Noninvasive sampling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive sampling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal sampling methods in adult amphibians. In this study, we compare microbiomes from two noninvasive sample types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina . We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal sampling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher diversity. Our results indicate that cloacal swabs were more similar to large intestine samples than were faecal samples, and small intestine samples were significantly different from both nonlethal sample types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal sampling of amphibian gut microbiota.

中文翻译：

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两栖动物肠道微生物组分析非致命性采样方法的比较。

用于研究肠道微生物的无创采样方法已广泛用于濒危物种的研究以及在操纵实验中进行时间监控的物种。尽管现有研究表明不同分类单元之间的非侵入性采样方法在准确性上存在差异，但尚未发表比较成年两栖动物非致命采样方法的研究。在这项研究中，我们比较了两种无创样品类型（粪便和泄殖腔拭子）的微生物组与成年甘蔗蟾蜍（Rinellla marina）大肠的微生物组。。我们使用16S rRNA基因测序来研究微生物群落如何沿消化道变化，以及哪种非致死性采样方法更能代表大肠微生物群。我们发现甘蔗蟾蜍的肠道菌群主要由拟杆菌，Proteobacteria和Firmicutes所控制，有趣的是，我们还发现了很高比例的Fusobacteria，它以前与海洋物种和青蛙免疫力的变化有关。蟾蜍的大肠和小肠的微生物组成相似，但大肠的多样性更高。我们的结果表明，泄殖腔拭子与大肠样本比粪便样本更相似，而小肠样本与两种非致死样本类型有显着差异。我们的研究为甘蔗蟾蜍肠道微生物组的未来研究提供了有价值的信息，并验证了泄殖腔拭子作为一种非致死性方法来研究大肠微生物组变化的有效性。这些数据为需要非致命性采样两栖动物肠道菌群的未来研究提供了见识。