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Gu T, Hu J, Yu L. Evolution and conservation genetics of pangolins. Integr Zool 2024; 19:426-441. [PMID: 38146613 DOI: 10.1111/1749-4877.12796] [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: 12/27/2023]
Abstract
Pangolins (Pholidota, Manidae) are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology (nail-like scales and a myrmecophagous diet) and being the victim of heavy poaching and worldwide trafficking. As such, pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species. Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics, which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins. This review comprehensively presents the hitherto advances in phylogeny, adaptive evolution, conservation genetics, and conservation genomics that are related to pangolins, which will provide an ample understanding of their diversity, molecular adaptation mechanisms, and evolutionary potentials. In addition, we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.
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Affiliation(s)
- Tongtong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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Zhang L, Tang X, Fan C, Ren S, Cheng Q, Zhou H, Liu K, Jia S, Zhang Y. Dysbiosis of Gut Microbiome Aggravated Male Infertility in Captivity of Plateau Pika. Biomolecules 2024; 14:403. [PMID: 38672421 PMCID: PMC11047922 DOI: 10.3390/biom14040403] [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: 01/30/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
Captivity is an important and efficient technique for rescuing endangered species. However, it induces infertility, and the underlying mechanism remains obscure. This study used the plateau pika (Ochotona curzoniae) as a model to integrate physiological, metagenomic, metabolomic, and transcriptome analyses and explore whether dysbiosis of the gut microbiota induced by artificial food exacerbates infertility in captive wild animals. Results revealed that captivity significantly decreased testosterone levels and the testicle weight/body weight ratio. RNA sequencing revealed abnormal gene expression profiles in the testicles of captive animals. The microbial α-diversity and Firmicutes/Bacteroidetes ratio were drastically decreased in the captivity group. Bacteroidetes and Muribaculaceae abundance notably increased in captive pikas. Metagenomic analysis revealed that the alteration of flora increased the capacity for carbohydrate degradation in captivity. The levels of microbe metabolites' short-chain fatty acids (SCFAs) were significantly high in the captive group. Increasing SCFAs influenced the immune response of captivity plateau pikas; pro-inflammatory cytokines were upregulated in captivity. The inflammation ultimately contributed to male infertility. In addition, a positive correlation was observed between Gastranaerophilales family abundance and testosterone concentration. Our results provide evidence for the interactions between artificial food, the gut microbiota, and male infertility in pikas and benefit the application of gut microbiota interference in threatened and endangered species.
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Affiliation(s)
- Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
| | - Xianjiang Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
| | - Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
| | - Shi’en Ren
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
| | - Qi Cheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
| | - Huakun Zhou
- Key Laboratory of Restoration Ecology of Cold Area in Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China;
| | - Kai Liu
- Qinghai Provincial Grassland Station, Xining 810008, China;
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (L.Z.); (X.T.); (C.F.); (S.R.); (Q.C.)
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Ning R, Li C, Xia M, Zhang Y, Gan Y, Huang Y, Zhang T, Song H, Zhang S, Guo W. Pseudomonas-associated bacteria play a key role in obtaining nutrition from bamboo for the giant panda ( Ailuropoda melanoleuca). Microbiol Spectr 2024; 12:e0381923. [PMID: 38305171 PMCID: PMC10913395 DOI: 10.1128/spectrum.03819-23] [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: 11/02/2023] [Accepted: 12/28/2023] [Indexed: 02/03/2024] Open
Abstract
Gut microbiota plays a vital role in obtaining nutrition from bamboo for giant pandas. However, low cellulase activity has been observed in the panda's gut. Besides, no specific pathway has been implicated in lignin digestion by gut microbiota of pandas. Therefore, the mechanism by which they obtain nutrients is still controversial. It is necessary to elucidate the precise pathways employed by gut microbiota of pandas to degrade lignin. Here, the metabolic pathways for lignin degradation in pandas were explored by comparing 209 metagenomic sequencing data from wild species with different feeding habits. Lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. The gut microbiome of wild bamboo-eating specialists was enriched with genes from pathways implicated in degrading ferulate and p-coumarate into acetyl-CoA and succinyl-CoA, which can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, was found to be the main bacteria to provide genes involved in lignin or lignin derivative degradation. Herein, three Pseudomonas-associated strains isolated from the feces of wild pandas showed the laccase, lignin peroxidase, and manganese peroxidase activity and extracellular lignin degradation ability in vitro. A potential mechanism for pandas to obtain nutrition from bamboo was proposed based on the results. This study provides novel insights into the adaptive evolution of pandas from the perspective of lignin metabolism. IMPORTANCE Although giant pandas only feed on bamboo, the mechanism of lignin digestion in pandas is unclear. Here, the metabolic pathways for lignin degradation in wild pandas were explored by comparing gut metagenomic from species with different feeding habits. Results showed that lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. Genes from pathways involved in degrading ferulate and p-coumarate via beta-ketoadipate pathway were also enriched in bamboo-eating pandas. The final products of the above process, such as acetyl-CoA, can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, mainly provides genes involved in lignin degradation. Herein, Pseudomonas-associated strains isolated from the feces of pandas could degrade extracellular lignin. These findings suggest that gut microbiome of pandas is crucial in obtaining nutrition from lignin via Pseudomonas, as the main lignin-degrading bacteria.
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Affiliation(s)
- Ruihong Ning
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Maohua Xia
- Beijing Key Laboratory of Captive Wildlife Technology, Beijing Zoo, Beijing, P.R. China
| | - Yu Zhang
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Yunong Gan
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, 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
| | - Tianyou Zhang
- Chimelong Safari Park in Guangdong Province, Guangzhou, China
| | - Haitao Song
- 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
| | - Siyuan Zhang
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Wei Guo
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
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Lu Y, Zhang L, Liu X, Lan Y, Wu L, Wang J, Wu K, Yang C, Lv R, Yi D, Zhuo G, Li Y, Shen F, Hou R, Yue B, Fan Z. Red pandas with different diets and environments exhibit different gut microbial functional composition and capacity. Integr Zool 2024. [PMID: 38420673 DOI: 10.1111/1749-4877.12813] [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] [Indexed: 03/02/2024]
Abstract
The red panda (Ailurus fulgens) is a distinctive mammal known for its reliance on a diet primarily consisting of bamboo. The gut microbiota and overall health of animals are strongly influenced by diets and environments. Therefore, conducting research to explore the taxonomical and functional variances within the gut microbiota of red pandas exposed to various dietary and environmental conditions could shed light on the dynamic complexities of their microbial communities. In this study, normal fecal samples were obtained from red pandas residing in captive and semi-free environments under different dietary regimes and used for metabolomic, 16S rRNA, and metagenomic sequencing analysis, with the pandas classified into four distinct cohorts according to diet and environment. In addition, metagenomic sequencing was conducted on mucus fecal samples to elucidate potential etiological agents of disease. Results revealed an increased risk of gastrointestinal diseases in red pandas consuming bamboo shoots due to the heightened presence of pathogenic bacteria, although an increased presence of microbiota-derived tryptophan metabolites appeared to facilitate intestinal balance. The red pandas fed bamboo leaves also exhibited a decrease in gut microbial diversity, which may be attributed to the antibacterial flavonoids and lower protein levels in leaves. Notably, red pandas residing in semi-free environments demonstrated an enriched gut microbial diversity. Moreover, the occurrence of mucus secretion may be due to an increased presence of species associated with diarrhea and a reduced level of microbiota-derived tryptophan metabolites. In summary, our findings substantiate the influential role of diet and environment in modulating the gut microbiota of red pandas, offering potential implications for improved captive breeding practices.
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Affiliation(s)
- Yunwei Lu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Liang Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Xu Liu
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yue Lan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Lixia Wu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Jiao Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Kongju Wu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Chaojie Yang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Ruiqing Lv
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Dejiao Yi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Guifu Zhuo
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Yan Li
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Fujun Shen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
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Bo T, Liu H, Liu M, Liu Q, Li Q, Cong Y, Luo Y, Wang Y, Yu B, Pu T, Wang L, Wang Z, Wang D. Mechanism of inulin in colic and gut microbiota of captive Asian elephant. MICROBIOME 2023; 11:148. [PMID: 37408039 DOI: 10.1186/s40168-023-01581-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/23/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Gut microbiota have a complex role on the survivability, digestive physiology, production, and growth performance in animals. Recent studies have emphasized the effects of prebiotics therapy on the gut disease, but the relationship between elephant gut-related diseases and prebiotics remains elusive. Here, a case study was undertaken to evaluate the mechanism of inulin treatment in colic in Asian elephant (Elephas maximus Linnaeus). METHODS Fecal samples were collected from a sick elephant and four healthy elephants. Analysis of microbial profile was carried out by 16S rRNA sequencing, and the short chain fatty acids were tested by gas chromatography. The physiological function of "inulin-microbiota" of elephant was verified in mice by fecal microbial transplantation (FMT). The expression of related proteins was determined by Western blotting and qPCR. RESULTS (1) Eating inulin can cure gut colic of the sick elephant and changed gut microbiota. (2) It was found that "inulin microbiota" from the post-treatment elephants can promote the proliferation of intestinal cells, increase the utilization of short chain fatty acids (SCFAs), maintain intestinal barrier, and reduce the inflammation in mice. (3) The mechanism was inulin-gut microbiota-SCFAs-immune barrier. CONCLUSIONS Inulin contributed to rehabilitate the gut microbiota and gut immune barrier of the elephant with colic. This provides reasonable verification for using prebiotics to treat the colic in captive elephants. Prebiotics will foresure play an increasingly important role in disease prevention and treatment of captive animals in the future. Video Abstract.
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Affiliation(s)
- Tingbei Bo
- School of Grassland Science, Beijing Forestry University, Beijing, 100091, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - He Liu
- Beijing key laboratory of captive wildlife technology, Beijing Zoo, Beijing, 100044, China.
| | - Min Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiyong Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Vector Control, School of Public Health, Shandong University, Jinan, 250012, China
| | - Qingduo Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yipeng Cong
- Beijing key laboratory of captive wildlife technology, Beijing Zoo, Beijing, 100044, China
| | - Yi Luo
- Beijing key laboratory of captive wildlife technology, Beijing Zoo, Beijing, 100044, China
| | - Yuqi Wang
- Beijing key laboratory of captive wildlife technology, Beijing Zoo, Beijing, 100044, China
| | - Bo Yu
- Beijing key laboratory of captive wildlife technology, Beijing Zoo, Beijing, 100044, China
| | - Tianchun Pu
- Beijing key laboratory of captive wildlife technology, Beijing Zoo, Beijing, 100044, China
| | - Lu Wang
- Beijing key laboratory of captive wildlife technology, Beijing Zoo, Beijing, 100044, China
| | - Zheng Wang
- Beijing key laboratory of captive wildlife technology, Beijing Zoo, Beijing, 100044, China
| | - Dehua Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- School of Life Science, Shandong University, Qingdao, 266237, China.
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Liu L, Dong Z, Ai S, Chen S, Dong M, Li Q, Zhou Z, Liu H, Zhong Z, Ma X, Hu Y, Ren Z, Fu H, Shu G, Qiu X, Peng G. Virulence-related factors and antimicrobial resistance in Proteus mirabilis isolated from domestic and stray dogs. Front Microbiol 2023; 14:1141418. [PMID: 37234544 PMCID: PMC10206225 DOI: 10.3389/fmicb.2023.1141418] [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: 01/10/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Introduction Proteus mirabilis is a multi-host pathogen that causes diseases of varying severity in a wide range of mammals, including humans. Proteus mirabilis is resistant to multiple antibiotics and has acquired the ability to produce expanded spectrum of β-lactamases, leading to serious public health problems. However, the available information on P. mirabilis isolated from feces of dogs, is still poorly understood, as is the correlation between its virulence-associated genes (VAGs) and antibiotic resistance genes (ARGs). Method In this study, we isolated 75 strains of P. mirabilis from 241 samples, and investigated the swarming motility, biofilm formation, antimicrobial resistance (AMR), distribution of VAGs and ARGs, as well as the presence of class 1, 2, and 3 integrons in these isolates. Results Our findings suggest a high prevalence of intensive swarming motility and strong biofilm formation ability among P. mirabilis isolates. Isolates were primarily resistant to cefazolin (70.67%) and imipenem (70.67%). These isolates were found to carry ureC, FliL, ireA, zapA, ptA, hpmA, hpmB, pmfA, rsbA, mrpA, and ucaA with varying prevalence levels of 100.00, 100.00, 100.00, 98.67, 98.67, 90.67, 90.67, 90.67, 90.67, 89.33, and 70.67%, respectively. Additionally, the isolates were found to carry aac(6')-Ib, qnrD, floR, blaCTX-M, blaCTX-M-2, blaOXA-1, blaTEM, tetA, tetB and tetM with varying prevalence levels of 38.67, 32.00, 25.33, 17.33, 16.00, 10.67, 5.33, 2.67, 1.33, and 1.33%, respectively. Among 40 MDR strains, 14 (35.00%) were found to carry class 1 integrons, 12 (30.00%) strains carried class 2 integrons, while no class 3 integrons was detected. There was a significant positive correlation between the class 1 integrons and three ARGs: blaTEM, blaCTX-M, and blaCTX-M-2. This study revealed that P. mirabilis strains isolated from domestic dogs exhibited a higher prevalence of MDR, and carried fewer VAGs but more ARGs compared to those isolated from stay dogs. Furthermore, a negative correlation was observed between VAGs and ARGs. Discussion Given the increasing antimicrobial resistance of P. mirabilis, veterinarians should adopt a prudent approach towards antibiotics administration in dogs to mitigate the emergence and dissemination of MDR strains that pose a potential threat to public health.
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Affiliation(s)
- Lijuan Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhiyou Dong
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shengquan Ai
- New Ruipeng Pet Healthcare Group, Chengdu, China
| | - Shanyu Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mengyao Dong
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qianlan Li
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ziyao Zhou
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Haifeng Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhijun Zhong
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoping Ma
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanchun Hu
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhihua Ren
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Hualin Fu
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Gang Shu
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xianmeng Qiu
- New Ruipeng Pet Healthcare Group, Chengdu, China
| | - Guangneng Peng
- Key Laboratory of Animal Disease and Human Health of Sichuan, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Yan D, Luo X, Tang J, Xu S, Huang K, Wang X, Feng T, Que T, Jia M, Guo X, Rehman SU, Li Z, Yang Y, Li K, Cui K, Ruan J, Liu Q. High-Quality Genomes of Pangolins: Insights into the Molecular Basis of Scale Formation and Adaption to Myrmecophagous Diet. Mol Biol Evol 2022; 40:6966006. [PMID: 36585823 PMCID: PMC9848057 DOI: 10.1093/molbev/msac262] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 01/01/2023] Open
Abstract
Pangolins are one of nature's most fascinating species being scales covered and myrmecophagous diet, yet relatively little is known about the molecular basis. Here, we combine the multi-omics, evolution, and fundamental proteins feature analysis of both Chinese and Malayan pangolins, highlighting the molecular mechanism of both myrmecophagous diet and scale formation, representing a fascinating evolutionary strategy to occupy the unique ecological niches. In contrast to conserved organization of epidermal differentiation complex, pangolin has undergone large scale variation and gene loss events causing expression pattern and function conversion that contribute to cornified epithelium structures on stomach to adapt myrmecophagous diet. Our assemblies also enable us to discover large copies number of high glycine-tyrosine keratin-associated proteins (HGT-KRTAPs). In addition, highly homogenized tandem array, amino content, and the specific expression pattern further validate the strong connection between the molecular mechanism of scale hardness and HGT-KRTAPs.
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Affiliation(s)
| | | | | | - Shanghua Xu
- Guangxi Forestry Research Institute, 530002 Nanning, China
| | - Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, 528225 Foshan, China,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Xiaobo Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Tong Feng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120 Shenzhen, China,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Tengcheng Que
- Guangxi Terrestrial Wildlife Rescue Research and Epidemic Disease Monitoring Centre, 530003 Nanning, China
| | - Miaomiao Jia
- Guangxi Forestry Research Institute, 530002 Nanning, China
| | - Xiaobing Guo
- Guangxi Forestry Research Institute, 530002 Nanning, China
| | - Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Yufeng Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 530005 Nanning, China
| | - Kaixiang Li
- Guangxi Forestry Research Institute, 530002 Nanning, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, 528225 Foshan, China
| | - Jue Ruan
- Corresponding authors: E-mails: ; ;
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Zhao Y, Zhang L, Tang X, Ren S, Zhang Y. Anthropogenic disturbance promotes the diversification of antibiotic resistance genes and virulence factors in the gut of plateau pikas (Ochotona curzoniae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1027941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The prevalence and transmission of antibiotic resistance genes (ARGs) and virulence factors (VFs) pose a great threat to public health. The importance of pollution in determining the occurrence of ARGs and VFs in wildlife is poorly understood. Using a metagenomic approach, this study investigates the composition and functional pathways of bacteria, ARGs, and VFs in the gut microbiome of Plateau pikas in regions of medical pollution (MPR), heavy tourist traffic (HTR), and no contamination (NCR). We found that the abundance of probiotic genera (Clostridium, Eubacterium, Faecalibacterium, and Roseburia) were significantly lower in the HTR. The metabolic pathways of replication and repair in the endocrine and nervous systems were significantly enriched in the MPR, whereas endocrine and metabolic diseases were significantly enriched in the NCR. The Shannon and Gini–Simpson α-diversity indices of ARGs were highest in the HTR, and there were significant differences in β-diversity among the three regions. The resistance of ARGs to glycopeptide antibiotics increased significantly in the MPR, whereas the ARGs for aminocoumarins increased significantly in the HTR. The diversity of mobile genetic elements (MGEs) was significantly higher in the MPR than in other regions. We observed a strong positive correlation between ARGs and pathogenic bacteria, and the network structure was the most complex in the MPR. There were significant differences in the β-diversity of VFs among the three regions. Medical pollution led to significant enrichment of fibronectin-binding protein and PhoP, whereas tourism-related pollution (in the HTR) led to significant enrichment of LPS and LplA1. Our study indicates that environmental pollution can affect the structure and function of gut microbes and disseminate ARGs and VFs via horizontal transmission, thereby posing a threat to the health of wild animals.
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Jiao W, Liu L, Zeng Z, Li L, Chen J. Differences in gut microbes in captive pangolins and the effects of captive breeding. Front Microbiol 2022; 13:1053925. [PMID: 36560954 PMCID: PMC9763570 DOI: 10.3389/fmicb.2022.1053925] [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: 09/26/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Intestinal microorganisms are crucial for health and have a significant impact on biological processes, such as metabolism, immunity, and neural regulation. Although pangolin are protected animals in China and listed as critically endangered (CR) level by The International Union for Conservation of Nature (IUCN), the population of wild pangolins has decreased sharply in recent decades. Captive breeding has been adopted to protect pangolins, but the survival is low due to gastrointestinal infections, diarrhea, and parasitic infections. Studies on intestinal microbes in pangolins may reveal the relationship between intestinal microorganisms and health and assist protection. To explore the relationship between intestinal microorganisms and pangolin health, blood parameters and intestinal microorganisms of 10 pangolins (two Manis pentadactyla and eight Manis javanica) were studied at the Shenzhen Wildlife Rescue Center. There is difference among adult Sunda pangolins (M. javanica), adult Chinese pangolins (M. pentadactyla) and sub-adult Sunda pangolins (M. javanica) in intestinal microbial composition, diversity and phenotypic diversity, which suggested that adult Sunda pangolins occupied more diversity and proportion of microbial species to resist environmental pressure than the others. Due to the captive breeding serum cortisol of pangolins was increased, and the intestinal microbial structure changed, which may affect immunity. This study provides a scientific basis for the rescue of pangolins through artificial breeding.
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Affiliation(s)
- Wenjing Jiao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China,*Correspondence: Wenjing Jiao
| | - Lina Liu
- Shenzhen Management Bureau of Natural Reserve, Guangdong, China
| | - Zhiliao Zeng
- Shenzhen Management Bureau of Natural Reserve, Guangdong, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China,Jinping Chen
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10
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To Save Pangolins: A Nutritional Perspective. Animals (Basel) 2022; 12:ani12223137. [PMID: 36428365 PMCID: PMC9686612 DOI: 10.3390/ani12223137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Pangolins are one of the world's most trafficked mammals. Since pangolins are highly adapted to ants and termites, they are important for controlling forest termite infestations. In addition to their ecological value, pangolins have economic and medicinal value. Currently, poaching and habitat destruction have radically reduced the number of pangolins, and Manis pentadactyla, Manis javanica, and Manis culionensis are now considered the most threatened pangolin species. In addition to the control of hunting and illegal trade, ex situ breeding is also a useful conservation method. However, many technical obstacles still limit the success of ex situ pangolin breeding. The special feeding traits of pangolins require a diet that meets nutritional and ethological needs. Based on the existing literature and practical experience, this review aims to compare the natural diet and successful diet in the human care of pangolins, to outline the key factors of successful ex situ maintenance from a dietary perspective, and the strategies to improve their conservation success in animal care centers and in the wild. The type of food used in successful pangolin protection agencies is quite variable in nutritional composition. In the diet of pangolins in the wild, the nutrient profile of different species of termites and ants and even the same species of termites and ants but different types (queens, soldiers, etc.) also displays differences. The crude protein content of some ants is higher than that of other foods, such as eggs, milk, and common cat food. The mineral and vitamin concentrations of ants also exceed many common food items, such as oil, meat, and eggs. However, not much is known about the bioavailability of minerals from ants and termites. Based on comparisons between foods, it is clear that the main difference between diets in the wild and in human care of pangolins is that the latter contains fewer insects and vitamins, such as vitamin E, vitamin A, and vitamin B2, and more carbohydrates and non-protein substances than the former. Although many successful dietary formulae have been developed, the pangolin's nutritional needs are still less well studied. A diet with the nutrient concentrations observed in the wild may add to successful ex situ conservation.
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Gao H, Dou H, Wei S, Sun S, Zhang Y, Hua Y. Local chronicles reveal the effect of anthropogenic and climatic impacts on local extinctions of Chinese pangolins ( Manis pentadactyla) in mainland China. Ecol Evol 2022; 12:e9388. [PMID: 36225832 PMCID: PMC9534744 DOI: 10.1002/ece3.9388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/18/2022] Open
Abstract
Anthropogenic and climatic factors affect the survival of animal species. Chinese pangolin is a critically endangered species, and identifying which variables lead to local extinction events is essential for conservation management. Local chronicles in China serve as long‐term monitoring data, providing a perspective to disentangle the roles of human impacts and climate changes in local extinctions. Therefore, we established generalized additive models to identify factors leading to local extinction with historical data from 1700–2000 AD in mainland China. Then we decreased the time scale and constructed extinction risk models using MaxEnt in a 30‐year transect (1970–2000 AD) to further assess extinction probability of extant Chinese pangolin populations. Lastly, we used principal component analysis to assess variation of related anthropogenic and climatic variables. Our results showed that the extinction probability increased with global warming and human population growth. An extinction risk assessment indicated that the population and distribution range of Chinese pangolins had been persistently shrinking in response to highly intensive human activities (main cause) and climate change. PCA results indicated that variability of climatic variables is greater than anthropogenic variables. Overall, the factors causing local extinctions are intensive human interference and drastic climatic fluctuations which induced by the effect of global warming. Approximately 28.10% of extant Chinese pangolins populations are confronted with a notable extinction risk (0.37 ≤ extinction probability≤0.93), specifically those in Southeast China, including Guangdong, Jiangxi, Zhejiang, Hunan and Fujian Provinces. To rescue this critically endangered species, we suggest strengthening field investigations, identifying the exact distribution range and population density of Chinese pangolins and further optimizing the network of nature reserves to improve conservation coverage on the landscape scale and alleviate human interference. Conservation practices that concentrate on the viability assessment of scattered populations could help to improve restoration strategies of the Chinese pangolin.
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Affiliation(s)
- Haiyang Gao
- Guangdong Provincial Key Laboratory of Silviculture, Protection and UtilizationGuangdong Academy of ForestryGuangzhouChina
| | - Hongliang Dou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and UtilizationGuangdong Academy of ForestryGuangzhouChina
| | - Shichao Wei
- Guangdong Provincial Key Laboratory of Silviculture, Protection and UtilizationGuangdong Academy of ForestryGuangzhouChina
| | - Song Sun
- Guangdong Provincial Key Laboratory of Silviculture, Protection and UtilizationGuangdong Academy of ForestryGuangzhouChina
| | - Yulin Zhang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and UtilizationGuangdong Academy of ForestryGuangzhouChina
| | - Yan Hua
- Guangdong Provincial Key Laboratory of Silviculture, Protection and UtilizationGuangdong Academy of ForestryGuangzhouChina
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Kapsetaki SE, Marquez Alcaraz G, Maley CC, Whisner CM, Aktipis A. Diet, Microbes, and Cancer Across the Tree of Life: a Systematic Review. Curr Nutr Rep 2022; 11:508-525. [PMID: 35704266 PMCID: PMC9197725 DOI: 10.1007/s13668-022-00420-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 11/09/2022]
Abstract
PURPOSE OF REVIEW Cancers are a leading cause of death in humans and for many other species. Diet has often been associated with cancers, and the microbiome is an essential mediator between diet and cancers. Here, we review the work on cancer and the microbiome across species to search for broad patterns of susceptibility associated with different microbial species. RECENT FINDINGS Some microbes, such as Helicobacter bacteria, papillomaviruses, and the carnivore-associated Fusobacteria, consistently induce tumorigenesis in humans and other species. Other microbes, such as the milk-associated Lactobacillus, consistently inhibit tumorigenesis in humans and other species. We systematically reviewed over a thousand published articles and identified links between diet, microbes, and cancers in several species of mammals, birds, and flies. Future work should examine a larger variety of host species to discover new model organisms for human preclinical trials, to better understand the observed variance in cancer prevalence across species, and to discover which microbes and diets are associated with cancers across species. Ultimately, this could help identify microbial and dietary interventions to diagnose, prevent, and treat cancers in humans as well as other animals.
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Affiliation(s)
- Stefania E Kapsetaki
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA.
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, USA.
| | - Gissel Marquez Alcaraz
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, USA
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, USA
| | - Corrie M Whisner
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA
| | - Athena Aktipis
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Psychology, Arizona State University, Tempe, AZ, USA
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Zhang K, Wang X, Gong X, Sui J. Gut Microbiome Differences in Rescued Common Kestrels (Falco tinnunculus) Before and After Captivity. Front Microbiol 2022; 13:858592. [PMID: 35794924 PMCID: PMC9251364 DOI: 10.3389/fmicb.2022.858592] [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: 01/20/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbes significantly impact animal health, yet research on the gut microbiota of most birds, especially raptors, is lacking. This study investigated the effects of dietary and environmental changes on the composition and abundance of gut microbiota in 17 rescued common kestrels (Falco tinnunculus) through 16S rRNA gene high-throughput sequencing of microorganisms in the feces of the birds. Firmicutes (relative abundance, 43.63%), Proteobacteria (37.26%), Actinobacteria (7.31%), and Bacteroidetes (5.48%) were the dominant phyla in the gut microbiota of the common kestrels. A comparison of the gut microbiota before and after captivity revealed that community composition and abundance of the common kestrel gut microbiota differed among different living conditions including diet and environment. At the phylum level, the abundance of Firmicutes was higher (P < 0.05), and that of Proteobacteria was lower (P < 0.05), after captivity (54.62 and 27.16%, respectively) compared with before captivity (33.67 and 46.41%, respectively), but no significant differences were found among other phyla. At the genus level, the abundance of Lactobacillus was higher (P < 0.05) after captivity (15.77%) compared with the abundance before captivity (5.02%). Hierarchical clustering and principal component analyses showed that common kestrels in different living conditions exhibited differences (P < 0.05) in gut microbiota at phylum and genus levels. Functional prediction of gene sequences using PICRUSt2 further revealed that pathways related to glucose metabolism and amino acid metabolism were enhanced (P < 0.05) after captivity. Collectively, the findings from this study demonstrated that the relative abundance of specific microbes in the gut of the rescued common kestrels either increased or decreased, and that dietary and environment changes might be the predominant factors affecting the gut microbiota of these birds during rescue or captivity.
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Captivity Shifts Gut Microbiota Communities in White-Lipped Deer (Cervus albirostris). Animals (Basel) 2022; 12:ani12040431. [PMID: 35203139 PMCID: PMC8868073 DOI: 10.3390/ani12040431] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/03/2022] [Accepted: 02/09/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Captivity is a common conservation method for endangered animals. However, a growing number of recent studies have shown that some animals in captivity might be in sub-health condition. The gut microbiota has been described as a complex, interactive internal system that has effects on diseases of the host with many interactions, and the occurrence of certain diseases is accompanied by changes and disorder of gut microbiota. We used16S rRNA sequencing technology and a mathematical model to find differences in gut microbiota composition and assembly processes. The results show that captivity might be unfavorable for white-lipped deer by shifting the gut microbiota composition and assembly process. Abstract White-lipped deer (Cervus albirostris) is a nationally protected wild animal species in China, as well as a unique and endangered species, according to the International Union for Conservation of Nature (IUCN) Red List. Captivity may alleviate the pressure from poaching and contribute to the repopulation and conservation of the population in the wild. The gut microbiota is described as a complex, interactive internal system that has effects on diseases of the host, with many interactions. However, the influence of captivity on the composition and assembly process of gut microbiota in white-lipped deer is unclear. This study applied high-throughput 16S rRNA sequencing technology to determine differences in the gut microbiota between captive (CW) and wild (WW) white-lipped deer. We used the null model, neutral community model, and niche width to identify whether captivity affects the composition and assembly process of gut microbiota. The results show that WW has a higher number of Firmicutes and a lower number of Bacteroidetes compared with CW at the phylum level, and it has more opportunistic pathogens and specific decomposition bacteria at the genus level. Principal coordinate analysis also indicated significant differences in the composition and function of gut microbiota in CW and WW. Moreover, the results reveal that captivity shifts the ecological assembly process of gut microbiota by raising the contribution of deterministic processes. In conclusion, our results demonstrate that captivity might potentially have an unfavorable effect on white-lipped deer by continually exerting selective pressure.
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Chiang E, Deblois CL, Carey HV, Suen G. Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing. Anim Microbiome 2022; 4:1. [PMID: 34980290 PMCID: PMC8722175 DOI: 10.1186/s42523-021-00154-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/12/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Hibernating animals experience extreme changes in diet that make them useful systems for understanding host-microbial symbioses. However, most of our current knowledge about the hibernator gut microbiota is derived from studies using captive animals. Given that there are substantial differences between captive and wild environments, conclusions drawn from studies with captive hibernators may not reflect the gut microbiota's role in the physiology of wild animals. To address this, we used Illumina-based sequencing of the 16S rRNA gene to compare the bacterial cecal microbiotas of captive and wild 13-lined ground squirrels (TLGS) in the summer. As the first study to use Illumina-based technology to compare the microbiotas of an obligate rodent hibernator across the year, we also reported changes in captive TLGS microbiotas in summer, winter, and spring. RESULTS Wild TLGS microbiotas had greater richness and phylogenetic diversity with less variation in beta diversity when compared to captive microbiotas. Taxa identified as core operational taxonomic units (OTUs) and found to significantly contribute to differences in beta diversity were primarily in the families Lachnospiraceae and Ruminococcaceae. Captive TLGS microbiotas shared phyla and core OTUs across the year, but active season (summer and spring) microbiotas had different alpha and beta diversities than winter season microbiotas. CONCLUSIONS This is the first study to compare the microbiotas of captive and wild rodent hibernators. Our findings suggest that data from captive and wild ground squirrels should be interpreted separately due to their distinct microbiotas. Additionally, as the first study to compare seasonal microbiotas of obligate rodent hibernators using Illumina-based 16S rRNA sequencing, we reported changes in captive TLGS microbiotas that are consistent with previous work. Taken together, this study provides foundational information for improving the reproducibility and experimental design of future hibernation microbiota studies.
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Affiliation(s)
- Edna Chiang
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Courtney L. Deblois
- Microbiology Doctoral Training Program, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hannah V. Carey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Garret Suen
- Present Address: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
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