Growth stage and interspecies interactions shape the cell biology and cell cycle characteristics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis.

The human gut is a densely populated environment where microbial cells face frequent nutrient fluctuations. While previous studies have identified changes in gene expression, protein concentrations, and metabolite levels, less is known about how gut bacteria respond to nutrient fluctuations at the cellular level. Here, we compared cell biological properties of B. thetaiotaomicron and R. intestinalis, two prevalent human gut microbiome members. Our comparison revealed distinct cellular properties of both bacteria during exponential growth in vitro, including a unique zonal peptidoglycan synthesis pattern in R. intestinalis. Upon nutrient depletion in stationary phase, we observed different cell morphological alterations, with B. thetaiotaomicron cells becoming wider and R. intestinalis cells shorter, accompanied by distinct intracellular changes. These alterations extended to other B. thetaiotaomicron strains, but not Roseburia species. By re-analyzing an existing RNA-seq dataset, we could link the cell biological response of both species to different alterations in gene expression in stationary phase. Finally, coculture experiments revealed a significant impact of interspecies interactions on cell morphological and transcriptomic properties of both bacteria. Together, our work provides insight into the unexplored cell biology of representative human gut microbiome members and how this is shaped by nutrient fluctuations and the presence of other species.