ArticleNature biotechnology2025
Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Emergent function, not microbial conformity: functional redundancy and the limits of taxonomic inference in microbiome genomics.Microbial genomics · 2026Review
- Isolation by distance promotes gut microbial strain divergence in wild mouse populations.Nature ecology & evolution · 2026Article
- Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate.bioRxiv : the preprint server for biology · 2026Article
- Fidelity in co-diversified symbiosis.Nature communications · 2026Article
- Enhancing the Signature Rose Aroma ofFoods (Basel, Switzerland) · 2026Article
- From genomes to interventions: computational strategies transforming parasitology.Frontiers in veterinary science · 2026Review
- Assessing live microbial therapeutic transmission.Gut microbes · 2025Review
- Leveraging FracMinHash Containment for GenomicbioRxiv : the preprint server for biology · 2025Article
- Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.Cancer research · 2025Review
- New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean.Environmental microbiome · 2025Article
- Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission.Microbiome · 2025Article
- Article
- Microsynteny is a powerful front for microbial strain tracking.Cell reports methods · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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.
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