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Zhang B, Shi M, Xu S, Zhang H, Li Y, Hu D. Analysis on Changes and Influencing Factors of the Intestinal Microbiota of Alpine Musk Deer between the Place of Origin and Migration. Animals (Basel) 2023; 13:3791. [PMID: 38136828 PMCID: PMC10740494 DOI: 10.3390/ani13243791] [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: 10/31/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In China, the population of wild musk deer, belonging to the family Moschidae, has drastically decreased in recent years owing to human activities and environmental changes. During the 1990s, artificial breeding of Alpine musk deer was conducted in Xinglong Mountain, Gansu Province, China, and their ex situ conservation was explored for over a decade. Ex situ protection is beneficial for expanding the population of animals and maintaining their genetic diversity; however, it can also induce metabolic diseases and parasitic infections and reduce reproductive capacity. The gut microbiota of animals has a considerable impact on host energy metabolism and immune regulation, thereby playing a crucial role in the overall health and reproductive success of the host. In this study, by comparing the differences in the intestinal microbiome of the musk deer according to their place of origin and migration, the changes in their gut microbiota and the influencing factors were explored to provide a theoretical basis for monitoring the health status of the musk deer. We used 16S rRNA high-throughput sequencing technology to analyze the structure and diversity of the gut microbiota of Alpine musk deer in Gansu (G, place of origin) and Sichuan (S, place of migration). The results showed that the dominant bacteria and genera in the intestinal microbiome of captive musk deer were similar in the places of origin and migration, but significant differences were observed in their relative abundance (p < 0.05). Regarding Firmicutes and Actinobacteria, which are related to plant cellulose digestion, the relative abundance in group G was higher than that in group S; regarding Proteobacteria and Verrucomicrobia, which are related to fat and starch intake, the relative abundance in group S was higher than that in group G; the relative abundance of Bacillus and Clostridium sensu stricto, which are related to fiber digestibility, was higher in group G than in group S; the relative abundance of conditional pathogens Acinetobacter and Escherichia-Shigella was higher in group S than in group G. The results of α and β diversity analysis also showed significant differences between the two groups (p < 0.05). The ACE and Shannon indices of musk deer in group G were considerably higher than those in group S, and the Simpson index of musk deer in group S was greater than that in group G, indicating that the abundance and diversity of intestinal microbiome were higher in musk deer of Gansu than those of Sichuan. Comparison of the changes in the intestinal microbiome of the musk deer according to the place of origin and migration showed that the plant cellulose content in the food of the musk deer, the fat content in the concentrated feed, and changes in the feeding environment have an impact on the intestinal microbiome. Effective monitoring of the health and immunity of the musk deer is crucial for ensuring their overall health, which in turn will aid in formulating a scientific and reasonable management plan for their conservation.
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Affiliation(s)
- Baofeng Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Minghui Shi
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Shanghua Xu
- Guangxi Forestry Research Institute, Nanning 530002, China
| | - Haonan Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yimeng Li
- Department of Life Sciences, National Natural History Museum of China, Beijing 100050, China
| | - Defu Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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Dahl SA, Seifert J, Camarinha-Silva A, Cheng YC, Hernández-Arriaga A, Hudler M, Windisch W, König A. Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats. MICROBIAL ECOLOGY 2023; 86:3082-3096. [PMID: 37875737 PMCID: PMC10640537 DOI: 10.1007/s00248-023-02308-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023]
Abstract
Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer's rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.
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Affiliation(s)
- Sarah-Alica Dahl
- Wildlife Biology and Management Unit, Chair of Animal Nutrition and Metabolism, Technical University of Munich, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany.
| | - Jana Seifert
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 10, 70599, Stuttgart, Germany
| | - Amélia Camarinha-Silva
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 10, 70599, Stuttgart, Germany
| | - Yu-Chieh Cheng
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 10, 70599, Stuttgart, Germany
| | - Angélica Hernández-Arriaga
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 10, 70599, Stuttgart, Germany
| | - Martina Hudler
- Game Management and Wildlife Management, Weihenstephan-Triesdorf University of Applied Sciences, Hans-Carl-von-Carlowitz-Platz 3, 85354, Freising, Germany
| | - Wilhelm Windisch
- TUM School of Life Sciences, Technical University of Munich, Liesel-Beckmann-Straße 2, 85354, Freising, Germany
| | - Andreas König
- Wildlife Biology and Management Unit, Chair of Animal Nutrition and Metabolism, Technical University of Munich, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
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Pacheco-Torres I, Hernández-Sánchez D, García-De la Peña C, Tarango-Arámbula LA, Crosby-Galván MM, Sánchez-Santillán P. Analysis of the Intestinal and Faecal Bacterial Microbiota of the Cervidae Family Using 16S Next-Generation Sequencing: A Review. Microorganisms 2023; 11:1860. [PMID: 37513032 PMCID: PMC10386072 DOI: 10.3390/microorganisms11071860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
The Cervidae family has a wide distribution due to its adaptation to numerous ecological environments, which allows it to develop a diverse microbial community in its digestive tract. Recently, research has focused on the taxonomic composition and functionality of the intestinal and faecal microbiota of different cervid species worldwide, as well as their microbial diversity and variation under different associated factors such as age, sex, diet, distribution, and seasonal variation. In addition, there is special interest in knowing how cervids act as reservoirs of zoonotic pathogenic microorganisms, which represent a threat to public health. This review provides a synthesis of the growing field of microbiota determination in cervids worldwide, focusing on intestinal and faecal samples using 16S next-generation sequencing. It also documents factors influencing microbial diversity and composition, the microorganisms reported as pathogenic/zoonotic, and the perspectives regarding the conservation of these species. Knowing the interactions between bacteria and cervid health can drive management and conservation strategies for these species and help develop an understanding of their evolutionary history and the interaction with emerging disease-causing microorganisms.
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Affiliation(s)
| | | | | | | | | | - Paulino Sánchez-Santillán
- Faculty of Veterinary Medicine and Zootechnics No. 2, Autonomous University of Guerrero, Cuajinicuilapa 41940, Mexico
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Wang Y, Xu B, Chen H, Yang F, Huang J, Jiao X, Zhang Y. Environmental factors and gut microbiota: Toward better conservation of deer species. Front Microbiol 2023; 14:1136413. [PMID: 36960286 PMCID: PMC10027939 DOI: 10.3389/fmicb.2023.1136413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/16/2023] [Indexed: 03/09/2023] Open
Abstract
Thousands of microbial species inhabiting the animal gut, collectively known as the gut microbiota, play many specific roles related to host nutrient metabolism and absorption, immune regulation, and protection from pathogenic bacteria. Gut microbiota composition is affected by several internal and external factors, such as the host genotype, dietary intake, breeding environment, and antibiotic exposure. As deer species are important members for maintaining ecosystem balance, understanding the effects of multiple factors on the gut microbiota of deer species, particularly endangered ones, is crucial. In this review, we summarize and discuss the factors that significantly affect the gut microbiota of deer and present the impacts of these factors on microbial composition. In particular, we focused on the changes in gut microbiota due to dietary differences under different conditions, including seasonal changes, different geographical locations, and captivity, as well as weaning and pathogen disturbance. Understanding the correlations between gut microbiota composition and its driving factors is important for evaluating and improving the captive breeding environment for better conservation of endangered deer species, and reintroducing wild deer populations in the future.
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Affiliation(s)
- Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Bo Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Huan Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Fang Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Jinlin Huang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Xin’an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- Xin’an Jiao,
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-Food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- *Correspondence: Yunzeng Zhang,
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Lafferty DJR, McKenney EA, Gillman SJ, Kailing CD, Walimaa MC, Kailing MJ, Roell BJ. The gut microbiome of wild American marten in the Upper Peninsula of Michigan. PLoS One 2022; 17:e0275850. [PMID: 36327319 PMCID: PMC9632765 DOI: 10.1371/journal.pone.0275850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 09/25/2022] [Indexed: 11/06/2022] Open
Abstract
Carnivores are ecologically important and sensitive to habitat loss and anthropogenic disruption. Here we measured trophic level and gut bacterial composition as proxies of carnivore ecological status across the Upper Peninsula, Michigan, for wild American marten (Martes americana; hereafter marten). In contrast to studies that have focused on omnivorous and herbivorous species, we find that marten, like other carnivore species without a cecum, are dominated by Firmicutes (52.35%) and Proteobacteria (45.31%) but lack Bacteroidetes. Additionally, a majority of the 12 major bacterial genera (occurring at ≥1%) are known hydrogen producers, suggesting these taxa may contribute to host energy requirements through fermentative production of acetate. Our study suggests that live trapping and harvest methods yield similar marten gut microbiome data. In addition, preserving undisturbed forest likely impacts marten ecology by measurably increasing marten trophic level and altering the gut microbiome. Our study underscores the utility of the gut microbiome as a tool to monitor the ecological status of wild carnivore populations.
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Affiliation(s)
- Diana J. R. Lafferty
- Department of Biology, Wildlife Ecology and Conservation Science Lab, Northern Michigan University, Marquette, Michigan, United States of America
- * E-mail:
| | - Erin A. McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Sierra J. Gillman
- School of Environment and Forest Sciences, University of Washington, Seattle, Washington, United States of America
| | - Chris D. Kailing
- Department of Biology, Wildlife Ecology and Conservation Science Lab, Northern Michigan University, Marquette, Michigan, United States of America
| | - Myles C. Walimaa
- Department of Earth, Environmental, and Geographical Sciences, Wildlife Ecology and Conservation Science Lab, Northern Michigan University, Marquette, Michigan, United States of America
| | - Macy J. Kailing
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Institute for Critical Technology and Applied Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Brian J. Roell
- Michigan Department of Natural Resources, Marquette, Michigan, United States of America
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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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Soare C, McNeilly TN, Seguino A. A review of potential risk factors linked to shiga toxin-producing Escherichia coli (STEC) in wild deer populations and the practices affecting the microbial contamination of wild deer carcasses with enteric bacteria. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Alterations in gut microbiota linked to provenance, sex, and chronic wasting disease in white-tailed deer (Odocoileus virginianus). Sci Rep 2021; 11:13218. [PMID: 34168170 PMCID: PMC8225879 DOI: 10.1038/s41598-021-89896-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/04/2021] [Indexed: 01/04/2023] Open
Abstract
Chronic wasting disease (CWD) is a fatal, contagious, neurodegenerative prion disease affecting both free-ranging and captive cervid species. CWD is spread via direct or indirect contact or oral ingestion of prions. In the gastrointestinal tract, prions enter the body through microfold cells (M-cells), and the abundance of these cells can be influenced by the gut microbiota. To explore potential links between the gut microbiota and CWD, we collected fecal samples from farmed and free-ranging white-tailed deer (Odocoileus virginianus) around the Midwest, USA. Farmed deer originated from farms that were depopulated due to CWD. Free-ranging deer were sampled during annual deer harvests. All farmed deer were tested for CWD via ELISA and IHC, and we used 16S rRNA gene sequencing to characterize the gut microbiota. We report significant differences in gut microbiota by provenance (Farm 1, Farm 2, Free-ranging), sex, and CWD status. CWD-positive deer from Farm 1 and 2 had increased abundances of Akkermansia, Lachnospireacea UCG-010, and RF39 taxa. Overall, differences by provenance and sex appear to be driven by diet, while differences by CWD status may be linked to CWD pathogenesis.
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The Comparative Analysis of the Ruminal Bacterial Population in Reindeer ( Rangifer tarandus L.) from the Russian Arctic Zone: Regional and Seasonal Effects. Animals (Basel) 2021; 11:ani11030911. [PMID: 33810167 PMCID: PMC8004722 DOI: 10.3390/ani11030911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 01/08/2023] Open
Abstract
Simple Summary The reindeer (Rangifer tarandus) is a unique ruminant that lives in arctic areas characterized by severe living conditions. Low temperatures and a scarce diet containing a high proportion of hard-to-digest components have contributed to the development of several adaptations that allow reindeer to have a successful existence in the Far North region. These adaptations include the microbiome of the rumen—a digestive organ in ruminants that is responsible for crude fiber digestion through the enzymatic activity of microorganisms. In this study, research was conducted on the ruminal microbiome of reindeer of the Nenets breed living in various climatic zones of the Russian Arctic (in the Yamalo-Nenetski Autonomous District and Nenetski Autonomous District. The impacts of the habitat, season of the year, sex, and age factors on the rumen microbiome were investigated. As a result, it was found that significant differences in the reindeer ruminal microbiome composition are associated with the region of habitat and change of seasons that the reindeer are exposed to. The distinctions mainly come down to different ratios of bacteria involved in the metabolism of volatile fatty acids and cellulose decomposition in the rumen, which is apparently a reflection of the different plant components in the diet in different regions and seasons. Abstract The reindeer (Rangifer tarandus L.) is a unique animal inhabitant of arctic regions. Low ambient temperatures and scant diets (primarily, lichens) have resulted in different evolutional adaptations, including the composition of the ruminal microbiota. In the study presented here, the effects of seasonal and regional aspects of the composition of the ruminal microbiota in reindeer (Nenets breed, 38 animals) were studied (wooded tundra from the Yamalo-Nenetski Autonomous District (YNAD) vs. from the Nenetski Autonomous District (NAD)). The ruminal content of calves (n = 12) and adult animals (n = 26, 15 males and 11 females) was sampled in the summer (n = 16) and winter seasons (n = 22). The composition of the ruminal microbial population was determined by the V3–V4 16S rRNA gene region sequencing. It was found that the population was dominated by Bacteroidetes and Firmicutes phyla, followed by Spirochaetes and Verrucomicrobia. An analysis of the community using non-metric multidimensional scaling and Bray–Curtis similarity metrics provided evidence that the most influential factors affecting the composition of ruminal microbiota are the region (p = 0.001) and season (p = 0.001); heat map analysis revealed several communities that are strongly affected by these two factors. In the summer season, the following communities were significantly larger compared to in the winter season: Coriobactriaceae, Erysipelothrihaceae, and Mycoplasmataceae. The following communities were significantly larger in the winter season compared to in summer: Paraprevotellaceae, Butyrivibrio spp., Succiniclasticum spp., Coprococcus spp., Ruminococcus spp., and Pseudobutyrivibrio spp. In NAD (tundra), the following communities were significantly larger in comparison to YNAD (wooded tundra): Verrucomicrobia (Verruco-5), Anaerolinaceae, PeHg47 Planctomycetes, cellulolytic Lachnospiraceae, and Succiniclasticum spp. The following bacterial groups were significantly larger in YNAD in comparison to NAD: cellulolytic Ruminococaceae, Dehalobacteriaceae, Veillionelaceae, and Oscilospira spp. The significant differences in the ruminal microbial population were primarily related to the ingredients of diets, affected by region and season. The summer-related increases in the communities of certain pathogens (Mycoplasmataceae, Fusobacterium spp., Porphyromonas endodentalis) were found. Regional differences were primarily related to the ratio of the species involved in ruminal cellulose degradation and ruminal fatty acids metabolism; these differences reflect the regional dissimilarities in botanical diet ingredients.
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Zhao W, Ren Z, Luo Y, Cheng J, Wang J, Wang Y, Yang Z, Yao X, Zhong Z, Yang W, Wu X. Metagenomics analysis of the gut microbiome in healthy and bacterial pneumonia forest musk deer. Genes Genomics 2021; 43:43-53. [PMID: 33428153 DOI: 10.1007/s13258-020-01029-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND The forest musk deer (FMD, Moschus berezovskii) is an threatened species in China. Bacterial pneumonia was found to seriously restrict the development of FMD captive breeding. Historical evidence has demonstrated the relationship between immune system and intestinal Lactobacillus in FMD. OBJECTIVE We sought to elucidate the differences in the gut microbiota of healthy and bacterial pneumonia FMD. METHODS The bacterial pneumonia FMD was demonstrated by bacterial and pathological diagnosis, and the gut microbiome of healthy and bacterial pneumonia FMD was sequenced and analysed. RESULTS There are three pathogens (Pseudomonas aeruginosa, Streptococcus equinus and Trueperella pyogenes) isolated from the bacterial pneumonia FMD individuals. Compared with the healthy group, the abundance of Firmicutes and Proteobacteria in the pneumonia group was changed, and a high level of Proteobacteria was found in the pneumonia group. In addition, a higher abundance of Acinetobacter (p = 0.01) was observed in the population of the pneumonia group compared with the healthy group. Several potentially harmful bacteria and disease-related KEGG subsystems were only found in the gut of the bacterial pneumonia group. Analysis of KEGG revealed that many genes related to type IV secretion system, type IV pilus, lipopolysaccharide export system, HTH-type transcriptional regulator/antitoxin MqsA, and ArsR family transcriptional regulator were significantly enriched in the metagenome of the bacterial pneumonia FMD. CONCLUSION Our results demonstrated that the gut microbiome was significantly altered in the bacterial pneumonia group. Overall, our research improves the understanding of the potential role of the gut microbiota in the FMD bacterial pneumonia.
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Affiliation(s)
- Wei Zhao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 610000, Sichuan, People's Republic of China
| | - Ziwei Ren
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 610000, Sichuan, People's Republic of China
| | - Yan Luo
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 610000, Sichuan, People's Republic of China.
| | - Jianguo Cheng
- Sichuan Institute of Musk Deer Breeding, Chengdu, 610000, Sichuan, People's Republic of China
| | - Jie Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 610000, Sichuan, People's Republic of China
| | - Yin Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 610000, Sichuan, People's Republic of China
| | - Zexiao Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 610000, Sichuan, People's Republic of China
| | - Xueping Yao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 610000, Sichuan, People's Republic of China
| | - Zhijun Zhong
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 610000, Sichuan, People's Republic of China
| | - Wei Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 610000, Sichuan, People's Republic of China
| | - Xi Wu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 610000, Sichuan, People's Republic of China
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Hu X, Xu Y, Liu G, Hu D, Wang Y, Zhang W, Zheng Y. The impact of anthelmintic treatment on gut bacterial and fungal communities in diagnosed parasite-free sika deer Cervus nippon. Appl Microbiol Biotechnol 2020; 104:9239-9250. [PMID: 32930840 DOI: 10.1007/s00253-020-10838-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/24/2020] [Accepted: 08/14/2020] [Indexed: 12/28/2022]
Abstract
The gut microbiota, including both bacterial and fungal communities, plays vital roles in the gut homeostasis of animals, and antibiotics can lead to disorders of these microbial communities. The use of anthelmintic treatment to control parasitic infection has long been a standard practice, although its impact on the gut microbiota of healthy sika deer is relatively unknown. This study used next-generation sequencing based on 16S/18S/ITS rRNA genes to investigate the shifts in fecal bacterial and fungal communities in parasite-free sika deer after treatment with fenbendazole and ivermectin tablets. The α-diversity of both bacterial and fungal communities was significantly decreased (P < 0.05) after treatment, as were the bacterial genus Bacteroides and fungal genus Candida (P < 0.05). The results of β-diversity, LEfSe analysis, core community's analysis, taxonomic composition, and functional prediction of fungal and bacterial communities confirmed the substantial impacts of anthelmintic treatment on the function and structure of the intestinal microbiota of sika deer. Nevertheless, many lines of evidence, including β-diversity, LEfSe analysis and functional prediction analysis, suggested that the anthelmintics exerted more significant influences on fungal communities than on bacterial communities, suggesting that more attention should be paid to the changes in fungal communities of sika deer under anthelmintic treatment. The present study provides evidence to support the assumption that anthelmintic drugs modify the gut microbiota of deer and serves as the first trial to test the potential effects of anthelmintics on mycobiota in ruminants using high-throughput sequencing techniques. Key Points • Anthelmintic treatment showed significant effects on the gut microbiota of sika deer. • Fungi were more strongly affected by anthelmintic treatment than bacteria. • The profile of mycobiota provides essential data that were previously absent.
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Affiliation(s)
- Xiaolong Hu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yongtao Xu
- College of forestry, Jiangxi Agricultural University, Nanchang, China
| | - Gang Liu
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Defu Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yihua Wang
- Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Weiwei Zhang
- College of forestry, Jiangxi Agricultural University, Nanchang, China.
| | - Yunlin Zheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China.
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12
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Maquia IS, Fareleira P, Videira e Castro I, Brito DRA, Soares R, Chaúque A, Ferreira-Pinto MM, Lumini E, Berruti A, Ribeiro NS, Marques I, Ribeiro-Barros AI. Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion. Microorganisms 2020; 8:E1291. [PMID: 32846974 PMCID: PMC7563409 DOI: 10.3390/microorganisms8091291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 01/19/2023] Open
Abstract
(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.
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Affiliation(s)
- Ivete Sandra Maquia
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
- TropiKMan Doctoral Program, Nova School of Business & Economics (Nova SBE), 2775-405 Carcavelos, Portugal
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Paula Fareleira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Isabel Videira e Castro
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Denise R. A. Brito
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Ricardo Soares
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Aniceto Chaúque
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - M. Manuela Ferreira-Pinto
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Erica Lumini
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Andrea Berruti
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Natasha S. Ribeiro
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - Isabel Marques
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Ana I. Ribeiro-Barros
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
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13
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Valdebenito JO, Martínez-de la Puente J, Castro M, Pérez-Hurtado A, Tejera G, Székely T, Halimubieke N, Schroeder J, Figuerola J. Association of insularity and body condition to cloacal bacteria prevalence in a small shorebird. PLoS One 2020; 15:e0237369. [PMID: 32804958 PMCID: PMC7430747 DOI: 10.1371/journal.pone.0237369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/23/2020] [Indexed: 11/18/2022] Open
Abstract
Do islands harbour less diverse disease communities than mainland? The island biogeography theory predicts more diverse communities on mainland than on islands due to more niches, more diverse habitats and availability of greater range of hosts. We compared bacteria prevalences of Campylobacter, Chlamydia and Salmonella in cloacal samples of a small shorebird, the Kentish plover (Charadrius alexandrinus) between two island populations of Macaronesia and two mainland locations in the Iberian Peninsula. Bacteria were found in all populations but, contrary to the expectations, prevalences did not differ between islands and mainland. Females had higher prevalences than males for Salmonella and when three bacteria genera were pooled together. Bacteria infection was unrelated to bird’s body condition but females from mainland were heavier than males and birds from mainland were heavier than those from islands. Abiotic variables consistent throughout breeding sites, like high salinity that is known to inhibit bacteria growth, could explain the lack of differences in the bacteria prevalence between areas. We argue about the possible drivers and implications of sex differences in bacteria prevalence in Kentish plovers.
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Affiliation(s)
- José O. Valdebenito
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- * E-mail:
| | - Josué Martínez-de la Puente
- Department of Wetland Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Seville, Spain
| | - Macarena Castro
- Instituto Universitario de Investigación Marina, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, Spain
| | - Alejandro Pérez-Hurtado
- Instituto Universitario de Investigación Marina, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, Spain
| | - Gustavo Tejera
- Canary Islands’ Ornithology and Natural History Group (GOHNIC), Buenavista del Norte, Tenerife, Canary Islands, Spain
| | - Tamás Székely
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
- Departmen of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary
| | | | - Julia Schroeder
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Jordi Figuerola
- Department of Wetland Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Seville, Spain
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14
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Ricci S, Sandfort R, Pinior B, Mann E, Wetzels SU, Stalder G. Impact of supplemental winter feeding on ruminal microbiota of roe deer Capreolus capreolus. WILDLIFE BIOLOGY 2019. [DOI: 10.2981/wlb.00572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Sara Ricci
- S. Ricci and G. Stalder ✉ , Res. Inst. of Wildlife Ecology, Dept of Interdisciplinary Life Sciences, Univ. of Veterinary Medicine, Austria, Savoyenstraße 1, AU-1160 Vienna, Austria. SR also at: Univ. of Camerino, Ca
| | - Robin Sandfort
- R. Sandfort, Inst. of Wildlife Biology and Game Management, Univ. of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Beate Pinior
- B. Pinior, Inst. for Veterinary Public Health, Dept for Farm Animals and Veterinary Public Health, Univ. of Veterinary Medicine, Vienna, Austria
| | - Evelyne Mann
- E. Mann and S. U. Wetzels, Inst. of Milk Hygiene, Milk Technology and Food Science, Dept for Farm Animal and Public Health in Veterinary Medicine, Univ. of Veterinary Medicine, Vienna, Austria
| | - Stefanie U. Wetzels
- E. Mann and S. U. Wetzels, Inst. of Milk Hygiene, Milk Technology and Food Science, Dept for Farm Animal and Public Health in Veterinary Medicine, Univ. of Veterinary Medicine, Vienna, Austria
| | - Gabrielle Stalder
- S. Ricci and G. Stalder ✉ , Res. Inst. of Wildlife Ecology, Dept of Interdisciplinary Life Sciences, Univ. of Veterinary Medicine, Austria, Savoyenstraße 1, AU-1160 Vienna, Austria. SR also at: Univ. of Camerino, Ca
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15
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Li J, Zhan S, Liu X, Lin Q, Jiang J, Li X. Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae. Front Microbiol 2018; 9:1823. [PMID: 30214431 PMCID: PMC6125396 DOI: 10.3389/fmicb.2018.01823] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Gastrointestinal microbiota may shape the adaptation of their hosts to different habitats and lifestyles, thereby driving their evolutionary diversification. It remains unknown if gastrointestinal microbiota diverge in congruence with the phylogenetic relationships of their hosts. To evaluate the phylosymbiotic relationships, here we analyzed the compositions of fecal microbiota of seven Cervinae species raised in the Chengdu Zoo. All sampled animals were kept in the same environmental condition and fed identical fodder for years. Results showed that Firmicutes and Bacteroidetes were dominant in their fecal microbiota. Even though some bacteria (e.g., Ruminococcaceae) were found to be common in the feces of all investigated species, some genera (e.g., Sharpea and Succinivibrio) were only observed in animals with particular digestive systems. As for the intraspecies variations of microbial communities, only a few operational taxonomic units (OTUs) were shared among replicates of the same host species although they accounted for most of the total abundance. Correlation was observed between the fecal microbiota divergence and host phylogeny, but they were not congruent completely. This may shed new light on the coevolution of host species and their microbiota.
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Affiliation(s)
- Jiaying Li
- Key Laboratory of Environmental and Applied Microbiology - Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | | | - Xuanzhen Liu
- Chengdu Zoo, Chengdu Institute of Wildlife, Chengdu, China
| | - Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology - Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jianping Jiang
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangzhen Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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16
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Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J. Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 2018; 11:1094-1119. [PMID: 30026800 PMCID: PMC6050181 DOI: 10.1111/eva.12600] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/02/2018] [Indexed: 12/12/2022] Open
Abstract
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
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Affiliation(s)
- Emma L. Carroll
- Scottish Oceans Institute and Sea Mammal Research UnitUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places Research InstituteCardiff UniversityCardiff, WalesUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Gregoire Leroy
- Animal Production and Health DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Alan Strand
- Grice Marine LaboratoryDepartment of BiologyCollege of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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17
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Hu X, Liu G, Li Y, Wei Y, Lin S, Liu S, Zheng Y, Hu D. High-Throughput Analysis Reveals Seasonal Variation of the Gut Microbiota Composition Within Forest Musk Deer ( Moschus berezovskii). Front Microbiol 2018; 9:1674. [PMID: 30093891 PMCID: PMC6070636 DOI: 10.3389/fmicb.2018.01674] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/04/2018] [Indexed: 01/08/2023] Open
Abstract
The gut microbiota plays a key role in the nutritional ecology of ruminants, and host diet has a significant effect on these microbial communities. Longitudinal studies assessing variation of seasonal microbiota in animals can provide a comparative context for interpreting the adaptive significance of such changes. However, few studies have investigated the effects of seasonally-related dietary shifts on the gut microbial communities of endangered forest musk deer (FMD), and the national breeding programs need this information to promote the growth of captive populations. The present study applied bacterial 16S rRNA genes based on high-throughput sequencing to profile the fecal microbial communities of FMD across four seasons. Microbial diversity was higher in seasons with dry leaf diets (winter and spring) compared to seasons with fresh leaf diets (summer and autumn). The dominant microbial phyla were Firmicutes and Bacteroidetes, and the core bacterial taxa also comprised mostly (94.40% of shared OTUs) Firmicutes (37 taxa) and Bacteroidetes (6 taxa), which were relatively stable across different seasons. The Firmicutes-Bacteroidetes ratio declined in seasons with fresh leaf diets relative to seasons with dry leaf diets, and the dominant genera among the four seasons showed no significant variation in abundance. This work explores the seasonal variation in the microbial communities of FMD for the first time, and reveals how gut microbial community dynamics vary seasonally in accordance with differences in dietary plants (fresh and dry leaf). These results indicate that the annual cyclic reconfiguration of FMD gut microbiota could be associated with shifts in dietary nutrients, which is important information to inform captive FMD management.
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Affiliation(s)
- Xiaolong Hu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Gang Liu
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Yimeng Li
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yuting Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Shaobi Lin
- Zhangzhou Pien Tze Huang Pharmaceutical, Co., Ltd., Zhangzhou, China
| | - Shuqiang Liu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yunlin Zheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Defu Hu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
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