Unravelling the Core and Accessory Genome Diversity of Enterobacteriaceae in Carbon Metabolism

Abstract

Enterobacteriaceae are commonly colonizing animal guts and impact health. While strain-specific metabolic features can promote gut colonization, we lack systematic knowledge regarding metabolic diversity and the core metabolism shared among Enterobacteriaceae. To address this gap, we have analyzed the pan-genome of nearly 20,000 genomes. We found that genes necessary for monosaccharide-fuelled mixed acid fermentation are part of the Enterobacteriaceae core genome, while most genes for anaerobic respiration and most carbohydrate utilization genes belong to the accessory genome. Understanding Enterobacteriaceaes metabolic capacity helps clarify the distinction of nutrients consumed by all Enterobacteriaceae, and niche-defining nutrient sources, which are genus-, species- or strain-specific. This knowledge sheds light on bacterial nutrient exploitation during gut colonization in health and disease, aiding in the development of targeted interventions for microbiome research and infectious disease control. The theoretical framework described here can also be adapted to analyze core physiological characteristics of other microbiota taxa.