Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
03 2022
03 2022
Historique:
received:
22
03
2021
accepted:
22
12
2021
pubmed:
7
1
2022
medline:
11
3
2022
entrez:
6
1
2022
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 34987055
pii: gr.275533.121
doi: 10.1101/gr.275533.121
pmc: PMC8896461
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
558-568Subventions
Organisme : NCI NIH HHS
ID : U01 CA217858
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA209997
Pays : United States
Informations de copyright
© 2022 Joseph et al.; Published by Cold Spring Harbor Laboratory Press.
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