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Yang S, Deng W, Li G, Jin L, Huang Y, He Y, Wu D, Li D, Zhang A, Liu C, Li C, Zhang H, Xu H, Penttinen P, Zhao K, Zou L. Reference gene catalog and metagenome-assembled genomes from the gut microbiome reveal the microbial composition, antibiotic resistome, and adaptability of a lignocellulose diet in the giant panda. ENVIRONMENTAL RESEARCH 2024; 245:118090. [PMID: 38163545 DOI: 10.1016/j.envres.2023.118090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.
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Affiliation(s)
- Shengzhi Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Wenwen Deng
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Guo Li
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Lei Jin
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Yongguo He
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Daifu Wu
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Anyun Zhang
- College of Life Science, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Chengxi Liu
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Hemin Zhang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, 610051, Sichuan, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Petri Penttinen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Deng F, Han Y, Huang Y, Li D, Chai J, Deng L, Wei M, Wu K, Zhao H, Yang G, Zhao J, Li Y, Wang C. A comprehensive analysis of antibiotic resistance genes in the giant panda gut. IMETA 2024; 3:e171. [PMID: 38868505 PMCID: PMC10989137 DOI: 10.1002/imt2.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 06/14/2024]
Abstract
In this study, we have successfully constructed a comprehensive database of metagenome-assembled genomes (MAGs) pertaining to the gut microbiota of the giant panda. Through our analysis, we have identified significant reservoirs of antibiotic resistance genes (ARGs), namely Escherichia coli, Citrobacter portucalensis, and Klebsiella pneumoniae. Furthermore, we have elucidated the primary contributors to ARGs, including Streptococcus alactolyticus and Clostridium SGBP116, in both captive and wild pandas. Additionally, our findings have demonstrated a higher prevalence of ARGs in the metagenome, with notable expression of the RPOB2 gene in S. alactolyticus. Crucially, 1217 ARGs shared homology with human gut ARGs, underscoring the interaction relationship between pandas and human microbiomes. These findings are instrumental in understanding the antibiotic resistance landscape in the giant panda's gut, providing a framework for developing strategies to combat antibiotic resistance and safeguard the health of this endangered species.
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Affiliation(s)
- Feilong Deng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and EngineeringFoshan UniversityFoshanChina
- Department of Animal Science, College of Life Science and EngineeringFoshan UniversityFoshanChina
| | - Yanhua Han
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and EngineeringFoshan UniversityFoshanChina
- Department of Animal Science, College of Life Science and EngineeringFoshan UniversityFoshanChina
| | - Yushan Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and EngineeringFoshan UniversityFoshanChina
- Department of Animal Science, College of Life Science and EngineeringFoshan UniversityFoshanChina
| | - Desheng Li
- National Conservation and Research Centre for Giant Pandas/China Conservation and Research Centre for the Giant PandaChengduChina
| | - Jianmin Chai
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and EngineeringFoshan UniversityFoshanChina
- Department of Animal Science, College of Life Science and EngineeringFoshan UniversityFoshanChina
| | - Linhua Deng
- National Conservation and Research Centre for Giant Pandas/China Conservation and Research Centre for the Giant PandaChengduChina
| | - Ming Wei
- National Conservation and Research Centre for Giant Pandas/China Conservation and Research Centre for the Giant PandaChengduChina
| | - Kai Wu
- National Conservation and Research Centre for Giant Pandas/China Conservation and Research Centre for the Giant PandaChengduChina
| | - HuaBin Zhao
- Department of Ecology, College of Life SciencesWuhan UniversityWuhanChina
| | - Guan Yang
- Department of Infectious Diseases and Public HealthCity University of Hong KongKowloon, Hong Kong, SARChina
| | - Jiangchao Zhao
- Department of Animal Science, Division of AgricultureUniversity of ArkansasFayettevilleArkansasUSA
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and EngineeringFoshan UniversityFoshanChina
- Department of Animal Science, College of Life Science and EngineeringFoshan UniversityFoshanChina
| | - Chengdong Wang
- National Conservation and Research Centre for Giant Pandas/China Conservation and Research Centre for the Giant PandaChengduChina
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