Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation

作者：Dionysios A. Antonopoulos, Susan M. Huse, Hilary G. Morrison, Thomas Mitchell Schmidt, Mitchell L. Sogin, Vincent Bensan Young · 发表于：Infection and Immunity · 年份：2009 · DOI：10.1128/iai.01520-08 · 被引用次数：570 · 研究领域：Gut microbiota and health、Clostridium difficile and Clostridium perfringens research、Probiotics and Fermented Foods

Shifts in microbial communities are implicated in the pathogenesis of a number of gastrointestinal diseases, but we have limited understanding of the mechanisms that lead to altered community structures. One difficulty with studying these mechanisms in human subjects is the inherent baseline variability of the microbiota in different individuals. In an effort to overcome this baseline variability, we employed a mouse model to control the host genotype, diet, and other possible influences on the microbiota. This allowed us to determine whether the indigenous microbiota in such mice had a stable baseline community structure and whether this community exhibited a consistent response following antibiotic administration. We employed a tag-sequencing strategy targeting the V6 hypervariable region of the bacterial small-subunit (16S) rRNA combined with massively parallel sequencing to determine the community structure of the gut microbiota. Inbred mice in a controlled environment harbored a reproducible baseline community that was significantly impacted by antibiotic administration. The ability of the gut microbial community to recover to baseline following the cessation of antibiotic administration differed according to the antibiotic regimen administered. Severe antibiotic pressure resulted in reproducible, long-lasting alterations in the gut microbial community, including a decrease in overall diversity. The finding of stereotypic responses of the indigenous microbiota to ecologi...