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Bo X, Chen J, Mu J, Dong X, Ren Z, Liu J, Wang S. Quercetin promotes the secretion of musk by regulating the hormone level and microbial structure of forest musk deer. Integr Zool 2024; 19:596-611. [PMID: 37789560 DOI: 10.1111/1749-4877.12763] [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] [Indexed: 10/05/2023]
Abstract
Musk is a scarce and precious medical resource secreted by male forest musk deer (FMD). Current research to promote musk secretion in FMD has used almost exclusively hormone injections, but this approach can be detrimental to the health of FMD. In order to conserve this endangered species as much as possible while increasing the production of musk, this study first used bioinformatics methods to predict the function of quercetin, a flavonoid that promotes testosterone (T) production and prevents late-onset male hypogonadism. On the basis of good prediction effect, different concentrations of quercetin were added to the diet of FMD. The results showed that quercetin could change the levels of T, luteinizing hormone releasing hormone, luteinizing hormone, and estradiol, and regulate the structure of intestinal microorganisms and musk microorganisms of FMD. Moreover, there is a correlation among musk components, hormones, intestinal microorganisms, and musk microorganisms, which indicates that the production of musk may be regulated by these three at the same time, and the addition of quercetin with 800 mg per kg diet could significantly increase the yield of muscone (P < 0.05), the most effective ingredient in musk. In addition, quercetin decreased the high level of cortisol during musk secretion, which may relieve the stress on FMD in this process. This may help to protect the health of FMD. Combined with the results of software prediction, we finally proposed a possible mechanism for the complex process of musk secretion in FMD with a view to providing ideas for further studies.
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Affiliation(s)
- Xinyu Bo
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Jialing Chen
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Jinzhan Mu
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Xianggui Dong
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Zhanjun Ren
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Jinyao Liu
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A & F University, Shaanxi, China
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2
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Mo Q, Yao H, Wu H, Zhao D. Impact of Environmental Food Intake on the Gut Microbiota of Endangered Père David's Deer: Primary Evidence for Population Reintroduction. Animals (Basel) 2024; 14:728. [PMID: 38473113 DOI: 10.3390/ani14050728] [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: 11/15/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 03/14/2024] Open
Abstract
Reintroduction has been successful in re-establishing several endangered wild animals in their historical habitats, including Père David's deer (Elaphurus davidianus). Continuous monitoring of reintroduced individuals is essential for improving the sustainability of ex situ conservation efforts. Despite an increased recognition of the significance of the gut microbiome for animal health, the correlation between diet and the gut microbiome in E. davidianus is unclear. In this study, 15 fresh fecal samples of E. davidianus were collected from Tianjin Qilihai Wetland and the association between dietary and gut microbiota composition was evaluated. Microscopic observations showed that Nymphoides peltata [relative density (RD = 0.3514), Phragmites australis (RD = 0.2662), Setaria viridis (RD = 0.1211), and Typha orientalis (RD = 0.1085) were the main dietary plants in the fecal samples. High-throughput 16S rRNA sequencing showed a predominance of the phyla Firmicutes and Proteobacteria and the genus Psychrobacillus (26.53%) in the gut microbiota. The RD of N. peltata was significantly positively correlated with the abundance of Firmicutes (p = 0.005) and the genus UCG-005 (p = 0.024). This study indicates a close association between food digestion and nutrient intake, providing basic monitoring data for the full reintroduction and recovery of wild E. davidianus.
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Affiliation(s)
- Qiying Mo
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Hongyu Yao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Hong Wu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
| | - Dapeng Zhao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin 300387, China
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3
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Lee W, Hayakawa T, Kiyono M, Yamabata N, Enari H, Enari HS, Fujita S, Kawazoe T, Asai T, Oi T, Kondo T, Uno T, Seki K, Shimada M, Tsuji Y, Langgeng A, MacIntosh A, Suzuki K, Yamada K, Onishi K, Ueno M, Kubo K, Hanya G. Diet-related factors strongly shaped the gut microbiota of Japanese macaques. Am J Primatol 2023; 85:e23555. [PMID: 37766673 DOI: 10.1002/ajp.23555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/08/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
Although knowledge of the functions of the gut microbiome has increased greatly over the past few decades, our understanding of the mechanisms governing its ecology and evolution remains obscure. While host genetic distance is a strong predictor of the gut microbiome in large-scale studies and captive settings, its influence has not always been evident at finer taxonomic scales, especially when considering among the recently diverged animals in natural settings. Comparing the gut microbiome of 19 populations of Japanese macaques Macaca fuscata across the Japanese archipelago, we assessed the relative roles of host genetic distance, geographic distance and dietary factors in influencing the macaque gut microbiome. Our results suggested that the macaques may maintain a core gut microbiome, while each population may have acquired some microbes from its specific habitat/diet. Diet-related factors such as season, forest, and reliance on anthropogenic foods played a stronger role in shaping the macaque gut microbiome. Among closely related mammalian hosts, host genetics may have limited effects on the gut microbiome since the hosts generally have smaller physiological differences. This study contributes to our understanding of the relative roles of host phylogeography and dietary factors in shaping the gut microbiome of closely related mammalian hosts.
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Affiliation(s)
- Wanyi Lee
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mieko Kiyono
- Graduate School of Human Development and Environment, Kobe University, Kobe, Hyogo, Japan
| | - Naoto Yamabata
- Institute of Natural and Environmental Sciences, University of Hyogo, Sanda, Hyogo, Japan
| | - Hiroto Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Haruka S Enari
- Faculty of Agriculture, Yamagata University, Wakabamachi, Tsuruoka, Yamagata, Japan
| | - Shiho Fujita
- Department of Behavioral Physiology and Ecology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Tatsuro Kawazoe
- Research Institute for Languages and Cultures of Asia and Africa, Tokyo University of Foreign Studies, Tokyo, Japan
| | - Takayuki Asai
- South Kyushu Wildlife Management Center, Kagoshima, Japan
| | - Toru Oi
- Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | | | - Takeharu Uno
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Kentaro Seki
- Tohoku Monkey and Mammal Management Center, Sendai, Miyagi, Japan
| | - Masaki Shimada
- Department of Animal Sciences, Teikyo University of Science, Uenohara, Yamanashi, Japan
| | - Yamato Tsuji
- Department of Science and Engineering, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
| | - Abdullah Langgeng
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | - Andrew MacIntosh
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Wildlife Research Center, Kyoto University, Kanrin, Inuyama, Japan
| | | | - Kazunori Yamada
- Graduate School of Human Sciences, Osaka University, Suita, Osaka, Japan
| | - Kenji Onishi
- Department of Early Childhood Education, Nara University of Education, Nara, Japan
| | - Masataka Ueno
- Faculty of Applied Sociology, Kindai University, Higashiosaka, Osaka, Japan
| | - Kentaro Kubo
- Cultural Asset Management Division, Board of Education, Oita-City, Japan
| | - Goro Hanya
- Center for Ecological Research, Kyoto University, Inuyama, Japan
- Primate Research Institute, Kyoto University, Inuyama, Japan
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4
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Zhai J, Sun X, Lu R, Hu X, Huang Z. Bibliometric Analysis of Global Trends in Research on Seasonal Variations in Gut Microbiota from 2012 to 2022. Microorganisms 2023; 11:2125. [PMID: 37630685 PMCID: PMC10458723 DOI: 10.3390/microorganisms11082125] [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: 07/20/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Seasons are the important influencing factor for gut microbiota, which in turn affects the ecology and evolution of the host. The seasonal variation in gut microbiota has increasingly attracted the attention of researchers and professionals worldwide. However, studies of seasonal variations in gut microbiota have not been systematically analyzed by bibliometrics or visual analysis. This study is based on 271 publications from 2012 to 2022 in the Web of Science Core Collection database (WOSCC) to analyze hot spots and trends in this field. The collaborations between different countries, institutions, authors, journals, and keywords were bibliometrically analyzed using Excel, CiteSpace (Version 6.2. R4), and VOSviewer (version 1.6.19) software. The number of publications has been increasing rapidly and shows a general upward trend. China and the Chinese Academy of Sciences are the country and institution contributing the most, respectively. The research hotspots and trends mainly include the diversity of gut microbiota communities in different seasons, the relationship between diet and gut microbiota in seasonal changes, and the relationship between gut microbiota and evolutionary adaptation in seasonal changes. This is the first bibliometric and visualization analysis of seasonal variations in gut microbiota, which may advance this field and lay the foundation for future research.
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Affiliation(s)
- Jiancheng Zhai
- Natural Reserve Planning and Research Institute, East China University of Technology, Nanchang 330013, China
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Xiao Sun
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330029, China
| | - Rui Lu
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Xueqin Hu
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
| | - Zhiqiang Huang
- Natural Reserve Planning and Research Institute, East China University of Technology, Nanchang 330013, China
- School of Earth Sciences, East China University of Technology, Nanchang 330013, China
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5
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Yao H, Mo Q, Wu H, Zhao D. How do living conditions affect the gut microbiota of endangered Père David's deer ( Elaphurus davidianus)? Initial findings from the warm temperate zone. PeerJ 2023; 11:e14897. [PMID: 36860766 PMCID: PMC9969852 DOI: 10.7717/peerj.14897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/24/2023] [Indexed: 03/03/2023] Open
Abstract
Reintroduction is an effective strategy in the conservation of endangered species under scientific monitoring. Intestinal flora plays an important role in the envir onmental adaptation of endangered Père David's deer (Elaphurus davidianus). In this study, 34 fecal samples from E. davidianus were collected from different habitats in Tianjin city of China to investigate differences in the intestinal flora under captive and semi-free-ranging conditions. Based on 16S rRNA high-throughput sequencing technology, a total of 23 phyla and 518 genera were obtained. Firmicutes was dominant in all individuals. At the genus level, UCG-005 (13.05%) and Rikenellaceae_RC9_gut_group (8.94%) were dominant in captive individuals, while Psychrobacillus (26.53%) and Pseudomonas (11.33%) were dominant in semi-free-ranging individuals. Alpha diversity results showed that the intestinal flora richness and diversity were significantly (P < 0.001) higher in captive individuals than in semi-free-ranging individuals. Beta diversity analysis also showed a significant difference (P = 0.001) between the two groups. In addition, some age- and sex-related genera such as Monoglobus were identified. In summary, the structure and diversity of intestinal flora showed significant habitat variation. This is the first time an analysis has been undertaken of the structural differences of the intestinal flora in Père David's deer, under different habitats in the warm temperate zone, providing a reference basis for the conservation of endangered species.
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6
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Zhang Z, Ding M, Sun Y, Khattak RH, Chen J, Teng L, Liu Z. Different living environments drive deterministic microbial community assemblages in the gut of Alpine musk deer ( Moschus chrysogaster). Front Microbiol 2023; 13:1108405. [PMID: 36713154 PMCID: PMC9880224 DOI: 10.3389/fmicb.2022.1108405] [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: 11/26/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023] Open
Abstract
Substantial variation in the environment directly causes remodeling of the colonized gut microbiota, controlling community diversity, and functions in the host to tune-up their adaptive states. However, the mechanisms of microbial community assembly in response to environmental changes remain unclear, especially in endangered ruminants. In this study, we analyzed the microbial communities of 37 fecal samples collected from captive and wild Alpine musk deer (Moschus chrysogaster) to characterize the complexity and assembly processes using 16S rRNA gene sequencing. We found significantly different diversities and compositions of gut microbiota among both groups associated with different living environments. Heterogeneous selection was the predominant factor regulating the gut microbiota community under similar climatic conditions, indicating that microbial community assembly was largely driven by deterministic mechanisms. The species co-occurrence network showed complex and tight connections with a higher positive correlation in the wild environment. Moreover, the captive group exhibited significant differences in chemoheterotrophy and fermentation compared with the wild group, but the opposite was observed in animal parasites or symbionts, which might be closely related to diet, energy supply, and healthcare of animals. This study provides a framework basis and new insights into understanding gut microbiota in different environments.
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Affiliation(s)
- Zhirong Zhang
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China
| | - Mengqi Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Yujiao Sun
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China,College of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Romaan Hayat Khattak
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China
| | - Junda Chen
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China
| | - Liwei Teng
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China,Key Laboratory of Conservation Biology, National Forestry and Grassland Administration, Harbin, China,*Correspondence: Liwei Teng ✉
| | - Zhensheng Liu
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, China,Key Laboratory of Conservation Biology, National Forestry and Grassland Administration, Harbin, China,Zhensheng Liu ✉
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7
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Blyton MDJ, Pascoe J, Hynes E, Soo RM, Hugenholtz P, Moore BD. The koala gut microbiome is largely unaffected by host translocation but rather influences host diet. Front Microbiol 2023; 14:1085090. [PMID: 36937253 PMCID: PMC10018171 DOI: 10.3389/fmicb.2023.1085090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/31/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction Translocation is a valuable and increasingly used strategy for the management of both threatened and overabundant wildlife populations. However, in some instances the translocated animals fail to thrive. Differences in diet between the source and destination areas may contribute to poor translocation outcomes, which could conceivably be exacerbated if the animals' microbiomes are unsuited to the new diet and cannot adapt. Methods In this study we tracked how the faecal microbiome of a specialist Eucalyptus folivore, the koala (Phascolarctos cinereus), changed over the course of a year after translocation. We assessed microbiome composition by 16S rRNA amplicon sequencing of faecal pellets. Results We found no significant overall changes in the faecal microbiomes of koalas post-translocation (n = 17) in terms of microbial richness, diversity or composition when compared to the faecal microbiomes of koalas from an untranslocated control group (n = 12). This was despite the translocated koalas feeding on a greater variety of Eucalyptus species after translocation. Furthermore, while differences between koalas accounted for half of the microbiome variation, estimated diets at the time of sampling only accounted for 5% of the variation in the koala microbiomes between sampling periods. By contrast, we observed that the composition of koala faecal microbiomes at the time of translocation accounted for 37% of between koala variation in post-translocation diet. We also observed that translocated koalas lost body condition during the first month post-translocation and that the composition of the koalas' initial microbiomes were associated with the magnitude of that change. Discussion These findings suggest that the koala gut microbiome was largely unaffected by dietary change and support previous findings suggesting that the koala gut microbiome influences the tree species chosen for feeding. They further indicate that future research is needed to establish whether the koalas' gut microbiomes are directly influencing their health and condition or whether aspects of the koala gut microbiomes are an indicator of underlying physiological differences or pathologies. Our study provides insights into how animal microbiomes may not always be affected by the extreme upheaval of translocation and highlights that responses may be host species-specific. We also provide recommendations to improve the success of koala translocations in the future.
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Affiliation(s)
- Michaela D. J. Blyton
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
- The University of Queensland, Australian Institute of Bioengineering and Nanotechnology, St Lucia, QLD, Australia
- *Correspondence: Michaela D. J. Blyton,
| | - Jack Pascoe
- Conservation Ecology Centre, Cape Otway, VIC, Australia
- School of Ecosystem and Forest Science, University of Melbourne, Parkville, VIC, Australia
| | | | - Rochelle M. Soo
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Ben D. Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
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Comparative study of the function and structure of the gut microbiota in Siberian musk deer and Forest musk deer. Appl Microbiol Biotechnol 2022; 106:6799-6817. [DOI: 10.1007/s00253-022-12158-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 11/02/2022]
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9
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You Z, Deng J, Liu J, Fu J, Xiong H, Luo W, Xiong J. Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer ( Cervus albirostris). PeerJ 2022; 10:e13753. [PMID: 35873913 PMCID: PMC9302429 DOI: 10.7717/peerj.13753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/28/2022] [Indexed: 01/17/2023] Open
Abstract
The gut microbiota has key physiological functions in host adaptation, although little is known about the seasonal changes in the composition and diversity of the gut microbiota in deer. In this study, seasonal variations (grassy and withering season) in the gut microbiota of white-lipped deer (Cervus albirostris), which lives in alpine environments, were explored through 16S rRNA high-throughput sequencing based on sixteen fecal samples collected from Gansu Qilian Mountain National Nature Reserve in China. At the phylum level, Firmicutes, Bacteroidota, and Actinobacteriota dominated the grassy season, while Firmicutes, Proteobacteria, and Actinobacteriota dominated the withering season. At the genus level, Carnobacterium dominated the grassy season, while Arthrobacter and Acinetobacter dominated the withering season. Alpha diversity results (Shannon: P = 0.01, ACE: P = 0.00, Chao1: P = 0.00) indicated that there was a difference in the diversity and richness of the gut microbiota between the two seasons, with higher diversity in the grassy season than in the withering season. Beta diversity results further indicated that there was a significant difference in the community structure between the two seasons (P = 0.001). In summary, the composition, diversity, and community structure of the gut microbiota showed significant seasonal variations, which could be explained by variations in the seasonal food availability, composition, diversity, and nutrition due to phenological alternations. The results of this study indicate that the gut microbiota can adapt to changes in the environment and provide the scientific basis for health assessment of white-lipped deer.
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Affiliation(s)
- Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Jing Deng
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Jialin Liu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Junhua Fu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Huan Xiong
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Wei Luo
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
| | - Jianli Xiong
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan Province, China
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10
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Chen S, Holyoak M, Liu H, Bao H, Ma Y, Dou H, Li G, Roberts NJ, Jiang G. Global warming responses of gut microbiota in moose (
Alces alces
) populations with different dispersal patterns. J Zool (1987) 2022. [DOI: 10.1111/jzo.12998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. Chen
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
| | - M. Holyoak
- Department of Environmental Science and Policy University of California Davis California USA
| | - H. Liu
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
- College of Forestry Hainan University Haikou China
| | - H. Bao
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
| | - Y. Ma
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
- Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - H. Dou
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization Guangdong Academy of Forestry Guangzhou China
| | - G. Li
- State Key Laboratory of Integrated Pest Management, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - N. J. Roberts
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
| | - G. Jiang
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area Northeast Forestry University Harbin China
- Northeast Asia Biodiversity Research Center Northeast Forestry University Harbin China
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11
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Cai W, Suding Z, Wang L, Hou Z, Liu D, Huang S, Xu J, Tao J. A new Eimeria coccidian species (Apicomplexa: Eimeriidae) from Père David's deer (Elaphurus davidianus Milne-Edwards, 1866) in Dafeng Milu National Nature Reserve in Jiangsu Province, eastern China. BMC Vet Res 2022; 18:213. [PMID: 35655211 PMCID: PMC9164372 DOI: 10.1186/s12917-022-03308-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
Background Eimeria coccidiosis is a significant intestinal parasitic disease, which can lead to weight loss, disease and even death of many animals. At present, there is no information about the prevalence of Eimeria among the world’s endangered species of Père David’s deer (Elaphurus davidianus). Therefore, the purpose of this study is to identify an unknown Eimeria genus in the Père David’s deer in Dafeng Milu National Nature Reserve, China. Results A new Eimeria species is described from Père David’s deer. Sporulated oocysts (n = 54) are pyriform, with a rough, yellowish brown, 2-layered oocyst wall (2.5 μm thick). A numerous small granules are dispersed randomly on the wall. Oocysts measured 41.2 (39.2–42.8) μm × 29.5 (27.9–30.5) μm, oocyst length/width (L/W) ratio, 1.4. Oocyst residuum, a polar granule and a polar cap are absent. The micropyle (3.5 μm wide) is present. Sporocysts are spindle shaped, 18.2 (16.5–20.0) μm × 10.5 (9.8–11.9) μm, sporocyst L/W ratio, 1.7 (1.5–1.9). A thin convex Stieda body is present and the sporocyst residuum is composed of numerous small granules less than 2.0 μm in diameter dispersed randomly. Each sporocyst contained 2 comma-shaped sporozoites in head-to-tail arrangement. A nucleus is located immediately anterior to the posterior, strong refractive and subspherical refractile body (~ 8 μm). Molecular analysis was conducted at the 18S, ITS-1 and COI loci. Conclusion Based on the morphological and molecular data, this isolate is a new species of coccidian parasite, which is named Eimeria davidianusi after its host, the Père David’s deer (Elaphurus davidianus). Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03308-2.
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Affiliation(s)
- Weimin Cai
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Zeyang Suding
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Lele Wang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Zhaofeng Hou
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Dandan Liu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Siyang Huang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Jinjun Xu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Jianping Tao
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, People's Republic of China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
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12
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Effect of Different Dietary Regimes on the Gut Microbiota and Fecal Metabolites of Père David’s Deer. Animals (Basel) 2022; 12:ani12050584. [PMID: 35268151 PMCID: PMC8909101 DOI: 10.3390/ani12050584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Père David’s deer is native to the middle and lower reaches of the Yangtze River and the Yellow River in China. However, the wild population became extinct in China around 1900. In 1986, 39 Père David’s deer were reintroduced into Dafeng. Up until now, its wild population has reached 2658, with a total of 6119 in 2021. At present, due to the continuous increase in the population, the repeated grazing on the same plants by the Père David’s deer has affected the re-growth of plants, which has led to insufficient natural food. Therefore, feeding supplement with silage is necessary. As a key nutritional factor, diet is the most important for the gut microbiota and metabolites of wild animals. In order to determine the effect of different dietary patterns on the nutrition and health of Père David’s deer in Dafeng Reserve in spring, we conducted a comprehensive analysis of Père David’s deer feces by UPLC-MS/MS and 16S rRNA gene sequencing to reveal its intestinal chemical environment and the differences in the fecal microbiome. Altogether, our data explored the significant changes in the gut microbiota and metabolic pathways during the transition from full silage to a combination diet with silage and plant in spring. These data provided important information to make more reasonable measures for Père David’s deer’s protection. Abstract A deep understanding of the effect of seasonal dietary changes on the nutrition and health of Père David’s deer in Dafeng Reserve will contribute greatly to Père David’s deer’s protection. In this reserve, there were three seasonal dietary regimes: feeding on naturally occurring plants (PLANT diet), silage (SILAGE diet), and a combination of natural plants and silage (COMB diet). To some extent, the COMB diet reflects the seasonal transition from silage to the all-natural plant diet, especially in early spring. However, little is known regarding the gut microbiota changes and metabolic consequences under the COMB diet. Based on 16S rRNA sequencing and ultra-high performance liquid chromatography combined with tandem mass spectrometry, the gut microbiota and fecal metabolites of Père David’s deer under these three diets were compared. Results showed the alpha diversity of the gut microbiota was significantly lower under the COMB diet compared to either the SILAGE or PLANT diets. Although no significant changes were observed in the core phyla, Firmicutes and Bacteroidetes, among the three dietary regimes, a significant lower abundance of several other phyla (Spirochaetes, Melainabacteria, Proteobacteria, and Verrucobacteria) was observed in the COMB diet compared to the SILAGE diet. A greater number of fecal metabolite differences was identified between the COMB and SILAGE or COMB and PLANT diets than between the SILAGE and PLANT diets, suggesting that the COMB diet had more of an effect on the metabolism of Père David’s deer. The integrated pathway analysis showed that several metabolic pathways were significantly affected by the different dietary regimes, such as tryptophan metabolism, vitamin metabolism, and the platelet activation pathways. These metabolic changes reflect the responses and adaptations of Père David’s deer to different diets. Taken overall, our data reveal the difference in the gut microbiota and metabolic pathways of Père David’s deer under three dietary regimes in Dafeng Reserve, which provides important information for Père David’s deer conservation.
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13
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Chen S, Holyoak M, Liu H, Bao H, Ma Y, Dou H, Jiang G. Effects of spatially heterogeneous warming on gut microbiota, nutrition and gene flow of a heat-sensitive ungulate population. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150537. [PMID: 34844317 DOI: 10.1016/j.scitotenv.2021.150537] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/19/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Effects of climate warming on trophic cascades are increasingly reported for large herbivores occupying northern latitudes. During the last 40 years, moose (Alces alces) in northeast China have lost nearly half of their historical distribution through their habitat shifting northwards. There are many possible causes of bottom-up and top-down effects of temperature and for moose in northeast China they are poorly understood. Of particular relevance are the effects of extrinsic environmental factors on gene flow, nutritional adaptions, and gut microbiota that occur as moose populations retreat northwards. We combined molecular biology, nutritional ecology and metagenomics to gain deeper mechanistic insights into the effects of temperature on moose populations. In this study, we revealed that the direction and intensity of gene flow is consistent with global warming driving retreats of moose populations. We interpret this as evidence for the northward movement of moose populations, with cooler northern populations receiving more immigrants and warmer southern populations supplying emigrants. Comparison across latitudes showed that warmer late spring temperatures were associated with plant community composition and facilitated related changes in moose protein and carbohydrate intake through altering forage availability, forage quality and diet composition. Furthermore, these nutrient shifts were accompanied by changes in gut microbial composition and functional pathways related to nutrient metabolism. This study provided insights into mechanisms driving effects of spatial heterogeneous warming on genetic, nutritional and physiological adaptions related to key demographic rates and patterns of survival of heat-sensitive ungulates along a latitude gradient. Understanding such changes helps to identify key habitat areas and plant species to ensure accurate assessment of population status and targeted management of moose populations.
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Affiliation(s)
- Shiyu Chen
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Marcel Holyoak
- Department of Environmental Science and Policy, University of California, Davis, CA 95616, USA
| | - Hui Liu
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; College of Forestry, Hainan University, Haikou 570228, China
| | - Heng Bao
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yingjie Ma
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichenxi Road, Chaoyang, Beijing 100101, China
| | - Hongliang Dou
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Guangshun Jiang
- Feline Research Center of National Forestry and Grassland Administration, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China.
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14
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Pannoni SB, Proffitt KM, Holben WE. Non-invasive monitoring of multiple wildlife health factors by fecal microbiome analysis. Ecol Evol 2022; 12:e8564. [PMID: 35154651 PMCID: PMC8826075 DOI: 10.1002/ece3.8564] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 01/04/2023] Open
Abstract
Fecal microbial biomarkers represent a less invasive alternative for acquiring information on wildlife populations than many traditional sampling methodologies. Our goal was to evaluate linkages between fecal microbiome communities in Rocky Mountain elk (Cervus canadensis) and four host factors including sex, age, population, and physical condition (body-fat). We paired a feature-selection algorithm with an LDA-classifier trained on elk differential bacterial abundance (16S-rRNA amplicon survey) to predict host health factors from 104 elk microbiomes across four elk populations. We validated the accuracy of the various classifier predictions with leave-one-out cross-validation using known measurements. We demonstrate that the elk fecal microbiome can predict the four host factors tested. Our results show that elk microbiomes respond to both the strong extrinsic factor of biogeography and simultaneously occurring, but more subtle, intrinsic forces of individual body-fat, sex, and age-class. Thus, we have developed and described herein a generalizable approach to disentangle microbiome responses attributed to multiple host factors of varying strength from the same bacterial sequence data set. Wildlife conservation and management presents many challenges, but we demonstrate that non-invasive microbiome surveys from scat samples can provide alternative options for wildlife population monitoring. We believe that, with further validation, this method could be broadly applicable in other species and potentially predict other measurements. Our study can help guide the future development of microbiome-based monitoring of wildlife populations and supports hypothetical expectations found in host-microbiome theory.
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Affiliation(s)
- Samuel B. Pannoni
- Franke College of Forestry and ConservationUniversity of MontanaMissoulaMontanaUSA
| | | | - William E. Holben
- Cellular, Molecular and Microbial Biology ProgramUniversity of MontanaMissoulaMontanaUSA
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15
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Yao R, Dai Q, Wu T, Yang Z, Chen H, Liu G, Zhu Y, Qi D, Yang X, Luo W, Gu X, Yang X, Zhu L. Fly-over phylogeny across invertebrate to vertebrate: The giant panda and insects share a highly similar gut microbiota. Comput Struct Biotechnol J 2021; 19:4676-4683. [PMID: 34504662 PMCID: PMC8390952 DOI: 10.1016/j.csbj.2021.08.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/30/2021] [Accepted: 08/16/2021] [Indexed: 01/19/2023] Open
Abstract
Many studies highlight that host phylogeny and diet are the two main factors influencing the animal gut microbiota. However, the internal mechanisms driving the evolution of animal gut microbiota may be more complex and complicated than we previously realized. Here, based on a large-scale meta-analysis of animal gut microbiota (16 s RNA gene data from approximately 1,800 samples; 108 metagenomes) across a wide taxonomic range of hosts, from invertebrate to vertebrate, we found high similarity in the gut microbial community (high proportion of Gammaproteobacteria (Pseudomonas)) of invertebrate insects and vertebrate bamboo-eating pandas (giant panda and red panda), which might be associated their plant-eating behavior and the presence of oxygen in the intestinal tract. A Pseudomonas strain-level analysis using 108 metagenomes further revealed that the response to either host niches or selection by the host might further lead to host-specific strains (or sub-strains) among the different hosts congruent with their evolutionary history. In this study, we uncovered new insights into the current understanding of the evolution of animals and their gut microbiota.
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Affiliation(s)
- Ran Yao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qinlong Dai
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Tonggui Wu
- East China Coastal Forest Ecosystem Long-term Research Station, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou Zhejiang, China
| | | | - Hua Chen
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Guoqi Liu
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Yudong Zhu
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Dunwu Qi
- Chengdu Giant Panda Breeding Center, Chengdu, China
| | - Xu Yang
- Chengdu Xinagai Information Technology Co., Ltd., Chengdu, China
| | - Wei Luo
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Xiaodong Gu
- Sichuan Station of Wildlife Survey and Management, Chengdu, China
| | - Xuyu Yang
- Sichuan Station of Wildlife Survey and Management, Chengdu, China
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Corresponding author.
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16
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Zhu L, Zhang Y, Cui X, Zhu Y, Dai Q, Chen H, Liu G, Yao R, Yang Z. Host Bias in Diet-Source Microbiome Transmission in Wild Cohabitating Herbivores: New Knowledge for the Evolution of Herbivory and Plant Defense. Microbiol Spectr 2021; 9:e0075621. [PMID: 34406815 PMCID: PMC8552726 DOI: 10.1128/spectrum.00756-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
It is commonly understood that dietary nutrition will influence the composition and function of the animal gut microbiome. However, the transmission of organisms from the diet-source microbiome to the animal gut microbiome in the natural environment remains poorly understood, and elucidating this process may help in understanding the evolution of herbivores and plant defenses. Here, we investigated diet-source microbiome transmission across a range of herbivores (insects and mammals) living in both captive and wild environments. We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. IMPORTANCE We discovered a host bias among cohabitating herbivores (leaf-eating insects and deer), where a significant portion of the herbivorous insect gut microbiome may originate from the diet, while in deer, only a tiny fraction of the gut microbiome is of dietary origin. We speculated that the putative difference in the oxygenation level in the host digestion systems would lead to these host biases in plant-source (diet) microbiome transmission due to the oxygenation living condition of the dietary plant's symbiotic microbiome. This study shed new light on the coevolution of herbivory and plant defense.
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Affiliation(s)
- Lifeng Zhu
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Yongyong Zhang
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Xinyuan Cui
- College of Life Sciences, Nanjing Norma University, Nanjing, China
| | - Yudong Zhu
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Qinlong Dai
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Hua Chen
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Guoqi Liu
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Ran Yao
- College of Life Sciences, Nanjing Norma University, Nanjing, China
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17
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Eddington HS, Carroll C, Larsen RT, McMillan BR, Chaston JM. Spatiotemporal variation in the fecal microbiota of mule deer is associated with proximate and future measures of host health. BMC Vet Res 2021; 17:258. [PMID: 34325697 PMCID: PMC8323208 DOI: 10.1186/s12917-021-02972-0] [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: 10/30/2020] [Accepted: 07/20/2021] [Indexed: 11/29/2022] Open
Abstract
Background Mule deer rely on fat and protein stored prior to the winter season as an energy source during the winter months when other food sources are sparse. Since associated microorganisms (‘microbiota’) play a significant role in nutrient metabolism of their hosts, we predicted that variation in the microbiota might be associated with nutrient storage and overwintering in mule deer populations. To test this hypothesis we performed a 16S rRNA marker gene survey of fecal samples from two deer populations in the western United States before and after onset of winter. Results PERMANOVA analysis revealed the deer microbiota varied interactively with geography and season. Further, using metadata collected at the time of sampling, we were able to identify different fecal bacterial taxa that could potentially act as bioindicators of mule deer health outcomes. First, we identified the abundance of Collinsella (family: Coriobacteriaceae) reads as a possible predictor of poor overwintering outcomes for deer herds in multiple locations. Second, we showed that reads assigned to the Bacteroides and Mollicutes Order RF39 were both positively correlated with deer protein levels, leading to the idea that these sequences might be useful in predicting mule deer protein storage. Conclusions These analyses confirm that variation in the microbiota is associated with season-dependent health outcomes in mule deer, which may have useful implications for herd management strategies. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-021-02972-0.
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Affiliation(s)
- Hyrum S Eddington
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Courtney Carroll
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Randy T Larsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Brock R McMillan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - John M Chaston
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA.
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18
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Zhu L, Wang J, Bahrndorff S. Editorial: The Wildlife Gut Microbiome and Its Implication for Conservation Biology. Front Microbiol 2021; 12:697499. [PMID: 34234768 PMCID: PMC8256134 DOI: 10.3389/fmicb.2021.697499] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/26/2021] [Indexed: 12/29/2022] Open
Affiliation(s)
- Lifeng Zhu
- Colleges of Life Science, Nanjing Normal University, Nanjing, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Simon Bahrndorff
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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19
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Zhu L, Zhang Z, Chen H, Lamer JT, Wang J, Wei W, Fu L, Tang M, Wang C, Lu G. Gut microbiomes of bigheaded carps and hybrids provide insights into invasion: A hologenome perspective. Evol Appl 2021; 14:735-745. [PMID: 33767748 PMCID: PMC7980309 DOI: 10.1111/eva.13152] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Gut microbiomes play an essential role in host survival and local adaptation and thus can facilitate the invasion of host species. Biological invasions have been shown to be linked to the genetic properties of alien host species. It is thus plausible that the holobiont, the host, and its associated microbiome act as an entity to drive invasion success. The bighead carp and silver carp (bigheaded carps), invasive species that exhibit extensive hybridization in the Mississippi River Basin (MRB), provided a unique model to test the holobiont hypothesis of invasion. Here, we investigated the microbiomes of foreguts and hindguts in bigheaded carps and their reciprocal hybrids reared in aquaculture ponds using 16S amplicons and the associated gene prediction. We found an admixed pattern in the gut microbiome community in bigheaded carp hybrids. The hybrid gut microbiomes showed special characteristics such as relatively high alpha diversity in the foregut, an increasing dissimilarity between foreguts and hindguts, and a remarkable proportion of genes coding for putative enzymes related to their digestion of main food resources (Cyanobacteria, cellulose, and chitin). The pond-reared hybrids had advantageous features in genes coding for putative enzymes related to their diet. The above results collectively suggested that the gut microbiomes of hybrids could be beneficial to their local adaptation (e.g., food resource utilization), which might have facilitated their invasion in the MRB. The gut microbial findings, along with the intrinsic genomic features likely associated with life-history traits revealed in our recent study, provide preliminary evidence supporting the holobiont hypothesis of invasion.
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Affiliation(s)
- Lifeng Zhu
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Zheng Zhang
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Hua Chen
- Mingke Biotechnology CenterHangzhouChina
| | - James T. Lamer
- Department of Biological SciencesWestern Illinois UniversityMacombILUSA
| | - Jun Wang
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of Agriculture and Rural Affair/National Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Wenzhi Wei
- College of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Lixia Fu
- College of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Minghu Tang
- Yangzhou Hanjiang National Carp Seed FarmYangzhouChina
| | - Chenghui Wang
- Key Laboratory of Freshwater Fisheries Germplasm ResourcesMinistry of Agriculture and Rural Affair/National Demonstration Center for Experimental Fisheries ScienceEducation/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghaiChina
| | - Guoqing Lu
- Department of BiologyUniversity of Nebraska at OmahaOmahaNEUSA
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20
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Zhu Z, Sun Y, Zhu F, Liu Z, Pan R, Teng L, Guo S. Seasonal Variation and Sexual Dimorphism of the Microbiota in Wild Blue Sheep ( Pseudois nayaur). Front Microbiol 2020; 11:1260. [PMID: 32670222 PMCID: PMC7332577 DOI: 10.3389/fmicb.2020.01260] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 05/18/2020] [Indexed: 01/18/2023] Open
Abstract
Microbiota of the wild blue sheep (Pseudois nayaur) presents a seasonal variation due to different dietary selection and feeding strategies from different ecological niches chosen by different sex in summer. To address those issues, we analyzed the variation of gut microbiota based on the material from the feces, with 16S rRNA and meta-genome aimed to explore seasonal and gender differences. The results indicate that seasonal dietary changes and gender differentiation, as expected, cause the variation in sheep's gut microbiota structure. The variation of the former is more significant than the latter. Dominant Firmicutes exists a significantly higher abundance in summer than that in winter. Subordinate Bacteroides expresses no seasonal difference between the two seasons. Compared with the winter group, the summer group is featured by abundant enzymes digesting cellulose and generating short-chain fatty acids (SCFAs), such as beta-glucosidase (EC: 3.2.1.21) for cellulose digestion, and butyrate kinase (EC:2.7.2.7) in butyrate metabolism, implying that the changes of the composition in intestinal flora allow the sheep to adapt to the seasonalized dietary selection through alternated microbial functions to reach the goal of facilitating the efficiency of energy harvesting. The results also show that the blue sheep expresses a prominent sexual dimorphism in the components of gut microbiota, indicating that the two sexes have different adaptations to the dietary selection, and demands for physical and psychological purposes. Thus, this study provides an example of demonstrating the principles and regulations of natural selection and environmental adaptation.
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Affiliation(s)
- Zhaoling Zhu
- College of Wildlife and Protected Area, Key Laboratory of Conservation Biology, State Forestry Administration, Northeast Forestry University, Harbin, China.,College of Economics and Management, Jiamusi University, Jiamusi, China
| | - Yewen Sun
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
| | - Feng Zhu
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
| | - Zhensheng Liu
- College of Wildlife and Protected Area, Key Laboratory of Conservation Biology, State Forestry Administration, Northeast Forestry University, Harbin, China
| | - Ruliang Pan
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China.,School of Human Sciences, The University of Western Australia, Perth, WA, United States.,International Centre of Biodiversity and Primate Conservation, Dali University, Dali, China
| | - Liwei Teng
- College of Wildlife and Protected Area, Key Laboratory of Conservation Biology, State Forestry Administration, Northeast Forestry University, Harbin, China
| | - Songtao Guo
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
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21
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Scheelings TF, Moore RJ, Van TTH, Klaassen M, Reina RD. No correlation between microbiota composition and blood parameters in nesting flatback turtles (Natator depressus). Sci Rep 2020; 10:8333. [PMID: 32433567 PMCID: PMC7239873 DOI: 10.1038/s41598-020-65321-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/27/2020] [Indexed: 02/07/2023] Open
Abstract
The microbiota is considered critical for normal vertebrate homeostasis and it may exert its effects at a local level within the gastrointestinal tract, or systemically through the production of bacterial metabolites. To date, investigations into the role that the microbiota plays in reptile physiology are rare. To address this knowledge gap, we explored the relationship between differences in microbial communities to see if they accounted for differences in haematology and biochemistry values, in different populations of nesting flatback turtles (Natator depressus). We found that microbiota composition was not correlated to any of the blood analytes we measured in flatbacks. This study is the first of its kind in reptiles and highlights the need for further investigations to determine mechanisms by which the microbiota influences the physiology and health of reptiles.
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Affiliation(s)
- T Franciscus Scheelings
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Victoria, 3800, Australia.
| | - Robert J Moore
- School of Science, RMIT University, Bundoora West Campus, Plenty Rd, Bundoora, Victoria, 3083, Australia
| | - Thi Thu Hao Van
- School of Science, RMIT University, Bundoora West Campus, Plenty Rd, Bundoora, Victoria, 3083, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Waurn Ponds, Victoria, 3216, Australia
| | - Richard D Reina
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Victoria, 3800, Australia
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22
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Zhang Z, Hu T, Lu G, Zhu L. Lessons from bamboo-eating pandas and their gut microbiome: Gut microbiome flow and applications. Evol Appl 2020; 13:615-619. [PMID: 32211055 PMCID: PMC7086052 DOI: 10.1111/eva.12915] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 12/26/2022] Open
Abstract
The giant panda is one of the most endangered mammals in the world, and many studies have revealed their evolutionary adaptation to the local environment (e.g., dietary cellulose and cyanide) on the evidences from population genetics and their gut microbiome. Here, based on the results of our analysis of the giant panda gut microbiome, we concluded that instability and resilience are the two primary characteristics of the giant panda gut microbiome. This basic information may have an impact on giant panda conservation, as well the management of other animal species.
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Affiliation(s)
- Zheng Zhang
- College of Life Sciences Nanjing Normal University Nanjing China
| | - Ting Hu
- College of Life Sciences Nanjing Normal University Nanjing China
| | - Guoqing Lu
- Department of Biology University of Nebraska Omaha Omaha NE USA
| | - Lifeng Zhu
- College of Life Sciences Nanjing Normal University Nanjing China
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23
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Sun Y, Sun Y, Shi Z, Liu Z, Zhao C, Lu T, Gao H, Zhu F, Chen R, Zhang J, Pan R, Li B, Teng L, Guo S. Gut Microbiota of Wild and Captive Alpine Musk Deer ( Moschus chrysogaster). Front Microbiol 2020; 10:3156. [PMID: 32038587 PMCID: PMC6985557 DOI: 10.3389/fmicb.2019.03156] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/30/2019] [Indexed: 12/17/2022] Open
Abstract
As for the wild animals, their diet components are always changed, so that we have to monitor such changes by analyzing the modification of intestinal microbial community. Such effort allows us to amend their conservation strategies and tactics accordingly so that they are able to appropriately adapt to the new environment and dietary selection. In this study we focus on the gut flora of two groups of an endangered species, Alpine musk deer (Moschus chrysogaster), wild group (WG) which is compared with that of the individuals of the same species but kept in the captivities (CG), a control group. Such a project is aimed to work out whether the composition of the gut microbes has significantly been changed due to captive feedings. To do so, we used 16S rRNA amplicon sequencing to characterize gut bacteria of the musk deer from the two groups. The results show that there is a significant difference in community structure of the bacteria: WG shows significant enrichment of Firmicutes and depletion of Bacteroidetes, while CG has a significant abundance of Proteobacteria and Euryarchaeota. Metagenomics was used to analyze the differences in functional enzymes between the two groups. The related results indicate that genes in WG are mostly related to the enzymes digesting cellulose and generating short-chain fatty acids (SCFAs) for signaling pathways, but CG shows enrichment in methanogenesis, including the CO2/H2 pathway and the methylotrophic pathway. Thus, this study indicates that the Firmicutes-rich gut microbiota in the WG enables individuals to maximize their energy intake from the cellulose, and has significant abundance of Euryarchaeota and methanogenesis pathways that allow them to reduce redundant energy consumption in methane metabolism, ensuring them to adapt to the wild environments.
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Affiliation(s)
- Yewen Sun
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
| | - Yujiao Sun
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,College of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Zhihui Shi
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
| | - Zhensheng Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,Key Laboratory of Wildlife Conservation, China State Forestry Administration, Harbin, China
| | - Chang Zhao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Taofeng Lu
- Institute of Laboratory Animal Science, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hui Gao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Feng Zhu
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
| | - Rui Chen
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
| | - Jun Zhang
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
| | - Ruliang Pan
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China.,School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
| | - Liwei Teng
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Songtao Guo
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
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24
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Sun CH, Liu HY, Liu B, Yuan BD, Lu CH. Analysis of the Gut Microbiome of Wild and Captive Père David's Deer. Front Microbiol 2019; 10:2331. [PMID: 31636626 PMCID: PMC6787558 DOI: 10.3389/fmicb.2019.02331] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/24/2019] [Indexed: 12/27/2022] Open
Abstract
Père David’s deer (Elaphurus davidianus or milu) is a highly endangered species originating from China, and many deer are currently being raised in captivity for gradual re-introduction to the wild. Wild and captive deer currently live in the same region but have vastly different diets. In this study, we used 16S rRNA high-throughput sequencing to identify the healthy core microbiome in the gut of wild and captive Père David’s deer and investigate how dietary factors influence the gut microbiome by comparing their differences. A core shared gut microbiome was identified in healthy Père David’s deer, which was similar to that of other ruminants, mainly comprising the phyla Firmicutes and Bacteroidetes. There were no differences in the richness or diversity of the gut microbiome between the wild and captive deer. However, PCA and ANOSIM demonstrated clear differences in the microbial community structure between the captive and wild deer, which mainly manifested as changes in the relative abundance of 39 bacterial genera. As the majority of these genera were not dominant in the deer gut, no significant difference was detected in functional modules related to the microbiome between the two groups. Therefore, the difference in dietary factors does not appear to affect the healthy core gut microbiome between captive and wild Père David’s deer, suggesting strong co-evolution and the possibility of re-establishment in the wild. These data could guide future applications of population management in Père David’s deer conservation.
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Affiliation(s)
- Cheng-He Sun
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hong-Yi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Bin Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.,Jiangsu Dafeng Père David's Deer National Nature Reserve, Yancheng, China
| | - Bao-Dong Yuan
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.,College of Biology and Food, Shangqiu Normal University, Shangqiu, China
| | - Chang-Hu Lu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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25
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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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26
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Yao R, Xu L, Lu G, Zhu L. Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation. Evol Bioinform Online 2019; 15:1176934319848438. [PMID: 31205409 PMCID: PMC6537485 DOI: 10.1177/1176934319848438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/15/2019] [Indexed: 11/16/2022] Open
Abstract
The relationship between animal conservation and the animal gut microbiome is a hot topic in current microbial ecology research. Our group has recently revealed that the occurrence of diverse combinations of gut microbial compositions and functions (metagenomics) in Père David's deer (Elaphurus davidianus) populations is likely to lead to increased evolutionary potential and resilience in response to environmental changes. Thus, considering the effects of diet on the gut microbiome and the importance of a stable gut microbial community to host health, we suggest that a transitional buffer period (with feeding on a regular diet and a diet from the translocation habitat) is needed before animal translocation. When the gut microbiome enters into relatively stable stages and adapts to the new diet from the translocation site, the time is suitable for translocation. Long-term monitoring of the gut microbiomes of translocated animals (by collecting fresh feces and carrying out next-generation sequencing) is still necessary after their translocation.
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Affiliation(s)
- Ran Yao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lianglaing Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guoqing Lu
- Department of Biology, University of Nebraska Omaha, Omaha, NE, USA
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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