Bifidobacterium bifidum suppresses gut inflammation caused by repeated antibiotic disturbance without recovering gut microbiome diversity in mice. Bifidobacterium bifidum suppresses antibiotic-induced inflammation

The gut microbiome is a dynamic community that significantly affects host health, frequently disturbed by medications such as antibiotics. Recently, probiotics have been proposed as a remedy for antibiotic-induced dysbiosis, but the efficacy of such treatments remains debated. The effect of specific antibiotic-probiotic combinations on the gut microbiome and host health requires further research. We used 40 female C57BL/6 mice and tested the effect of three different antibiotics: vancomycin, amoxicillin, and ciprofloxacin. Antibiotic administration was followed by one of the following recovery treatments: Bifidobacterium bifidum JCM 1254 as a probiotic; fecal transplants; or natural recovery. Each antibiotic administration and recovery treatment was repeated 3 times over 9 weeks. We used the Shannon Index and Chao1 Index to determine gut microbiome diversity and assessed recovery by quantifying the magnitude of microbial shift using the Bray-Curtis Index of Dissimilarity. We determined the community composition based on the V3–V4 regions of the 16S ribosomal RNA gene. To assess host health, we measured body weight and cecum weight, as well as mRNA expression of inflammation-related genes in the intestine by Reverse-Transcription quantitative PCR. Results show that community response varied by the type of antibiotic used, with vancomycin having the most significant effects. As a result, the effect of probiotics and fecal transplants also varied by antibiotic type. For vancomycin, the first antibiotic disturbance substantially increased the relative abundance of inflammatory species in the phylum Proteobacteria, such as Proteus, but the effect of subsequent disturbances was less pronounced, suggesting that the gut microbiome is affected by past disturbance events. Furthermore, although gut microbiome diversity did not recover, probiotic supplementation was effective in limiting cecum size enlargement and colonic inflammation caused by vancomycin. However, for amoxicillin and ciprofloxacin, the relative abundances of proinflammatory species were not greatly affected, and consequently, the effect of probiotic supplementation on community structure, cecum weight, and expression of inflammation-related genes was comparatively negligible. These results indicate that probiotic supplementation is effective, but only when antibiotics cause proinflammatory species-induced gut inflammation, suggesting that the efficacy of probiotic supplementation is strongly influenced by the type of disturbance introduced to the community.