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Tang K, Wang Y, Wu M, Wang S, Fu C, Zhang Z, Fu Y. Metabarcoding of fecal DNA reveals the broad and flexible diet of a globally endangered bird. Curr Zool 2023; 69:501-513. [PMID: 37637316 PMCID: PMC10449430 DOI: 10.1093/cz/zoac071] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/02/2022] [Indexed: 08/29/2023] Open
Abstract
Knowing the diet of endangered wild animals is a prerequisite for species-specific conservation and habitat management. The Sichuan partridge Arborophila rufipectus is a globally endangered Galliformes species endemic to the mountains of southwest China. Existing information on the diet of this species is biased and fragmented owing to traditional observation methods. Little is known about their dietary composition or how they respond to temporal variations in food resources throughout the year. In this study, a dietary analysis was performed on 60 fecal samples using DNA Metabarcoding of invertebrates and plants to determine the primary animal and plant components of the diet across 3 critical periods of adult life history (breeding, postbreeding wandering, and overwintering). Preys from the dipteran order, followed by the lepidopteran and araneaen spp., were the predominant, animal-derived foods. Symplocos, Rubus, Celastrus, Holboellia, and Actinidia spp. supply a large abundance of fruits and seeds for this omnivorous bird. Substantial temporal dietary changes among the 3 periods and a general shift toward lower dietary diversity during the breeding season were observed, suggesting that the Sichuan partridge can adjust their diet according to the availability of food resources and their own needs. Characterizing the composition and seasonal changes in Sichuan partridge diets informs the habitat management of native flora (the plant taxa that can generate berries and seeds, such as Symplocos, Rubus, Celastrus, and Holboellia, which are likely of conservation interest) to achieve full life-cycle conservation.
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Affiliation(s)
- Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Yufeng Wang
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Mengling Wu
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Shufang Wang
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Changkun Fu
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yiqiang Fu
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
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Oparina OS, Oparin ML, Kudryavtsev AY, Oparina AM. Characteristics of Great Bustard (Otis tarda) (Otididae, Aves) Habitats in the Trans-Volga Region according to Food Availability during the Chick Rearing Period. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022100272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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3
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Lu Z, Li S, Wang M, Wang C, Meng D, Liu J. Comparative Analysis of the Gut Microbiota of Three Sympatric Terrestrial Wild Bird Species Overwintering in Farmland Habitats. Front Microbiol 2022; 13:905668. [PMID: 35928156 PMCID: PMC9343720 DOI: 10.3389/fmicb.2022.905668] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota of wild birds are affected by complex factors, and cross-species transmission may pose challenges for the host to maintain stable gut symbionts. Farmland habitats are environments strongly manipulated by humans, and the environmental characteristics within a large area are highly consistent. These features provide the ideal natural conditions for conducting cross-species comparative studies on gut microbiota among wild birds. This study aimed to investigate and compare the gut microbiota of three common farmland-dependent bird species, Great Bustard (Otis tarda dybowskii), Common Crane (Grus grus), and Common Coot (Fulica atra), in a homogeneous habitat during the wintering period. The results indicated that under the combined action of similar influencing factors, the gut microbiota of different host species did not undergo adaptive convergence, maintained relatively independent structures, and exhibited host-driven signals. In addition, we also detected various pathogenic genera that may cause outbreaks of periodic infections among sympatric migratory birds. We conclude that phylosymbiosis may occur between some wild birds and their gut microbiota. Usage of non-invasive methods to monitor the changes in the gut microbiota of wild bird fecal samples has important implications for the conservation of endangered species.
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Affiliation(s)
- Zhiyuan Lu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Sisi Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Derong Meng
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- *Correspondence: Jingze Liu,
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4
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Lu Z, Li S, Li H, Wang Z, Meng D, Liu J. The gut microbiota of wild wintering great bustard ( Otis tarda dybowskii): survey data from two consecutive years. PeerJ 2021; 9:e12562. [PMID: 34909281 PMCID: PMC8641483 DOI: 10.7717/peerj.12562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/07/2021] [Indexed: 01/08/2023] Open
Abstract
Background The composition of the intestinal microbiota plays a significant role in modulating host health. It serves as a sensitive evaluation indicator and has substantial implications in protecting endangered species. Great Bustards are typical farmland-dependent wintering birds that are highly susceptible to the interference of human activities. However, information regarding their gut microbiota remains scarce. Methods To ensure a comprehensive analysis of this crucial data, we collected fecal samples from wild Great Bustards at their wintering habitat for two consecutive years. High-throughput sequencing of the 16S rRNA gene was subsequently applied to characterize their core gut microbiota and determine whether the gut microbial composition was similar or varied interannually. Results The gut microbiota of the Great Bustard was primarily comprised of four phyla: Firmicutes (82.87%), Bacteroidetes (7.98%), Proteobacteria (4.49%), and Actinobacteria (3.67%), accounting for 99.01% of the microbial community in all samples. Further analysis revealed 22 genera of core microbes and several pathogens. Notably, there were no significant differences in the alpha-diversity and beta-diversity between the two sample groups from different years. Conclusions This study provides essential information for assessing the health and developing targeted protective measures of this threatened species.
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Affiliation(s)
- Zhiyuan Lu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.,College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Sisi Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.,Hebei Key Laboratory of Wetland Ecology and Conservation, Hengshui, China
| | - Hongxia Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhucheng Wang
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Derong Meng
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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5
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Zhuo Y, Kessler M, Wang M, Xu W, Xu F, Yang W. Habitat suitability assessment for the Great Bustard Otis tarda tarda in Tacheng Basin, western China. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Liu G, Zhang S, Zhao X, Li C, Gong M. Advances and Limitations of Next Generation Sequencing in Animal Diet Analysis. Genes (Basel) 2021; 12:genes12121854. [PMID: 34946803 PMCID: PMC8701983 DOI: 10.3390/genes12121854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 02/07/2023] Open
Abstract
Diet analysis is a critical content of animal ecology and the diet analysis methods have been constantly improving and updating. Contrary to traditional methods of high labor intensity and low resolution, the next generation sequencing (NGS) approach has been suggested as a promising tool for dietary studies, which greatly improves the efficiency and broadens the application range. Here we present a framework of adopting NGS and DNA metabarcoding into diet analysis, and discuss the application in aspects of prey taxa composition and structure, intra-specific and inter-specific trophic links, and the effects of animal feeding on environmental changes. Yet, the generation of NGS-based diet data and subsequent analyses and interpretations are still challenging with several factors, making it possible still not as widely used as might be expected. We suggest that NGS-based diet methods must be furthered, analytical pipelines should be developed. More application perspectives, including nutrient geometry, metagenomics and nutrigenomics, need to be incorporated to encourage more ecologists to infer novel insights on they work.
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Affiliation(s)
- Gang Liu
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Shumiao Zhang
- Beijing Milu Ecological Research Center, Beijing 100076, China;
| | - Xinsheng Zhao
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Chao Li
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
| | - Minghao Gong
- Key Laboratory of Wetland Ecological Function and Restoration in Beijing City, Wetland Research Institute of Chinese Academy of Forestry Sciences, Beijing 100091, China; (G.L.); (X.Z.); (C.L.)
- Correspondence: ; Tel.: +86-010-62884159
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7
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Li C, Liu Y, Gong M, Zheng C, Zhang C, Li H, Wen W, Wang Y, Liu G. Diet-induced microbiome shifts of sympatric overwintering birds. Appl Microbiol Biotechnol 2021; 105:5993-6005. [PMID: 34272578 DOI: 10.1007/s00253-021-11448-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/21/2021] [Accepted: 06/27/2021] [Indexed: 11/29/2022]
Abstract
Gut microbiota have a significant impact on host physiology and health, and host genetics and diet are considered as two important factors, but it is difficult to discriminate the influence of each single factor (host or diet) on gut microbiota under natural conditions. Moreover, current studies of avian microbiota mainly focus on domestic or captive birds, and it is still uncertain how host and diet take part in changing avian gut microbiota composition, diversity, and function in the wild. Here, high-throughput sequencing of 16S rRNA was used to identify the gut microbiota communities for sympatric wintering Great Bustards and Common Cranes at different diets. The results showed that 8.87% operational taxonomic units (OTUs) were shared among all sampling birds; in contrast, 39.43% of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways were common among all individuals, indicating the existence of gut microbiota conservatism both in microbiota structure and function. Microbiota abundance and diversity differed between Great Bustards and Common Cranes in a specific wintering site, and microbiota variation was detected for the same host species under two different sites, suggesting that the change of gut microbiota was induced by both host and diet. Furthermore, we found that changes of both microbial communities and functional pathways were larger between hosts than those between diets, which revealed that host might be the dominant factor determining microbiota characteristics and function, while diet further drove the divergence of gut microbiota. Gut microbiota functions appeared to be more conserved than bacterial community structure, indicating that different bacteria may function in a similar way, while microbiota OTU diversity might not be necessarily associated with functional diversity. With diet shifting, gut microbiota changed both in terms of microbial communities and functional pathways for the sympatric birds, which implies that avian habitats and their physiological microbiota would be influenced by different farmland management regimes. KEY POINTS: • Gut microbiota can be shaped by both diets and hosts in sympatric species. • Host was the dominant factor shaping the gut microbiota communities and functional pathways. • Gut microbiota were conservative both in structure and in function, but more conservative in function.
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Affiliation(s)
- Chao Li
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yan Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China
| | - Minghao Gong
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Changming Zheng
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, 100044, China
| | - Huixin Li
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wanyu Wen
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yuhang Wang
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Gang Liu
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China.
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8
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Liu G, Meng D, Gong M, Li H, Wen W, Wang Y, Zhou J. Effects of Sex and Diet on Gut Microbiota of Farmland-Dependent Wintering Birds. Front Microbiol 2020; 11:587873. [PMID: 33262746 PMCID: PMC7688461 DOI: 10.3389/fmicb.2020.587873] [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: 08/05/2020] [Accepted: 10/19/2020] [Indexed: 01/17/2023] Open
Abstract
Gut microbiota plays an important role for bird biological and ecological properties, and sex and diet may be important intrinsic and extrinsic factors influencing gut microbial communities. However, sex difference of gut microbiota has been rarely investigated in free-living birds, and it remains unclear how sex and diet interactively affect avian gut microbiota composition and diversity, particularly under natural conditions. Here we used non-invasive molecular sexing technique to sex the fecal samples collected from two wintering sites of Great Bustard, which is the most sexually dimorphic among birds, as well as a typical farmland-dependent wintering bird. High-throughput sequencing of 16S was applied to identify the gut microbiota communities for both sexes under two diets (wheat_corn and rice_peanut). The results showed that 9.74% of common microbiota taxa was shared among four groups (sex vs. diet), revealing the conservatism of gut microbiota. Microbiota diversity, composition and abundance varied on different diets for male and female Great Bustards, suggesting that the gut microbiota was interactively influenced by both sex and diet. Under the wheat_corn diet, females had higher abundances of the phylum Verrucomicrobia than males, but lower Bacteroidetes and Firmicutes compared to males; meanwhile, the microbiota diversity and evenness were higher for males than females. In contrast, under the rice_peanut diet, females were more colonized by the phylum Firmicutes than males, but less by the phylum Bacteroidetes; while males had lower microbiota diversity and evenness than females. This study investigated the impacts of sex and diet on microbiota of Great Bustards, and highlights the need of new studies, perhaps with the same methodology, taking into account bird ages, flock size, breeding or health status, which will contribute to the understanding of ecology and conservation of this vulnerable species.
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Affiliation(s)
- Gang Liu
- Research Institute of Wetland, Chinese Academy of Forestry, Beijing, China.,Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
| | - Derong Meng
- Biology Department of Cangzhou Normal College, Cangzhou, China
| | - Minghao Gong
- Research Institute of Wetland, Chinese Academy of Forestry, Beijing, China.,Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
| | - Huixin Li
- Research Institute of Wetland, Chinese Academy of Forestry, Beijing, China.,Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
| | - Wanyu Wen
- Research Institute of Wetland, Chinese Academy of Forestry, Beijing, China.,Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
| | - Yuhang Wang
- Research Institute of Wetland, Chinese Academy of Forestry, Beijing, China.,Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
| | - Jingying Zhou
- Tumuji National Nature Reserve, Inner Mongolia, China
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9
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da Silva LP, Mata VA, Lopes PB, Lopes RJ, Beja P. High-resolution multi-marker DNA metabarcoding reveals sexual dietary differentiation in a bird with minor dimorphism. Ecol Evol 2020; 10:10364-10373. [PMID: 33072265 PMCID: PMC7548197 DOI: 10.1002/ece3.6687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/25/2020] [Accepted: 07/28/2020] [Indexed: 11/11/2022] Open
Abstract
Although sexual dietary differentiation is well known in birds, it is usually linked with significant morphological dimorphism between males and females, with lower differentiation reported in sexually monomorphic or only slightly dimorphic species. However, this may be an artifact of poor taxonomic resolution achieved in most conventional dietary studies, which may be unable to detect subtle intraspecific differentiation in prey consumption. Here, we show the power of multi‐marker metabarcoding to address these issues, focusing on a slightly dimorphic generalist passerine, the black wheatear Oenanthe leucura. Using markers from four genomic regions (18S, 16S, COI, and trnL), we analyzed fecal droppings collected from 93 adult black wheatears during the breeding season. We found that sexes were rather similar in bill and body features, though males had a slightly thicker bill and longer wings and tail than females. Diet was dominated in both sexes by a very wide range of arthropod species and a few fleshy fruits, but the overall diet diversity was higher for males than females, and there was a much higher frequency of occurrence of ants in female (58%) than male (29%) diets. We hypothesize that the observed sexual differentiation was likely related to females foraging closer to their offspring on abundant prey, while males consumed a wider variety of prey while foraging more widely. Overall, our results suggest that dietary sexual differentiation in birds may be more widespread than recognized at present and that multi‐marker DNA metabarcoding is a particularly powerful tool to unveiling such differences.
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Affiliation(s)
- Luís P da Silva
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | - Vanessa A Mata
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | | | - Ricardo J Lopes
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | - Pedro Beja
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal.,CIBIO-InBIO Research Center in Biodiversity and Genetic Resources Institute of Agronomy University of Lisbon Lisbon Portugal
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10
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Bird S, Prewer E, Kutz S, Leclerc L, Vilaça ST, Kyle CJ. Geography, seasonality, and host-associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal. Ecol Evol 2019; 9:13202-13217. [PMID: 31871639 PMCID: PMC6912892 DOI: 10.1002/ece3.5768] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/19/2019] [Accepted: 09/25/2019] [Indexed: 12/17/2022] Open
Abstract
The Canadian Arctic is an extreme environment with low floral and faunal diversity characterized by major seasonal shifts in temperature, moisture, and daylight. Muskoxen (Ovibos moschatus) are one of few large herbivores able to survive this harsh environment. Microbiome research of the gastrointestinal tract may hold clues as to how muskoxen exist in the Arctic, but also how this species may respond to rapid environmental changes. In this study, we investigated the effects of season (spring/summer/winter), year (2007-2016), and host genetic structure on population-level microbiome variation in muskoxen from the Canadian Arctic. We utilized 16S rRNA gene sequencing to characterize the fecal microbial communities of 78 male muskoxen encompassing two population genetic clusters. These clusters are defined by Arctic Mainland and Island populations, including the following: (a) two mainland sampling locations of the Northwest Territories and Nunavut and (b) four locations of Victoria Island. Between these geographic populations, we found that differences in the microbiome reflected host-associated genetic cluster with evidence of migration. Within populations, seasonality influenced bacterial diversity with no significant differences between years of sampling. We found evidence of pathogenic bacteria, with significantly higher presence in mainland samples. Our findings demonstrate the effects of seasonality and the role of host population-level structure in driving fecal microbiome differences in a large Arctic mammal.
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Affiliation(s)
- Samantha Bird
- Forensic Science ProgramTrent UniversityPeterboroughONCanada
| | - Erin Prewer
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
| | - Susan Kutz
- Faculty of Veterinary MedicineUniversity of CalgaryCalgaryABCanada
- Canadian Wildlife Health CooperativeAlberta NodeFaculty of Veterinary MedicineUniversity of CalgaryCalgaryABCanada
| | | | - Sibelle T. Vilaça
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
- Biology DepartmentTrent UniversityPeterboroughONCanada
| | - Christopher J. Kyle
- Forensic Science ProgramTrent UniversityPeterboroughONCanada
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
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11
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da Silva LP, Mata VA, Lopes PB, Pereira P, Jarman SN, Lopes RJ, Beja P. Advancing the integration of multi-marker metabarcoding data in dietary analysis of trophic generalists. Mol Ecol Resour 2019; 19:1420-1432. [PMID: 31332947 PMCID: PMC6899665 DOI: 10.1111/1755-0998.13060] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 06/16/2019] [Accepted: 06/19/2019] [Indexed: 01/01/2023]
Abstract
The application of DNA metabarcoding to dietary analysis of trophic generalists requires using multiple markers in order to overcome problems of primer specificity and bias. However, limited attention has been given to the integration of information from multiple markers, particularly when they partly overlap in the taxa amplified, and vary in taxonomic resolution and biases. Here, we test the use of a mix of universal and specific markers, provide criteria to integrate multi‐marker metabarcoding data and a python script to implement such criteria and produce a single list of taxa ingested per sample. We then compare the results of dietary analysis based on morphological methods, single markers, and the proposed combination of multiple markers. The study was based on the analysis of 115 faeces from a small passerine, the Black Wheatears (Oenanthe leucura). Morphological analysis detected far fewer plant taxa (12) than either a universal 18S marker (57) or the plant trnL marker (124). This may partly reflect the detection of secondary ingestion by molecular methods. Morphological identification also detected far fewer taxa (23) than when using 18S (91) or the arthropod markers IN16STK (244) and ZBJ (231), though each method missed or underestimated some prey items. Integration of multi‐marker data provided far more detailed dietary information than any single marker and estimated higher frequencies of occurrence of all taxa. Overall, our results show the value of integrating data from multiple, taxonomically overlapping markers in an example dietary data set.
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Affiliation(s)
- Luís P da Silva
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,CEF, Center for Functional Ecology - Science for People & the Planet, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Vanessa A Mata
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | | | - Paulo Pereira
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Simon N Jarman
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,School of Biological Sciences, University of Western Australia, Perth, WA, Australia.,Environomics Future Science Platform, CSIRO National Collections and Marine Infrastructure, Crawley, WA, Australia
| | - Ricardo J Lopes
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Pedro Beja
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, Institute of Agronomy, University of Lisbon, Lisbon, Portugal
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