Abstract Background Nutritional interventions have been considered an alternative rationale for preventing Inflammatory Bowel Diseases. The investigation of their impact on the gut microbiota is a fundamental question since shifts in the composition of the commensal bacterial community are required for the onset and maintenance of colitis. Therefore, in this study, we investigated the effects of two types of cheeses, fermented by probiotic propionibacteria. One experimental single-strain cheese was solely fermented by Propionibacterium freudenreichii CIRM-BIA129. Another was an Emmental made in industrial conditions using the same propionic strain, in combination with Lactobacillus delbrueckii CNRZ327 and Streptococcus thermophilus LMD-9, as starters. Both kinds of cheese were tested in healthy conditions and the context of DSS-induced colitis in conventional C57BL6 mice and the gut microbiota was investigated. Results Based on the metagenomic analysis, our results suggest that cheese consumption, whatever the kind of cheese, did not disturb the typical microbial community, although the Emmental intake increased symbionts population as Romboutsia sp. and partially increased Akkermansia muciniphila . Furthermore, metabolic pathway reconstruction analysis suggests that A. muciniphila may produce acetate through sulfate assimilatory metabolism and may cooperate with other commensal species in tryptophan and glutamate metabolism to produce indole and gamma-aminobutyric acid. Considering the colitis context, the consumption of the Single-strain cheese restored some of the impaired microbiome metabolic functions, while Emmental cheese promoted the increase of Ligilactobacillus murinus. This bacterium presented several genes involved in producing metabolites and adhesin proteins with potential immunomodulatory activity. Conclusions This study concludes that the Emmental cheese effects increased the microbiota's capacity to produce metabolites involved in gut-brain axis regulation in intestinal homeostasis condition and, therefore, may represent a potential therapy for inflammatory neurodegenerative diseases. Regarding the colitis context, our results support the beneficial properties of functional Emmental cheese by suggesting possible anti-inflammatory mechanisms based on the promotion of Lg. murinus interaction with the host.