Dynamical and highly personalized responses in the microbial composition and short-chain fatty acids of the human gut microbiome to inulin intervention
Inulin is widely used as a prebiotic to modulate the composition and short-chain fatty acids (SCFAs) metabolism of the human gut microbiota. While studies have revealed that the response of gut microbiota to inulin intervention can be personalized, characterization of the individualized dynamics following inulin intervention remains incomplete and requires further investigation, aimed at enhancing personalized nutritional interventions. In this study, we tracked the compositional and SCFAs metabolic shifts in the gut microbiome for 10 days of inulin intervention in a cohort of 20 healthy volunteers. We found that inulin exerts profound and personalized effects on the dynamics of the human gut microbiota compositions, while exhibiting a relatively moderate influence on the stool SCFA profiles. In addition, we observed inter-individual differences in the response patterns to inulin during temporal microbial shifts. Furthermore, we observed that alterations in stool SCFA profiles did not consistently align with changes in the gut microbiota compositional profiles, and notably, the baseline microbiota profile did not exhibit a correlation with the inulin-induced microbiota response. Specifically, inulin selectively enriched particular species, including Bifidobacterium adolescentis, Bifidobacterium longum, Anaerostipes hadrus, and Bacteroides xylanisolvens. Moreover, we evaluated whether in vitro culture of human stool-derived microbial communities can be used to predict the personalized responses to inulin. We found that the compositional changes in vitro (i.e. inulin stimulates the growth for certain species) were comparable with in vivo observations, while personalized responses in SCFAs were not consistent between in vitro and in vivo. Our study highlights significant individual differences in response to inulin, thereby advocating for further research based on larger cohort studies in human populations rather than relying on in vitro culturing to assess and predict inulin's prebiotic benefits.