德国马克斯·普朗克生物研究所Ruth E. Ley研究团队利用同源分析，对复杂微生物群进行菌株追踪来揭示每种微生物的进化模式。相关论文于2024年6月19日发表在《自然—生物技术》杂志上。

据介绍，微生物通过单核苷酸突变和结构变化（如重组、插入和缺失）分化成不同菌株。大多数菌株比较方法都是量化单核苷酸多态性（SNPs）的差异，不涉及结构变化。然而，重组是包括人类病原体在内的许多物种表型多样化的重要调控因素。

研究人员开发了SynTracker，这是一种利用基因组同源性（同源基因组区域中序列块的顺序），结合元基因组或基因组组装来进行微生物菌株比较的工具。基因组同源性是目前菌株比较工具未参考的丰富基因组信息来源。SynTracker对SNP的灵敏度低，不需要数据库，测序错误对其影响很低。

在追踪元基因组数据中的菌株时，它的表现优于现有工具，尤其适合噬菌体、质粒和其他低数据量的情况。将SynTracker与基于SNP的工具结合，应用于单物种数据集和人类肠道元基因组，可以检测出富含点突变或结构变化的菌株，从而有助于深入了解微生物的原位进化。

附：英文原文

Title: Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution

Author: Enav, Hagay, Paz, Inbal, Ley, Ruth E.

Issue&Volume: 2024-06-19

Abstract: Microbial species diversify into strains through single-nucleotide mutations and structural changes, such as recombination, insertions and deletions. Most strain-comparison methods quantify differences in single-nucleotide polymorphisms (SNPs) and are insensitive to structural changes. However, recombination is an important driver of phenotypic diversification in many species, including human pathogens. We introduce SynTracker, a tool that compares microbial strains using genome synteny—the order of sequence blocks in homologous genomic regions—in pairs of metagenomic assemblies or genomes. Genome synteny is a rich source of genomic information untapped by current strain-comparison tools. SynTracker has low sensitivity to SNPs, has no database requirement and is robust to sequencing errors. It outperforms existing tools when tracking strains in metagenomic data and is particularly suited for phages, plasmids and other low-data contexts. Applied to single-species datasets and human gut metagenomes, SynTracker, combined with an SNP-based tool, detects strains enriched in either point mutations or structural changes, providing insights into microbial evolution in situ.

DOI: 10.1038/s41587-024-02276-2

Source: https://www.nature.com/articles/s41587-024-02276-2