摘要
      肠道微生物群是抗微生物耐药性基因（ARGs）的蓄水池。根据目前的测序方法，很难将ARGs分配给它们的微生物宿主，特别是如果这些ARGs位于质粒上。最近开发了宏基因组染色体构象捕获方法（meta3C和Hi-C），将细菌基因与系统发育标记联系起来，从而有可能在微生物组范围内将ARGs分配给宿主。
在这里，我们生成了一个人类粪便样本的meta3C数据集，并使用之前发表的meta3C和Hi-C数据集来研究人类肠道微生物组中ARGs的细菌宿主。发现映射到重复元素的序列读取会在meta3C和Hi-C数据中造成问题噪声，并可能重要地扭曲解释。我们提供了一种策略，通过丢弃映射到重复元素和重叠群末端的读数来提高信噪比。我们还展示了在对照中使用刺突来量化meta3C和Hi-C协议中的交联步骤是否成功的重要性。
在过滤虚假链接后，在所有数据集中有87个ARG与其细菌宿主相连，包括我们生成的meta3C数据集中的27个ARG。我们表明，共生肠道细菌是ARGs的重要宿主，编码氨基糖苷类和四环素抗性的基因在人类肠道厌氧共生菌中广泛存在。
Abstract
The gut microbiota is a reservoir for antimicrobial resistance genes (ARGs). With current sequencing methods, it is difficult to assign ARGs to their microbial hosts, particularly if these ARGs are located on plasmids. Metagenomic chromosome conformation capture approaches (meta3C and Hi-C), have recently been developed to link bacterial genes to phylogenetic markers, thus potentially allowing the assignment of ARGs to their hosts on a microbiome-wide scale.

Here, we generated a meta3C dataset of a human stool sample and used previously published meta3C and Hi-C datasets to investigate bacterial hosts of ARGs in the human gut microbiome. Sequence reads mapping to repetitive elements were found to cause problematic noise in, and may importantly skew interpretation of, meta3C and Hi-C data. We provide a strategy to improve the signal-to-noise ratio by discarding reads that map to repetitive elements and to the end of contigs. We also show the importance of using spike-in controls to quantify whether the cross-linking step in meta3C and Hi-C protocols has been successful.

After filtering for spurious links, 87 ARGs were linked to their bacterial hosts across all datasets, including 27 ARGs in the meta3C dataset we generated. We show that commensal gut bacteria are an important reservoir for ARGs, with genes encoding for aminoglycoside and tetracycline resistance being widespread in anaerobic commensals of the human gut.

https://www.biorxiv.org/content/10.1101/2022.11.05.514866v1.abstract