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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The data supporting the findings of this study are available within the paper and its supplementary information files. Reads from infant samples are available under BioProject PRJNA294605 (SRA studies SRP052967, SRP114966 and SRP012558; and SRA accessions SRR5405607 to SRR5406014), reads from Zymo samples are available under BioProject PRJNA648136 and de novo assembled genomes are available at https://doi.org/10.6084/m9.figshare.c.4740080.v1.
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This research was supported by the National Institutes of Health (NIH) under award no. RAI092531A to J.F.B. and M.J.M., the Alfred P. Sloan Foundation under grant no. APSF-2012-10-05 to J.F.B., a National Science Foundation Graduate Research Fellowship to M.R.O. under grant no. DGE 1106400 and Chan Zuckerberg Biohub. The study was approved by the University of Pittsburgh Institutional Review Board (protocol no. PRO10090089).
J.F.B. is a founder of Metagenomi.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Figs. 1–7.
Information related to inStrain benchmarking.
Ability of inStrain, MIDAS and MetaPhlAn2 to detect genomes present in the Zymo samples using public reference genomes.
Raw data related to comparison of SNV detection by metagenomic inStrain analysis compared with isolate sequencing.
Strain-level comparisons within infant samples, between infant coReads and strain identities.
Abundance of subspecies in all infants, individual samples and controls, and information about subspecies genomes and representatives.
Detailed SNS and SNV information for Enterococcus faecalis bacteriophage subspecies 482_10.ph.
inStrain program documentation.
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Olm, M.R., Crits-Christoph, A., Bouma-Gregson, K. et al. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat Biotechnol (2021). https://doi.org/10.1038/s41587-020-00797-0