ArticleThe ISME journal2021
Benchmarking microbial growth rate predictions from metagenomes.
Article in The ISME journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 89 citations in OpenAlex.
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- Metabolic modelling reveals the aging-associated decline of host-microbiome metabolic interactions in mice.Nature microbiology · 2025Article
- Legacies of temperature fluctuations promote stability in marine biofilm communities.Nature communications · 2025Article
- A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry.Nature communications · 2025Article
- Genome-resolved adaptation strategies ofApplied and environmental microbiology · 2025Article
- Priestia megaterium cells are primed for surviving lethal doses of antibiotics and chemical stress.Communications biology · 2025Article
- Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria.mSphere · 2025Article
- The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards.Microbiome · 2025Review
- 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
- Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing.ISME communications · 2025Article
- A new selective force driving metabolic gene clustering.mSystems · 2024Article
- Soil viral-host interactions regulate microplastic-dependent carbon storage.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The biogeography of soil microbiome potential growth rates.Nature communications · 2024Article
- Global patterns in the growth potential of soil bacterial communities.Nature communications · 2024Article
- Gram-positive bacteria are primed for surviving lethal doses of antibiotics and chemical stress.bioRxiv : the preprint server for biology · 2024Article
- DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses.NAR genomics and bioinformatics · 2024Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Growth rates are central to understanding microbial interactions and community dynamics. Metagenomic growth estimators have been developed, specifically codon usage bias (CUB) for maximum growth rates and "peak-to-trough ratio" (PTR) for in situ rates. Both were originally tested with pure cultures, but natural populations are more heterogeneous, especially in individual cell histories pertinent to PTR. To test these methods, we compared predictors with observed growth rates of freshly collected marine prokaryotes in unamended seawater. We prefiltered and diluted samples to remove grazers and greatly reduce virus infection, so net growth approximated gross growth. We sampled over 44 h for abundances and metagenomes, generating 101 metagenome-assembled genomes (MAGs), including Actinobacteria, Verrucomicrobia, SAR406, MGII archaea, etc. We tracked each MAG population by cell-abundance-normalized read recruitment, finding growth rates of 0 to 5.99 per day, the first reported rates for several groups, and used these rates as benchmarks. PTR, calculated by three methods, rarely correlated to growth (r ~-0.26-0.08), except for rapidly growing γ-Proteobacteria (r ~0.63-0.92), while CUB correlated moderately well to observed maximum growth rates (r = 0.57). This suggests that current PTR approaches poorly predict actual growth of most marine bacterial populations, but maximum growth rates can be approximated from genomic characteristics.
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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.