ArticleProceedings of the National Academy of Sciences of the United States of America2021
Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 papers.
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153 citing papers in PubMed, 289 citations in OpenAlex.
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- Evolutionary constraints on RNA polymerase gene positioning in the genome of fast-growing bacteria.Nucleic acids research · 2026Article
- Circularization of 23S rRNA but not 16S rRNA within archaeal ribosomes.Genome biology · 2026Article
- Constant trouble with prolines-navigating a global translation dilemma.Nucleic acids research · 2026Review
- Constructing a "periodic table" of bacteria to map diversity in trait space.The ISME journal · 2026Article
- Conservation agriculture buffers persistent carbon loss under warming by microbial adaptation.The ISME journal · 2026Article
- Genomic traits associated with copiotrophy decouple from maximum growth rate predictions along temperature gradients.The ISME journal · 2026Article
- Host life-history strategy is a critical determinant of virulent phage infection propensity.The ISME journal · 2026Article
- Lifestyle differentiation among marine denitrifying microorganisms.The ISME journal · 2026Article
- Article
93 more citing papers are in PubMed but not listed here.
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3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Maximal growth rate is a basic parameter of microbial lifestyle that varies over several orders of magnitude, with doubling times ranging from a matter of minutes to multiple days. Growth rates are typically measured using laboratory culture experiments. Yet, we lack sufficient understanding of the physiology of most microbes to design appropriate culture conditions for them, severely limiting our ability to assess the global diversity of microbial growth rates. Genomic estimators of maximal growth rate provide a practical solution to survey the distribution of microbial growth potential, regardless of cultivation status. We developed an improved maximal growth rate estimator and predicted maximal growth rates from over 200,000 genomes, metagenome-assembled genomes, and single-cell amplified genomes to survey growth potential across the range of prokaryotic diversity; extensions allow estimates from 16S rRNA sequences alone as well as weighted community estimates from metagenomes. We compared the growth rates of cultivated and uncultivated organisms to illustrate how culture collections are strongly biased toward organisms capable of rapid growth. Finally, we found that organisms naturally group into two growth classes and observed a bias in growth predictions for extremely slow-growing organisms. These observations ultimately led us to suggest evolutionary definitions of oligotrophy and copiotrophy based on the selective regime an organism occupies. We found that these growth classes are associated with distinct selective regimes and genomic functional potentials.
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