Mapping and understanding bacterial metabolism with multi-omics approaches: from E. coli to microbiomes
While the reaction stoichiometry of bacterial metabolism is well mapped, its dynamic nature remains less understood. In my talk, I will show how we combine CRISPR methods with mass spectrometry to examine bacterial metabolism. For example, CRISPR interference in 7,177 E. coli strains revealed a general metabolic robustness that maintains cellular fitness despite decreased enzyme levels. Key findings include the identification of gene-specific buffering mechanisms, which compensate a CRISPRi-knockdown by upregulation of genes that are near the CRISPRi target. Additionally, we created 15,120 E. coli mutants with point mutations in essential genes and analysis with mass spectrometry revealed mutant-specific metabolic changes, which show that simple point mutations can induce overproduction of various metabolites. Screening the 15,120 E. coli mutants for antibiotic resistance highlighted the relevance of metabolism for the efficacy antibiotics. Metabolism-mediated resistance mechanisms were drug-specific and dependent on distinct metabolic functions such as nucleotide biosynthesis. I will also show how we apply these methods to synthetic bacterial communities to identify metabolic interactions in the microbiome.