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InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains

Matthew R. Olm, Alexander Crits-Christoph, Keith Bouma-Gregson, Brian Firek, Michael J. Morowitz, Jillian F. Banfield
doi: https://doi.org/10.1101/2020.01.22.915579
Matthew R. Olm
1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
2Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Alexander Crits-Christoph
2Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Keith Bouma-Gregson
3Office of Information Management and Analysis, California State Water Resources Control Board, Sacramento, CA, USA
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Brian Firek
4Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Michael J. Morowitz
4Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Jillian F. Banfield
1Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
5Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
6Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
7Chan Zuckerberg Biohub, San Francisco, CA, USA.
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  • For correspondence: jbanfield@berkeley.edu
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Abstract

Coexisting microbial cells of the same species often exhibit genetic differences that can affect phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a program that utilizes metagenomic paired reads to profile intra-population genetic diversity (microdiversity) across whole genomes and compare populations in a microdiversity-aware manner, dramatically increasing genomic comparison accuracy 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 via cesarean section harbored Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital versus maternal microbiomes. Genomic loci showing diversity within an infant included variants found in 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 copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 23, 2020.
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InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains
Matthew R. Olm, Alexander Crits-Christoph, Keith Bouma-Gregson, Brian Firek, Michael J. Morowitz, Jillian F. Banfield
bioRxiv 2020.01.22.915579; doi: https://doi.org/10.1101/2020.01.22.915579
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InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains
Matthew R. Olm, Alexander Crits-Christoph, Keith Bouma-Gregson, Brian Firek, Michael J. Morowitz, Jillian F. Banfield
bioRxiv 2020.01.22.915579; doi: https://doi.org/10.1101/2020.01.22.915579

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