Animals under managed care in zoos and aquariums are ideal surrogate study subjects for endangered species that are difficult to obtain in the wild. We compared the fecal and oral microbiomes of healthy, managed African penguins (Spheniscus demersus) to those of other domestic and wild vertebrate hosts to determine how host identity, diet, and environment shape the penguin microbiome. The African penguin oral microbiome was more similar to that of piscivorous marine mammals, suggesting that diet and a marine environment together play a strong role in shaping the oral microbiome. Conversely, the penguin cloaca/fecal microbiome was more similar to that of other birds, suggesting that host phylogeny plays a significant role in shaping the gut microbiome. Although the penguins were born under managed care, they had a gut microbiome more similar to that of wild bird species compared to domesticated (factory-farmed) birds, suggesting that the managed care environment and diet resemble those experienced by wild birds. Finally, the microbiome composition at external body sites was broadly similar to that of the habitat, suggesting sharing of microbes between animals and their environment. Future studies should link these results to microbial functional capacity and host health, which will help inform conservation efforts.

动物园和水族馆中受管理照顾的动物是难以在野外获得的濒危物种的理想替代研究对象。我们将健康、管理的非洲企鹅（ Spheniscus demersus ）的粪便和口腔微生物组与其他家养和野生脊椎动物宿主的粪便和口腔微生物组进行了比较，以确定宿主身份、饮食和环境如何塑造企鹅微生物组。非洲企鹅的口腔微生物组与食鱼海洋哺乳动物的口腔微生物组更相似，这表明饮食和海洋环境在塑造口腔微生物组方面发挥着重要作用。相反，企鹅泄殖腔/粪便微生物组与其他鸟类更相似，表明宿主系统发育在塑造肠道微生物组方面发挥着重要作用。尽管企鹅是在管理护理下出生的，但与驯养（工厂化养殖）鸟类相比，它们的肠道微生物组与野生鸟类更相似，这表明管理护理环境和饮食与野生鸟类的经历相似。最后，身体外部部位的微生物组组成与栖息地的微生物组组成大致相似，这表明动物与其环境之间存在微生物共享。未来的研究应该将这些结果与微生物功能能力和宿主健康联系起来，这将有助于为保护工作提供信息。