Deciphering oxidative stress responses in human gut microbes and fecal microbiota: a cultivation-based approach

Chronic inflammation creates an oxidative environment, altering the gut microbiota. However, the mechanisms underlying oxidative stress-induced community changes remain poorly understood, owing to the complexity of the host environment, high inter-individual variability, and a lack of comparative data on stress tolerance across intestinal taxa. To address this, we developed an in vitro cultivation approach to assess the effects of oxidative stress, induced by 12 concentrations each of hydrogen peroxide (H₂O₂) and oxygen (O₂), on 41 intestinal strains and seven adults' fecal microbiota. Fusicatenibacter saccharivorans and Lachnospira eligens emerged as particularly sensitive taxa in both pure cultures and complex communities. Oxidative stress also reduced butyrate-producing taxa, like Agathobacter and Anaerostipes, along with total butyrate levels. In contrast, facultative anaerobes, like Escherichia-Shigella and Enterococcus, were largely unaffected, and Bacteroides showed high resilience. Notably, the impact of oxidative stress varied among individuals, with numerous genera showing taxon-specific changes depending on the host microbiota composition. These findings underscore the importance of considering individual microbiota backgrounds when assessing oxidative stress effects on microbial communities. Our study provides a tolerance profile of gut microbes to oxidative stress, reveals overlooked taxa involved in community restructuring, and introduces a screening tool to characterize individual microbial and metabolic responses.