ArticleNature biotechnology2021
inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 356 papers, 1 of them a synthesis that pooled it.
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Who cites it
356 citing papers in PubMed, 1 synthesis or guideline pooled it, 550 citations in OpenAlex.
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- 15-strain live biotherapeutic product or same donor fecal microbiota transplant for recurrent Clostridioides difficile infection: a randomized phase 1b trial.Nature medicine · 2026Trial
- Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial.Nature communications · 2025Trial
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- Gut microbial markers of immunotherapy response in melanoma: a cross-cohort analysis including the first Russian dataset.Gut microbes · 2026Article
- Community-wide adaptive evolution of gut bacteria during dietary transitions.bioRxiv : the preprint server for biology · 2026Article
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- Species and strain sharing in the vaginal microbiome of mothers and their adult daughters.Cell reports · 2026Article
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- The planktonic microbiome of the Great Barrier Reef.Nature · 2026Article
- Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau.Nature communications · 2026Article
- ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.Microbiology spectrum · 2026Article
- Citywide metagenomics reveals microbial community and resistome dynamics in urban wastewater.Nature communications · 2026Article
- The faecal microbiome and carriage of Salmonella in Australian captive pythons.FEMS microbiology ecology · 2026Article
- Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.Nature communications · 2026Article
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- Distance-Limited Larval Replenishment in the Deep-Sea Mussel Gigantidas platifrons Challenges Connectivity-Based Conservation Planning.Molecular ecology · 2026Article
- Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils.Nature microbiology · 2026Article
296 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 3 institutions in 1 country.
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Abstract
Coexisting microbial cells of the same species often exhibit genetic variation that can affect phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a program that uses metagenomic paired reads to profile intra-population genetic diversity (microdiversity) across whole genomes and compares microbial populations in a microdiversity-aware manner, greatly increasing the accuracy of genomic comparisons when benchmarked against existing methods. We use inStrain to profile >1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born by cesarean section harbor Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital rather than maternal microbiomes. Genomic loci that show diversity in individual infants include variants found between other infants, possibly reflecting inoculation from diverse hospital-associated sources. inStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison.
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