室内饲养对高原鼠兔肠道微生物群落构建过程的影响

群落生态构建过程是近年来微生物群落生态学的研究热点。室内饲养可引起肠道菌群的剧烈变化，这种改变是否会影响群落的构建过程，一直未见报道。本文以高原鼠兔 (Ochotona curzoniae) 为对象，采用16S rRNA测序技术，探讨室内饲养和野生高原鼠兔肠道微生物群落在结构、功能以及群落构建过程等方面的差异。结果表明，在繁殖季节，室内饲养组的群落多样性指数和均匀度指数均显著低于野外组；群落丰度指数和群落覆盖度指数在非繁殖季节显著高于繁殖季节。拟杆菌门 (Bacteroidetes) 在室内饲养组显著富集，而厚壁菌门 (Firmicute) 和浮霉菌门 (Planctomycetes) 在野外组显著富集；在野外组，Epsilonbacteraeota和软壁菌门 (Tenericutes) 在繁殖季节显著富集。菌群功能分析显示，室内饲养组与野生组在细胞通讯和心血管疾病通路存在显著差异；野外组繁殖季节与非繁殖季节肠道菌群功能在氨基酸代谢、碳水化合物代谢和脂质代谢等通路存在显著差异。中性模型拟合结果表明，室内饲养明显降低了菌群构建的随机过程。野外组生理状态也会降低菌群构建的随机性。本研究证明室内饲养和宿主生理状态均会对高原鼠兔肠道菌群组成及群落构建产生影响，此结果为实现高原鼠兔室内繁殖提供了新的理论基础。

Effects of captivity on the assembly process of microbiota communities of plateau pikas

Revealing the community assembly process is helpful to better understand the mechanism of biodiversity generation and maintenance, which has been an emerging topic in microbial community ecology in recent years. Studies have shown that captivity can cause drastic changes in the composition and diversity of intestinal microbiotas, however, whether captivity can alter the assembly processes of gut bacterial communities in plateau pikas is still unknown. Here, we employed 16S rRNA gene-based large-scale structural profiling to explore the effect of captivity and breeding status on the gut microbial composition, diversity, functions, and assembly processes in plateau pikas (Ochotona curzoniae). The results showed that the community richness and community coverage index of captivity animals were significantly lower than those of wild groups. For the wild groups, the indexes were significantly higher in non-breeding groups than those of breeding groups. The relative abundance of Bacteroidetes was significantly higher in the captivity group than that of the wild groups, while the relative abundance of Firmicutes and Planctomycetes were significantly higher in wild groups than those of the captivity group. For the wild groups, the richness of Epsilonbacteraeota and Tenericutes were higher in the breeding period group than those of the non-breeding group. The results of functional prediction revealed that the abundance of genes involved in cardiovascular disease and cell communication were significantly different between captivity and wild breeding groups. The abundance of genes involved in the pathway of amino acid metabolism, carbohydrate metabolism, and lipid metabolism enriched in non-breeding groups compared with breeding groups. The results of neutral model revealed that captivity reduced the importance of stochastic processes in governing the bacterial community assembly, while breeding status increased the importance of stochastic processes in structuring the community assembly. Our results provided new insights on the effects of captivity on the microbial composition, diversity, function, and assembly processes and the interactions between microbiotas and physiological state of plateau pika, which provided a new theoretical basis to promote the possibility of successful reproduction in laboratory.