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Kaczvinsky C, Levy H, Preston S, Youngflesh C, Clucas G, Lynch HJ, Hart T, Smith AL. The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins (Pygoscelis papua) in their natural environment. Sci Rep 2024; 14:17933. [PMID: 39095393 PMCID: PMC11297207 DOI: 10.1038/s41598-024-66460-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 07/01/2024] [Indexed: 08/04/2024] Open
Abstract
The microbiome is a key factor in the health, well-being, and success of vertebrates, contributing to the adaptive capacity of the host. However, the impact of geographic and biotic factors that may affect the microbiome of wild birds in polar environments is not well defined. To address this, we determined the bacterial 16S rRNA gene sequence profiles in faecal samples from pygoscelid penguin populations in the Scotia Arc, focusing on gentoo penguins. This mesopredatory group breeds in defined colonies across a wide geographic range. Since diet could influence microbiome structure, we extracted dietary profiles from a eukaryotic 18S rRNA gene sequence profile. The bacterial microbiome profiles were considered in the context of a diverse set of environmental and ecological measures. Integrating wide geographic sampling with bacterial 16S and eukaryotic 18S rRNA gene sequencing of over 350 faecal samples identified associations between the microbiome profile and a suite of geographic and ecological factors. Microbiome profiles differed according to host species, colony identity, distance between colonies, and diet. Interestingly there was also a relationship between the proportion of host DNA (in relation to total 18S rRNA gene signal) and the microbiome, which may reflect gut passage time. Colony identity provided the strongest association with differences in microbiome profiles indicating that local factors play a key role in the microbiome structure of these polar seabirds. This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. Other factors including diet and host species also associate with variation in microbiome profile, and in at least some locations, the microbiome composition varies considerably between individuals. Given the variation in penguin microbiomes associated with diverse factors there is potential for disruption of microbiome associations at a local scale that could influence host health, productivity, and immunological competence. The microbiome represents a sensitive indicator of changing conditions, and the implications of any changes need to be considered in the wider context of environmental change and other stressors.
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Affiliation(s)
- Chloe Kaczvinsky
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Hila Levy
- Office of Science and Technology Policy, Executive Office of the President, 1650 Pennsylvania Avenue, Washington, DC, 20504, USA
| | - Stephen Preston
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Casey Youngflesh
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Gemma Clucas
- Cornell Lab of Ornithology, 159 Sapsucker Woods Rd., Ithaca, NY, 14850, USA
| | - Heather J Lynch
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
- Institute for Advanced Computational Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Tom Hart
- Oxford Brookes University, Gypsy Lane, Headington, Oxford, OX3 0BP, UK.
| | - Adrian L Smith
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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Tang K, Tao L, Wang Y, Wang Q, Fu C, Chen B, Zhang Z, Fu Y. Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation. Appl Environ Microbiol 2023; 89:e0074723. [PMID: 37272815 PMCID: PMC10305732 DOI: 10.1128/aem.00747-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023] Open
Abstract
Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.
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Affiliation(s)
- Keyi Tang
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Ling Tao
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yufeng Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Qiong Wang
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Changkun Fu
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Benping Chen
- Laojunshan National Nature Reserve Administration, Pingshan, Sichuan, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yiqiang Fu
- Ministry of Education Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
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Kong Z, Wei T, Liu B, Li Y, Wang Y, Ma Z, Tian J, Li Y. Diel modifications in the oral and anal microflora of the Pygoscelis papua Penguins. BIOL RHYTHM RES 2023. [DOI: 10.1080/09291016.2023.2185388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Affiliation(s)
- Zhongren Kong
- Dalian Key Laboratory of Conservation Biology for Endangered Marine Mammals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, China
| | - Tingyu Wei
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Baozhan Liu
- Center of Eco-environmental Monitoring and Scientific Research, Administration of Ecology and Environment of Haihe River Basin and Beihai Sea Area, ministry of Ecology and Environment of People`s Republic of China, Tianjin, China
| | - Yanqiu Li
- Dalian Sun Asia Tourism Holding Co, Ltd, Dalian, Liaoning, China
| | - Yufei Wang
- Huludao City Comprehensive Law Enforcement of Agriculture, Huludao, Liaoning, China
| | - Zhi Ma
- Dalian Jinpu New Area Marine Development Affairs Service Center, Dalian, Liaoning, China
| | - Jiashen Tian
- Dalian Key Laboratory of Conservation Biology for Endangered Marine Mammals, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, China
| | - Yingdong Li
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, Liaoning, China
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Molecular dietary analysis of Adélie (Pygoscelis adeliae) and Gentoo (Pygoscelis papua) penguins breeding sympatrically on Antarctic Ardley Island using fecal DNA. Polar Biol 2022. [DOI: 10.1007/s00300-022-03051-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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