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

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.

肠道微生物组（gut microbiome）是一类动态群落，可显著影响宿主健康，且常受抗生素（antibiotics）等药物的干扰。近年来，益生菌（probiotics）被提出用于缓解抗生素诱导的菌群失调，但此类治疗的有效性仍存在争议。特定抗生素-益生菌联合疗法对肠道微生物组及宿主健康的影响仍需进一步研究。本研究使用40只雌性C57BL/6小鼠，测试了三种不同抗生素：万古霉素（vancomycin）、阿莫西林（amoxicillin）及环丙沙星（ciprofloxacin）的作用。抗生素给药后，分别采用以下三种恢复干预措施：以两歧双歧杆菌JCM 1254（Bifidobacterium bifidum JCM 1254）作为益生菌干预、粪便移植，或自然恢复。每轮抗生素给药与恢复干预在9周内重复3次。本研究采用香农指数（Shannon Index）与Chao1指数（Chao1 Index）评估肠道微生物组多样性，并通过布赖-柯蒂斯相异指数（Bray-Curtis Index of Dissimilarity）量化微生物移位程度，以此评估恢复效果。基于16S核糖体RNA基因（16S ribosomal RNA gene）的V3–V4区测定群落组成。为评估宿主健康状况，我们测量了小鼠体重与盲肠重量，并通过逆转录定量PCR（Reverse-Transcription quantitative PCR）检测肠道内炎症相关基因的mRNA表达水平。研究结果显示，群落响应因所用抗生素类型而异，其中万古霉素的影响最为显著。相应地，益生菌与粪便移植的效果也随抗生素类型发生变化。针对万古霉素，首次抗生素干预可显著提升变形菌门（Proteobacteria）中变形杆菌属（Proteus）等促炎物种的相对丰度，但后续干预的影响则相对较弱，表明肠道微生物组会受既往干预事件的影响。此外，尽管肠道微生物组多样性未能恢复，但补充益生菌可有效限制万古霉素诱导的盲肠体积增大与结肠炎症。然而，对于阿莫西林与环丙沙星，促炎物种的相对丰度并未受到显著影响，因此补充益生菌对群落结构、盲肠重量及炎症相关基因表达的影响相对可忽略。上述结果表明，补充益生菌仅在抗生素引发促炎物种介导的肠道炎症时才具有有效性，提示益生菌补充的疗效强烈受群落所受干扰类型的影响。