Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA.
Department of Medicine, The University of Chicago, Chicago, IL, USA.
Nat Methods. 2023 Nov;20(11):1672-1682. doi: 10.1038/s41592-023-02025-4. Epub 2023 Oct 12.
Host-microbe interactions have been linked to health and disease states through the use of microbial taxonomic profiling, mostly via 16S ribosomal RNA gene sequencing. However, many mechanistic insights remain elusive, in part because studying the genomes of microbes associated with mammalian tissue is difficult due to the high ratio of host to microbial DNA in such samples. Here we describe a microbial-enrichment method (MEM), which we demonstrate on a wide range of sample types, including saliva, stool, intestinal scrapings, and intestinal mucosal biopsies. MEM enabled high-throughput characterization of microbial metagenomes from human intestinal biopsies by reducing host DNA more than 1,000-fold with minimal microbial community changes (roughly 90% of taxa had no significant differences between MEM-treated and untreated control groups). Shotgun sequencing of MEM-treated human intestinal biopsies enabled characterization of both high- and low-abundance microbial taxa, pathways and genes longitudinally along the gastrointestinal tract. We report the construction of metagenome-assembled genomes directly from human intestinal biopsies for bacteria and archaea at relative abundances as low as 1%. Analysis of metagenome-assembled genomes reveals distinct subpopulation structures between the small and large intestine for some taxa. MEM opens a path for the microbiome field to acquire deeper insights into host-microbe interactions by enabling in-depth characterization of host-tissue-associated microbial communities.
宿主-微生物相互作用通过微生物分类分析得到了健康和疾病状态的联系，主要是通过 16S 核糖体 RNA 基因测序。然而，许多机制上的见解仍然难以捉摸，部分原因是由于在这些样本中，宿主与微生物 DNA 的比例很高，因此研究与哺乳动物组织相关的微生物基因组非常困难。在这里，我们描述了一种微生物富集方法（MEM），我们在广泛的样本类型上进行了验证，包括唾液、粪便、肠刮片和肠黏膜活检。MEM 通过将宿主 DNA 减少 1000 多倍，同时对微生物群落的变化最小（大约 90%的分类群在 MEM 处理组和未处理对照组之间没有显著差异），从而实现了高通量的人类肠道活检微生物宏基因组特征描述。MEM 处理的人类肠道活检的鸟枪法测序能够对胃肠道中沿长轴的高丰度和低丰度微生物分类群、途径和基因进行纵向特征描述。我们报告了直接从人类肠道活检中构建相对丰度低至 1%的细菌和古菌的宏基因组组装基因组。宏基因组组装基因组的分析揭示了一些分类群在小肠和大肠之间存在明显的亚群结构。MEM 通过能够深入描述与宿主组织相关的微生物群落，为微生物组领域深入了解宿主-微生物相互作用开辟了道路。
