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Dietary changes and lifestyle shifts affect the gut microbiomes of giant pandas
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  • Lei Jin,
  • Shengzhi Yang,
  • Caiwu Li,
  • Daifu Wu,
  • Yongguo He,
  • Bei Li,
  • Guiquan Zhang,
  • Yaowu Xiong,
  • Rongping Wei,
  • Guo Li,
  • Hongning Wu,
  • Wenwen Deng,
  • Yan Huang,
  • Hemin Zhang,
  • Likou Zou
Shengzhi Yang
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Yongguo He
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Guiquan Zhang
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Yaowu Xiong
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Rongping Wei
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Hongning Wu
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Wenwen Deng
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Hemin Zhang
China Conservation and Research Center for the Giant Panda
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Abstract

Gut microbiota (GM) are important for the health of giant pandas (Ailuropoda melanoleuca, GP), in addition to the utilization of bamboo in their diets. However, it’s not fully understood how diet conversions and environmental factors contribute to the compositions of giant panda GM. Consequently, we evaluated how dietary changes and lifestyle shifts influence the GM of giant pandas using high-throughput sequencing and genome-resolved metagenomics. The gut microbial communities of giant pandas were more similar when their hosts exhibited the same diets or lifestyles. High fiber diets significantly increased the diversity (Shannon index) and decreased the richness (Chao1 index) of gut bacterial communities (p < 0.05). In addition, the abundances of Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium significantly increased with bamboo consumption (Non-parametric factorial Kruskal-Wallis sum-rank test, LDA>4). Reconstruction of 60 metagenome-assembled-genomes (MAGs) indicated that these bacteria were likely responsible for bamboo digestion via gene complements involved in cellulose, hemicellulose, and lignin degradation. Further, the biodiversity of GM in wild or reintroduced pandas were higher than those of wild-training pandas, especially fungal communities. The GM structure in reintroduced giant pandas notably converged to that of wild pandas. These results revealed Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium may contribute to lignocellulose digestion in GP. Captivity generally led to decreased biodiversity of GM in giant pandas. Adaptations to increased environmental threats or stressors may aid the conversion of reintroduced giant panda GM to those like wild pandas. In summary, we indicated that diet and lifestyle could influence GM remarkably in GP.