RT Journal Article
SR Electronic
T1 Accurate and robust inference of microbial growth dynamics from metagenomic sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.02.02.429365
DO 10.1101/2021.02.02.429365
A1 Tyler A. Joseph
A1 Philippe Chlenski
A1 Tal Korem
A1 Itsik Pe’er
YR 2021
UL http://biorxiv.org/content/early/2021/02/02/2021.02.02.429365.abstract
AB 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 CoPTR (Compute PTR): a tool for computing PTRs from complete reference genomes and assemblies. We show that CoPTR is more accurate than the current state-of-the-art, while also providing more PTR estimates overall. We further develop 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 irritable bowel disease. We show that PTRs have high inter-individual variation, are only loosely correlated with relative abundances, and are associated with disease status. We conclude by demonstrating how PTRs can be combined with relative abundances and metabolomics to investigate their effect on the microbiome.Availability CoPTR is available from https://github.com/tyjo/coptr, with documentation on https://coptr.readthedocs.io.Competing Interest StatementThe authors have declared no competing interest.