ArticlemSystems2022
Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Linking Plant Metabolomics with Fungal Functional Dynamics Reveals a Noncanonical S-R-C Adaptive Trajectory.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Organic carbon oxidation state shapes fermentative methanogenic microbiomes and controls greenhouse gas fluxes.Nature communications · 2026Article
- Genomic traits associated with copiotrophy decouple from maximum growth rate predictions along temperature gradients.The ISME journal · 2026Article
- Conservation agriculture buffers persistent carbon loss under warming by microbial adaptation.The ISME journal · 2026Article
- Constructing a "periodic table" of bacteria to map diversity in trait space.The ISME journal · 2026Article
- Soil Nutrient Enrichment Induces Trade-Offs in Bacterial Life-History Strategies Promoting Plant Productivity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Comparative genomics reveals adaptive traits in novel Antarctic lithic cyanobacteria.BMC genomics · 2025Article
- Relative abundances of bacterial phyla are strong indicators of community-scale microbial growth rates in soil.Environmental microbiome · 2025Article
- Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information.Nature communications · 2025Article
- Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria.mSphere · 2025Article
- Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.PeerJ · 2025Article
- Global patterns in the growth potential of soil bacterial communities.Nature communications · 2024Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion.The ISME journal · 2024Article
- Growth rate is a dominant factor predicting the rhizosphere effect.The ISME journal · 2023Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Trait inference from mixed-species assemblages is a central problem in microbial ecology. Frequently, sequencing information from an environment is available, but phenotypic measurements from individual community members are not. With the increasing availability of molecular data for microbial communities, bioinformatic approaches that map metagenome to (meta)phenotype are needed. Recently, we developed a tool, gRodon, that enables the prediction of the maximum growth rate of an organism from genomic data on the basis of codon usage patterns. Our work and that of other groups suggest that such predictors can be applied to mixed-species communities in order to derive estimates of the average community-wide maximum growth rate. Here, we present an improved maximum growth rate predictor designed for metagenomes that corrects a persistent GC bias in the original gRodon model for metagenomic prediction. We benchmark this predictor with simulated metagenomic data sets to show that it has superior performance on mixed-species communities relative to earlier models. We go on to provide guidance on data preprocessing and show that calling genes from assembled contigs rather than directly from reads dramatically improves performance. Finally, we apply our predictor to large-scale metagenomic data sets from marine and human microbiomes to illustrate how community-wide growth prediction can be a powerful approach for hypothesis generation. Altogether, we provide an updated tool with clear guidelines for users about the uses and pitfalls of metagenomic prediction of the average community-wide maximal growth rate.
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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.