Most knowledge of the vertebrate gut microbiota comes from fecal samples; due to difficulties involved in sample collection, the upper intestinal microbiota is poorly understood in wild animals despite its potential to inform broad interpretations about host-gut microbe relationships under natural conditions. Here, we used 16S rRNA gene sequencing to characterize the microbiota of wild coyotes (Canis latrans) along the gastrointestinal tract, including samples from the duodenum, jejunum, ileum, caecum, ascending and descending colon, and feces. We used this intestinal profile to (1) quantify how intestinal site and individual identity interact to shape the microbiota in an uncontrolled setting, and (2) evaluate whether the fecal microbiota adequately represent other intestinal sites. Microbial communities in the large intestine were distinct from those in the small intestine, with higher diversity and a greater abundance of anaerobic taxa. Within each of the small and large intestine, individual identity explained significantly more among-sample variation than specific intestinal sites, revealing the importance of individual variation in the microbiota of free-living animals. Fecal samples were not an adequate proxy for studying upper intestinal environments, as they contained only half the amplicon sequence variants (ASVs) present in the small intestine at three- to four-fold higher abundances. Our study is a unique biogeographical investigation of the microbiota using free-living mammals rather than livestock or laboratory organisms and provides a foundational understanding of the gastrointestinal microbiota in a wild canid.

有关脊椎动物肠道菌群的大多数知识都来自粪便样本。由于样品采集过程中的困难，尽管在自然条件下有可能为宿主-肠道微生物之间的关系提供广泛的解释，但在野生动物中对上部肠道菌群的了解却很少。在这里，我们使用了16S rRNA基因测序来表征野生土狼（Canis latrans）沿胃肠道，包括十二指肠，空肠，回肠，盲肠，升结肠和降结肠以及粪便的样本。我们使用此肠道特征来（1）量化肠道部位和个体身份如何在不受控制的环境中相互作用以塑造微生物群，以及（2）评价粪便微生物群是否足以代表其他肠道部位。大肠中的微生物群落不同于小肠中的微生物群落，具有更高的多样性和更大的厌氧生物分类单元。在每个小肠和大肠中，个体身份解释的样本间变异要比特定的肠道部位大得多，这揭示了个体变异在自由生存动物微生物群中的重要性。粪便样品不足以研究上部肠道环境，因为它们仅含有小肠中一半的扩增子序列变异体（ASV），其丰度高三至四倍。我们的研究是使用自由生存的哺乳动物而非牲畜或实验室生物对微生物群进行的独特生物地理调查，并为野生犬科动物的胃肠道微生物群提供了基础知识。