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Hu Y, Hu Y, Zhou W, Wei F. Conservation Genomics and Metagenomics of Giant and Red Pandas in the Wild. Annu Rev Anim Biosci 2024; 12:69-89. [PMID: 37863091 DOI: 10.1146/annurev-animal-021022-054730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Giant pandas and red pandas are endangered species with similar specialized bamboo diet and partial sympatric distribution in China. Over the last two decades, the rapid development of genomics and metagenomics research on these species has enriched our knowledge of their biology, ecology, physiology, genetics, and evolution, which is crucial and useful for their conservation. We describe the evolutionary history, endangerment processes, genetic diversity, and population structure of wild giant pandas and two species of red pandas (Chinese and Himalayan red pandas). In addition, we explore how genomics and metagenomics studies have provided insight into the convergent adaptation of pandas to the specialized bamboo diet. Finally, we discuss how these findings are applied to effective conservation management of giant and red pandas in the wild and in captivity to promote the long-term persistence of these species.
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Affiliation(s)
- Yisi Hu
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fuwen Wei
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Feng H, Cao F, Jin T, Wang L. Forest fragmentation causes an isolated population of the golden takin (Budorcas taxicolor bedfordi Thomas, 1911) (Artiodactyla: Bovidae) in the Qinling Mountains (China). BMC ZOOL 2024; 9:2. [PMID: 38287429 PMCID: PMC10826085 DOI: 10.1186/s40850-024-00192-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
Budorcas taxicolor bedfordi is a rare animal uniquely distributed in the Qinling Mountains (China). Human disturbance and habitat fragmentation have directly affected the survival of B. t. bedfordi. It is urgent to clarify the genetic diversity and genetic structure of the B. t. bedfordi population and implement effective conservation measures. In this study, 20 new polymorphic microsatellite loci were isolated by Illumina sequencing. The genetic diversity and population structure of 124 B. t. bedfordi individuals from three populations (Niubeliang population, Zhouzhi population, and Foping population) were analysed according to these 20 microsatellite loci. Our results indicated that B. t. bedfordi had a low level of genetic variability and that there was inbreeding in the three populations. The population genetic structure analyses showed that the Niubeliang population had a trend of differentiation from other populations. National roads can affect population dispersal, while ecological corridors can promote population gene exchange. None of the three B. t. bedfordi populations experienced bottleneck effects. For conservation management plans, the Zhouzhi population and Foping population should be considered one management unit, and the Niubeliang population should be considered another management unit. We suggest building an ecological corridor to keep the habitat connected and formulating tourism management measures to reduce the influence of human disturbance on B. t. bedfordi.
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Affiliation(s)
- Hui Feng
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, 710032, Xi'an, China.
| | - Fangjun Cao
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, 710032, Xi'an, China
| | - Tiezhi Jin
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, 710032, Xi'an, China
| | - Lu Wang
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, 710032, Xi'an, China
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Yang S, Lan T, Wei R, Zhang L, Lin L, Du H, Huang Y, Zhang G, Huang S, Shi M, Wang C, Wang Q, Li R, Han L, Tang D, Li H, Zhang H, Cui J, Lu H, Huang J, Luo Y, Li D, Wan QH, Liu H, Fang SG. Single-nucleus transcriptome inventory of giant panda reveals cellular basis for fitness optimization under low metabolism. BMC Biol 2023; 21:222. [PMID: 37858133 PMCID: PMC10588165 DOI: 10.1186/s12915-023-01691-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 08/25/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Energy homeostasis is essential for the adaptation of animals to their environment and some wild animals keep low metabolism adaptive to their low-nutrient dietary supply. Giant panda is such a typical low-metabolic mammal exhibiting species specialization of extremely low daily energy expenditure. It has low levels of basal metabolic rate, thyroid hormone, and physical activities, whereas the cellular bases of its low metabolic adaptation remain rarely explored. RESULTS In this study, we generate a single-nucleus transcriptome atlas of 21 organs/tissues from a female giant panda. We focused on the central metabolic organ (liver) and dissected cellular metabolic status by cross-species comparison. Adaptive expression mode (i.e., AMPK related) was prominently displayed in the hepatocyte of giant panda. In the highest energy-consuming organ, the heart, we found a possibly optimized utilization of fatty acid. Detailed cell subtype annotation of endothelial cells showed the uterine-specific deficiency of blood vascular subclasses, indicating a potential adaptation for a low reproductive energy expenditure. CONCLUSIONS Our findings shed light on the possible cellular basis and transcriptomic regulatory clues for the low metabolism in giant pandas and helped to understand physiological adaptation response to nutrient stress.
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Affiliation(s)
- Shangchen Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
| | - Rongping Wei
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Ling Zhang
- China Wildlife Conservation Association, Beijing, 100714, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8000, Aarhus, Denmark
| | - Hanyu Du
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yunting Huang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guiquan Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Shan Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengdong Wang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Lei Han
- College of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China
| | - Dan Tang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hemin Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China
| | - Jie Cui
- The Genome Synthesis and Editing Platform, BGI-Shenzhen, Shenzhen, 518120, China
| | - Haorong Lu
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jinrong Huang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, 8000, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, China
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8000, Aarhus, Denmark
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, China.
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China.
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F, Wei F. PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation. MICROBIOME 2023; 11:221. [PMID: 37805557 PMCID: PMC10559513 DOI: 10.1186/s40168-023-01657-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 08/23/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples. RESULTS The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes. CONCLUSIONS Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract.
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Affiliation(s)
- Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingyue Qu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenqiang Zuo
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Wang
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangqing Zhao
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Wang Y, Swaisgood RR, Wei W, Zhou H, Yuan F, Hong M, Han H, Zhang Z. Signal detection theory applied to giant pandas: Do pandas go out of their way to make sure their scent marks are found? Ecol Evol 2023; 13:e10517. [PMID: 37706159 PMCID: PMC10495809 DOI: 10.1002/ece3.10517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/17/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023] Open
Abstract
Inter-animal communication allows signals released by an animal to be perceived by others. Scent-marking is the primary mode of such communication in giant pandas (Ailuropoda melanoleuca). Signal detection theory propounds that animals choose the substrate and location of their scent marks so that the signals released are transmitted more widely and last longer. We believe that pandas trade-off scent-marking because they are an energetically marginal species and it is costly to generate and mark chemical signals. Existing studies only indicate where pandas mark more frequently, but their selection preferences remain unknown. This study investigates whether the marking behavior of pandas is consistent with signal detection theory. Feces count, reflecting habitat use intensity, was combined with mark count to determine the selection preference for marking. The results showed that pandas preferred to mark ridges with animal trails and that most marked tree species were locally dominant. In addition, marked plots and species were selected for lower energy consumption and a higher chance of being detected. Over 90% of the marks used were the longest-surviving anogenital gland secretion marks, and over 80% of the marks were oriented toward animal trails. Our research demonstrates that pandas go out of their way to make sure their marks are found. This study not only sheds light on the mechanisms of scent-marking by pandas but also guides us toward more precise conservation of the panda habitat.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan ProvinceNanchongChina
| | - Ronald R. Swaisgood
- Conservation Science and Wildlife HealthSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
| | - Wei Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan ProvinceNanchongChina
| | - Hong Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan ProvinceNanchongChina
| | - Feiyun Yuan
- Sichuan Tibetan Area Expressway Co., LtdChengduChina
- Sichuan LuShi Expressway Co., LtdChengduChina
| | - Mingsheng Hong
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan ProvinceNanchongChina
| | - Han Han
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan ProvinceNanchongChina
| | - Zejun Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchongChina
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan ProvinceNanchongChina
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Deng F, Wang C, Li D, Peng Y, Deng L, Zhao Y, Zhang Z, Wei M, Wu K, Zhao J, Li Y. The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host's dietary adaption to bamboo. MICROBIOME 2023; 11:180. [PMID: 37580828 PMCID: PMC10424351 DOI: 10.1186/s40168-023-01603-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/19/2023] [Indexed: 08/16/2023]
Abstract
BACKGROUND The gut microbiota of the giant panda (Ailuropoda melanoleuca), a global symbol of conservation, are believed to be involved in the host's dietary switch to a fibrous bamboo diet. However, their exact roles are still largely unknown. RESULTS In this study, we first comprehensively analyzed a large number of gut metagenomes giant pandas (n = 322), including 98 pandas sequenced in this study with deep sequencing (Illumina) and third-generation sequencing (nanopore). We reconstructed 408 metagenome-assembled genomes (MAGs), and 148 of which (36.27%) were near complete. The most abundant MAG was classified as Streptococcus alactolyticus. A pairwise comparison of the metagenomes and meta-transcriptomes in 14 feces revealed genes involved in carbohydrate metabolism were lower, but those involved in protein metabolism were greater in abundance and expression in giant pandas compared to those in herbivores and omnivores. Of note, S. alactolyticus was positively correlated to the KEGG modules of essential amino-acid biosynthesis. After being isolated from pandas and gavaged to mice, S. alactolyticus significantly increased the relative abundance of essential amino acids in mice jejunum. CONCLUSIONS The study highlights the unique protein metabolic profiles in the giant panda's gut microbiome. The findings suggest that S. alactolyticus is an important player in the gut microbiota that contributes to the giant panda's dietary adaptation by more involvement in protein rather than carbohydrate metabolism. Video Abstract.
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Affiliation(s)
- Feilong Deng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Guangdong, China
| | - Chengdong Wang
- China Conservation and Research Center of Giant Panda, Key Laboratory of SFGA on Conservation Biology of Rare Animals in The Giant Panda National Park (CCRCGP), Sichuan, 611830, Dujiangyan, China
| | - Desheng Li
- China Conservation and Research Center of Giant Panda, Key Laboratory of SFGA on Conservation Biology of Rare Animals in The Giant Panda National Park (CCRCGP), Sichuan, 611830, Dujiangyan, China
| | - Yunjuan Peng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Guangdong, China
| | - Linhua Deng
- China Conservation and Research Center of Giant Panda, Key Laboratory of SFGA on Conservation Biology of Rare Animals in The Giant Panda National Park (CCRCGP), Sichuan, 611830, Dujiangyan, China
| | - Yunxiang Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Guangdong, China
| | - Zhihao Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Guangdong, China
| | - Ming Wei
- China Conservation and Research Center of Giant Panda, Key Laboratory of SFGA on Conservation Biology of Rare Animals in The Giant Panda National Park (CCRCGP), Sichuan, 611830, Dujiangyan, China
| | - Kai Wu
- China Conservation and Research Center of Giant Panda, Key Laboratory of SFGA on Conservation Biology of Rare Animals in The Giant Panda National Park (CCRCGP), Sichuan, 611830, Dujiangyan, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, AR, Fayetteville, USA.
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.
- School of Life Science and Engineering, Foshan University, Guangdong, China.
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Yan Z, Xu Q, Yao Y, Ayala J, Hou R, Wang H. Fecal Metabolomics Reveals the Foraging Strategies of Giant Pandas for Different Parts of Bamboo. Animals (Basel) 2023; 13:ani13081278. [PMID: 37106841 PMCID: PMC10135075 DOI: 10.3390/ani13081278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/01/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Climate change-induced food shortages pose major threats to wildlife conservation, and the exclusive reliance of giant pandas on bamboo makes them particularly vulnerable. The aim of this study was to provide insight into the reasons for the foraging strategies of giant pandas to selectively forage for different bamboo parts (bamboo shoot, culm, and leaf) during different seasons. This study used a metabolomic approach to analyze the fecal metabolites of giant pandas and conducted a correlation analysis with their gut microbiota. The results indicate that the fecal metabolites of giant pandas differ significantly depending on the bamboo parts they forage on, with higher sugar content observed when they consume bamboo culm with high fiber content. By functional annotation, culm group metabolites were enriched in the galactose metabolic pathway, while shoot group metabolites were enriched in the phenylalanine, tyrosine and tryptophan biosynthesis pathways. Moreover, Streptococcus showed a significant positive correlation with glucose and acetic acid content. Therefore, the foraging strategy of giant pandas is based on the ability to utilize the nutrient content of different bamboo parts. Captive feeding and habitat construction should enrich bamboo species to allow them to express their natural foraging strategies and improve their welfare and reproductive status.
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Affiliation(s)
- Zheng Yan
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Qin Xu
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Ying Yao
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - James Ayala
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu 610081, China
- Sichuan Academy of Giant Panda, Chengdu 610081, China
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Zeng Y, Han H, Gong Y, Qubi S, Chen M, Qiu L, Huang Y, Zhou H, Wei W. Feeding habits and foraging patch selection strategy of the giant panda in the Meigu Dafengding National Nature Reserve, Sichuan Province, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49125-49135. [PMID: 36773257 DOI: 10.1007/s11356-023-25769-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/02/2023] [Indexed: 04/16/2023]
Abstract
Despite retaining a digestive system with carnivorous characteristics, the giant panda has now specialized to eat bamboo. Therefore, research on its feeding habits and foraging strategies has always been an important field in the study of giant panda population ecology. Located in the core distribution area of the giant panda population in the Liangshan mountains, the Meigu Dafengding Nature Reserve acts as the link between the major panda reserves in the Liangshan mountains and the key corridor zone connecting the giant panda populations in the east and west. This study was performed in 2017 and aimed to determine the feeding habits of giant pandas in this region, the heterogeneity of food resources in different seasons, and the selection strategy for foraging patches. To achieve this, we used the line transect method to investigate the giant panda population, collected fresh feces, analyzed the nutritional composition of bamboo samples, and set up a sampling grid of foraging patches in different seasonal distribution areas. It was found that wild giant pandas in the region spend most of the year at lower elevations(1939-3296 m) foraging for Yushania maculata and Yushania ailuropodina, and only move to higher elevations(2844-3770 m) in summer for Bashania fangiana. Their preferred foraging patches(n = 65) had certain topographical features, such as gentle slopes(< 25°) and closer proximity to water sources(< 500 m), and the nutritional quality of bamboo resources in foraging patches was significantly better than in those they avoided or rarely used. The food habits and foraging patch selection strategies of giant pandas in the Liangshan and Qinling mountains are relatively similar, and the results of this study can help provide a scientific basis for the conservation and management of wild giant panda habitats in different mountain regions.
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Affiliation(s)
- Ying Zeng
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Han Han
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, Science and Technology Department of Sichuan Province, Nanchong, China
| | - Yihua Gong
- Sichuan Meigu Dafengding National Nature Reserve Administration, Meigu, China
| | - Shibu Qubi
- Sichuan Meigu Dafengding National Nature Reserve Administration, Meigu, China
| | - Minghua Chen
- Sichuan Meigu Dafengding National Nature Reserve Administration, Meigu, China
| | - Lan Qiu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Youyou Huang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Hong Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, Science and Technology Department of Sichuan Province, Nanchong, China
| | - Wei Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China.
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province, Science and Technology Department of Sichuan Province, Nanchong, China.
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Wang S, Li Y, Zhou J, Jiang K, Chen J, Ye Z, Xue H, Bu W. The anthropogenic effect of land use on population genetics of Malcus inconspicuus. Evol Appl 2022; 16:98-110. [PMID: 36699121 PMCID: PMC9850013 DOI: 10.1111/eva.13512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022] Open
Abstract
Since the beginning of the Holocene era, human activities have seriously impacted animal habitats and vegetative environments. Species that are dependent on natural habitats or with narrow niches might be more severely affected by habitat changes. Malcus inconspicuus is distributed in subtropical China and highly dependent on the mountain environment. Our study investigated the role of the mountainous landscape in the historical evolution of M. inconspicuus and the impact of Holocene human activities on it. A phylogeographical approach was implemented with integrative datasets including double-digest restriction site-associated DNA (ddRAD), mitochondrial data, and distribution data. Three obvious clades and an east-west phylogeographical pattern were found in subtropical China. Mountainous landscape has "multifaceted" effects on the evolutionary history of M. inconspicuus, it has contributed to population differentiation, provided glacial refuges, and provided population expansion corridors during the postglacial period. The effective population size (Ne) of M. inconspicuus showed a sharp decline during the Holocene era, which revealed a significantly negative correlation with the development of cropland in a hilly area at the same time and space. It supported that the species which are highly dependent on natural habitats might undergo greater impact when the habitat was damaged by agricultural activities and we should pay more attention to them, especially in the land development of their distribution areas.
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Affiliation(s)
- Shujing Wang
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Yanfei Li
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Jiayue Zhou
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Kun Jiang
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Juhong Chen
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Zhen Ye
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Huaijun Xue
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
| | - Wenjun Bu
- Institute of Entomology, College of Life SciencesNankai UniversityTianjinChina
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10
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Liu S, Li C, Yan W, Jin S, Wang K, Wang C, Gong H, Wu H, Fu X, Deng L, Lei C, He M, Wang H, Cheng Y, Wang Q, Lin S, Huang Y, Li D, Yang X. Using Blood Transcriptome Analysis to Determine the Changes in Immunity and Metabolism of Giant Pandas with Age. Vet Sci 2022; 9:vetsci9120667. [PMID: 36548828 PMCID: PMC9784451 DOI: 10.3390/vetsci9120667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/18/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
A low reproductive rate coupled with human activities has endangered the giant panda, a species endemic to southwest China. Although giant pandas feed almost exclusively on bamboo, they retain carnivorous traits and suffer from carnivorous diseases. Additionally, their immune system is susceptible to aging, resulting in a reduced ability to respond to diseases. This study aimed to determine the genes and pathways expressed differentially with age in blood tissues. The differentially expressed genes in different age groups of giant pandas were identified by RNA-seq. The elderly giant pandas had many differentially expressed genes compared with the young group (3 years old), including 548 upregulated genes and 401 downregulated genes. Further, functional enrichment revealed that innate immune upregulation and adaptive immune downregulation were observed in the elderly giant pandas compared with the young giant pandas. Meanwhile, the immune genes in the elderly giant pandas changed considerably, including genes involved in innate immunity and adaptive immunity such as PLSCR1, CLEC7A, CCL5, CCR9, and EPAS1. Time series analysis found that giant pandas store glycogen by prioritizing fat metabolism at age 11, verifying changes in the immune system. The results reported in this study will provide a foundation for further research on disease prevention and the energy metabolism of giant pandas.
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Affiliation(s)
- Song Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Caiwu Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Wenjun Yan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Senlong Jin
- Sichuan Wolong National Nature Reserve Administration, Wenchuan 623006, China
| | - Kailu Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Chengdong Wang
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Huiling Gong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Xue Fu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Linhua Deng
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Changwei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Ming He
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Yanxi Cheng
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Qian Wang
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Shanshan Lin
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
| | - Desheng Li
- China Conservation and Research Center for the Giant Panda, Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Chengdu 610083, China
- Correspondence: (D.L.); (X.Y.)
| | - Xin Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
- Correspondence: (D.L.); (X.Y.)
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11
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Specific Gene Duplication and Loss of Cytochrome P450 in Families 1-3 in Carnivora (Mammalia, Laurasiatheria). Animals (Basel) 2022; 12:ani12202821. [PMID: 36290207 PMCID: PMC9597770 DOI: 10.3390/ani12202821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary In this study we investigated the specific duplication and loss events of cytochrome P450 (CYP) genes in families 1-3 in Carnivora. These genes have been recognized as essential detoxification enzymes, and, using genomic data, we demonstrated a synteny analysis of the CYP coding cluster and a phylogenetic analysis of these genes. We discovered the CYP2Cs and CYP3As expansion in omnivorous species such as the badger, the brown bear, the black bear, and the dog. Furthermore, phylogenetic analysis revealed the evolution of CYP2Cs and 3As in Carnivora. These findings are essential for the appropriate estimation of pharmacokinetics or toxicokinetic in wild carnivorans. Abstract Cytochrome P450s are among the most important xenobiotic metabolism enzymes that catalyze the metabolism of a wide range of chemicals. Through duplication and loss events, CYPs have created their original feature of detoxification in each mammal. We performed a comprehensive genomic analysis to reveal the evolutionary features of the main xenobiotic metabolizing family: the CYP1-3 families in Carnivora. We found specific gene expansion of CYP2Cs and CYP3As in omnivorous animals, such as the brown bear, the black bear, the dog, and the badger, revealing their daily phytochemical intake as providing the causes of their evolutionary adaptation. Further phylogenetic analysis of CYP2Cs revealed Carnivora CYP2Cs were divided into CYP2C21, 2C41, and 2C23 orthologs. Additionally, CYP3As phylogeny also revealed the 3As’ evolution was completely different to that of the Caniformia and Feliformia taxa. These studies provide us with fundamental genetic and evolutionary information on CYPs in Carnivora, which is essential for the appropriate interpretation and extrapolation of pharmacokinetics or toxicokinetic data from experimental mammals to wild Carnivora.
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Kang L, Luo W, Dai Q, Zhou H, Wei W, Tang J, Han H, Yuan Y, Long J, Zhang Z, Hong M. Giant pandas' staple food bamboo phyllosphere fungal community and its influencing factors. Front Microbiol 2022; 13:1009588. [PMID: 36246256 PMCID: PMC9561849 DOI: 10.3389/fmicb.2022.1009588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/06/2022] [Indexed: 11/21/2022] Open
Abstract
Giant pandas have developed a series of foraging strategies to adapt to their special bamboo diets. Although bamboo is an important food resource for giant pandas in Liziping National Nature Reserve (Liziping NR), China, there are relatively few studies on their phyllosphere fungal community and its influencing factors. Herein, we used ITS1 amplification and metagenomic sequencing to analyze the phyllosphere fungi diversity and functions (KEGG, CAZyme, and antibiotic resistance gene) and explore the influencing factors for the three giant pandas foraging bamboo species (Arundinaria spanostachya, AS; Yushania lineolate, YL; and Fargesia ferax, FF) over different seasons (spring vs. autumn) in Liziping NR, China. We found that Ascomycota and Basidiomycota were the most dominant phyla in the bamboo phyllosphere. The alpha diversity (e.g., the Sobs index and Shannon index) was relatively higher in autumn samples than in spring samples, and the community structure differed significantly between the three bamboo species in spring and autumn. Some biotic and abiotic variables (e.g., the elevation and mean base diameter of bamboo) significantly influenced the abundance, diversity, and community structure of the bamboo phyllosphere fungal community. Moreover, the functional analysis showed the differences in the glycoside hydrolase community and antibiotic resistance gene (ARG) profile between spring and autumn samples. Co-occurrence network modeling suggested that AS phyllosphere fungal communities in autumn employed a much more complex network than that in spring, and the abundance of multidrug, tetracycline, and glycopeptide resistance genes was high and closely correlated with other ARGs. These results indicate that fungal community's abundance, diversity, and community structure are mainly affected by the season, host species, and elevation. The season and host species are major factors affecting the biological functions (KEGG and CAZyme), ARGs, and interactions between sympatric bacterial and fungal communities in bamboo phyllosphere. This integrated study can provide a reference basis for the seasonal management of bamboo resources foraged by wild giant pandas, and predict the risk of antibiotic resistance in bamboo phyllosphere fungal flora in Liziping NR (Xiaoxiangling mountains), China.
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Affiliation(s)
- Liwen Kang
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Wei Luo
- Liziping National Nature Reserve Administration, Ya’an, China
| | - Qinglong Dai
- Liziping National Nature Reserve Administration, Ya’an, China
| | - Hong Zhou
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Wei Wei
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Junfeng Tang
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Han Han
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Yuan Yuan
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Juejie Long
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Zejun Zhang
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Mingsheng Hong
- Liziping Giant Panda’s Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
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13
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Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats. THE ISME JOURNAL 2022; 16:1980-1992. [PMID: 35568757 PMCID: PMC9107070 DOI: 10.1038/s41396-022-01247-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022]
Abstract
Bamboo rats (Rhizomys pruinosus) are among the few mammals that lives on a bamboo-based diet which is mainly composed of lignocellulose. However, the mechanisms of adaptation of their gut microbiome and metabolic systems in the degradation of lignocellulose are largely unknown. Here, we conducted a multi-omics analysis on bamboo rats to investigate the interaction between their gut microbiomes and metabolic systems in the pre- and post-weaning periods, and observed significant relationships between dietary types, gut microbiome, serum metabolome and host gene expression. For comparison, published gut microbial data from the famous bamboo-eating giant panda (Ailuropoda melanoleuca) were also used for analysis. We found that the adaptation of the gut microbiome of the bamboo rat to a lignocellulose diet is related to a member switch in the order Bacteroidales from family Bacteroidaceae to family Muribaculaceae, while for the famous bamboo-eating giant panda, several aerobes and facultative anaerobes increase after weaning. The conversion of bacteria with an increased relative abundance in bamboo rats after weaning enriched diverse carbohydrate-active enzymes (CAZymes) associated with lignocellulose degradation and functionally enhanced the biosynthesis of amino acids and B vitamins. Meanwhile, the circulating concentration of short-chain fatty acids (SCFAs) derived metabolites and the metabolic capacity of linoleic acid in the host were significantly elevated. Our findings suggest that fatty acid metabolism, including linoleic acid and SCFAs, are the main energy sources for bamboo rats in response to the low-nutrient bamboo diet.
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14
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Branch HA, Klingler AN, Byers KJRP, Panofsky A, Peers D. Discussions of the "Not So Fit": How Ableism Limits Diverse Thought and Investigative Potential in Evolutionary Biology. Am Nat 2022; 200:101-113. [PMID: 35737982 DOI: 10.1086/720003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
AbstractEvolutionary biology and many of its foundational concepts are grounded in a history of ableism and eugenics. The field has not made a concerted effort to divest our concepts and investigative tools from this fraught history, and as a result, an ableist investigative lens has persisted in present-day evolutionary research, limiting the scope of research and harming the ability to communicate and synthesize knowledge about evolutionary processes. This failure to divest from our eugenicist and ableist history has harmed progress in evolutionary biology and allowed principles from evolutionary biology to continue to be weaponized against marginalized communities in the modern day. To rectify this problem, scholars in evolutionary research must come to terms with how the history of the field has influenced their investigations and work to establish a new framework for defining and investigating concepts such as selection and fitness.
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15
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Wang X, Su DF, Jablonski NG, Ji X, Kelley J, Flynn LJ, Deng T. Earliest giant panda false thumb suggests conflicting demands for locomotion and feeding. Sci Rep 2022; 12:10538. [PMID: 35773284 PMCID: PMC9246853 DOI: 10.1038/s41598-022-13402-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/24/2022] [Indexed: 11/11/2022] Open
Abstract
Of the many peculiarities that enable the giant panda (Ailuropoda melanoleuca), a member of the order Carnivora, to adapt to life as a dedicated bamboo feeder, its extra “thumb” is arguably the most celebrated yet enigmatic. In addition to the normal five digits in the hands of most mammals, the giant panda has a greatly enlarged wrist bone, the radial sesamoid, that acts as a sixth digit, an opposable “thumb” for manipulating bamboo. We report the earliest enlarged radial sesamoid, already a functional opposable “thumb,” in the ancestral panda Ailurarctos from the late Miocene site of Shuitangba in Yunnan Province, China. However, since the late Miocene, the “thumb” has not enlarged further because it must be balanced with the constraints of weight bearing while walking in a plantigrade posture. This morphological adaptation in panda evolution thus reflects a dual function of the radial sesamoid for both bamboo manipulation and weight distribution. The latter constraint could be the main reason why the panda’s false thumb never evolved into a full digit. This crude “thumb” suggests that the origin of the panda’s dedicated bamboo diet goes back to as early as 6–7 Ma.
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Affiliation(s)
- Xiaoming Wang
- Department of Vertebrate Paleontology, Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA, 90007, USA. .,Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China.
| | - Denise F Su
- Institute of Human Origins and School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
| | - Nina G Jablonski
- Department of Anthropology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Xueping Ji
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.,Yunnan Institute of Cultural Relics and Archaeology, 15-1, Chunmingli, Chunyuan Xiaoqu, Kunming, 650118, Yunnan, China
| | - Jay Kelley
- Institute of Human Origins and School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lawrence J Flynn
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Tao Deng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
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16
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Han H, Swaisgood RR, Qiu L, Chen Y, Zhang Z. Down‐listing pandas and upgrading conservation: China setting an example to preserve wildlife worldwide. Anim Conserv 2022. [DOI: 10.1111/acv.12803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- H. Han
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province Science and Technology Department of Sichuan Province Chengdu China
| | - R. R. Swaisgood
- Institute for Conservation Research San Diego Zoo Global Escondido Escondido CA USA
| | - L. Qiu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province Science and Technology Department of Sichuan Province Chengdu China
| | - Y. Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province Science and Technology Department of Sichuan Province Chengdu China
| | - Z. Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province Science and Technology Department of Sichuan Province Chengdu China
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17
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Zheng Y, Zhou Y, Huang Y, Wang H, Guo H, Yuan B, Zhang J. Transcriptome sequencing of black and white hair follicles in the giant panda. Integr Zool 2022; 18:552-568. [PMID: 35500067 DOI: 10.1111/1749-4877.12652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the completion of the draft assembly of the giant panda genome sequence, RNA sequencing technology has been widely used in genetic research on giant pandas. We used RNA-seq to examine black and white hair follicle samples from adult pandas. By comparison with the giant panda genome, 75 963 SNP loci were labeled, 2 426 differentially expressed genes were identified, and 2 029 new genes were discovered, among which 631 were functionally annotated. A cluster analysis of the differentially expressed genes showed that they were mainly related to the Wnt signaling pathway, ECM-receptor interaction, the p53 signaling pathway and ribosome processing. The enrichment results showed that there were significant differences in the regulatory networks of hair follicles with different colors during the transitional stage of hair follicle resting growth, which may play a regulatory role in melanin synthesis during growth. In conclusion, our results provide new insights and more data support for research on the color formation in giant pandas. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yi Zheng
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Yingmin Zhou
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in The Giant Panda National Park, China
| | - Yijie Huang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Haoqi Wang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Haixiang Guo
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Bao Yuan
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
| | - Jiabao Zhang
- Department of Laboratory Animals, Jilin Provincial Key Laboratory of Animal Model, Jilin University, Changchun, China
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18
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Xie Y, Wang S, Wu S, Gao S, Meng Q, Wang C, Lan J, Luo L, Zhou X, Xu J, Gu X, He R, Yang Z, Peng X, Hu S, Yang G. Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:366-381. [PMID: 34487863 PMCID: PMC9684166 DOI: 10.1016/j.gpb.2021.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/17/2021] [Accepted: 08/25/2021] [Indexed: 01/05/2023]
Abstract
Baylisascaris schroederi, a roundworm (ascaridoid) parasite specific to the bamboo-feeding giant panda (Ailuropoda melanoleuca), represents a leading cause of mortality in wild giant panda populations. Here, we present a 293-megabase chromosome-level genome assembly of B. schroederi to infer its biology, including host adaptations. Comparative genomics revealed an evolutionary trajectory accompanied by host-shift events in ascaridoid parasite lineages after host separations, suggesting their potential for transmission and rapid adaptation to new hosts. Genomic and anatomical lines of evidence, including expansion and positive selection of genes related to the cuticle and basal metabolisms, indicate that B. schroederi undergoes specific adaptations to survive in the sharp-edged bamboo-enriched gut of giant pandas by structurally increasing its cuticle thickness and efficiently utilizing host nutrients through gut parasitism. Additionally, we characterized the secretome of B. schroederi and predicted potential drug and vaccine targets for new control strategies. Overall, this genome resource provides new insights into the host adaptation of B. schroederi to the giant panda as well as the host-shift events in ascaridoid parasite lineages. Our findings on the unique biology of B. schroederi will also aid in the development of prevention and treatment measures to protect giant panda populations from roundworm parasitism.
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Affiliation(s)
- Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Sen Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuangyang Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Department of Oncology and Pathology, Karolinska Institutet, Stockholm 17164, Sweden
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingshu Meng
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chengdong Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Jingchao Lan
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Li Luo
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Xuan Zhou
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Zijiang Yang
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD 20740, USA
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Chengdu 611130, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
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19
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Urine Metabolomics Reveals the Effects of Confined Environment on Mating Choice in Adult Male Giant Pandas. Physiol Behav 2022; 249:113744. [DOI: 10.1016/j.physbeh.2022.113744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/20/2022] [Accepted: 02/14/2022] [Indexed: 12/19/2022]
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20
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Huang G, Wang L, Li J, Hou R, Wang M, Wang Z, Qu Q, Zhou W, Nie Y, Hu Y, Ma Y, Yan L, Wei H, Wei F. Seasonal shift of the gut microbiome synchronizes host peripheral circadian rhythm for physiological adaptation to a low-fat diet in the giant panda. Cell Rep 2022; 38:110203. [PMID: 35045306 DOI: 10.1016/j.celrep.2021.110203] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/15/2021] [Accepted: 12/13/2021] [Indexed: 01/01/2023] Open
Abstract
Characteristics of the gut microbiome vary synchronously with changes in host diet. However, the underlying effects of these fluctuations remain unclear. Here, we performed fecal microbiota transplantation (FMT) of diet-specific feces from an endangered mammal (the giant panda) into a germ-free mouse model. We demonstrated that the butyrate-producing bacterium Clostridium butyricum was more abundant during shoot-eating season than during the leaf-eating season, congruent with the significant increase in host body mass. Following season-specific FMT, the microbiota of the mouse model resembled that of the donor, and mice transplanted with the microbiota from the shoot-eating season grew faster and stored more fat. Mechanistic investigations revealed that butyrate extended the upregulation of hepatic circadian gene Per2, subsequently increasing phospholipid biosynthesis. Validation experiments further confirmed this causal relationship. This study demonstrated that seasonal shifts in the gut microbiome affect growth performance, facilitating a deeper understanding of host-microbe interactions in wild mammals.
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Affiliation(s)
- Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Le Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Li
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Meng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhilin Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingyue Qu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yonggang Nie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Yingjie Ma
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Yan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China; State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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21
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Hu Y, Bernatchez L. Fuwen Wei-Recipient of the 2021 Molecular Ecology Prize. Mol Ecol 2021; 31:31-36. [PMID: 34962012 DOI: 10.1111/mec.16306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/01/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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22
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Yue C, Luo X, Ma X, Zhang D, Yan X, Deng Z, Li Y, Liu Y, An J, Fan X, Li L, Su X, Hou R, Cao S, Liu S. Contrasting Vaginal Bacterial Communities Between Estrus and Non-estrus of Giant Pandas ( Ailuropoda melanoleuca). Front Microbiol 2021; 12:707548. [PMID: 34557168 PMCID: PMC8453077 DOI: 10.3389/fmicb.2021.707548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/30/2021] [Indexed: 11/14/2022] Open
Abstract
Bacterial infection and imbalance of bacterial community in the genitourinary system of giant panda could affect the reproductive health. In severe cases, it can also lead to abortion. In this study, 13 of vaginal secretions in the estrue (E) group and seven of vaginal secretions in the non-estrue (NE) group were used to study the composition and diversity of vaginal bacterial communities between estrus and non-estrus by 16S rRNA gene sequencing analysis. The results showed that the vaginal microbiome in giant pandas shared the same top five abundant species between estrus and non-estrus at the phylum level. However, the vaginal microbiome changed significantly during estrus at the genus level. In top 10 genera, the abundance of Escherichia, Streptococcus, and Bacteroides in the E group was significantly higher than that in the NE group (p<0.05); Azomonas, Porphyromonas, Prevotella, Campylobacter, and Peptoniphilus in the NE group was significantly higher than that in the E group (p<0.05). The richness and diversity of vaginal microbiome in giant panda on estrus were significantly lower than those on non-estrus (p<0.05). It is noteworthy that the abundance of Streptococcus, Escherichia, and Bacteroides of vagina in giant pandas maintained low abundance in the daily. Whereas, they increased significantly during estrus period, which may play an important role in female giant pandas during estrus period. It was hypothesized that hormones may be responsible for the changes in the vaginal microbiome of giant pandas between estrus and no-estrus stages.
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Affiliation(s)
- Chanjuan Yue
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
| | - Xue Luo
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China.,College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoping Ma
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dongsheng Zhang
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
| | - Xia Yan
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
| | - Zeshuai Deng
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
| | - Yunli Li
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
| | - Yuliang Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
| | - Junhui An
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
| | - Xueyang Fan
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
| | - Lin Li
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
| | - Xiaoyan Su
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
| | - Suizhong Cao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Songrui Liu
- Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Sichuan Academy of Giant Panda, Chengdu, China
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23
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Wang L, Huang G, Hou R, Qi D, Wu Q, Nie Y, Zuo Z, Ma R, Zhou W, Ma Y, Hu Y, Yang Z, Yan L, Wei F. Multi-omics reveals the positive leverage of plant secondary metabolites on the gut microbiota in a non-model mammal. MICROBIOME 2021; 9:192. [PMID: 34548111 PMCID: PMC8456708 DOI: 10.1186/s40168-021-01142-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 08/10/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Flavonoids are important plant secondary metabolites (PSMs) that have been widely used for their health-promoting effects. However, little is known about overall flavonoid metabolism and the interactive effects between flavonoids and the gut microbiota. The flavonoid-rich bamboo and the giant panda provide an ideal system to bridge this gap. RESULTS Here, integrating metabolomic and metagenomic approaches, and in vitro culture experiment, we identified 97 flavonoids in bamboo and most of them have not been identified previously; the utilization of more than 70% flavonoid monomers was attributed to gut microbiota; the variation of flavonoid in bamboo leaves and shoots shaped the seasonal microbial fluctuation. The greater the flavonoid content in the diet was, the lower microbial diversity and virulence factor, but the more cellulose-degrading species. CONCLUSIONS Our study shows an unprecedented landscape of beneficial PSMs in a non-model mammal and reveals that PSMs remodel the gut microbiota conferring host adaptation to diet transition in an ecological context, providing a novel insight into host-microbe interaction. Video abstract.
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Affiliation(s)
- Le Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangping Huang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
| | - Qi Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yonggang Nie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenqiang Zuo
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458, Guangzhou, China
| | - Rui Ma
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
| | - Wenliang Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yingjie Ma
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhisong Yang
- Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Li Yan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 511458, Guangzhou, China.
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24
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Yao Y, Xu Q, He X, Wang H, Yan H, Gao J, Hou R, Li X, Wang H. Preliminary investigation on iodine nutrition in captive giant pandas. J Trace Elem Med Biol 2021; 67:126780. [PMID: 34023729 DOI: 10.1016/j.jtemb.2021.126780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 04/12/2021] [Accepted: 05/10/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND/OBJECTIVE The giant panda belongs to the family Ursidae and, as a species of bear, still retains the simple digestive system of a Carnivoran. However, under the pressure of a specific habitat they had to adapt to a plant mono-diet consisting of bamboo with different species and growth stages around the year. A plant-based diet has relatively low iodine content with risk of iodine deficiency. Furthermore, bamboo contains cyanogenic glycosides releasing cyanide whose detoxification metabolite the thiocyanate acts as antagonist against iodine uptake and storage in the thyroid. To date very little is known about the iodine nutritional status of the giant panda, thus this study was conducted to receive the first information about the iodine nutrition of captive giant panda. SUBJECTS/METHODS Here we investigated the iodine content of bamboo with different plant parts/vegetation stage and species and further compounds of the captive giant panda diet. Next, the urinary iodine (UI) and urinary thiocyanate (UT) levels of infant, sub-adult, adult and geriatric captive giant pandas was measured during the periods when the pandas consume both bamboo leaves- and culm (bamboo leaf-culm stage). Afterwards, the UI of 19 adult giant pandas was measured again for the different iodine intake during bamboo shoot stage. Finally, in this study part also the fecal iodine concentration was analyzed for calculation of total iodine excretion in relation to the iodine intake. RESULTS Bamboo leaves had the highest iodine content (453 μg/kg dry matter (DM)), followed by the shoots (84 μg/kg DM, p < 0.05), while bamboo culm had the lowest value (12 μg/kg DM, p < 0.05). During bamboo leaf-culm stage, giant pandas of different age groups had different UI and UT levels (p < 0.05). Furthermore, UI and UT were positively correlated among sub-adult, adult and geriatric giant pandas (p < 0.05). In adult giant pandas during bamboo shoot stage, the iodine excretion in feces was not different from that in urine while their total iodine excretion was less than their iodine intake (p < 0.05). Moreover, during bamboo shoot stage, the UI level of adult giant pandas was much lower than noted during bamboo leaf-culm stage (p < 0.05). CONCLUSIONS Our results indicate that UI of captive giant pandas was related to their age as well as to the vegetation stage/part of bamboo they consumed reflecting a different periodic iodine supply. Thiocyanate and fecal excretion should be emphasized when considering the iodine nutrition of giant pandas.
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Affiliation(s)
- Ying Yao
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China
| | - Qin Xu
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China
| | - Xin He
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China
| | - Haiyan Wang
- Key Laboratory of Trace Element Nutrition of National Health Commission of the People's Republic of China, Department of Trace Element Nutrition, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, 100050, Beijing, China
| | - Honglin Yan
- School of Life Science and Engineering, Southwest University of Science and Technology, 621010, Mianyang, China
| | - Jie Gao
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China
| | - Xiuwei Li
- Key Laboratory of Trace Element Nutrition of National Health Commission of the People's Republic of China, Department of Trace Element Nutrition, National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, 100050, Beijing, China.
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China; Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, 610081, Chengdu, China; Sichuan Academy of Giant Panda, 610081, Chengdu, China.
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25
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Rudolf AM, Wu Q, Li L, Wang J, Huang Y, Togo J, Liechti C, Li M, Niu C, Nie Y, Wei F, Speakman JR. A single nucleotide mutation in the dual-oxidase 2 ( DUOX2) gene causes some of the panda's unique metabolic phenotypes. Natl Sci Rev 2021; 9:nwab125. [PMID: 35251670 PMCID: PMC8890364 DOI: 10.1093/nsr/nwab125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/11/2021] [Accepted: 06/10/2021] [Indexed: 12/25/2022] Open
Abstract
The giant panda (Ailuropoda melanoleuca) is an iconic bear native to China, famous for eating almost exclusively bamboo. This unusual dietary behavior for a carnivore is enabled by several key adaptations including low physical activity, reduced organ sizes and hypothyroidism leading to lowered energy expenditure. These adaptive phenotypes have been hypothesized to arise from a panda-unique single-nucleotide mutation in the dual-oxidase 2 (DUOX2) gene, involved in thyroid hormone synthesis. To test this hypothesis, we created genome-edited mice carrying the same point mutation as the panda and investigated its effect on metabolic phenotype. Homozygous mice were 27% smaller than heterozygous and wild-type ones, had 13% lower body mass-adjusted food intake, 55% decreased physical activity, lower mass of kidneys (11%) and brain (5%), lower serum thyroxine (T4: 36%), decreased absolute (12%) and mass-adjusted (5%) daily energy expenditure, and altered gut microbiota. Supplementation with T4 reversed the effects of the mutation. This work uses a state-of-the-art genome editing approach to demonstrate the link between a single-nucleotide mutation in a key endocrine-related gene and profound adaptive changes in the metabolic phenotype, with great importance in ecology and evolution.
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Affiliation(s)
- Agata M Rudolf
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Wu
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Li
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Huang
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jacques Togo
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Christopher Liechti
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
| | - Min Li
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chaoqun Niu
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonggang Nie
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuwen Wei
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Centre of Excellence for Animal Ecology and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - John R Speakman
- State Key Laboratory of Molecular Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
- Centre of Excellence for Animal Ecology and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Shenzhen Key Laboratory of Metabolic Health, Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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26
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Vallittu PK, Varrela J, Salo J, Rengui L, Shanshan L, Shan H, Zhang H, Niemelä P. Temporomandibular joint and Giant Panda's (Ailuropoda melanoleuca) adaptation to bamboo diet. Sci Rep 2021; 11:14252. [PMID: 34244613 PMCID: PMC8271028 DOI: 10.1038/s41598-021-93808-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 06/28/2021] [Indexed: 11/09/2022] Open
Abstract
Here, we present new evidence that evolutionary adaptation of the Ailuripodinae lineage to bamboo diet has taken place by morphological adaptations in the masticatory system. The giant panda in the wild and in captivity removes without an exception the outer skin of all bamboo shoots, rich in abrasive and toxic compounds, by the highly adapted premolars P3 and P4. The temporomandibular joint (TMJ) allows sidewise movement of the jaw and the premolars can, in a cusp-to-cusp position, remove the poorly digestible outer skin of the bamboo before crushing the bamboo with molars. Based on the evidence presented here, we suggest that adaptation of TMJ to lateral movement for enabling cusp-to-cusp contact of premolars is the crucial evolutionary factor as which we consider the key to understand the Ailuropodinae lineage adaptive pathway to utilize the bamboo resource.
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Affiliation(s)
- Pekka K Vallittu
- Department of Biomaterials Science, Institute of Dentistry, University of Turku, Lemminkäisenkatu 2, 20520, Turku, Finland. .,City of Turku Welfare Division, Turku, Finland.
| | - Juha Varrela
- City of Turku Welfare Division, Turku, Finland.,Department of Oral Development and Orthodontics, Institute of Dentistry, University of Turku, Turku, Finland
| | - Jukka Salo
- Biodiversity Unit, University of Turku, Turku, Finland
| | - Li Rengui
- China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Dujiangyan, Sichuan, China.,Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, Sichuan, China
| | - Ling Shanshan
- China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Dujiangyan, Sichuan, China.,Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, Sichuan, China
| | - Huang Shan
- China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Dujiangyan, Sichuan, China.,Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, Sichuan, China
| | - Hemin Zhang
- China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, Dujiangyan, Sichuan, China.,Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, Sichuan, China
| | - Pekka Niemelä
- Biodiversity Unit, University of Turku, Turku, Finland
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27
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Hu Y, Yu L, Fan H, Huang G, Wu Q, Nie Y, Liu S, Yan L, Wei F. Genomic Signatures of Coevolution between Nonmodel Mammals and Parasitic Roundworms. Mol Biol Evol 2021; 38:531-544. [PMID: 32960966 PMCID: PMC7826172 DOI: 10.1093/molbev/msaa243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antagonistic coevolution between host and parasite drives species evolution. However, most of the studies only focus on parasitism adaptation and do not explore the coevolution mechanisms from the perspective of both host and parasite. Here, through the de novo sequencing and assembly of the genomes of giant panda roundworm, red panda roundworm, and lion roundworm parasitic on tiger, we investigated the genomic mechanisms of coevolution between nonmodel mammals and their parasitic roundworms and those of roundworm parasitism in general. The genome-wide phylogeny revealed that these parasitic roundworms have not phylogenetically coevolved with their hosts. The CTSZ and prolyl 4-hydroxylase subunit beta (P4HB) immunoregulatory proteins played a central role in protein interaction between mammals and parasitic roundworms. The gene tree comparison identified that seven pairs of interactive proteins had consistent phylogenetic topology, suggesting their coevolution during host–parasite interaction. These coevolutionary proteins were particularly relevant to immune response. In addition, we found that the roundworms of both pandas exhibited higher proportions of metallopeptidase genes, and some positively selected genes were highly related to their larvae’s fast development. Our findings provide novel insights into the genetic mechanisms of coevolution between nonmodel mammals and parasites and offer the valuable genomic resources for scientific ascariasis prevention in both pandas.
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Affiliation(s)
- Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Lijun Yu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Huizhong Fan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yonggang Nie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Shuai Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Li Yan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Jin L, Huang Y, Yang S, Wu D, Li C, Deng W, Zhao K, He Y, Li B, Zhang G, Xiong Y, Wei R, Li G, Wu H, Zhang H, Zou L. Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:145316. [PMID: 33517011 DOI: 10.1016/j.scitotenv.2021.145316] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/02/2021] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
Gut microbiota (GM) are important for the health of giant pandas (GPs), in addition to the utilization of bamboo in their diets. However, it is not fully understood how diet, habitat environment and lifestyle contribute to the composition of GM in GP. Consequently, we evaluated how dietary changes, habitat environment conversions and lifestyle shifts influence the GM of GPs using high-throughput sequencing and genome-resolved metagenomics. The GM of GPs were more similar when their hosts exhibited the same diet. High fiber diets significantly increased the diversity and decreased the richness of gut bacterial communities alone or interacted with the age factor (p < 0.05). The abundances of Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium significantly increased during diet conversion process (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. While habitat environment may play a more important role in shaping the GM of GP, lifestyle can also greatly affect bacterial communities. The GM structure in reintroduced GPs notably converged to that of wild pandas. Importantly, the main bacterial genera of wild GPs could aid in lignin degradation, while those of reintroduced GPs were related to cellulose and hemicellulose digestion. Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium may contribute to lignocellulose digestion in GP. The results revealed that diet conversion, habitat environment and lifestyle could remarkably influence the GM of GP. In addition, results suggested that increasing the ability of lignin degradation with GM may aid to change the GM of reintroduced pandas to resemble those of wild pandas.
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Affiliation(s)
- Lei Jin
- College of Resources, Sichuan Agricultural University, Chengdu, 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, China
| | - Shengzhi Yang
- College of Resources, Sichuan Agricultural University, Chengdu, 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, 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, China
| | - Wenwen Deng
- 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, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, 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, China
| | - Bei Li
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Guiquan 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, China
| | - Yaowu Xiong
- 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, China
| | - Rongping Wei
- 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, China
| | - Guo 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, China
| | - Hongning 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, 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, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, China.
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Liu H, Tang Y, Ni Y, Fang G. Laterality in Responses to Acoustic Stimuli in Giant Pandas. Animals (Basel) 2021; 11:ani11030774. [PMID: 33799531 PMCID: PMC8000618 DOI: 10.3390/ani11030774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/18/2021] [Accepted: 03/09/2021] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Functional lateralization in the auditory system has been widely studied. Accordingly, behavioral laterality responses affected by acoustic stimuli have been observed in many vertebrate species. In this study, we assessed giant pandas’ behavioral responses to different acoustic stimuli in order to examine cerebral lateralization. We concluded that adult giant pandas showed a left-hemisphere bias in response to positive acoustic stimuli. Furthermore, we found the specific valence of cerebral lateralization for different categories of acoustic stimuli, of which some were relevant to the lateralization while others were not relevant. Our findings support an evolutionary strategy that giant pandas process auditory signals similar to other mammals. Abstract Cerebral lateralization is a common feature present in many vertebrates and is often observed in response to various sensory stimuli. Numerous studies have proposed that some vertebrate species have a right hemisphere or left hemisphere dominance in response to specific types of acoustic stimuli. We investigated lateralization of eight giant pandas (Ailuropoda melanoleuca) by using a head turning paradigm and twenty-eight acoustic stimuli with different emotional valences which included twenty-four conspecific and four non-conspecific acoustic stimuli (white noise, thunder, and vocalization of a predator). There was no significant difference in auditory laterality in responses to conspecific or non-conspecific sounds. However, the left cerebral hemisphere processed the positive stimuli, whereas neither of the two hemispheres exhibited a preference for processing the negative stimuli. Furthermore, the right hemisphere was faster than the left hemisphere in processing emotional stimuli and conspecific stimuli. These findings demonstrate that giant pandas exhibit lateralization in response to different acoustic stimuli, which provides evidence of hemispheric asymmetry in this species.
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Affiliation(s)
- He Liu
- Beijing Key Laboratory of Captive Wildlife Technology, Beijing Zoo, No 137 Xizhimenwai Street, Beijing 100044, China; (H.L.); (Y.N.)
| | - Yezhong Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, Chengdu 610041, China;
| | - Yanxia Ni
- Beijing Key Laboratory of Captive Wildlife Technology, Beijing Zoo, No 137 Xizhimenwai Street, Beijing 100044, China; (H.L.); (Y.N.)
| | - Guangzhan Fang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9 Section 4, Renmin Nan Road, Chengdu 610041, China;
- Correspondence: ; Tel.: +86-28-82890628
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Fowler NL, Spady TJ, Wang G, Leopold BD, Belant JL. Denning, metabolic suppression, and the realisation of ecological opportunities in Ursidae. Mamm Rev 2021. [DOI: 10.1111/mam.12246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Nicholas L. Fowler
- Global Wildlife Conservation Center State University of New York College of Environmental Science and Forestry 1 Forestry Drive Syracuse NY13210USA
| | - Thomas J. Spady
- Department of Biological Sciences California State University San Marcos San Marcos CA92096USA
| | - Guiming Wang
- Department of Wildlife, Fisheries, and Aquaculture Mississippi State UniversityMississippi State Box 9690MS39762USA
| | - Bruce D. Leopold
- Department of Wildlife, Fisheries, and Aquaculture Mississippi State UniversityMississippi State Box 9690MS39762USA
| | - Jerrold L. Belant
- Global Wildlife Conservation Center State University of New York College of Environmental Science and Forestry 1 Forestry Drive Syracuse NY13210USA
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Zhao S, Li C, Zhu T, Jin L, Deng W, Zhao K, He Y, Li G, Xiong Y, Li T, Li B, Huang Y, Zhang H, Zou L. Diversity and Composition of Gut Bacterial Community in Giant Panda with Anorexia. Curr Microbiol 2021; 78:1358-1366. [PMID: 33646379 DOI: 10.1007/s00284-021-02424-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/10/2021] [Indexed: 01/02/2023]
Abstract
The giant panda (GP) is the most precious animal in China. Gastrointestinal tract disease, especially associated with dysbiosis of gut microbiota, is the leading cause of death in GPs. Here, we performed 16S rRNA high-throughput sequencing to investigate the gut microbiota of GPs having symptoms of anorexia. Results showed that gut microbiota of GP with anorexia had lower richness (Chao1 index) than the healthy GP. However, no significant differences in alpha diversity were observed. There is a significance in the microbial structure between anorexia and healthy GPs. The abundance of phylum Firmicutes (99.23% ± 7.1%), unidentified genus Clostridiales (24.75% ± 2.5%), was significantly higher in the subadult anorexia group (P < 0.01), and that of the unidentified genus Clostridiales (4.53% ± 1.2%) was also significantly higher in the adult anorexia group (P < 0.01). Weissella and Streptococcus were found to be decreased in both anorexia groups. The decreased abundance of Weissella (0.02% ± 0.0%, 0.08% ± 0.0%) and Streptococcus (73.89% ± 4.3%, 91.15% ± 7.6%) and increase in Clostridium may cause symptoms of anorexia in giant pandas. The correlation analysis indicated that there is a symbiotic relationship among Streptococcus, Leuconostoc, Weissella, and Bacillus which are classified as probiotics (r > 0.6, P < 0.05). Importantly, a negative correlation has been found between Streptococcus and unidentified_Clostridium in two groups (r > 0.6, P < 0.05). Our results suggested that Streptococcus might be used as probiotics to control the growth of Clostridium causing the anorexia.
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Affiliation(s)
- Siyue Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Caiwu Li
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China
- Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, Sichuan, China
| | - Tao Zhu
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China
- Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, Sichuan, China
| | - Lei Jin
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wenwen Deng
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China
| | - Ke Zhao
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yongguo He
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China
- Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, Sichuan, China
| | - Guo Li
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China
| | - Yaowu Xiong
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China
- Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, Sichuan, China
| | - Ti Li
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China
- Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, Sichuan, China
| | - Bei Li
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Huang
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China
- Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, Sichuan, China
| | - Hemin Zhang
- Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for Giant Panda, Dujiangyan, Sichuan, China
- Qionglai Mountains Conservation Biology of Endangered Wild Animals and Plants National Permanent Scientific Research Base, Dujiangyan, Sichuan, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China.
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Shen H, Li C, He M, Huang Y, Wang J, Wang M, Yue B, Zhang X. Immune profiles of male giant panda (Ailuropoda melanoleuca) during the breeding season. BMC Genomics 2021; 22:143. [PMID: 33639852 PMCID: PMC7916315 DOI: 10.1186/s12864-021-07456-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
Background The giant panda (Ailuropoda melanoleuca) is a threatened endemic Chinese species and a flagship species of national and global conservation concern. Life history theory proposes that reproduction and immunity can be mutually constraining and interrelated. Knowledge of immunity changes of male giant pandas during the breeding season is limited. Results Here, we researched peripheral blood gene expression profiles associated with immunity. Thirteen captive giant pandas, ranging from 9 to 11 years old, were divided into two groups based on their reproductive status. We identified 318 up-regulated DEGs and 43 down-regulated DEGs, which were enriched in 87 GO terms and 6 KEGG pathways. Additionally, we obtained 45 immune-related genes with altered expression, mostly up-regulated, and identified four hub genes HSPA4, SUGT1, SOD1, and IL1B in PPI analysis. These 45 genes were related to pattern recognition receptors, autophagy, peroxisome, proteasome, natural killer cell, antigen processing and presentation. SUGT1 and IL1B were related to pattern recognition receptors. HSP90AA1 was the most up-regulated gene and is a member of heat shock protein 90 family. HSP90 contributes to the translocation of extracellular antigen. KLRD1 encodes CD94, whose complex is an inhibitor of the cytotoxic activity of NK cells, was down-regulated. IGIP, which has the capability of inducing IgA production by B cells, was down-regulated, suggesting low concentration of IgA in male giant pandas. Our results suggest that most immune-related genes were up-regulated and more related to innate immune than adaptive immune. Conclusions Our results indicated that breeding male giant pandas presented an immunoenhancement in innate immunity, enhanced antigen presentation and processing in cellular immunity compared to non-breeding males. The humoral immunity of male giant pandas may show a tendency to decrease during the breeding season. This study will provide a foundation for further studies of immunity and reproduction in male giant pandas. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07456-x.
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Affiliation(s)
- Haibo Shen
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Ming He
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Jing Wang
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Minglei Wang
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, PR China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, China.
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Mustafa GR, Li C, Zhao S, Jin L, He X, Shabbir MZ, He Y, Li T, Deng W, Xu L, Xiong Y, Zhang G, Zhang H, Huang Y, Zou L. Metagenomic analysis revealed a wide distribution of antibiotic resistance genes and biosynthesis of antibiotics in the gut of giant pandas. BMC Microbiol 2021; 21:15. [PMID: 33413128 PMCID: PMC7792088 DOI: 10.1186/s12866-020-02078-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/20/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The gut microbiome is essential for the host's health and serves as an essential reservoir of antibiotic resistance genes (ARGs). We investigated the effects of different factors, including the dietary shifts and age, on the functional characteristics of the giant panda's gut microbiome (GPs) through shotgun metagenome sequencing. We explored the association between gut bacterial genera and ARGs within the gut based on network analysis. RESULTS Fecal samples (n=60) from captive juvenile, adult, and geriatric GPs were processed, and variations were identified in the gut microbiome according to different ages, the abundance of novel ARGs and the biosynthesis of antibiotics. Among 667 ARGs identified, nine from the top ten ARGs had a higher abundance in juveniles. For 102 ARGs against bacteria, a co-occurrence pattern revealed a positive association for predominant ARGs with Streptococcus. A comparative KEGG pathways analysis revealed an abundant biosynthesis of antibiotics among three different groups of GPs, where it was more significantly observed in the juvenile group. A co-occurrence pattern further revealed a positive association for the top ten ARGs, biosynthesis of antibiotics, and metabolic pathways. CONCLUSION Gut of GPs serve as a reservoir for novel ARGs and biosynthesis of antibiotics. Dietary changes and age may influence the gut microbiome's functional characteristics; however, it needs further studies to ascertain the study outcomes.
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Affiliation(s)
- Ghulam Raza Mustafa
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, 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), Dujiangyan, 611830, China
| | - Siyue Zhao
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lei Jin
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xueping He
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Muhammad Zubair Shabbir
- Institute of Microbiology, The University of Veterinary and Animal Sciences, Lahore, 54600, Pakistan
| | - 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), Dujiangyan, 611830, China
| | - Ti 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), Dujiangyan, 611830, China
| | - Wenwen Deng
- 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), Dujiangyan, 611830, China
| | - Lin Xu
- 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), Dujiangyan, 611830, China
| | - Yaowu Xiong
- 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), Dujiangyan, 611830, China
| | - Guiquan 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), Dujiangyan, 611830, 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), Dujiangyan, 611830, 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), Dujiangyan, 611830, China.
| | - Likou Zou
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, 611130, China.
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Lai XL, Zhou WL, Gao HL, Wang M, Gao K, Zhang BW, Wei FW, Nie YG. Impact of sympatric carnivores on den selection of wild giant pandas. Zool Res 2020; 41:273-280. [PMID: 32279465 PMCID: PMC7231472 DOI: 10.24272/j.issn.2095-8137.2020.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Interspecific killing is a primary reason for the low survival rates of some animal species. The giant panda (Ailuropoda melanoleuca) is an altricial eutherian mammal and thus, in comparison to other infants, panda cubs are highly vulnerable, which may significantly influence the selection of breeding sites by females. Here, we used infrared camera traps to monitor giant panda dens for 5.5 years in Foping National Nature Reserve (FNNR) to determine how interspecific factors affect den selection by wild female pandas. Results indicated that Asian black bears (Ursusthibetanus), yellow-throated martens (Martes flavigula), leopard cats (Prionailurus bengalensis), and masked palm civets (Paguma larvata) visited the dens frequently, and the presence of these species negatively influenced den selection by female pandas. Interestingly, the presence of rodents and terrestrial birds appeared to indicate den safety, and female giant pandas were not averse and even preferred dens with a high abundance index of rodents and terrestrial birds. The den suitability index (DSI) was a reliable tool for evaluating whether dens were suitable for female giant pandas to give birth to and rear cubs, with preference for dens with high DSI values. This study increases our understanding of the den selection criteria of female giant pandas and the main threats to the survival of their cubs, thus providing important guidance for the conservation and management of this species.
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Affiliation(s)
- Xin-Lei Lai
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China.,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Liang Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua-Lei Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Gao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Bao-Wei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China. E-mail:
| | - Fu-Wen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yong-Gang Nie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
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Effects of ecological factors on growth of Arundinaria spanostachya shoots in Liziping National Nature Reserve, China. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Dong J, Liu S, Zhang Y, Dai Y, Wu Q. A New Alignment-Free Whole Metagenome Comparison Tool and Its Application on Gut Microbiomes of Wild Giant Pandas. Front Microbiol 2020; 11:1061. [PMID: 32612579 PMCID: PMC7309450 DOI: 10.3389/fmicb.2020.01061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 04/29/2020] [Indexed: 11/13/2022] Open
Abstract
The comparison of metagenomes is crucial for studying the relationship between microbial communities and environmental factors. One recently published alignment-free whole metagenome comparison method based on k-mer frequencies, Libra, showed higher resolutions than the present fastest method, Mash, on whole metagenomic sequencing reads, but it did not perform as well on the assembled contigs. Here, we developed a new alignment-free tool, KmerFreqCalc, for the comparison of the whole metagenomic data, which first calculated the frequencies of both forward and reverse complementary sequences of k-mers like Mash and then computed the cosine distance between the samples based on k-mer frequency vectors like Libra. We applied KmerFreqCalc on the assembled contigs of the gut microbiomes of wild giant pandas and compared the results to Libra and Mash. The results indicated that KmerFreqCalc was able to detect the subtle difference between giant panda samples caused by seasonal diet change, showing better clustering than Libra and Mash. Therefore, KmerFreqCalc has high resolution and accuracy for assembled contigs, being very suitable for comparison of samples with low dissimilarity.
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Affiliation(s)
- Jiuhong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuai Liu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China.,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yaran Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Li Y, Ma G, Zhou Q, Li Y, Huang Z. Nutrient contents predict the bamboo-leaf-based diet of Assamese macaques living in limestone forests of southwest Guangxi, China. Ecol Evol 2020; 10:5570-5581. [PMID: 32607175 PMCID: PMC7319238 DOI: 10.1002/ece3.6297] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/23/2020] [Accepted: 03/30/2020] [Indexed: 12/03/2022] Open
Abstract
Determining the nutrient factors influencing food choice provides important insight into the feeding strategy of animals, which is crucial for understanding their behavioral response to environmental changes. A bamboo-leaf-based diet is rare among mammals. Animals' food choice and nutritional goals have been explained by several frameworks; however, the influence of nutrients on food choice in bamboo-leaf-based macaques is not yet available. Assamese macaques (Macaca assamensis) inhabiting limestone forests are characterized by such a bamboo-leaf-based diet, predominantly consuming young leaves of Bonia saxatilis, a shrubby, karst-endemic bamboo. We studied the feeding behavior of one group of Assamese macaques using instantaneous scan sampling in limestone forests of the Guangxi Nonggang National Nature Reserve in southwest Guangxi, China. We compared the nutrient content of staple food and nonfood items and examine the role of key nutrients in the food selection of macaques. Our results showed that young leaves of bamboo B. saxatilis contained more water, crude protein, phosphorus, and less tannin than nonfood items. Furthermore, staple foods contained a higher content of water and less content of calcium than nonfood items. More specifically, quantities of water, crude protein, calcium, and phosphorus in food items were critical factors affecting feeding time on a specific plant item. Our results suggest that young bamboo leaves could meet macaques' required protein and water intake, while enabling them to maintain their mineral balance, consequently facilitating to maintain the primates' bamboo-leaf-diet in the limestone forest. Our findings confirm the effects of nutrient contents in food choice of Assamese macaques, highlighting the importance of the nutrient contents in maintaining their bamboo-based diet and the need to increase the knowledge on their nutritional strategy adapted to the bamboo-dominated diet inhabiting the unique limestone habitat.
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Affiliation(s)
- Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Guangzhi Ma
- School of Life SciencesSouth China Normal UniversityGuangzhouChina
| | - Qihai Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Youbang Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Zhonghao Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
- School of Life SciencesSouth China Normal UniversityGuangzhouChina
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38
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Hu X, Wang G, Shan L, Sun S, Hu Y, Wei F. TAS2R20 variants confer dietary adaptation to high-quercitrin bamboo leaves in Qinling giant pandas. Ecol Evol 2020; 10:5913-5921. [PMID: 32607200 PMCID: PMC7319149 DOI: 10.1002/ece3.6327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/11/2022] Open
Abstract
Sensitivity to bitter tastes provides animals with an important means of interacting with their environment and thus, influences their dietary preferences. Genetic variants encoding functionally distinct receptor types contribute to variation in bitter taste sensitivity. Our previous study showed that two nonsynonymous sites, A52V and Q296H, in the TAS2R20 gene are directionally selected in giant pandas from the Qinling Mountains, which are speculated to be the causative base-pair changes of Qinling pandas for the higher preference for bamboo leaves in comparison with other pandas. Here, we used functional expression in engineered cells to identify agonists of pTAS2R20 (i.e., giant panda's TAS2R20) and interrogated the differences in perception in the in vitro responses of pTAS2R20 variants to the agonists. Our results show that pTAS2R20 is specifically activated by quercitrin and that pTAS2R20 variants exhibit differences in the sensitivity of their response to the agonist. Compared with pTAS2R20 in pandas from other areas, the receptor variant with A52V and Q296H, which is most commonly found in Qinling pandas, confers a significantly decreased sensitivity to quercitrin. We subsequently quantified the quercitrin content of the leaves of bamboo distributed in the Qinling Mountains, which was found to be significantly higher than that of the leaves of bamboo from panda habitats in other areas. Our results suggest that the decreased sensitivity to quercitrin in Qinling pandas results in higher-quercitrin-containing bamboo leaves to be tasting less bitter to them and thus, influences their dietary preference. This study illustrates the genetic adaptation of Qinling pandas to their environments and provides a fine example of the functional effects of directional selection in the giant panda.
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Affiliation(s)
- Xiangxu Hu
- Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guan Wang
- Department of Laboratory MedicineBoston Children’s Hospital and Harvard Medical SchoolBostonMAUSA
| | - Lei Shan
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Shuyan Sun
- Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
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39
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Kerley GIH, Beest M, Cromsigt JPGM, Pauly D, Shultz S. The Protected Area Paradox and refugee species: The giant panda and baselines shifted towards conserving species in marginal habitats. CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Graham I. H. Kerley
- Centre for African Conservation Ecology Nelson Mandela University Port Elizabeth South Africa
| | - Mariska Beest
- Centre for African Conservation Ecology Nelson Mandela University Port Elizabeth South Africa
- Copernicus Institute of Sustainable Development Utrecht University Utrecht The Netherlands
| | - Joris P. G. M. Cromsigt
- Centre for African Conservation Ecology Nelson Mandela University Port Elizabeth South Africa
- Copernicus Institute of Sustainable Development Utrecht University Utrecht The Netherlands
- Department of Wildlife, Fish & Environmental Studies Swedish University of Agricultural Sciences Umeå Sweden
| | - Daniel Pauly
- Institute for the Oceans and Fisheries The University of British Columbia Vancouver BC Canada
| | - Susanne Shultz
- School of Earth and Environmental Sciences University of Manchester Manchester UK
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40
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He X, Hsu WH, Hou R, Yao Y, Xu Q, Jiang D, Wang L, Wang H. Comparative genomics reveals bamboo feeding adaptability in the giant panda ( Ailuropoda melanoleuca). Zookeys 2020; 923:141-156. [PMID: 32292275 PMCID: PMC7142162 DOI: 10.3897/zookeys.923.39665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/18/2019] [Indexed: 11/12/2022] Open
Abstract
The giant panda (Ailuropoda melanoleuca) is one of the world's most endangered mammals and remains threatened as a result of intense environmental and anthropogenic pressure. The transformation and specialization of the giant panda's diet into a herbivorous diet have resulted in unique adaptabilities in many aspects of their biology, physiology and behavior. However, little is known about their adaptability at the molecular level. Through comparative analysis of the giant panda's genome with those of nine other mammalian species, we found some genetic characteristics of the giant panda that can be associated with adaptive changes for effective digestion of plant material. We also found that giant pandas have similar genetic characteristics to carnivores in terms of olfactory perception but have similar genetic characteristics to herbivores in terms of immunity and hydrolytic enzyme activity. Through the analysis of gene family expansion, 3752 gene families were found, which were enriched in functions such as digestion. A total of 93 genes under positive selection were screened out and gene enrichment identified these genes for the following processes: negative regulation of cellular metabolic process, negative regulation of nitrogen compound metabolic process, negative regulation of macromolecule metabolic process and negative regulation of metabolic process. Combined with the KEGG pathway, it was found that genes such as CREB3L1, CYP450 2S1, HSD11B2, LRPAP1 play a key role in digestion. These genes may have played a key role in the pandas' adaptation to its bamboo diet.
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Affiliation(s)
- Xin He
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China.,Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Walter H Hsu
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China.,Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Ying Yao
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China.,Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Qin Xu
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China.,Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Dandan Jiang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China.,Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Longqiong Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China.,Sichuan Academy of Giant Panda, Chengdu, 610081, China
| | - Hairui Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081, China.,Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, 610081, China.,Sichuan Academy of Giant Panda, Chengdu, 610081, China
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41
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Du L, Liu Q, Shen F, Fan Z, Hou R, Yue B, Zhang X. Transcriptome analysis reveals immune-related gene expression changes with age in giant panda ( Ailuropoda melanoleuca) blood. Aging (Albany NY) 2020; 11:249-262. [PMID: 30641486 PMCID: PMC6339791 DOI: 10.18632/aging.101747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/26/2018] [Indexed: 12/24/2022]
Abstract
The giant panda (Ailuropoda melanoleuca), an endangered species endemic to western China, has long been threatened with extinction that is exacerbated by highly contagious and fatal diseases. Aging is the most well-defined risk factor for diseases and is associated with a decline in immune function leading to increased susceptibility to infection and reduced response to vaccination. Therefore, this study aimed to determine which genes and pathways show differential expression with age in blood tissues. We obtained 210 differentially expressed genes by RNA-seq, including 146 up-regulated and 64 down-regulated genes in old pandas (18-21yrs) compared to young pandas (2-6yrs). We identified ISG15, STAT1, IRF7 and DDX58 as the hub genes in the protein-protein interaction network. All of these genes were up-regulated with age and played important roles in response to pathogen invasion. Functional enrichment analysis indicated that up-regulated genes were mainly involved in innate immune response, while the down-regulated genes were mainly related to B cell activation. These may suggest that the innate immunity is relatively well preserved to compensate for the decline in the adaptive immune function. In conclusion, our findings will provide a foundation for future studies on the molecular mechanisms underlying immune changes associated with ageing.
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Affiliation(s)
- Lianming Du
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China.,Institute for Advanced Study, Chengdu University, Chengdu 610106, China
| | - Qin Liu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China.,College of Life Sciences and Food Engineering, Yibin University, Yibin 644000, China
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Zhenxin Fan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
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42
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Guo W, Chen Y, Wang C, Ning R, Zeng B, Tang J, Li C, Zhang M, Li Y, Ni Q, Ni X, Zhang H, li D, Zhao J, Li Y. The carnivorous digestive system and bamboo diet of giant pandas may shape their low gut bacterial diversity. CONSERVATION PHYSIOLOGY 2020; 8:coz104. [PMID: 32190328 PMCID: PMC7066643 DOI: 10.1093/conphys/coz104] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/16/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
The gut microbiota diversity of eight panda cubs was assessed during a dietary switch.Gut microbiota diversity of panda cubs significantly decreased after bamboo consumption.Carnivorous species living on a plant-based diet possess low microbial diversity.Mice were fed a bamboo diet but did not display low gut microbiota diversity. Giant pandas have an exclusive diet of bamboo; however, their gut microbiotas are more similar to carnivores than herbivores in terms of bacterial composition and their functional potential. This is inconsistent with observations that typical herbivores possess highly diverse gut microbiotas. It is unclear why the gut bacterial diversity of giant pandas is so low. Herein, the dynamic variations in the gut microbiota of eight giant panda cubs were measured using 16S rRNA gene paired-end sequencing during a dietary switch. Similar data from red panda (an herbivorous carnivore) and carnivorous species were compared with that of giant pandas. In addition, mice were fed a high-bamboo diet (80% bamboo and 20% rat feed) to determine whether a bamboo diet could lower the gut bacterial diversity in a non-carnivorous digestive tract. The diversity of giant panda gut microbiotas decreased significantly after switching from milk and complementary food to bamboo diet. Carnivorous species living on a plant-based diet, including giant and red pandas, possess a lower microbial diversity than other carnivore species. Mouse gut microbiota diversity significantly increased after adding high-fibre bamboo to their diet. Findings suggest that a very restricted diet (bamboo) within a carnivorous digestive system might be critical for shaping a low gut bacterial diversity in giant pandas.
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Affiliation(s)
- Wei Guo
- Department of Laboratory Medicine, School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, 783 Xindu Road, Xindu, Chengdu, Sichuan, 610500, China
| | - Yinfeng Chen
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Chengdong Wang
- Department of Feeding, China Conservation and Research Center for the Giant Panda, 155 Xianfeng Road, Ya’an, Sichuan, 611830, China
| | - Ruihong Ning
- Department of Laboratory Medicine, School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, 783 Xindu Road, Xindu, Chengdu, Sichuan, 610500, China
| | - Bo Zeng
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Jingsi Tang
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Caiwu Li
- Department of Feeding, China Conservation and Research Center for the Giant Panda, 155 Xianfeng Road, Ya’an, Sichuan, 611830, China
| | - Mingwang Zhang
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Yan Li
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Qingyong Ni
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Xueqin Ni
- Department of animal medicine, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Hemin Zhang
- Department of Feeding, China Conservation and Research Center for the Giant Panda, 155 Xianfeng Road, Ya’an, Sichuan, 611830, China
| | - Desheng li
- Department of Feeding, China Conservation and Research Center for the Giant Panda, 155 Xianfeng Road, Ya’an, Sichuan, 611830, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, 2404 North University Avenue Little Rock, Fayetteville, Arkansas, 72207, USA
| | - Ying Li
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
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43
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Jensen DA, Ma K, Svenning J. Steep topography buffers threatened gymnosperm species against anthropogenic pressures in China. Ecol Evol 2020; 10:1838-1855. [PMID: 32128120 PMCID: PMC7042744 DOI: 10.1002/ece3.5983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 11/08/2022] Open
Abstract
China is one of the most species-rich countries in the world, harboring many rare gymnosperms. Following recent human-led loss of forests, China is now experiencing increases in forest cover resulting from efforts of reforestation schemes. As anthropogenic activities have previously been found to interact with topography in shaping forest cover in China and considering the large human population and the ongoing population increase of the country, it is important to understand the role of anthropogenic pressures relative to environmental drivers for shaping species distributions here. Based on the well-established relationship between human population density and topography, we propose a hypothesis for explaining species distributions in a country dominated by human activities, predicting that species are more likely to occur in areas of steep topography under medium human population densities compared to low and high human population densities. Using species occurrence data from the Chinese Vascular Plant Distribution Database along with a common SDM method (maximum entropy modeling), we tested this hypothesis. Our results show that steep topography has the highest importance for predicting Chinese gymnosperm species occurrences in general, and threatened species specifically, in areas of medium human population densities. Consequently, these species are more often found in areas of steep terrain, supporting the proposed hypothesis. Results from this study highlight the need to include topographically heterogeneous habitats when planning new protected areas for species conservation.
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Affiliation(s)
- Ditte Arp Jensen
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE)Department of BioscienceAarhus UniversityAarhus CDenmark
- Section for Ecoinformatics and BiodiversityDepartment of BioscienceAarhus UniversityAarhus CDenmark
- Sino‐Danish Center for Education and Research (SDC)Water and Environment Programme, Eastern Yanqihu CampusUniversity of Chinese Academy of SciencesBeijingChina
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental ChangeInstitute of BotanyChinese Academy of SciencesBeijingChina
| | - Jens‐Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE)Department of BioscienceAarhus UniversityAarhus CDenmark
- Section for Ecoinformatics and BiodiversityDepartment of BioscienceAarhus UniversityAarhus CDenmark
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44
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Li P, Smith KK. Comparative skeletal anatomy of neonatal ursids and the extreme altriciality of the giant panda. J Anat 2019; 236:724-736. [PMID: 31792960 DOI: 10.1111/joa.13127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 12/11/2022] Open
Abstract
Mammalian neonates are born at a wide range of maturity levels. Altricial newborns are born with limited sensory agency and require extensive parental care. In contrast, precocial neonates are relatively mature physically and often capable of independent function shortly after birth. In extant mammals, placental newborns vary from altricial to precocial, while marsupials and monotremes are all extremely altricial at birth. Bears (family Ursidae) have one of the lowest neonatal-maternal mass ratios in placental mammals, and are thought to also have the most altricial placental newborns. In particular, giant pandas (Ailuropoda melanoleuca) are thought to be exceptionally altricial at birth, and possibly marsupial-like. Here we used micro-computer (micro-computed) tomography scanning to visualize the skeletal anatomy of ursid neonates and compare their skeletal maturity with the neonates of other caniform outgroups. Specifically, we asked whether ursid neonates have exceptionally altricial skeletons at birth compared with other caniform neonates. We found that most bear neonates are similar to outgroup neonates in levels of skeletal ossification, with little variation in degree of ossification between ursine bears neonates (i.e. bears of the subfamily Ursinae). Perinatal giant pandas, however, have skeletal maturity levels most similar to a 42-45-day-old beagle fetus (~70% of total beagle gestation period). No bear exhibits the skeletal heterochronies seen in marsupial development. With regards to skeletal development, ursine bears are not exceptionally altricial relative to other caniform outgroups, but characterized largely by the drastic difference between newborn and adult body sizes. A review on the existing hypotheses for ursids' unique reproductive strategy suggests that the extremely small neonatal-maternal mass ratio of ursids may be related to the recent evolution of large adult body size, while life history characteristics retained an ancestral condition. A relatively short post-implantation gestation time may be the proximal mechanism behind the giant panda neonates' small size relative to maternal size and altricial skeletal development at birth.
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Affiliation(s)
- Peishu Li
- Department of Biology, Duke University, Durham, NC, USA.,Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
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45
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Ren J, Shen F, Zhang L, Sun J, Yang M, Yang M, Hou R, Yue B, Zhang X. Single-base-resolution methylome of giant panda's brain, liver and pancreatic tissue. PeerJ 2019; 7:e7847. [PMID: 31637123 PMCID: PMC6800980 DOI: 10.7717/peerj.7847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/08/2019] [Indexed: 11/20/2022] Open
Abstract
The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals, and its conservation has significant ecosystem and cultural service value. Cytosine DNA methylation (5mC) is a stable epigenetic modification to the genome and has multiple functions such as gene regulation. However, DNA methylome of giant panda and its function have not been reported as of yet. Bisulfite sequencing was performed on a 4-day-old male giant panda's brain, liver and pancreatic tissues. We found that the whole genome methylation level was about 0.05% based on reads normalization and mitochondrial DNA was not methylated. Three tissues showed similar methylation tendency in the protein-coding genes of their genomes, but the brain genome had a higher count of methylated genes. We obtained 467 and 1,013 different methylation regions (DMR) genes in brain vs. pancreas and liver, while only 260 DMR genes were obtained in liver vs pancreas. Some lncRNA were also DMR genes, indicating that methylation may affect biological processes by regulating other epigenetic factors. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that low methylated promoter, high methylated promoter and DMR genes were enriched at some important and tissue-specific items and pathways, like neurogenesis, metabolism and immunity. DNA methylation may drive or maintain tissue specificity and organic functions and it could be a crucial regulating factor for the development of newborn cubs. Our study offers the first insight into giant panda's DNA methylome, laying a foundation for further exploration of the giant panda's epigenetics.
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Affiliation(s)
- Jianying Ren
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Fujun Shen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Liang Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Jie Sun
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Miao Yang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Mingyu Yang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
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Yao R, Yang Z, Zhang Z, Hu T, Chen H, Huang F, Gu X, Yang X, Lu G, Zhu L. Are the gut microbial systems of giant pandas unstable? Heliyon 2019; 5:e02480. [PMID: 31687574 PMCID: PMC6819816 DOI: 10.1016/j.heliyon.2019.e02480] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/11/2019] [Accepted: 09/12/2019] [Indexed: 12/29/2022] Open
Abstract
Animals have stable dominant gut microbiomes under similar diets. Similar diets can also lead to similar gut microbial communities within host species levels. Giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens) have had long-term and stable bamboo diets, and seem well adapted to this highly fibrous diet. When compared to the gut microbiomes of Père David's deer (Elaphurus davidianus), humans, cheetah (Acinonyx jubatus), black-backed jackal (Canis-mesomelas), and black bear (Ursus thibetanus), giant panda gut microbiomes have high variation in the abundance of Pseudomonadaceae and Clostridiaceae, and are somewhat unstable. This high instability and dissimilarity may reflect an unstable gut environment, perturbation or selective pressure because of their carnivorous gastrointestinal system. A short digestive tract, brief digestion time and fast intestinal peristalsis may result in higher oxygen concentrations that select for the growth of aerobes and facultative anaerobes in giant pandas. Potential selection of high proportion of Pseudomonadaceae in giant panda (GP-HP) and red panda gut microbiomes may arise because of their postulated ability to degrade secondary compounds (e.g., cyanide compounds and aromatic compounds). However, high proportion of Clostridiaceae (GP-HF) may focus on cellulose and hemicellulose digestion. Thus, GP-HP and GP-HF groups have high dissimilarity on the functional level. These findings show that long-term similarities in diet do not always lead to similar or stable gut microbial system within the same host species and that other factors can drive the selection of gut taxa.
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Affiliation(s)
- Ran Yao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zhisong Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637002, China
| | - Zheng Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ting Hu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Hua Chen
- Shanghai Biozeron Bioinfmatics Center, Shanghai, 201800, China
| | - Feng Huang
- Sichuan Lizhiping Giant Panda National Nature Reserve, Shimian, China
| | - Xiaodong Gu
- Sichuan Station of Wild Life Survey and Management, Chengdu, 610082, China
| | - Xuyu Yang
- Sichuan Station of Wild Life Survey and Management, Chengdu, 610082, China
| | - Guoqing Lu
- University of Nebraska at Omaha, Omaha, USA
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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47
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Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil. Nat Commun 2019; 10:4201. [PMID: 31519986 PMCID: PMC6744486 DOI: 10.1038/s41467-019-12133-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 08/23/2019] [Indexed: 12/30/2022] Open
Abstract
As Charles Darwin anticipated, living fossils provide excellent opportunities to study evolutionary questions related to extinction, competition, and adaptation. Ginkgo (Ginkgo biloba L.) is one of the oldest living plants and a fascinating example of how people have saved a species from extinction and assisted its resurgence. By resequencing 545 genomes of ginkgo trees sampled from 51 populations across the world, we identify three refugia in China and detect multiple cycles of population expansion and reduction along with glacial admixture between relict populations in the southwestern and southern refugia. We demonstrate multiple anthropogenic introductions of ginkgo from eastern China into different continents. Further analyses reveal bioclimatic variables that have affected the geographic distribution of ginkgo and the role of natural selection in ginkgo’s adaptation and resilience. These investigations provide insights into the evolutionary history of ginkgo trees and valuable genomic resources for further addressing various questions involving living fossil species. Ginkgo is one of the living fossils from the plant kingdom. Here, authors conduct population genomics analyses to reveal its refugia and demographic history, and provide evidence of multiple anthropogenic introductions of ginkgo from eastern China into different continents.
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48
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Zhao S, Li C, Li G, Yang S, Zhou Y, He Y, Wu D, Zhou Y, Zeng W, Li T, Qu Y, Li B, Deng W, Jin L, Yu X, Huang Y, Zhang H, Zou L. Comparative Analysis of Gut Microbiota Among the Male, Female and Pregnant Giant Pandas ( Ailuropoda Melanoleuca). Open Life Sci 2019; 14:288-298. [PMID: 33817162 PMCID: PMC7874769 DOI: 10.1515/biol-2019-0032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 01/14/2019] [Indexed: 12/13/2022] Open
Abstract
The giant panda (GP) was the most endangered species in China, and gut microbiota plays a vital role in host health. To determine the differences of the gut microbiota among the male, female and pregnant GPs, a comparative analysis of gut microbiota in GPs was carried out by 16S rRNA and ITS high-throughput sequencing. In 16S rRNA sequencing, 435 OTUs, 17 phyla and 182 genera were totally detected. Firmicutes (53.6%) was the predominant phylum followed by Proteobacteria (37.8%) and Fusobacteria (7.1%). Escherichia/Shigella (35.9%) was the most prevalent genus followed by Streptococcus (25.9%) and Clostridium (11.1%). In ITS sequencing, 920 OTUs, 6 phyla and 322 genera were also detected. Ascomycota (71.3%) was the predominant phylum followed by Basidiomycota (28.4%) and Zygomycota (0.15%). Purpureocillium (4.4%) was the most prevalent genus followed by Cladosporium (2.5%) and Pezicula (2.4%). Comparative analysis indicated that the male GPs harbor a higher abundance of phylum Firmicutes than female GPs with the contribution from genus Streptococcus. Meanwhile, the female GPs harbor a higher abundance of phylum Proteobacteria than male GPs with the contribution from genus Escherichia/ Shigella. In addition, the shift in bacteria from female to pregnant GPs indicated that phylum Firmicutes increased significantly with the contribution from Clostridium in the gut, which may provide an opportunity to study possible associations with low reproduction of the GPs.
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Affiliation(s)
- Siyue Zhao
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Caiwu Li
- China Conservation and Research Center for Giant Panda, 611830, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), 611830, Wolong, China
| | - Guo Li
- China Conservation and Research Center for Giant Panda, 611830, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), 611830, Wolong, China
| | - Shengzhi Yang
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Yingming Zhou
- China Conservation and Research Center for Giant Panda, 611830, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), 611830, Wolong, China
| | - Yongguo He
- China Conservation and Research Center for Giant Panda, 611830, Dujiangyan, Sichuan, China
| | - Daifu Wu
- China Conservation and Research Center for Giant Panda, 611830, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), 611830, Wolong, China
| | - Yu Zhou
- China Conservation and Research Center for Giant Panda, 611830, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), 611830, Wolong, China
| | - Wen Zeng
- China Conservation and Research Center for Giant Panda, 611830, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), 611830, Wolong, China
| | - Ti Li
- China Conservation and Research Center for Giant Panda, 611830, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), 611830, Wolong, China
| | - Yuanyuan Qu
- China Conservation and Research Center for Giant Panda, 611830, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), 611830, Wolong, China
| | - Bei Li
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Wenwen Deng
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Lei Jin
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Xiumei Yu
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Yan Huang
- China Conservation and Research Center for Giant Panda, 611830, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), 611830, Wolong, China
| | - Hemin Zhang
- China Conservation and Research Center for Giant Panda, 611830, Dujiangyan, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), 611830, Wolong, China
| | - Likou Zou
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
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Nie Y, Wei F, Zhou W, Hu Y, Senior AM, Wu Q, Yan L, Raubenheimer D. Giant Pandas Are Macronutritional Carnivores. Curr Biol 2019; 29:1677-1682.e2. [PMID: 31056385 DOI: 10.1016/j.cub.2019.03.067] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/13/2019] [Accepted: 03/27/2019] [Indexed: 01/21/2023]
Abstract
Giant pandas are unusual in belonging to a primarily carnivorous clade and yet being extremely specialized herbivores that feed almost exclusively on highly fibrous bamboo [1]. Paradoxically, they appear inconsistently adapted to their plant diet, bearing a mix of herbivore and carnivore traits. Herbivore traits include a skull, jaw musculature, and dentition that are adapted for fibrous diets and a specialized "pseudo-thumb" used for handling bamboo [2, 3]. They have lost functional versions of the T1R1 gene codes for umami taste receptors, which are often associated with meat eating [3]. They also have an herbivore-like subcellular distribution of the metabolic enzyme alanine: glyoxylate aminotransferase [4]. But meanwhile, giant pandas have a digestive tract [5], digestive enzymes [6], and a gut microbiota composition that resemble those of carnivores and not of herbivores [6, 7]. We draw on recent developments in multi-dimensional niche theory [8] to examine this apparent paradox. We show that the pandas' diet clustered in a macronutrient space among carnivores and was distinct from that of herbivores. The similarity with carnivore diets applied not only to the ingested diet but also to the absorbed diet, with the absorbed macronutrient ratios similar to those of the ingested foods. Comparison of the macronutrient composition of pandas' milk with those of other species shows that the carnivore-like dietary macronutrient composition extends across the life cycle. These results cast new light on the seemingly incongruous constellation of dietary adaptations in pandas, suggesting that the transition from carnivorous and omnivorous ancestry to specialized herbivory might be less abrupt than it might otherwise appear.
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Affiliation(s)
- Yonggang Nie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wenliang Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Alistair M Senior
- The Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia
| | - Qi Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Yan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - David Raubenheimer
- The Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia
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50
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Sheng GL, Basler N, Ji XP, Paijmans JL, Alberti F, Preick M, Hartmann S, Westbury MV, Yuan JX, Jablonski NG, Xenikoudakis G, Hou XD, Xiao B, Liu JH, Hofreiter M, Lai XL, Barlow A. Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations. Curr Biol 2019; 29:1695-1700.e6. [DOI: 10.1016/j.cub.2019.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/28/2019] [Accepted: 04/09/2019] [Indexed: 11/30/2022]
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