美国西奈山伊坎医学院Gang Fang研究小组取得一项新突破。他们研发了mEnrich-seq，可对微生物组中感兴趣的细菌类群进行甲基化引导富集测序。这一研究成果发表在2024年1月4日出版的国际学术期刊《自然—方法学》上。

研发人员研发了mEnrich-seq（其中 "m "代表甲基化，seq代表测序），用于在测序前从元基因组DNA中富集感兴趣的类群。其核心思想是利用天然细菌DNA甲基化的自体与非自体分化，合理选择对甲基化敏感的限制性酶单独或组合使用，在富集目标类群的同时清除宿主和背景类群。

将这一想法与文库制备程序相结合并付诸于多种应用，研究人员从人类尿液和粪便样本中富集（高达117倍）致病或有益细菌，包括难以培养或丰度较低的物种。mEnrich-seq为微生物组研究提供了一种多功能且经济高效的方法，用于对感兴趣的不同分类群进行选择性测序。

据悉，元基因组学实现了对微生物组的全面研究。然而，如果能对特定感兴趣的细菌类群进行测序，而非大多数背景类群进行测序，那么许多应用都将受益匪浅。

附：英文原文

Title: mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome

Author: Cao, Lei, Kong, Yimeng, Fan, Yu, Ni, Mi, Tourancheau, Alan, Ksiezarek, Magdalena, Mead, Edward A., Koo, Tonny, Gitman, Melissa, Zhang, Xue-Song, Fang, Gang

Issue&Volume: 2024-01-04

Abstract: Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which ‘m’ stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self versus nonself differentiation by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes, individually or in combination, to deplete host and background taxa while enriching targeted taxa. This idea is integrated with library preparation procedures and applied in several applications to enrich (up to 117-fold) pathogenic or beneficial bacteria from human urine and fecal samples, including species that are hard to culture or of low abundance. We assessed 4,601 bacterial strains with mapped methylomes so far and showed broad applicability of mEnrich-seq. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest.

DOI: 10.1038/s41592-023-02125-1

Source: https://www.nature.com/articles/s41592-023-02125-1