ArticleNature communications2020
High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli.
Article in Nature communications, 2020. 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, 93 citations in OpenAlex.
- Distinct transcription factor network dynamics underlie early and long-term adaptation to rifampicin inmSystems · 2026Article
- Collateral sensitivity-harnessing microbial vulnerabilities as a solution to antimicrobial resistance.Molecular biology reports · 2026Review
- Simultaneous optimization of lignocellulosic sugar catabolism via systematic laboratory evolution under complex selection pressure.Nature communications · 2026Article
- Function-specific epistasis shapes evolutionary trajectories towards antibiotic resistance.Nature communications · 2026Article
- GeneScanner: profiling genetic variation across bacterial populations.Microbial genomics · 2026Article
- Navigating the copper highway: bacterial strategies for cytoplasmic import.Journal of inorganic biochemistry · 2026Review
- Transport of the abundant intestinal amino acid glutamine by the enteric pathogenMicrobiology (Reading, England) · 2026Article
- Advances in adaptive laboratory evolution applications forSynthetic and systems biotechnology · 2025Review
- Reinforcement learning for adaptive control of phenotypically heterogeneous bacterial populations.bioRxiv : the preprint server for biology · 2025Article
- Considering Metabolic Context in Enzyme Evolution and Design.Biochemistry · 2025Review
- Review
- Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales.Annual review of biophysics · 2025Review
- Spatial structure facilitates evolutionary rescue by drug resistance.PLoS computational biology · 2025Article
- Genetic properties underlying transcriptional variability across different perturbations.Nature communications · 2025Article
- Menadione reduces the expression of virulence- and colonization-associated genes inMicrobiology (Reading, England) · 2025Article
- Quantitative analysis of relationship between mutation rate and speed of adaptation under antibiotic exposure in Escherichia coli.PLoS genetics · 2025Article
- Multiple routes for non-physiological l-threonine uptake inFrontiers in microbiology · 2025Article
- Distribution and Antibiotic Resistance Analysis of 13,048 Clinically Common Isolates.Infection and drug resistance · 2025Article
- Genetic adaptation to amoxicillin in Escherichia coli: The limited role of dinB and katE.PloS one · 2025Article
- Soft Modes as a Predictive Framework for Low Dimensional Biological Systems across Scales.ArXiv · 2024Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the constraints that shape the evolution of antibiotic resistance is critical for predicting and controlling drug resistance. Despite its importance, however, a systematic investigation of evolutionary constraints is lacking. Here, we perform a high-throughput laboratory evolution of Escherichia coli under the addition of 95 antibacterial chemicals and quantified the transcriptome, resistance, and genomic profiles for the evolved strains. Utilizing machine learning techniques, we analyze the phenotype-genotype data and identified low dimensional phenotypic states among the evolved strains. Further analysis reveals the underlying biological processes responsible for these distinct states, leading to the identification of trade-off relationships associated with drug resistance. We also report a decelerated evolution of β-lactam resistance, a phenomenon experienced by certain strains under various stresses resulting in higher acquired resistance to β-lactams compared to strains directly selected by β-lactams. These findings bridge the genotypic, gene expression, and drug resistance gap, while contributing to a better understanding of evolutionary constraints for antibiotic resistance.
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