Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time

Genetics, diet, and other environmental exposures are thought to be major factors in the development and composition of the intestinal microbiota of animals. However, the relative contributions of these factors in adult animals, as well as variation with time in a variety of important settings, are still not fully understood. We studied a population of inbred, female mice fed the same diet and housed under the same conditions. We collected fecal samples from 46 individual mice over two weeks, sampling four of these mice for periods as long as 236 days for a total of 190 samples, and determined the phylogenetic composition of their microbial communities after analyzing 1,849,990 high-quality pyrosequencing reads of the 16S rRNA gene V3 region. Even under these controlled conditions, we found significant inter-individual variation in community composition, as well as variation within an individual over time, including increases in alpha diversity during the first 2 months of co-habitation. Some variation was explained by mouse membership in different cage and vendor shipment groups. The differences among individual mice from the same shipment group and cage were still significant. Overall, we found that 23% of the variation in intestinal microbiota composition was explained by changes within the fecal microbiota of a mouse over time, 12% was explained by persistent differences among individual mice, 14% by cage, and 18% by shipment group. Our findings suggest that the microbiota of controlled populations of inbred laboratory animals may not be as uniform as previously thought, that animal rearing and handling may account for some variation, and that as yet unidentified factors may explain additional components of variation in the composition of the microbiota within populations and individuals over time. These findings have implications for the design and interpretation of experiments involving laboratory animals.

遗传、饮食及其他环境暴露被认为是影响动物肠道菌群（intestinal microbiota）发育与组成的核心因素。然而，上述因素在成年动物中的相对贡献，以及多种重要场景下菌群随时间的变化规律，目前仍未得到完全阐明。本研究以饲喂相同饲料、饲养于统一环境中的近交系雌性小鼠（inbred mice）为研究对象。研究人员在两周内采集了46只个体小鼠的粪便样本，其中4只小鼠的采样时长长达236天，最终共获得190份样本；通过对16S rRNA基因V3区（16S rRNA gene V3 region）的1,849,990条优质焦磷酸测序（pyrosequencing）读段进行分析，确定了其微生物群落的系统发育组成。即便在上述可控实验条件下，研究仍发现菌群群落组成存在显著的个体间差异，同时单一个体的菌群也随时间发生变化，包括同居初期前2个月内α多样性（alpha diversity）的升高。部分差异可归因于小鼠所属的不同笼舍与供应商运输组，但即便来自同一运输组且处于同一笼舍的个体小鼠，其菌群差异仍具有统计学显著性。整体而言，本研究发现肠道菌群组成的变异中，23%可由单只小鼠粪便菌群随时间的变化所解释，12%源于个体间的持续性差异，14%归因于笼舍因素，18%则与运输组相关。研究结果表明，受控饲养的近交系实验动物的肠道菌群可能并不如此前预想的那般均一；动物饲养与操作流程可解释部分菌群变异，而尚未被探明的因素则可进一步解释种群内及个体内菌群组成随时间推移产生的额外变异。上述发现对涉及实验动物的实验设计与结果解读均具有重要参考价值。