The vertebrate gastrointestinal tract is colonised by microbiota that have a major effect on the host’s health, physiology and phenotype. Once introduced into captivity, however, the gut microbial composition of free-living individuals can change dramatically. At present, little is known about gut microbial changes associated with adaptation to a synanthropic lifestyle in commensal species, compared with their non-commensal counterparts. Here, we compare the taxonomic composition and diversity of bacterial and fungal communities across three gut sections in synanthropic house mouse (Mus musculus) and a closely related non-synanthropic mound-building mouse (Mus spicilegus). Using Illumina sequencing of bacterial 16S rRNA amplicons, we found higher bacterial diversity in M. spicilegus and detected 11 bacterial operational taxonomic units with significantly different proportions. Notably, abundance of Oscillospira, which is typically higher in lean or outdoor pasturing animals, was more abundant in non-commensal M. spicilegus. ITS2-based barcoding revealed low diversity and high uniformity of gut fungi in both species, with the genus Kazachstania clearly dominant. Though differences in gut bacteria observed in the two species can be associated with their close association with humans, changes due to a move from commensalism to captivity would appear to have caused larger shifts in microbiota.

中文翻译：

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拟人化如何影响肠道细菌组和霉菌组：比较两种具有不同生态学的小鼠。

脊椎动物胃肠道被微生物群定殖，微生物群对宿主的健康，生理和表型有重要影响。但是，一旦被圈养，自由生活者的肠道微生物组成就会发生巨大变化。目前，与共生物种相比，与共生物种适应同食生活方式有关的肠道微生物变化知之甚少。在这里，我们比较了人类合掌鼠（Mus musculus）和密切相关的非人类土墩小鼠（Mus spicilegus）三个肠道部分的细菌和真菌群落的分类学组成和多样性。使用细菌的16S rRNA扩增子的Illumina测序，我们发现M中的细菌多样性更高。并检测到11个细菌操作分类单位，比例明显不同。值得注意的是，在瘦肉型或室外牧草动物中，通常在较高水平的颤藻中的含量较高，而在非共生性的孢子藻中则更为丰富。基于ITS2的条形码显示这两种物种的肠道真菌均具有较低的多样性和较高的均一性，而Kazachstania属显然占优势。尽管在这两个物种中观察到的肠道细菌差异可能与它们与人类的密切关联有关，但由于从共鸣向圈养转变的变化似乎引起了微生物群的较大变化。基于ITS2的条形码显示这两种物种的肠道真菌均具有较低的多样性和较高的均一性，而Kazachstania属显然占优势。尽管在这两个物种中观察到的肠道细菌差异可能与它们与人类的密切关联有关，但由于从共鸣向圈养转变的变化似乎引起了微生物群的较大变化。基于ITS2的条形码显示这两种物种的肠道真菌均具有较低的多样性和较高的均一性，而Kazachstania属显然占优势。尽管在这两个物种中观察到的肠道细菌差异可能与它们与人类的密切关联有关，但由于从共鸣向圈养转变的变化似乎引起了微生物群的较大变化。