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Open AccessArticle

Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas (Ailuropoda melanoleuca)

1
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
2
School of Laboratory Medicine/Sichuan Provincial EngineeringLaboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu 610500, China
3
China Conservation and Research Center for the Giant Panda, Ya’an 611830, Sichuan, China
4
Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
*
Authors to whom correspondence should be addressed.
Genes 2019, 10(10), 827; https://doi.org/10.3390/genes10100827
Received: 2 September 2019 / Revised: 14 October 2019 / Accepted: 16 October 2019 / Published: 20 October 2019
(This article belongs to the Section Microbial Genetics and Genomics)
Captive breeding has been used as an effective approach to protecting endangered animals but its effect on the gut microbiome and the conservation status of these species is largely unknown. The giant panda is a flagship species for the conservation of wildlife. With integrated efforts including captive breeding, this species has been recently upgraded from “endangered” to “vulnerable” (IUCN 2016). Since a large proportion (21.8%) of their global population is still captive, it is critical to understand how captivity changes the gut microbiome of these pandas and how such alterations to the microbiome might affect their future fitness and potential impact on the ecosystem after release into the wild. Here, we use 16S rRNA (ribosomal RNA) marker gene sequencing and shotgun metagenomics sequencing to demonstrate that the fecal microbiomes differ substantially between wild and captive giant pandas. Fecal microbiome diversity was significantly lower in captive pandas, as was the diversity of functional genes. Additionally, captive pandas have reduced functional potential for cellulose degradation but enriched metabolic pathways for starch metabolism, indicating that they may not adapt to a wild diet after being released into the wild since a major component of their diet in the wild will be bamboo. Most significantly, we observed a significantly higher level of amylase activity but a lower level of cellulase activity in captive giant panda feces than those of wild giant pandas, shown by an in vitro experimental assay. Furthermore, antibiotic resistance genes and virulence factors, as well as heavy metal tolerance genes were enriched in the microbiomes of captive pandas, which raises a great concern of spreading these genes to other wild animals and ecosystems when they are released into a wild environment. Our results clearly show that captivity has altered the giant panda microbiome, which could have unintended negative consequences on their adaptability and the ecosystem during the reintroduction of giant pandas into the wild. View Full-Text
Keywords: captivity; gut microbiome; giant pandas; enzyme activity; antibiotic resistance genes; metagenomics; diversity; metal tolerance genes; virulence factors captivity; gut microbiome; giant pandas; enzyme activity; antibiotic resistance genes; metagenomics; diversity; metal tolerance genes; virulence factors
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MDPI and ACS Style

Guo, W.; Mishra, S.; Wang, C.; Zhang, H.; Ning, R.; Kong, F.; Zeng, B.; Zhao, J.; Li, Y. Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas (Ailuropoda melanoleuca). Genes 2019, 10, 827.

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