Data on the gut microbiota (GM) of wild animals are key to studies on evolutionary biology (host–GM interactions under natural selection), ecology and conservation biology (GM as a fitness component closely connected to the environment). Wildlife GM sampling often requires non-invasive techniques or sampling from dead animals. In a controlled experiment profiling microbial 16S rRNA in 52 house mice (Mus musculus) from eight families and four genetic backgrounds, we studied the effects of live- and snap-trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared CM from individuals sampled 16–18 h after death with those in live traps and caged controls, and caecal and faecal GM collected from mice in live-traps. Sampling delay did not affect GM composition, validating data from fresh cadavers or snap-trapped animals. Animals trapped overnight displayed a slight but significant difference in GM composition to the caged controls, though the change only had negligible effect on GM diversity, composition and inter-individual divergence. Hence, the trapping process appears not to bias GM profiling. Despite their significant difference, caecal and faecal microbiota were correlated in composition and, to a lesser extent, diversity. Both showed congruent patterns of inter-individual divergence following the natural structure of the dataset. Thus, the faecal microbiome represents a good non-invasive proxy of the caecal microbiome, making it suitable for detecting biologically relevant patterns. However, care should be taken when analysing mixed datasets containing both faecal and caecal samples.

野生动物肠道微生物群 (GM) 的数据是进化生物学（自然选择下的宿主-GM 相互作用）、生态学和保护生物学（GM 作为与环境密切相关的适应性成分）研究的关键。野生动物转基因采样通常需要非侵入性技术或从死动物身上采样。在对 52 只家鼠 ( Mus musculus ) 的微生物 16S rRNA 进行分析的对照实验中) 来自八个家族和四个遗传背景，我们研究了活体诱捕和快速诱捕对小型哺乳动物 GM 的影响，并评估了非新鲜粪便微生物群作为盲肠 GM 代表的适用性。我们比较了死后 16-18 小时采样的个体的 CM 与活体陷阱和笼中对照的个体，以及从活体陷阱中的小鼠收集的盲肠和粪便 GM。采样延迟不影响转基因成分，验证来自新鲜尸体或捕捉动物的数据。被困过夜的动物在转基因成分方面与关在笼子里的对照组有轻微但显着的差异，尽管这种变化对转基因多样性、成分和个体间差异的影响微乎其微。因此，诱捕过程似乎不会影响 GM 分析。尽管它们存在显着差异，盲肠和粪便微生物群在组成上相关，在较小程度上与多样性相关。两者都显示了遵循数据集自然结构的个体间差异的一致模式。因此，粪便微生物组代表了盲肠微生物组的良好非侵入性代表，使其适用于检测生物学相关模式。但是，在分析包含粪便和盲肠样本的混合数据集时应小心。