School of Agriculture, Food and Wine, University of Adelaide, SA, Glen Osmond, Australia.
Queensland Facility for Advanced Bioinformatics, School of Medicine, Menzies Health Institute Queensland, Griffith University, Southport, Qld, Australia.
Mol Ecol Resour. 2020 Jul;20(4):844-855. doi: 10.1111/1755-0998.13139. Epub 2020 Feb 19.
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.
非侵入性采样方法广泛应用于濒危物种的研究和在操纵实验期间进行的时间监测。虽然现有研究表明，不同类群的非侵入性采样方法在准确性上存在差异，但尚未有研究比较成年两栖动物的非致死性采样方法。在这项研究中，我们比较了成年甘蔗蟾蜍 Rhinella marina 的两种非侵入性样本类型（粪便和泄殖腔拭子）与大肠的微生物组。我们使用 16S rRNA 基因测序来研究微生物群落如何沿着消化道变化，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，甘蔗蟾蜍的肠道微生物群主要由拟杆菌门、变形菌门和厚壁菌门组成，有趣的是，我们还看到了相当比例的 Fusobacteria，Fusobacteria 以前与海洋物种和青蛙免疫力的变化有关。甘蔗蟾蜍的大小肠具有相似的微生物组成，但大肠表现出更高的多样性。我们的结果表明，与粪便样本相比，泄殖腔拭子与大肠样本更相似，而小肠样本与两种非致死性样本类型均有显著差异。我们的研究为未来研究甘蔗蟾蜍肠道微生物组提供了有价值的信息，并验证了使用泄殖腔拭子作为研究大肠微生物组变化的非致死性方法的有效性。这些数据为未来需要非致死性采样的两栖动物肠道微生物组研究提供了见解。
