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Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.

ABSTRACT: Patterns of sequencing coverage along a bacterial genome-summarized by a peak-to-trough ratio (PTR)-have been shown to accurately reflect microbial growth rates, revealing a new facet of microbial dynamics and host-microbe interactions. Here, we introduce Compute PTR (CoPTR): a tool for computing PTRs from complete reference genomes and assemblies. Using simulations and data from growth experiments in simple and complex communities, we show that CoPTR is more accurate than the current state of the art while also providing more PTR estimates overall. We further develop a theory formalizing a biological interpretation for PTRs. Using a reference database of 2935 species, we applied CoPTR to a case-control study of 1304 metagenomic samples from 106 individuals with inflammatory bowel disease. We show that growth rates are personalized, are only loosely correlated with relative abundances, and are associated with disease status. We conclude by showing how PTRs can be combined with relative abundances and metabolomics to investigate their effect on the microbiome.

SUBMITTER: Joseph TA

PROVIDER: S-EPMC8896461 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.

Joseph Tyler A TA Chlenski Philippe P Litman Aviya A Korem Tal T Pe'er Itsik I

Genome research 20220105 3

Patterns of sequencing coverage along a bacterial genome-summarized by a peak-to-trough ratio (PTR)-have been shown to accurately reflect microbial growth rates, revealing a new facet of microbial dynamics and host-microbe interactions. Here, we introduce Compute PTR (CoPTR): a tool for computing PTRs from complete reference genomes and assemblies. Using simulations and data from growth experiments in simple and complex communities, we show that CoPTR is more accurate than the current state of t ...[more]

PMID: 34987055

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Dataset Information

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.

Publications

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.

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