AUTHOR=Wang Xiaochen , Wang Ziming , Pan Huijuan , Qi Jiwei , Li Dayong , Zhang Liye , Shen Ying , Xiang Zuofu , Li Ming 

TITLE=Captivity Influences the Gut Microbiome of Rhinopithecus roxellana

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.763022

DOI=10.3389/fmicb.2021.763022

ISSN=1664-302X

ABSTRACT=<p><italic>Ex situ</italic> (captivity in zoos) is regarded as an important form of conservation for endangered animals. Many studies have compared differences in the gut microbiome between captive and wild animals, but few have explained those differences at the functional level due to the limited amount of 16S rRNA data. Here, we compared the gut microbiome of captive and wild <italic>Rhinopithecus roxellana</italic>, whose high degree of dietary specificity makes it a good subject to observe the effects of the captive environment on their gut microbiome, by performing a metagenome-wide association study (MWAS). The Chao1 index was significantly higher in the captive <italic>R. roxellana</italic> cohort than in the wild cohort, and the Shannon index of captive <italic>R. roxellana</italic> was higher than that of the wild cohort but the difference was not significant. A significantly increased ratio of <italic>Prevotella</italic>/<italic>Bacteroides</italic>, which revealed an increased ability to digest simple carbohydrates, was found in the captive cohort. A significant decrease in the abundance of Firmicutes and enrichment of genes related to the pentose phosphate pathway were noted in the captive cohort, indicating a decreased ability of captive monkeys to digest fiber. Additionally, genes required for glutamate biosynthesis were also significantly more abundant in the captive cohort than in the wild cohort. These changes in the gut microbiome correspond to changes in the composition of the diet in captive animals, which has more simple carbohydrates and less crude fiber and protein than the diet of the wild animals. In addition, more unique bacteria in captive <italic>R. roxellana</italic> were involved in antibiotic resistance (<italic>Acinetobacter</italic>) and diarrhea (<italic>Desulfovibrio piger</italic>), and in the prevention of diarrhea (<italic>Phascolarctobacterium succinatutens</italic>) caused by <italic>Clostridioides difficile</italic>. Accordingly, our data reveal the cause-and-effect relationships between changes in the exact dietary composition and changes in the gut microbiome on both the structural and functional levels by comparing of captive and wild <italic>R. roxellana</italic>.</p>