Captivity and urbanization have distinct effects on the gut microbiome of deer mice (Peromyscus maniculatus)

Animals in captive and urbanized environments encounter evolutionarily novel conditions shaped by humans, such as altered diets, exposure to human bacteria, and potentially medical interventions. These environments have been demonstrated to affect gut microbial composition and diversity independently, but have not yet been studied together. By sequencing the gut microbiomes of deer mice living in rural, urban, zoo, and laboratory settings, we sought to identify (1) whether gut microbiomes respond similarly to captivity regardless of differences in husbandry conditions and (2) whether urbanization and captivity induce parallel composition and diversity shifts in the gut microbiome. We found that the gut microbiomes of captive mice were distinct from those of free-living mice, indicating captivity had a consistent effect on the deer mouse microbiome regardless of location, lineage, or husbandry conditions for a population. Additionally, the gut microbiome composition, diversity and bacterial load of free-living urban mice were distinct from those of captive or rural mice. Together, these results indicate that gut microbial changes associated with captivity and urbanization are likely not a shared response to increased exposure to humans but rather are shaped by environmental features intrinsic to captive and urban conditions.

栖息于圈养与城市化环境中的动物，会面临人类塑造的、演化层面全新的生存条件，例如饮食结构改变、接触人源细菌，以及可能存在的医疗干预措施。已有研究证实，这两类环境均可独立影响宿主肠道微生物组（gut microbiome）的组成与多样性，但目前尚无研究将二者结合开展探讨。
本研究对栖息于野外乡村、城市、动物园及实验室环境中的鹿鼠（deer mice）开展肠道微生物组测序，旨在明确两个科学问题：（1）无论饲养管理条件存在何种差异，圈养环境是否会对肠道微生物组产生一致的影响；（2）城市化与圈养是否会引发肠道微生物组在组成与多样性层面出现相似的改变。
研究结果显示，圈养鹿鼠的肠道微生物组与野生鹿鼠存在显著差异，表明无论种群的栖息地点、遗传谱系或饲养管理条件存在何种差异，圈养环境对鹿鼠肠道微生物组均具有一致的影响。
此外，城市野生鹿鼠的肠道微生物组组成、多样性及细菌载量（bacterial load），均与圈养鹿鼠或乡村野生鹿鼠存在显著差异。
综合来看，上述结果表明，与圈养和城市化相关的肠道微生物组改变，并非源于宿主对人类接触增加的共有响应，而是由圈养与城市化环境所固有的特有环境特征所塑造。