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Bensch HM, Lundin D, Tolf C, Waldenström J, Zöttl M. Environmental effects rather than relatedness determine gut microbiome similarity in a social mammal. J Evol Biol 2023; 36:1753-1760. [PMID: 37584218 DOI: 10.1111/jeb.14208] [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: 12/09/2022] [Revised: 04/27/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
In social species, group members commonly show substantial similarity in gut microbiome composition. Such similarities have been hypothesized to arise either by shared environmental effects or by host relatedness. However, disentangling these factors is difficult, because group members are often related, and social groups typically share similar environmental conditions. In this study, we conducted a cross-foster experiment under controlled laboratory conditions in group-living Damaraland mole-rats (Fukomys damarensis) and used 16S amplicon sequencing to disentangle the effects of the environment and relatedness on gut microbiome similarity and diversity. Our results show that a shared environment is the main factor explaining gut microbiome similarity, overshadowing any effect of host relatedness. Together with studies in wild animal populations, our results suggest that among conspecifics environmental factors are more powerful drivers of gut microbiome composition similarity than host genetics.
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Affiliation(s)
- Hanna M Bensch
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
- Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
| | - Daniel Lundin
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
| | - Conny Tolf
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
| | - Jonas Waldenström
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
| | - Markus Zöttl
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, Kalmar, Sweden
- Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
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Risely A, Müller-Klein N, Schmid DW, Wilhelm K, Clutton-Brock TH, Manser MB, Sommer S. Climate change drives loss of bacterial gut mutualists at the expense of host survival in wild meerkats. GLOBAL CHANGE BIOLOGY 2023; 29:5816-5828. [PMID: 37485753 DOI: 10.1111/gcb.16877] [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: 10/11/2022] [Accepted: 06/24/2023] [Indexed: 07/25/2023]
Abstract
Climate change and climate-driven increases in infectious disease threaten wildlife populations globally. Gut microbial responses are predicted to either buffer or exacerbate the negative impacts of these twin pressures on host populations. However, examples that document how gut microbial communities respond to long-term shifts in climate and associated disease risk, and the consequences for host survival, are rare. Over the past two decades, wild meerkats inhabiting the Kalahari have experienced rapidly rising temperatures, which is linked to the spread of tuberculosis (TB). We show that over the same period, the faecal microbiota of this population has become enriched in Bacteroidia and impoverished in lactic acid bacteria (LAB), a group of bacteria including Lactococcus and Lactobacillus that are considered gut mutualists. These shifts occurred within individuals yet were compounded over generations, and were better explained by mean maximum temperatures than mean rainfall over the previous year. Enriched Bacteroidia were additionally associated with TB exposure and disease, the dry season and poorer body condition, factors that were all directly linked to reduced future survival. Lastly, abundances of LAB taxa were independently and positively linked to future survival, while enriched taxa did not predict survival. Together, these results point towards extreme temperatures driving an expansion of a disease-associated pathobiome and loss of beneficial taxa. Our study provides the first evidence from a longitudinally sampled population that climate change is restructuring wildlife gut microbiota, and that these changes may amplify the negative impacts of climate change through the loss of gut mutualists. While the plastic response of host-associated microbiotas is key for host adaptation under normal environmental fluctuations, extreme temperature increases might lead to a breakdown of coevolved host-mutualist relationships.
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Affiliation(s)
- Alice Risely
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
- School of Science, Engineering, and the Environment, Salford University, Salford, UK
| | - Nadine Müller-Klein
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Dominik W Schmid
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Kerstin Wilhelm
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
| | - Tim H Clutton-Brock
- Large Animal Research Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Mammal Research Institute, University of Pretoria, Pretoria, South Africa
- Kalahari Research Trust, Kuruman River Reserve, Van Zylsrus, Northern Cape, South Africa
| | - Marta B Manser
- Mammal Research Institute, University of Pretoria, Pretoria, South Africa
- Kalahari Research Trust, Kuruman River Reserve, Van Zylsrus, Northern Cape, South Africa
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Simone Sommer
- Institute for Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany
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Bensch HM, Tolf C, Waldenström J, Lundin D, Zöttl M. Bacteroidetes to Firmicutes: captivity changes the gut microbiota composition and diversity in a social subterranean rodent. Anim Microbiome 2023; 5:9. [PMID: 36765400 PMCID: PMC9912604 DOI: 10.1186/s42523-023-00231-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND In mammals, the gut microbiota has important effects on the health of their hosts. Recent research highlights that animal populations that live in captivity often differ in microbiota diversity and composition from wild populations. However, the changes that may occur when animals move to captivity remain difficult to predict and factors generating such differences are poorly understood. Here we compare the bacterial gut microbiota of wild and captive Damaraland mole-rats (Fukomys damarensis) originating from a population in the southern Kalahari Desert to characterise the changes of the gut microbiota that occur from one generation to the next generation in a long-lived, social rodent species. RESULTS We found a clear divergence in the composition of the gut microbiota of captive and wild Damaraland mole-rats. Although the dominating higher-rank bacterial taxa were the same in the two groups, captive animals had an increased ratio of relative abundance of Firmicutes to Bacteroidetes compared to wild animals. The Amplicon Sequence Variants (ASVs) that were strongly associated with wild animals were commonly members of the same bacterial families as those strongly associated with captive animals. Captive animals had much higher ASV richness compared to wild-caught animals, explained by an increased richness within the Firmicutes. CONCLUSION We found that the gut microbiota of captive hosts differs substantially from the gut microbiota composition of wild hosts. The largest differences between the two groups were found in shifts in relative abundances and diversity of Firmicutes and Bacteroidetes.
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Affiliation(s)
- Hanna M. Bensch
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden ,Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
| | - Conny Tolf
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Jonas Waldenström
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Daniel Lundin
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Markus Zöttl
- grid.8148.50000 0001 2174 3522Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Linnaeus University, 391 82 Kalmar, Sweden ,Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
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