ArticleNature2015
Long-term phenotypic evolution of bacteria.
Article in Nature, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 100 citations in OpenAlex.
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- Genome-based predictions of metabolic preferences and substrate phenotypes in psychrotrophic bacteria from permafrost environments.Microbiology spectrum · 2026Article
- Metagenome-scale Modeling to Assess Microbiome Metabolic Complementarity for Precision Microbiota Transplantation Therapies.bioRxiv : the preprint server for biology · 2026Article
- Bacterial proteome foundation model enhances functional prediction from enzymes to ecological interactions.bioRxiv : the preprint server for biology · 2026Article
- Beyond Resistance: Phenotypic Plasticity in Bacterial Responses to Antibiotics, Oxidative Stress and Antimicrobial Photodynamic Inactivation.Molecules (Basel, Switzerland) · 2026Review
- Experimental mapping of bacterial fitness landscapes reveals eco-evolutionary fingerprints.Scientific reports · 2025Article
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- The metabolic domestication syndrome of budding yeast.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Survival strategies ofFood science and biotechnology · 2023Review
- Functional comparison of metabolic networks across species.Nature communications · 2023Article
- Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis.NPJ biofilms and microbiomes · 2023Article
- Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli.G3 (Bethesda, Md.) · 2022Article
- A Pan-Draft Metabolic Model Reflects Evolutionary Diversity across 332 Yeast Species.Biomolecules · 2022Article
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- Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics.PLoS genetics · 2022Article
- Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome.Communications biology · 2022Article
- A better index for analysis of co-occurrence and similarity.Science advances · 2022Article
- Whole genome analysis of3 Biotech · 2021Article
- SiGMoiD: A super-statistical generative model for binary data.PLoS computational biology · 2021Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
For many decades comparative analyses of protein sequences and structures have been used to investigate fundamental principles of molecular evolution. In contrast, relatively little is known about the long-term evolution of species' phenotypic and genetic properties. This represents an important gap in our understanding of evolution, as exactly these proprieties play key roles in natural selection and adaptation to diverse environments. Here we perform a comparative analysis of bacterial growth and gene deletion phenotypes using hundreds of genome-scale metabolic models. Overall, bacterial phenotypic evolution can be described by a two-stage process with a rapid initial phenotypic diversification followed by a slow long-term exponential divergence. The observed average divergence trend, with approximately similar fractions of phenotypic properties changing per unit time, continues for billions of years. We experimentally confirm the predicted divergence trend using the phenotypic profiles of 40 diverse bacterial species across more than 60 growth conditions. Our analysis suggests that, at long evolutionary distances, gene essentiality is significantly more conserved than the ability to utilize different nutrients, while synthetic lethality is significantly less conserved. We also find that although a rapid phenotypic evolution is sometimes observed within the same species, a transition from high to low phenotypic similarity occurs primarily at the genus level.
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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.