The impact of Functional foods on the gut microbiota is a fundamental question since shifts in bacterial composition are associated with inflammation progression. Therefore, this study investigated the effects of two types of cheeses fermented by probiotic bacteria in C57BL6 mice either in healthy conditions or in dextran sulfate sodium (DSS)-induced colitis. One cheese was fermented by Propionibacterium freudenreichii CIRM-BIA129. A second kind of cheese was made in industrial conditions to reproduce Emmental but using the above-mentioned strain in combination with Lactobacillus delbrueckii CNRZ327 and Streptococcus thermophilus LMD-9 as starters. The gut microbiota was investigated by shotgun metagenomic sequencing and the taxonomic and functional profiles were assessed through sequence alignment to NCBI taxonomy and KEGG pathways databases. Our results suggest that both treatments did not disturb the microbial community ecology. Emmental intake increased symbionts as Romboutsia and Akkermansia muciniphila. Furthermore, metabolic pathway analysis suggests that A. muciniphila may produce bioactive metabolites as acetate and cooperate with other commensal species to produce indole and gamma-aminobutyric acid. Mice with colitis have restored some of the impaired microbiome metabolic functions when treated with cheese fermented only by Propionibacterium, while the Emmental cheese promoted the increase of Ligilactobacillus murinus. This taxon presented several genes with immunomodulatory activity potential. This study provides insights for engineering functional cheeses to increase beneficial bacteria in the gut. However, further studies are required to investigate their role in regulating the gut-brain axis. Moreover, possible anti-inflammatory mechanisms based on the promotion of Lg. murinus interaction with the host was suggested.