Gut microbial communities play critical roles in the biological functions of their host, such as mediating nutrient absorption, digesting food components the host cannot, and offering protection against enteric pathogens. Extensive research on gut microbial communities has been conducted on mammals, including humans and rodents, but much less work has been done in birds. Furthermore, much of the research on host–microbe interactions make use of faecal samples and rectal/cloacal swabs as a proxy for intestinal samples, which can be difficult to obtain directly. However, little is known about the overlap between the microbial communities of the gut, faeces and swabs, which limits interpretability of results based on faecal samples and swabs. To address this gap in knowledge, we compared the microbiome from five sample types – proventriculus, small intestine, large intestine, cloacal swabs and faeces – across individual Zebra Finches Taeniopygia guttata housed in constant conditions with a standardized diet. We compared diversity and community composition through 16S rRNA gene sequencing. Our results show that microbial communities from both cloacal swabs and faeces were distinct from proventriculus and small intestinal samples, but generally indistinguishable from large intestinal samples, indicating that these non‐lethal samples may be useful proxies for large intestinal bacterial communities. Gaining insight into non‐invasive sampling techniques for passerines has implications for studies of gut microbial diversity and abundance in wild bird populations. Furthermore, reliable non‐lethal sampling is necessary for experiments where repeated sampling is required.

中文翻译：

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对一只雀形目鸟类非致命性肠道微生物组采样方法的评估

肠道微生物群落在其宿主的生物学功能中起着至关重要的作用，例如介导营养吸收，消化宿主无法消化的食物成分以及提供针对肠道病原体的保护。已经对包括人类和啮齿动物在内的哺乳动物进行了肠道微生物群落的广泛研究，但是在鸟类中所做的工作却少得多。此外，许多关于宿主与微生物相互作用的研究都利用粪便样本和直肠/泄殖腔拭子代替肠道样本，而这可能很难直接获得。然而，对肠道，粪便和拭子的微生物群落之间的重叠知之甚少，这限制了基于粪便样本和拭子的结果的可解释性。为了解决这一知识鸿沟，我们比较了五种样本类型的微生物组：前体，Taeniopygia guttata可以在恒定条件下以标准化饮食饲养。我们通过16S rRNA基因测序比较了多样性和群落组成。我们的结果表明，泄殖腔拭子和粪便中的微生物群落与原肠和小肠样本不同，但通常与大肠样本没有区别，这表明这些非致死性样本可能是大肠细菌群落的有用代理。深入了解雀形目的非侵入性采样技术，对研究野生鸟类种群中肠道微生物的多样性和丰度具有重要意义。此外，对于需要重复采样的实验，可靠的非致命采样是必需的。