Revisiting nitrogen assimilation strategies in the mammalian gut: lessons from Enterobacteriaceae as pathobiont models and a challenge to the limitation paradigm

The intestinal microbiome is dependent on nitrogen to support growth, yet the extent of nitrogen-limitation for microbial expansion in the mammalian gut remains debated. Classical perspectives describe the colon as nitrogen-limited due to the early absorption of dietary nitrogen in the small intestine, prompting the evolution of nitrogen-scavenging. In this mini-review, we focus on Enterobacteriaceae, facultative anaerobes, and clinically relevant pathobionts to examine nitrogen-scavenging and -assimilation systems. Drawing from in vitro, in vivo and ex vivo mono-colonization murine studies in Escherichia coli and Klebsiella pneumoniae, we highlight findings that introduced a paradigm shift by showing that nitrogen-scavenging mechanisms may be dispensable under certain conditions. Rather than refuting nitrogen limitation, we propose a re-evaluation of nutrient limitation in the gut, and a more nuanced model, with carbon and energy sources emerging as potential bottlenecks. This minireview emphasizes Enterobacteriaceae as a pathobiont model for investigating nitrogen metabolism and outlines key knowledge gaps to be addressed in future studies.