Inflammatory bowel disease (IBD) is a complex relapsing inflammatory disease in the gut and is driven by complicated host-gut microbiome interactions. Gut commensals have shown different functions in IBD prevention and treatment. To gain a mechanistic understanding of how different commensals affect intestinal inflammation, we compared the protective effects of six probiotics (belonging to the genera <em>Akkermansia</em>, <em>Bifidobacterium</em>, <em>Clostridium</em>, and <em>Enterococcus</em>) on dextran sulfate sodium (DSS)-induced colitis in mice with or without gut microbiota. Anti-inflammatory properties (ratio of IL-10 and IL-12) of these strains were also evaluated in an in vitro mesenteric lymph nodes (MLN) co-culture system. Results showed that four probiotics (belonging to the species <em>B. breve</em>, <em>B. bifidum</em>, and <em>E. faecalis</em>) can alleviate colitis in normal mice. The probiotic strains differed in regulating the intestinal microbiota, cytokines (IL-10, IL-1β and IFN-γ), and tight junction function (Zonulin-1 and Occludin). By constrast, <em>A. muciniphila</em> AH39 and <em>C. butyricum</em> FHuNHHMY49T1 were not protective. Interestingly, <em>B. breve</em> JSNJJNM2 with high anti-inflammatory potential in the MLN model could relieve colitis symptoms in Abx-treated mice. Meanwhile, <em>E. faecalis</em> FJSWX25M1 induced low levels of cytokines in vitro and showed no beneficial effects. Therefore, we provided insight into the clinical application of probiotics in IBD treatment.