技术构建高质量基因组组装结果，用于与宏基因组数据进行对比分析。