Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time.
Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time.
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DOI：
10.1371/journal.pone.0142825
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Relman DA
中科院分区：
文献类型：
--
作者：
Hoy YE;Bik EM;Lawley TD;Holmes SP;Monack DM;Theriot JA;Relman DA
遗传、饮食和其他环境暴露被认为是动物肠道微生物群发育和组成的主要因素。然而，这些因素在成年动物中的相对贡献，以及在各种重要环境中随时间的变化，仍然没有完全了解。我们研究了一群近亲繁殖的雌性老鼠，它们吃同样的食物，住在同样的条件下。我们在两周内收集了46只小鼠的粪便样本，其中4只小鼠的采样时间长达236天，总共190个样本，并通过分析16S rRNA基因V3区域的1,849,990个高质量pyrosequencing reads，确定了它们微生物群落的系统发育组成。即使在这些控制条件下，我们也发现了群落组成的显著个体间差异，以及个体内部随时间的变化，包括在同居的前两个月α多样性的增加。在不同的笼子和供应商装运组中小鼠的成员数解释了一些差异。同一装运组和笼子的小鼠个体间差异仍然显著。总的来说，我们发现肠道微生物群组成的23%的变化可以通过小鼠粪便微生物群随时间的变化来解释，12%可以通过个体小鼠之间的持续差异来解释，14%可以通过笼子来解释，18%可以通过运输组来解释。我们的研究结果表明，近亲繁殖实验动物的控制种群的微生物群可能不像以前认为的那样均匀，动物饲养和处理可能解释了一些变化，并且尚未确定的因素可能解释了种群和个体内微生物群组成随时间变化的其他组成部分。这些发现对涉及实验动物的实验的设计和解释具有启示意义。
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.