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Abstract

Microbial species diversify into separate strains through mutation, recombination, and gene loss/acquisition. Elucidating mechanisms driving the genomic diversity of species residing within complex microbiomes remains biased towards mutation, because current strain tracking methods are focused on SNPs and are relatively insensitive to structural changes in genomes. To complement these methods, we developed a tool that compares strains using synteny - the conservation of the order of sequence blocks in homologous genomic regions in pairs of metagenomic assemblies. As a standalone tool, our tool allows improved microbial strain tracking within and between hosts. The combined use of our tool and SNP-based tools in metagenome analysis allows the identification of species undergoing high rates of structural change with low rates of mutation, or conversely, high rates of structural change with low mutation rates, providing a novel window into different modes of evolution on a per-species basis in complex microbiomes.