biostudies-literatureUnknownFavate JSNIGMS NIH HHSChanges in an organism's environment, genome, or gene expression patterns can lead to changes in its metabolism. The metabolic phenotype can be under selection and contributes to adaptation. However, the networked and convoluted nature of an organism's metabolism makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the Long-Term Evolution Experiment (LTEE) with <i>E. coli</i> as a model to understand how mutations can eventually affect metabolism and perhaps fitness. We used mass-spectrometry to broadly survey the metabolomes of the ancestral strains and all 12 evolved lines. We combined this metabolic data with mutation and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesisbioRxiv : the preprint server for biology2023.02.15.528756https://www.ebi.ac.uk/biostudies/studies/S-EPMC9985142biostudies-literatureLinking genotypic and phenotypic changes in the <i>E. coli</i> Long-Term Evolution Experiment using metabolomics.PMC9985142R35 GM147566R35 GM124976Shah PYadavalli SSFavate JSSu XSkalenko KSChiles EfalseLinking genotypic and phenotypic changes in the <i>E. coli</i> Long-Term Evolution Experiment using metabolomics.Changes in an organism's environment, genome, or gene expression patterns can lead to changes in its metabolism. The metabolic phenotype can be under selection and contributes to adaptation. However, the networked and convoluted nature of an organism's metabolism makes relating mutations, metabolic changes, and effects on fitness challenging. To overcome this challenge, we use the Long-Term Evolution Experiment (LTEE) with <i>E. coli</i> as a model to understand how mutations can eventually affect metabolism and perhaps fitness. We used mass-spectrometry to broadly survey the metabolomes of the ancestral strains and all 12 evolved lines. We combined this metabolic data with mutation and expression data to suggest how mutations that alter specific reaction pathways, such as the biosynthesis2023-01-01T00:00:00Z2023 May2025-08-16T03:06:17.517Z2025-04-05T18:34:29.037ZS-EPMC99851423687420310.1101/2023.02.15.528756