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Donohue ME, Hert ZL, Karrick CE, Rowe AK, Wright PC, Randriamanandaza LJ, Zakamanana F, Nomenjanahary ES, Everson KM, Weisrock DW. Lemur Gut Microeukaryotic Community Variation Is Not Associated with Host Phylogeny, Diet, or Habitat. MICROBIAL ECOLOGY 2023; 86:2149-2160. [PMID: 37133496 DOI: 10.1007/s00248-023-02233-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/26/2023] [Indexed: 05/04/2023]
Abstract
Identifying the major forces driving variation in gut microbiomes enhances our understanding of how and why symbioses between hosts and microbes evolved. Gut prokaryotic community variation is often closely associated with host evolutionary and ecological variables. Whether these same factors drive variation in other microbial taxa occupying the animal gut remains largely untested. Here, we present a one-to-one comparison of gut prokaryotic (16S rRNA metabarcoding) and microeukaryotic (18S rRNA metabarcoding) community patterning among 12 species of wild lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological niche diversity. We found that while lemur gut prokaryotic community diversity and composition vary with host taxonomy, diet, and habitat, gut microeukaryotic communities have no detectable association with any of these factors. We conclude that gut microeukaryotic community composition is largely random, while gut prokaryotic communities are conserved among host species. It is likely that a greater proportion of gut microeukaryotic communities comprise taxa with commensal, transient, and/or parasitic symbioses compared with gut prokaryotes, many of which form long-term relationships with the host and perform important biological functions. Our study highlights the importance of greater specificity in microbiome research; the gut microbiome contains many "omes" (e.g., prokaryome, eukaryome), each comprising different microbial taxa shaped by unique selective pressures.
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Affiliation(s)
- Mariah E Donohue
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA.
| | - Zoe L Hert
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Carly E Karrick
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Amanda K Rowe
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Patricia C Wright
- Department of Anthropology, Stony Brook University, Stony Brook, NY, USA
- Centre ValBio Research Station, Ranomafana, MD, USA
| | | | | | | | - Kathryn M Everson
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, 101 T.H.M. Building, Lexington, KY, 40506, USA
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Yue L, Wang C, Meng B, Xie B, Cao H, Su H, Zhang M. The Food Niche Overlap and Interspecific Relationship between the Sympatric Tibetan Macaque and Grey Snub-Nosed Monkey. Animals (Basel) 2023; 13:2536. [PMID: 37570344 PMCID: PMC10417265 DOI: 10.3390/ani13152536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Assessing the trophic niche and interspecific relationships between related species and determining how the species maintain differences in nutritional niches while coexisting in the same area are important topics in ecological research. Therefore, exploring the mechanism of food resource utilization, competition and coexistence among species distributed in the same region is important. In this study, we used fecal samples and metagenome sequencing technology to study the plant feeding habits and coexistence mechanisms of Tibetan macaques (Macaca thibetana) and grey snub-nosed monkeys (Rhinopithecus brelichi) within the same area. In the winter of 2020, we collected a total of 40 fecal samples from Tibetan macaques and grey snub-nosed monkeys; of those, 29 samples were considered valid and were analyzed using DNA metabarcoding. The results showed that in winter, Tibetan macaques consumed plants from 117 families and 184 genera, whereas grey snub-nosed monkeys consumed plants from 109 families and 165 genera. Diversity analysis revealed that there was a significant difference in the food composition of Tibetan macaques and grey snub-nosed monkeys. Tibetan macaques had a broader food niche width than grey snub-nosed monkeys at the family and genus levels. In winter, the food niches of Tibetan macaques and grey snub-nosed monkeys almost entirely overlapped (0.99). Our research provides detailed dietary data for Tibetan macaques and grey snub-nosed monkeys and valuable information that can aid in conservation efforts targeting these species.
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Affiliation(s)
- Li Yue
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
| | - Cheng Wang
- Zhangjiajie Giant Salamander National Nature Reserve Affairs Center, Zhangjiajie 427400, China
| | - Bingshun Meng
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
| | - Bo Xie
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
| | - Heqin Cao
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
| | - Haijun Su
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
| | - Mingming Zhang
- College of Forestry, Research Center for Biodiversity and Nature Conservation, Guizhou University, Guiyang 550025, China
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Schneider J, Brun L, Taberlet P, Fumagalli L, van de Waal E. Molecular assessment of dietary variation in neighbouring primate groups. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Judith Schneider
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Loïc Brun
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Inkawu Vervet Project, Mawana Game Reserve Swart Mfolozi South Africa
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine Université Grenoble Alpes, CNRS Grenoble France
- UiT – The Arctic University of Norway, Tromsø Museum Tromsø Norway
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Human Institute of Forensic Taphonomy, University Centre of Legal Medicine Lausanne‐Geneva Lausanne University Hospital and University of Lausanne Lausanne Switzerland
| | - Erica van de Waal
- Inkawu Vervet Project, Mawana Game Reserve Swart Mfolozi South Africa
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Centre for Functional Biodiversity, School of Life Sciences University of KwaZulu‐Natal Pietermaritzburg South Africa
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Brun L, Schneider J, Carrió EM, Dongre P, Taberlet P, van de Waal, Fumagalli L. Focal vs. fecal: Seasonal variation in the diet of wild vervet monkeys from observational and DNA metabarcoding data. Ecol Evol 2022; 12:e9358. [PMID: 36203642 PMCID: PMC9526031 DOI: 10.1002/ece3.9358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/12/2022] [Accepted: 09/05/2022] [Indexed: 11/08/2022] Open
Abstract
Assessing the diet of wild animals reveals valuable information about their ecology and trophic relationships that may help elucidate dynamic interactions in ecosystems and forecast responses to environmental changes. Advances in molecular biology provide valuable research tools in this field. However, comparative empirical research is still required to highlight strengths and potential biases of different approaches. Therefore, this study compares environmental DNA and observational methods for the same study population and sampling duration. We employed DNA metabarcoding assays targeting plant and arthropod diet items in 823 fecal samples collected over 12 months in a wild population of an omnivorous primate, the vervet monkey (Chlorocebus pygerythrus). DNA metabarcoding data were subsequently compared to direct observations. We observed the same seasonal patterns of plant consumption with both methods; however, DNA metabarcoding showed considerably greater taxonomic coverage and resolution compared to observations, mostly due to the construction of a local plant DNA database. We found a strong effect of season on variation in plant consumption largely shaped by the dry and wet seasons. The seasonal effect on arthropod consumption was weaker, but feeding on arthropods was more frequent in spring and summer, showing overall that vervets adapt their diet according to available resources. The DNA metabarcoding assay outperformed also direct observations of arthropod consumption in both taxonomic coverage and resolution. Combining traditional techniques and DNA metabarcoding data can therefore not only provide enhanced assessments of complex diets and trophic interactions to the benefit of wildlife conservationists and managers but also opens new perspectives for behavioral ecologists studying whether diet variation in social species is induced by environmental differences or might reflect selective foraging behaviors.
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Affiliation(s)
- Loïc Brun
- Laboratory for Conservation Biology, Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
| | - Judith Schneider
- Laboratory for Conservation Biology, Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
| | - Eduard Mas Carrió
- Laboratory for Conservation Biology, Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
| | - Pooja Dongre
- Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
- Inkawu Vervet ProjectMawana Game Reserve, Swart MfoloziKwaZulu NatalSouth Africa
| | - Pierre Taberlet
- Laboratoire d'Ecologie AlpineUniversité Grenoble Alpes, CNRSGrenobleFrance
- UiT – The Arctic University of Norway, Tromsø MuseumTromsøNorway
| | - van de Waal
- Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
- Inkawu Vervet ProjectMawana Game Reserve, Swart MfoloziKwaZulu NatalSouth Africa
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and Evolution, BiophoreUniversity of LausanneLausanneSwitzerland
- Swiss Human Institute of Forensic Taphonomy, University Centre of Legal Medicine Lausanne‐Geneva, Lausanne University Hospital and University of LausanneLausanneSwitzerland
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Donohue ME, Rowe AK, Kowalewski E, Hert ZL, Karrick CE, Randriamanandaza LJ, Zakamanana F, Nomenjanahary S, Andriamalala RY, Everson KM, Law AD, Moe L, Wright PC, Weisrock DW. Significant effects of host dietary guild and phylogeny in wild lemur gut microbiomes. ISME COMMUNICATIONS 2022; 2:33. [PMID: 37938265 PMCID: PMC9723590 DOI: 10.1038/s43705-022-00115-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 04/27/2023]
Abstract
Mammals harbor diverse gut microbiomes (GMs) that perform critical functions for host health and fitness. Identifying factors associated with GM variation can help illuminate the role of microbial symbionts in mediating host ecological interactions and evolutionary processes, including diversification and adaptation. Many mammals demonstrate phylosymbiosis-a pattern in which more closely-related species harbor more similar GMs-while others show overwhelming influences of diet and habitat. Here, we generated 16S rRNA sequence data from fecal samples of 15 species of wild lemurs across southern Madagascar to (1) test a hypothesis of phylosymbiosis, and (2) test trait correlations between dietary guild, habitat, and GM diversity. Our results provide strong evidence of phylosymbiosis, though some closely-related species with substantial ecological niche overlap exhibited greater GM similarity than expected under Brownian motion. Phylogenetic regressions also showed a significant correlation between dietary guild and UniFrac diversity, but not Bray-Curtis or Jaccard. This discrepancy between beta diversity metrics suggests that older microbial clades have stronger associations with diet than younger clades, as UniFrac weights older clades more heavily. We conclude that GM diversity is predominantly shaped by host phylogeny, and that microbes associated with diet were likely acquired before evolutionary radiations within the lemur families examined.
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Affiliation(s)
- Mariah E Donohue
- Department of Biology, University of Kentucky, Lexington, KY, USA.
| | - Amanda K Rowe
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, New York, NY, USA
| | - Eric Kowalewski
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Zoe L Hert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Carly E Karrick
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | | | | | - Stela Nomenjanahary
- Anthropobiologie et Développement Durable, Université Antananarivo, Antananarivo, Madagascar
| | - Rostant Y Andriamalala
- Anthropobiologie et Développement Durable, Université Antananarivo, Antananarivo, Madagascar
| | | | - Audrey D Law
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Luke Moe
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Patricia C Wright
- Centre ValBio Research Station, Ranomafana, Madagascar
- Department of Anthropology, Stony Brook University, Stony Brook, New York, NY, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
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Heymann EW. Opossums. An adaptive radiation of New World marsupials, by Robert S. Voss & Sharon A. Jansa. Primates 2021. [PMCID: PMC8410692 DOI: 10.1007/s10329-021-00931-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eckhard W. Heymann
- Verhaltensökologie & Soziobiologie, Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Kellnerweg 4, 37077 Göttingen, Germany
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