ArticleGenome research2022
Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.
Article in Genome research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 58 citations in OpenAlex.
- Isolation by distance promotes gut microbial strain divergence in wild mouse populations.Nature ecology & evolution · 2026Article
- Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts.Cell reports. Medicine · 2026Article
- Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD.Nature communications · 2026Article
- Article
- Multiplexed PCR to measureApplied and environmental microbiology · 2025Article
- An integrative approach for imaging and quantitative analysis of gut microbiota growthBiophysics reports · 2025Article
- Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information.Nature communications · 2025Article
- Sustainable Food Waste Management in Anaerobic Digesters: Prediction of the Organic Load Impact by Metagenome-Scale Metabolic Modeling.Environmental science & technology · 2025Article
- Metabolic modelling reveals the aging-associated decline of host-microbiome metabolic interactions in mice.Nature microbiology · 2025Article
- Genome-resolved adaptation strategies ofApplied and environmental microbiology · 2025Article
- Comparative Analysis of Growth Dynamics and Relative Abundances of Gut Microbiota Influenced by Ketogenic Diet.Phenomics (Cham, Switzerland) · 2025Article
- Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria.mSphere · 2025Article
- Impact of trace metal supplementation on anaerobic biological methanation under hydrogen and carbon dioxide starvation.NPJ biofilms and microbiomes · 2025Article
- Eco-evolutionary robustness of wild bacterial communities to experimental perturbation.The ISME journal · 2025Article
- Integration of metatranscriptomics data improves the predictive capacity of microbial community metabolic models.The ISME journal · 2025Article
- Explainable rule-based prediction of cultivation media for microbes.Computational and structural biotechnology journal · 2025Article
- MAGs-based genomic comparison of gut significantly enriched microbes in obese individuals pre- and post-bariatric surgery across diverse locations.Frontiers in cellular and infection microbiology · 2025Article
- A new selective force driving metabolic gene clustering.mSystems · 2024Article
- Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome.Cell genomics · 2024Article
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes.Genome biology · 2024Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.