High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage.

Document Type

Article

Publication Date

11-23-2018

Keywords

JGM

JAX Source

Nat Commun 2018 Nov 23; 9(1):4956

Volume

9

Issue

1

First Page

4956

Last Page

4956

ISSN

2041-1723

PMID

30470746

DOI

https://doi.org/10.1038/s41467-018-07240-8

Grant

GM126893, AI119231

Abstract

We developed Growth Rate InDex (GRiD) for estimating in situ growth rates of ultra-low coverage (>0.2×) and de novo-assembled metagenomes. Applying GRiD to human and environmental metagenomic datasets to demonstrate its versatility, we uncovered new associations with previously uncharacterized bacteria whose growth rates were associated with several disease characteristics or environmental interactions. In addition, with GRiD-MG (metagenomic), a high-throughput implementation of GRiD, we estimated growth dynamics of 1756 bacteria species from a healthy skin metagenomic dataset and identified a new Staphylococcus-Corynebacterium antagonism likely mediated by antimicrobial production in the skin. GRiD-MG significantly increases the ability to extract growth rate inferences from complex metagenomic data with minimal input from the user.

Comments

We thank Asaf Peer for making GRiD installation possible through Bioconda, Wei Zhou for providing the genomes used in creating the GRiD database, and Elizabeth Fleming for sequence library preparation. We thank the Oh lab for critical commentary and algorithm testing

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