Title

Metagenomic growth rate inferences of strains in situ.

Document Type

Article

Publication Date

4-22-2020

Keywords

JGM

JAX Source

Sci Adv 2020 Apr 22; 6(17):eaaz2299

PMID

32494636

DOI

https://doi.org/10.1126/sciadv.aaz2299

Grant

GM126893,AI119231,NS105539,AI124733,AR075174,AR073562

Abstract

We developed a method for strain-level metagenomic estimation of growth rate (SMEG) for inferring growth rates of bacterial subspecies, or strains, from complex metagenomic samples. We applied our method, which is based on both reference strains and de novo approaches, to different gut metagenomic datasets, accurately identifying an outbreak-associated Escherichia coli strain and a previously unidentified association of an Akkermansia muciniphila strain in cancer immunotherapy responders. SMEG resolves strain-specific growth rates from mixtures of commensal or pathogenic strains to provide new insights into microbial interactions and disease associations at the strain level. SMEG is available for download at https://github.com/ohlab/SMEG.

Comments

We would like to thank the Microbial Genomic Services and M. Adams of The Jackson Laboratory for their support in sequencing, and M. Adams and the Oh laboratory for critical reading of the manuscript.

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