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.

微生物物种通过单核苷酸突变和结构变化（例如重组、插入和缺失）多样化为菌株。大多数菌株比较方法量化单核苷酸多态性 (SNP) 的差异，并且对结构变化不敏感。然而，重组是许多物种（包括人类病原体）表型多样化的重要驱动因素。我们介绍了 SynTracker，这是一种使用基因组同线性（同源基因组区域中序列块的顺序）以宏基因组组装体或基因组对的形式比较微生物菌株的工具。基因组同线性是当前菌株比较工具尚未开发的丰富的基因组信息来源。 SynTracker 对 SNP 的敏感性较低，无需数据库，并且对测序错误具有鲁棒性。在跟踪宏基因组数据中的菌株时，它的性能优于现有工具，并且特别适合噬菌体、质粒和其他低数据环境。 SynTracker 应用于单物种数据集和人类肠道宏基因组，与基于 SNP 的工具相结合，可以检测富含点突变或结构变化的菌株，从而提供对微生物原位进化的见解。