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Giacomini A, Lakim MB, Tuh FYY, Hitchings M, Consuegra S, Webster TU, Wells K. Host-Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban-Rural Ecotone. Mol Ecol 2025; 34:e17782. [PMID: 40289691 PMCID: PMC12100590 DOI: 10.1111/mec.17782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Revised: 04/15/2025] [Accepted: 04/17/2025] [Indexed: 04/30/2025]
Abstract
Global change and urbanisation profoundly alter wildlife habitats, driving native animals into novel habitats while increasing the co-occurrence between native and invasive species. Host-microbiome associations are shaped by host traits and environmental features, but little is known about their plasticity in co-occurring native and invasive species across urban-rural gradients. Here, we explored gut microbiomes of four sympatric small mammal species along an urban-rural ecotone in Borneo, one of the planet's oldest rainforest regions experiencing recent urban expansion. Host species identity was the strongest determinant of microbiome composition, while land use and spatial proximity shaped microbiome similarity within and among the three rat species. The urban-dwelling rat Rattus rattus had a microbiome composition more similar to that of the native, urban-adapted rat Sundamys muelleri (R. rattus' strongest environmental niche overlap), than to the closely related urban-dwelling R. norvegicus. The urban-dwelling shrew Suncus murinus presented the most distinct microbiome. The microbiome of R. norvegicus was the most sensitive to land use intensity, exhibiting significant alterations in composition and bacterial abundance across the ecotone. Our findings suggest that environmental niche overlap among native and invasive species promotes similar gut microbiomes. Even for omnivorous urban-dwellers with a worldwide distribution like R. norvegicus, gut microbiomes may change across fine-scale environmental gradients. Future research needs to confirm whether land use intensity can be a strong selective force on mammalian gut microbiomes, influencing the way in which native and invasive species are able to exploit novel environments.
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Affiliation(s)
| | | | | | | | - Sofia Consuegra
- Department of BiosciencesSwansea UniversitySwanseaUK
- Laboratorio de Biotecnología AcuáticaInstituto de Investigaciones Marinas (IIM‐CSIC)VigoSpain
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2
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Li J, Shao Z, Cheng K, Yang Q, Ju H, Tang X, Zhang S, Li J. Coral-associated Symbiodiniaceae exhibit host specificity but lack phylosymbiosis, with Cladocopium and Durusdinium showing different cophylogenetic patterns. THE NEW PHYTOLOGIST 2025. [PMID: 40317738 DOI: 10.1111/nph.70184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Accepted: 04/09/2025] [Indexed: 05/07/2025]
Abstract
Altering the composition of the Symbiodiniaceae community to adapt to anomalous sea water warming represents a potential survival mechanism for scleractinian corals. However, the processes of Symbiodiniaceae assembly and long-standing evolution of coral-Symbiodiniaceae interactions remain unclear. Here, we utilized ITS2 (internal transcribed spacer 2) amplicon sequencing and the SymPortal framework to investigate the diversity and specificity of Symbiodiniaceae across 39 scleractinian coral species. Furthermore, we tested phylosymbiosis and cophylogeny between coral hosts and their Symbiodiniaceae. In our study, environmental samples exhibited the highest Symbiodiniaceae diversity. Cladocopium and Durusdinium dominated the Symbiodiniaceae communities, with significant β-diversity differences among coral species. Additionally, host specificity was widespread in Symbiodiniaceae, especially Durusdinium spp., yet lacked a phylosymbiotic pattern. Moreover, Cladocopium spp. showed cophylogenetic congruence with their hosts, while there was no evidence for Durusdinium spp. Furthermore, host switching was the predominant evolutionary event, implying its contribution to Cladocopium diversification. These findings suggest that Symbiodiniaceae assembly does not recapitulate host phylogeny, and host specificity alone does not drive phylosymbiosis or cophylogeny. As environmental reservoirs, free-living Symbiodiniaceae may influence symbiotic communities. Additionally, Durusdinium-coral associations lack cophylogenetic signals, indicating more flexible partnerships than Cladocopium. Overall, our results enhance understanding of Symbiodiniaceae assembly and coral-Symbiodiniaceae evolutionary interactions.
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Affiliation(s)
- Jiaxin Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Zhuang Shao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Keke Cheng
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Huimin Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xiaoyu Tang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Sanya National Marine Ecosystem Research Station, Chinese Academy of Sciences, Sanya, 572000, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Sanya National Marine Ecosystem Research Station, Chinese Academy of Sciences, Sanya, 572000, China
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Liu Y, Li X, Kormas KA, Li Y, Li H, Li J. Variable phylosymbiosis and cophylogeny patterns in wild fish gut microbiota of a large subtropical river. mSphere 2025; 10:e0098224. [PMID: 40152595 PMCID: PMC12039269 DOI: 10.1128/msphere.00982-24] [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: 11/20/2024] [Accepted: 02/25/2025] [Indexed: 03/29/2025] Open
Abstract
The persistence and specificity of fish host-microbial interaction during evolution is an important part of exploring the host-microbial symbiosis mechanism. However, it remains unclear how the environmental and host factors shape fish host-microbe symbiotic relationships in subtropical rivers with complex natural environments. Freshwater fish are important consumers in rivers and lakes and are considered keystone species in maintaining the stability of food webs there. In this study, patterns and mechanisms shaping gut microbiota community in 42 fish species from the Pearl River, in the subtropical zone of China, were investigated. The results showed that fish host specificity is a key driver of gut microbiota evolution and diversification. Different taxonomic levels of the host showed different degrees of contribution to gut microbiota variation. Geographical location and habitat type were the next most important factors in shaping gut microbiota across the 42 fishes, followed by diet and gut trait. Our results emphasized the contribution of stochastic processes (drift and homogenizing dispersal) in the gut microbial community assembly of freshwater fishes in the middle and lower reaches of the Pearl River. Phylosymbiosis is evident at both global and local levels, which are jointly shaped by complex factors including ecological or host physiological filtration and evolutionary processes. The core microbiota showed co-evolutionary relationships of varying degrees with different taxonomic groups. We speculate that host genetic isolation or habitat variation facilitates the heterogeneous selection (deterministic process), which occurs and results in different host-core bacterium specificity. IMPORTANCE Freshwater fish are regarded as the dominant consumers in rivers and lakes. Due to their diverse feeding modes, fish significantly enhance the trophic link and nutrient recycling/retention in aquatic habitats. For this, they are often considered keystone species in maintaining the stability of food webs in rivers and lakes. A significant part of fish nutrition is essentially mediated by their gut microbiota, which can enhance fish tolerance to fluctuations in external resources and improve the efficiency of nutrients extracted from various food sources. As gut bacterial symbionts have a profound impact on the nutrition and development of their hosts, as well as their overall fitness, it is critical to answer the question of how hosts maintain these benefits by procuring or inheriting these vital symbionts, which is still largely unanswered, especially for freshwater fish. Our study provides new insights into the co-evolutionary relationship between wild fish and their symbiotic microbiome, the hidden diversity of gut microbiome, and the ecological adaptation potential of wild freshwater fish.
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Affiliation(s)
- Yaqiu Liu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Xinhui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Konstantinos Ar. Kormas
- Department of Ichthyology & Aquatic Environment, University of Thessaly, Volos, Thessalia Sterea Ellada, Greece
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Huifeng Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
- Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou, Guangdong, China
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Li Y, Liu C, Wang Y, Li M, Zou S, Hu X, Chen Z, Li M, Ma C, Obi CJ, Zhou X, Zou Y, Tang M. Urban wild bee well-being revealed by gut metagenome data: A mason bee model. INSECT SCIENCE 2025. [PMID: 40287860 DOI: 10.1111/1744-7917.70051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 02/18/2025] [Accepted: 03/07/2025] [Indexed: 04/29/2025]
Abstract
Wild bees are ecologically vital but increasingly threatened by anthropogenic activities, leading to uncertain survival and health outcomes in urban environments. The gut microbiome contains features indicating host health and reflecting long-term evolutionary adaptation and acute reactions to real-time stressors. Moving beyond bacteria, we propose a comprehensive analysis integrating diet, bacteriome, virome, resistome, and their association to understand the survival status of urban lives better. We conducted a study on mason bees (Osmia excavata) across 10 urban agricultural sites in Suzhou, China, using shotgun gut metagenome sequencing for data derived from total gut DNA. Our findings revealed that most ingested pollen originated from Brassica crops and the unexpected garden tree Plantanus, indicating that floral resources at the 10 sites supported Osmia but with limited plant diversity. Varied city landscapes revealed site-specific flowers that all contributed to Osmia sustenance. The gut bacterial community, dominated by Gammaproteobacteria, showed remarkable structural stability across 8 sites but suggested perturbations at 2 sites. Antibiotic resistance gene profiles highly varied across 10 sites with prevalent unclassified drug classes, highlighting environmental threats to both bees and humans. The virome analysis identified honeybee pathogens, suggesting potential virus spillover. Many unknown bacteriophages were detected, some of which targeted the core gut bacteria, underscoring their role in maintaining gut homeostasis. These multifaceted metagenomic insights hold the potential to predict bee health and identify environmental threats, thereby guiding probiotic development and city management for effective bee conservation.
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Affiliation(s)
- Yiran Li
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Chengweiran Liu
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Yiran Wang
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Muhan Li
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Shasha Zou
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Xingyu Hu
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Zhiwei Chen
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Mingrui Li
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Changsheng Ma
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
- Key Laboratory of Pesticide Assessment, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Chinonye Jennifer Obi
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yi Zou
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
| | - Min Tang
- Department of Biosciences and Bioinformatics, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu Province, China
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5
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Carruthers LV, Nordmeyer SC, Anderson TJ, Chevalier FD, Le Clec'h W. Organ-specific microbiomes of Biomphalaria snails. Anim Microbiome 2025; 7:40. [PMID: 40275375 PMCID: PMC12023355 DOI: 10.1186/s42523-025-00403-1] [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: 08/15/2024] [Accepted: 04/01/2025] [Indexed: 04/26/2025] Open
Abstract
BACKGROUND The microbiome is increasingly recognized to shape many aspects of its host biology and is a key determinant of health and disease. The microbiome may influence transmission of pathogens by their vectors, such as mosquitoes or aquatic snails. We previously sequenced the V4 region of the bacterial 16S rRNA gene from the hemolymph (blood) of Biomphalaria spp. snails, vectors of the human blood fluke (schistosomes). We showed that snail hemolymph harbored an abundant and diverse microbiome. This microbiome is distinct from the water environment and can discriminate snail species and populations. As hemolymph bathes snail organs, we then investigated the heterogeneity of the microbiome in these organs. RESULTS We dissected ten snails for each of two different species (B. alexandrina and B. glabrata) and collected their hemolymph and organs (ovotestis, hepatopancreas, gut, and stomach). We also ground in liquid nitrogen four whole snails of each species. We sampled the water in which the snails were living (environmental controls). Sequencing the 16S rRNA gene revealed organ-specific microbiomes. These microbiomes harbored a lower diversity than the hemolymph microbiome, and the whole-snail microbiome. The organ microbiomes tend to cluster by physiological function. In addition, we showed that the whole-snail microbiome is more similar to hemolymph microbiome. CONCLUSIONS These results are critical for future work on snail microbiomes and show the necessity of sampling individual organ microbiomes to provide a complete description of snail microbiomes.
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Affiliation(s)
- Lauren V Carruthers
- School of Infection and Immunity, University of Glasgow, Glasgow, G12 8TA, UK
- Keltic Pharma Therapeutics, The Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, G11 6EW, UK
| | | | - Timothy Jc Anderson
- Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, 78245, USA
| | - Frédéric D Chevalier
- Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, 78245, USA.
| | - Winka Le Clec'h
- Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, 78245, USA.
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6
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Melero-Jiménez IJ, Sorokin Y, Merlin A, Li J, Couce A, Friedman J. Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium. Nat Commun 2025; 16:3482. [PMID: 40216843 PMCID: PMC11992082 DOI: 10.1038/s41467-025-58742-1] [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: 07/16/2024] [Accepted: 04/01/2025] [Indexed: 04/14/2025] Open
Abstract
Populations facing lethal environmental change can escape extinction through rapid genetic adaptation, a process known as evolutionary rescue. Despite extensive study, evolutionary rescue is largely unexplored in mutualistic communities, where it is likely constrained by the less adaptable partner. Here, we explored empirically the likelihood, population dynamics, and genetic mechanisms underpinning evolutionary rescue in an obligate mutualism involving cross-feeding of amino acids between auxotrophic Escherichia coli strains. We found that over 80% of populations overcame a severe decline when exposed to two distinct types of abrupt, lethal stress. Of note, in all cases only one of the strains survived by metabolically bypassing the auxotrophy. Crucially, the mutualistic consortium exhibited greater sensitivity to both stressors than a prototrophic control strain, such that reversion to autonomy was sufficient to alleviate stress below lethal levels. This sensitivity was common across other stresses, suggesting it may be a general feature of amino acid-dependent obligate mutualisms. Our results reveal that evolutionary rescue may depend critically on the specific genetic and physiological details of the interacting partners, adding rich layers of complexity to the endeavor of predicting the fate of microbial communities facing intense environmental deterioration.
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Affiliation(s)
- Ignacio J Melero-Jiménez
- Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
- Departamento de Botánica y Fisiología Vegetal, Universidad de Málaga, Campus de Teatinos s/n, 29071, Málaga, Spain.
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM), 28223, Madrid, Spain.
| | - Yael Sorokin
- Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ami Merlin
- Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jiawei Li
- Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alejandro Couce
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM), 28223, Madrid, Spain.
| | - Jonathan Friedman
- Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
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7
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Zhou N, Zheng Q, Liu Y, Huang Z, Feng Y, Chen Y, Hu F, Zheng H. Strain diversity and host specificity of the gut symbiont Gilliamella in Apis mellifera, Apis cerana and Bombus terrestris. Microbiol Res 2025; 293:128048. [PMID: 39813751 DOI: 10.1016/j.micres.2025.128048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 12/15/2024] [Accepted: 01/02/2025] [Indexed: 01/18/2025]
Abstract
Social bees, with their specialized gut microbiota and societal transmission between individuals, provide an ideal model for studying host-gut microbiota interactions. While the functional disparities arising from strain-level diversity of gut symbionts and their effects on host health have been studied in Apis mellifera and bumblebees, studies focusing on host-specific investigations of individual strains across different honeybee hosts remain relatively unexplored. In this study, the complete genomic sequences of 17 strains of Gilliamella from A. mellifera, Apis cerana and Bombus terrestris were analyzed. The analysis revealed that the strains of A. mellifera display a more expansive genomic and functional content compared to the strains of A. cerana and B. terrestris. Phylogenetic analysis showed a deep divergence among the Gilliamella strains from different hosts. Additionally, biochemistry tests and antibiotic susceptibility tests revealed that gut strains from A. mellifera exhibited a more extensive pathway for carbohydrate metabolism and a greater resistance to antibiotics than gut strains from A. cerana and B. terrestris. Strains from A. mellifera and A. cerana showed higher colonization efficiency and competitive ability whithin their respective host species, indicating a higher degree of host-specific adaptation of local gut microbiota. In addition, colonization by A. mellifera-derived strain triggers a stronger transcriptional response in the host than A. cerana-derived strain. The variation in the number of differentially expressed genes and the involvement of distinct signaling pathways across these two host species suggest species-specific adaptations to Gilliamella strains. These findings suggest that despite occupying similar niches in the bee gut, strain-level variations can influence microbial functions, and their impact on host physiological functions may vary across different strains.
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Affiliation(s)
- Nihong Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiulan Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yao Liu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhichu Huang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ye Feng
- Institute of Translational Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yanping Chen
- Bee Research Laboratory, USDA-ARS, Beltsville, MD, USA
| | - Fuliang Hu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huoqing Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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8
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Sun H, Hanson MA, Walsh SK, Imrie RM, Raymond B, Longdon B. Varying phylogenetic signal in susceptibility to four bacterial pathogens across species of Drosophilidae. Proc Biol Sci 2025; 292:20242239. [PMID: 40237085 PMCID: PMC12001086 DOI: 10.1098/rspb.2024.2239] [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: 09/19/2024] [Revised: 02/11/2025] [Accepted: 03/14/2025] [Indexed: 04/17/2025] Open
Abstract
Bacterial infections are a major threat to public health. Pathogen host shifts-where a pathogen jumps from one host species to another-are important sources of emerging infectious diseases. However, compared with viruses, we know relatively little about the factors that determine whether bacteria can infect a novel host, such as how host phylogenetics constrains variation in pathogen host range and the link between host phylogeny and the infectivity and virulence of a pathogen. Here, we experimentally examined susceptibility to bacterial infections using a panel of 36 Drosophilidae species and four pathogens (Providencia rettgeri, Pseudomonas entomophila, Enterococcus faecalis, Staphylococcus aureus). The outcomes of infection differed greatly among pathogens and across host species. The host phylogeny explains a considerable amount of variation in susceptibility, with the greatest phylogenetic signal for P. rettgeri infection, explaining 94% of the variation in mortality. Positive correlations were observed between mortality and bacterial load for three out of the four pathogens. Correlations in susceptibility between the four pathogens were positive but largely non-significant, suggesting susceptibility is mostly pathogen-specific. These results suggest that susceptibility to bacterial pathogens may be predicted by the host phylogeny, but the effect may vary in magnitude between different bacteria.
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Affiliation(s)
- Hongbo Sun
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Cornwall, UK
| | - Mark A. Hanson
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Cornwall, UK
| | - Sarah K. Walsh
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Cornwall, UK
- Environment and Sustainability Institute, University of Exeter, Cornwall, UK
| | - Ryan M. Imrie
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Cornwall, UK
| | - Ben Raymond
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Cornwall, UK
| | - Ben Longdon
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Cornwall, UK
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9
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Wallace MA, Wille M, Geoghegan J, Imrie RM, Holmes EC, Harrison XA, Longdon B. Making sense of the virome in light of evolution and ecology. Proc Biol Sci 2025; 292:20250389. [PMID: 40169018 PMCID: PMC11961256 DOI: 10.1098/rspb.2025.0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2025] [Revised: 03/07/2025] [Accepted: 03/07/2025] [Indexed: 04/03/2025] Open
Abstract
Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.
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Affiliation(s)
- Megan A. Wallace
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Penryn, Cornwall, UK
| | - Michelle Wille
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jemma Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ryan M. Imrie
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Penryn, Cornwall, UK
| | - Edward C. Holmes
- School of Medical Sciences, University of Sydney, Sydney, Australia
| | - Xavier A. Harrison
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Penryn, Cornwall, UK
| | - Ben Longdon
- Centre for Ecology and Conservation, Faculty of Environment, Science and Economy, University of Exeter, Penryn, Cornwall, UK
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10
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Mazel F, Prasad A, Engel P. Host specificity of gut microbiota associated with social bees: patterns and processes. Microbiol Mol Biol Rev 2025:e0008023. [PMID: 40111037 DOI: 10.1128/mmbr.00080-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2025] Open
Abstract
SUMMARYGut microbes provide benefits to some animals, but their distribution and effects across diverse hosts are still poorly described. There is accumulating evidence for host specificity (i.e., a pattern where different microbes tend to associate with distinct host lineages), but the causes and consequences of this pattern are unclear. Combining experimental tests in the laboratory with broad surveys in the wild is a promising approach to gaining a comprehensive and mechanistic understanding of host specificity prevalence, origin, and importance. Social bees represent an ideal testbed for this endeavor because they are phylogenetically and functionally diverse, with host-specific, stable, and tractable gut microbiota. Furthermore, the western honeybee (Apis mellifera) is an emerging experimental model system for studying microbiota-host interactions. In this review, we summarize data on the prevalence and strength of host specificity of the social bee gut microbiota (bumblebees, stingless bees, and honeybees), as well as the potential and proven ecological and molecular mechanisms that maintain host specificity. Overall, we found that host specificity in bees is relatively strong and likely results from several processes, including host filtering mediated by the immune system and priority effects. However, more research is needed across multiple social bee species to confirm these findings. To help future research, we summarize emerging hypotheses in the field and propose several experimental and comparative tests. Finally, we conclude this review by highlighting the need to understand how host specificity can influence host health.
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Affiliation(s)
- Florent Mazel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- NCCR Microbiomes, Lausanne, Switzerland
| | - Aiswarya Prasad
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- NCCR Microbiomes, Lausanne, Switzerland
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Zubillaga-Martín D, Solórzano-García B, Yanez-Montalvo A, de León-Lorenzana A, Falcón LI, Vázquez-Domínguez E. Gut microbiota signatures of the three Mexican primate species, including hybrid populations. PLoS One 2025; 20:e0317657. [PMID: 40100798 PMCID: PMC11918351 DOI: 10.1371/journal.pone.0317657] [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: 09/05/2024] [Accepted: 01/02/2025] [Indexed: 03/20/2025] Open
Abstract
Diversity of the gut microbiota has proven to be related with host physiology, health and behavior, influencing host ecology and evolution. Gut microbial community relationships often recapitulate primate phylogeny, suggesting phylosymbiotic associations. Howler monkeys (Alouatta) have been a model for the study of host-gut microbiota relationships, showing the influence of different host related and environmental factors. Differences in life-history traits and feeding behavior with other atelids, like spider monkeys, may reveal distinct patterns of bacterial gut communities, yet few wild populations have been studied; likewise, gut microbiota studies of hybrid populations are mostly lacking. We analyzed diversity and abundance patterns of the gut microbiota of wild populations of the three Mexican primates Ateles geoffroyi, Alouatta palliata and A. pigra from different regions across its distribution in the country, including sympatric localities and the Alouatta hybrid zone. Interspecific differences in gut microbial diversity were higher than intraspecific differences, concordant with phylosymbiosis. Ateles harbored the more differentiated diversity with a major presence of rare taxa, while differences were less strong between Alouatta species. Hybrids had a microbial diversity in-between their parental species, yet also showing unique microbe taxa. Genetic distances between Alouatta individuals correlated positively with their gut microbial dissimilarities. Results show that interspecific and intraspecific overall diversity, abundance and composition patterns are affected by environment, geographic distribution and host genetics. Our study provides the first comprehensive study of gut microbiota of the three Mexican primates and hybrid populations.
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Affiliation(s)
- Diego Zubillaga-Martín
- Laboratorio de Genética y Ecología, Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Brenda Solórzano-García
- Laboratorio de Parasitología y Medicina de la Conservación, ENES-Mérida U.N.A.M., Ucú, Yucatán, México
| | - Alfredo Yanez-Montalvo
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Unidad Mérida, Universidad Nacional Autónoma de México, Ucú, Yucatán, México
| | - Arit de León-Lorenzana
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Unidad Mérida, Universidad Nacional Autónoma de México, Ucú, Yucatán, México
| | - Luisa I. Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Unidad Mérida, Universidad Nacional Autónoma de México, Ucú, Yucatán, México
| | - Ella Vázquez-Domínguez
- Laboratorio de Genética y Ecología, Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Wang X, Hao J, Zhang C, Zhu P, Gao Q, Liu D, Nie M, Jia J, Qi D. Differences and correlation analysis of feeding habits and intestinal microbiome in Schizopygopsis microcephalus and Ptychobarbus kaznakovi in the upper reaches of Yangtze River. Front Microbiol 2025; 16:1513401. [PMID: 40135055 PMCID: PMC11935114 DOI: 10.3389/fmicb.2025.1513401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Accepted: 02/17/2025] [Indexed: 03/27/2025] Open
Abstract
Background The intestinal microbiota has co-evolved with the host to establish a stable and adaptive microbial community that is essential for maintaining host health and facilitating food digestion. Food selection is a critical factor influencing variations in gut microbial composition, shaping gut microbiome communities, and determining the ecological niches of fish. Methods In this study, high-throughput amplicon sequencing of 16S rRNA and 18S rRNA was utilized to compare the dietary and gut microbial differences between Schizopygopsis microcephalus and Ptychobarbus kaznakovi, both collected from the same sites in the Tuotuo River and Tongtian River, which are tributaries of the Yangtze River. We compared the microbial community structure, diet composition, and diversity between the two fish species using various analytical methods, including LefSe, α-diversity and β-diversity analyses. Additionally, we constructed co-occurrence networks to determine their correlations. Results and discussion The alpha diversity results indicated that S. microcephalus exhibited higher intestinal microbiota and feeding diversity compared to P. kaznakovi. Furthermore, the beta diversity results revealed significant differences in both intestinal microbiota and eukaryotic communities between the two species. The dominant bacterial phyla in both S. microcephalus and P. kaznakovi included Proteobacteria, Firmicutes, Actinobacteriota, Chloroflexi, and Verrucomicrobiota; however, Firmicutes was significantly more abundant in P. kaznakovi (P = 0.006), while Actinobacteriota was significantly higher (P = 0.019) in S. microcephalus at the phylum level. The primary food sources for S. microcephalus and P. kaznakovi were identified as Streptophyta (54.41%, 77.50%) and Cercozoa (8.67%, 1.94%), with Bacillariophyta (25.65%) was also the main food of constituting a major component of the diet for S. microcephalus. These differences suggested that S. microcephalus and P. kaznakovi occupy distinct dietary niches. To further explore the relationship between gut microbiota and feeding habits, we identified significant correlations between various food components and the gut microbial community through co-occurrence networks. This study enhances our understanding of the co-evolution and co-adaptation between host gut microbiota and feeding behaviors in sympatric fish species.
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Affiliation(s)
- Xinyu Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Jiahui Hao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Cunfang Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Ping Zhu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Dan Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Miaomiao Nie
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Junmei Jia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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Dias BDC, Lamarca AP, Machado DT, Kloh VP, de Carvalho FM, Vasconcelos ATR. Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans. Anim Microbiome 2025; 7:20. [PMID: 40033444 PMCID: PMC11874851 DOI: 10.1186/s42523-025-00379-y] [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: 07/31/2024] [Accepted: 01/21/2025] [Indexed: 03/05/2025] Open
Abstract
Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host's genetic background and social habits cooperate synergistically as a hidden force modulating the host's physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species.
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Affiliation(s)
- Beatriz do Carmo Dias
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Alessandra Pavan Lamarca
- Laboratório de Bioinformática e Evolução Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Douglas Terra Machado
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Vinicius Prata Kloh
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
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WAN B, CHEN G, POON ESK, FUNG HS, LAU A, SIN SYW. Environmental factors and host sex influence the skin microbiota structure of Hong Kong newt (Paramesotriton hongkongensis) in a coldspot of chytridiomycosis in subtropical East Asia. Integr Zool 2025; 20:236-255. [PMID: 38872359 PMCID: PMC11897979 DOI: 10.1111/1749-4877.12855] [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] [Indexed: 06/15/2024]
Abstract
Chytridiomycosis, an infectious skin disease caused by the chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans, poses a significant threat to amphibian biodiversity worldwide. Antifungal bacteria found on the skin of chytrid-resistant amphibians could potentially provide defense against chytridiomycosis and lower mortality rates among resistant individuals. The Hong Kong newt (Paramesotriton hongkongensis) is native to East Asia, a region suspected to be the origin of chytrids, and has exhibited asymptomatic infection, suggesting a long-term coexistence with the chytrids. Therefore, the skin microbiota of this resistant species warrant investigation, along with other factors that can affect the microbiota. Among the 149 newts sampled in their natural habitats in Hong Kong, China, putative antifungal bacteria were found in all individuals. There were 314 amplicon sequence variants distributed over 25 genera of putative antifungal bacteria; abundant ones included Acinetobacter, Flavobacterium, and Novosphingobium spp. The skin microbiota compositions were strongly influenced by the inter-site geographical distances. Despite inter-site differences, we identified some core skin microbes across sites that could be vital to P. hongkongensis. The dominant cores included the family Comamonadaceae, family Chitinophagaceae, and class Betaproteobacteria. Moreover, habitat elevation and host sex also exhibited significant effects on skin microbiota compositions. The antifungal bacteria found on these newts offer an important resource for conservation against chytridiomycosis, such as developing probiotic treatments for susceptible species.
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Affiliation(s)
- Bowen WAN
- School of Biological SciencesThe University of Hong KongHong KongChina
| | - Guoling CHEN
- School of Biological SciencesThe University of Hong KongHong KongChina
| | | | - Hon Shing FUNG
- School of Biological SciencesThe University of Hong KongHong KongChina
| | - Anthony LAU
- Science UnitLingnan UniversityHong KongChina
| | - Simon Yung Wa SIN
- School of Biological SciencesThe University of Hong KongHong KongChina
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15
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Donohue ME, Lamb A, Absangba AE, Noromalala E, Weisenbeck DR, Stumpf RM, Wright PC. Why Didn't the Sifaka Cross the Road? Divergence of Propithecus edwardsi Gut Microbiomes Across Geographic Barriers in Ranomafana National Park, Madagascar. Am J Primatol 2025; 87:e23732. [PMID: 39905243 PMCID: PMC11794673 DOI: 10.1002/ajp.23732] [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: 10/26/2023] [Revised: 01/02/2025] [Accepted: 01/03/2025] [Indexed: 02/06/2025]
Abstract
This study uses a biogeographic framework to identify patterns of gut microbiome divergence in an endangered lemur species endemic to Madagascar's southeastern rainforests, the Milne-Edwards's sifaka (Propithecus edwardsi). Specifically, we tested the effects of (1) geographic barriers, (2) habitat disturbance, and (3) geographic distance on gut microbiome alpha and beta diversity. We selected 10 social groups from 4 sites in Ranomafana National Park with varied histories of selective logging. Sites were spaced between 4 and 17 km apart falling on either side of two parallel barriers to animal movement: the Namorona River and the RN25 highway. Using 16S rRNA metabarcoding, we found the greatest beta diversity differentiation to occur between social groups, with significant divisions on opposite sides of geographic barriers (road/river). Habitat disturbance had the most significant effect on alpha diversity, though, contrary to many other studies, disturbance was associated with higher microbial species richness. Without biomedical context, it is unclear whether microbiome differences observed herein are neutral, adaptive, or maladaptive. However, microbiome divergence associated with the road/river may be a symptom of reduced host gene flow, warranting further investigation and perhaps conservation action (e.g., construction of wildlife bridges). Finally, this work demonstrates that significant microbiome variation can accrue over small sampling areas, lending new insight into host-microbe-environmental interactions.
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Affiliation(s)
- Mariah E. Donohue
- Department of BiologyUniversity of KentuckyLexingtonKentuckyUSA
- Department of Biological SciencesBinghamton UniversityBinghamtonNew YorkUSA
| | - Alicia Lamb
- Department of Ecology and EvolutionStony Brook UniversityStony BrookNew YorkUSA
- The Wild CenterTupper LakeNew YorkUSA
| | - Abigail E. Absangba
- Department of AnthropologyUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
- Department of AnthropologyNew York UniversityNew YorkNew YorkUSA
| | - Eliette Noromalala
- Anthropobiologie et Développement DurableUniversité AntananarivoAntananarivoMarylandUSA
- Department of AnthropologyThe University of Texas at AustinAustinTexasUSA
| | | | - Rebecca M. Stumpf
- Department of AnthropologyUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Patricia C. Wright
- Centre ValBio Research StationFianarantsoaMarylandUSA
- Department of AnthropologyStony Brook UniversityStony BrookNew YorkUSA
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16
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DuBose JG, Crook TB, Matzkin LM, Haselkorn TS. The relative importance of host phylogeny and dietary convergence in shaping the bacterial communities hosted by several Sonoran Desert Drosophila species. J Evol Biol 2025; 38:180-189. [PMID: 39587684 DOI: 10.1093/jeb/voae143] [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: 06/11/2024] [Revised: 10/11/2024] [Accepted: 11/21/2024] [Indexed: 11/27/2024]
Abstract
Complex eukaryotes vary greatly in the mode and extent that their evolutionary histories have been shaped by the microbial communities that they host. A general understanding of the evolutionary consequences of host-microbe symbioses requires that we understand the relative importance of host phylogenetic divergence and other ecological processes in shaping variation in host-associated microbial communities. To contribute to this understanding, we described the bacterial communities hosted by several Drosophila species native to the Sonoran Desert of North America. Our sampling consisted of four species that span multiple dietary shifts to cactophily, as well as the dietary generalist D. melanogaster, allowing us to partition the influences of host phylogeny and extant ecology. We found that bacterial communities were compositionally indistinguishable when considering incidence only but varied when considering the relative abundances of bacterial taxa. Variation in community composition was not explained by host phylogenetic divergence but could be partially explained by dietary variation. In support of the important role of diet as a source of ecological selection, we found that specialist cactophilic Drosophila deviated more from neutral predictions than dietary generalists. Overall, our findings provide insight into the evolutionary and ecological factors that shape host-associated microbial communities in a natural context.
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Affiliation(s)
- James G DuBose
- Department of Biology, University of Central Arkansas, Conway, AR, United States
- Department of Biology, Emory University, Atlanta, GA, United States
| | - Thomas Blake Crook
- Department of Biology, University of Central Arkansas, Conway, AR, United States
| | - Luciano M Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ, United States
- BIO5 Institute, University of Arizona, Tucson, AZ, United States
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Tamara S Haselkorn
- Department of Biology, University of Central Arkansas, Conway, AR, United States
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Chaib De Mares M, Arciniegas Castro E, Ulloa MA, Torres JM, Sierra MA, Butler DJ, Mason CE, Zambrano MM, Moncada B, Reyes Muñoz A. Distinct bacteria display genus and species-specific associations with mycobionts in paramo lichens in Colombia. FEMS Microbiol Ecol 2025; 101:fiaf010. [PMID: 39880798 PMCID: PMC11800485 DOI: 10.1093/femsec/fiaf010] [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: 07/09/2024] [Revised: 01/13/2025] [Accepted: 01/27/2025] [Indexed: 01/31/2025] Open
Abstract
Lichens are complex symbiotic systems where fungi interact with an extracellular arrangement of one or more photosynthetic partners and an indeterminate number of other microbes. Recently, specific lichen-microbial community associations have been proposed. In this study, we aimed to characterize the differences in bacteria associated with closely related lichens, under a defined set of environmental conditions in Colombian paramos. Our goal was to determine if there is a correlation between microbiota and host divergence in lichen species belonging to the genus Sticta. We found that specific microbiota are defined by their mycobiont at the genus level. Further, distinct bacterial families show differences among the three studied genera, and specific amplicon sequence variants further discriminate among lichen species within each genus. A geographic component also determines the composition of these microbial communities among lichen species. Our functional analysis revealed that fungal partners play a key role in synthesizing complex polysaccharides, while bacterial-derived antioxidants and photoprotective mechanisms contribute to desiccation tolerance in lichens. These insights highlight the complex interactions within lichen symbioses that could be relevant in environments such as the paramo ecosystem.
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Affiliation(s)
- Maryam Chaib De Mares
- Grupo de Biología Molecular Teórica y Evolutiva, Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá 111321, Colombia
- Corporación Corpogen, Bogotá 110311, Colombia
- Grupo de Max Planck Tándem en Biología Computacional y Ecología Microbiana, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá 111711, Colombia
| | - Emerson Arciniegas Castro
- Corporación Corpogen, Bogotá 110311, Colombia
- Grupo Colombiano de Liquenología, Licenciatura en Biología, Facultad de Ciencias y Educación, Universidad Distrital Francisco José de Caldas, Bogotá 110311, Colombia
| | - Maria Alejandra Ulloa
- Grupo de Max Planck Tándem en Biología Computacional y Ecología Microbiana, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá 111711, Colombia
| | - Jean Marc Torres
- Grupo Colombiano de Liquenología, Licenciatura en Biología, Facultad de Ciencias y Educación, Universidad Distrital Francisco José de Caldas, Bogotá 110311, Colombia
- Laboratório de Ecologia e Biologia Evolutiva, Instituto de Biociĕncias, Universidade Federal de Mato Grosso do Sul, Av. Costa e Silva, S/N, Campo Grande, MS 79070-900, Brazil
| | - Maria A Sierra
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10065, USA
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Christopher E Mason
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | | | - Bibiana Moncada
- Grupo Colombiano de Liquenología, Licenciatura en Biología, Facultad de Ciencias y Educación, Universidad Distrital Francisco José de Caldas, Bogotá 110311, Colombia
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Alejandro Reyes Muñoz
- Grupo de Max Planck Tándem en Biología Computacional y Ecología Microbiana, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá 111711, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63110, USA
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Camper BT, Kanes AS, Laughlin ZT, Manuel RT, Bewick SA. Transgressive hybrids as hopeful holobionts. MICROBIOME 2025; 13:19. [PMID: 39844274 PMCID: PMC11752726 DOI: 10.1186/s40168-024-01994-8] [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: 04/24/2024] [Accepted: 12/02/2024] [Indexed: 01/24/2025]
Abstract
BACKGROUND Hybridization between evolutionary lineages has profound impacts on the fitness and ecology of hybrid progeny. In extreme cases, the effects of hybridization can transcend ecological timescales by introducing trait novelty upon which evolution can act. Indeed, hybridization can even have macroevolutionary consequences, for example, as a driver of adaptive radiations and evolutionary innovations. Accordingly, hybridization is now recognized as a motor for macrobial evolution. By contrast, there has been substantially less progress made towards understanding the positive eco-evolutionary consequences of hybridization on holobionts. Rather, the emerging paradigm in holobiont literature is that hybridization disrupts symbiosis between a host lineage and its microbiome, leaving hybrids at a fitness deficit. These conclusions, however, have been drawn based on results from predominantly low-fitness hybrid organisms. Studying "dead-end" hybrids all but guarantees finding that hybridization is detrimental. This is the pitfall that Dobzhansky fell into over 80 years ago when he used hybrid sterility and inviability to conclude that hybridization hinders evolution. Goldschmidt, however, argued that rare saltational successes-so-called hopeful monsters-disproportionately drive positive evolutionary outcomes. Goldschmidt's view is now becoming a widely accepted explanation for the prevalence of historical hybridization in extant macrobial lineages. Aligning holobiont research with this broader evolutionary perspective requires recognizing the importance of similar patterns in host-microbiome systems. That is, rare and successful "hopeful holobionts" (i.e., hopeful monsters at the holobiont scale) might be disproportionately responsible for holobiont evolution. If true, then it is these successful systems that we should be studying to assess impacts of hybridization on the macroevolutionary trajectories of host-microbiome symbioses. RESULTS In this paper, we explore the effects of hybridization on the gut (cloacal) and skin microbiota in an ecologically successful hybrid lizard, Aspidoscelis neomexicanus. Specifically, we test the hypothesis that hybrid lizards have host-associated (HA) microbiota traits strongly differentiated from their progenitor species. Across numerous hybrid microbiota phenotypes, we find widespread evidence of transgressive segregation. Further, microbiota restructuring broadly correlates with niche restructuring during hybridization. This suggests a relationship between HA microbiota traits and ecological success. CONCLUSION Transgressive segregation of HA microbiota traits is not only limited to hybrids at a fitness deficit but also occurs in ecologically successful hybrids. This suggests that hybridization may be a mechanism for generating novel and potentially beneficial holobiont phenotypes. Supporting such a conclusion, the correlations that we find between hybrid microbiota and the hybrid niche indicate that hybridization might change host microbiota in ways that promote a shift or an expansion in host niche space. If true, hybrid microbiota restructuring may underly ecological release from progenitors. This, in turn, could drive evolutionary diversification. Using our system as an example, we elaborate on the evolutionary implications of host hybridization within the context of holobiont theory and then outline the next steps for understanding the role of hybridization in holobiont research. Video Abstract.
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Affiliation(s)
| | | | | | - Riley Tate Manuel
- Department of Biological Sciences, Clemson University, Clemson, SC, 29631, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sharon Anne Bewick
- Department of Biological Sciences, Clemson University, Clemson, SC, 29631, USA
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Carruthers LV, Nordmeyer SC, Anderson TJC, Chevalier FD, Le Clec’h W. Organ-Specific Microbiomes of Biomphalaria Snails. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.06.11.598555. [PMID: 38915569 PMCID: PMC11195231 DOI: 10.1101/2024.06.11.598555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Background The microbiome is increasingly recognized to shape many aspects of its host biology and is a key determinant of health and disease. The microbiome may influence transmission of pathogens by their vectors, such as mosquitoes or aquatic snails. We previously sequenced the V4 region of the bacterial 16S rRNA gene from the hemolymph (blood) of Biomphalaria spp. snails, vectors of the human blood fluke schistosome. We showed that snail hemolymph harbored an abundant and diverse microbiome. This microbiome is distinct from the water environment and can discriminate snail species and populations. As hemolymph bathes snail organs, we then investigated the heterogeneity of the microbiome in these organs. Results We dissected ten snails for each of two different species (B. alexandrina and B. glabrata) and collected their hemolymph and organs (ovotestis, hepatopancreas, gut, and stomach). We also ground in liquid nitrogen four whole snails of each species. We sampled the water in which the snails were living (environmental controls). Sequencing the 16S rRNA gene revealed organ-specific microbiomes. These microbiomes harbored a lower diversity than the hemolymph microbiome, and the whole-snail microbiome. The organ microbiomes tend to cluster by physiological function. In addition, we showed that the whole-snail microbiome is more similar to hemolymph microbiome. Conclusions These results are critical for future work on snail microbiomes and show the necessity of sampling individual organ microbiomes to provide a complete description of snail microbiomes.
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Affiliation(s)
| | | | | | | | - Winka Le Clec’h
- Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX 78258
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Li Q, Chen Y, Zhang J, Zhang S, Li J. Specificity of benthic invertebrate gill-associated microbiome contributes to host fitness to localized heterogeneous environment in the cold seep. THE SCIENCE OF THE TOTAL ENVIRONMENT 2025; 958:177861. [PMID: 39644640 DOI: 10.1016/j.scitotenv.2024.177861] [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: 06/09/2023] [Revised: 11/28/2024] [Accepted: 11/29/2024] [Indexed: 12/09/2024]
Abstract
The deep hydrocarbon fluids discharged into the water column at cold seeps create diverse and heterogeneous habitats on the seafloor. Symbiosis is essential for the survival of marine life in extreme deep-sea environments. Although the symbiotic relationship between chemoautotrophic bacteria and invertebrates has been reported, our understanding of these host-microbe interactions under heterogeneous environment remains limited. In this study, we evaluated the bacterial community structures, histological and subcellular localization, and potential functions of the gill microbiomes of six invertebrates in the Haima cold seep, South China Sea. The results showed distinct gill-associated microbiomes in these six invertebrates. Gigantidas haimaensis and Archivesica marissinica exhibit a highly dependent symbiotic relationship with their intracellular gill symbionts, characterized by a simple composition. In contrast, Alvinocaris longirostris, Shinkaia crosnieri, Phymorhynchus buccinoides, and Paraescarpia echinospica display a loosely dependent association with their extracellular gill-associated microbes, which are notably complex in composition. Moreover, gill microbiome specificity was seen among six invertebrates and host selection could be an underlying mechanism. The potential functional components of these six invertebrate gill microbiomes contribute to host fitness in heterogeneous local environments. The results obtained from our study provide insights into the ecology and evolution of host-microbe interactions and the underlying mechanisms in extreme marine environments. This information is critical for predicting the responses of benthic fauna to environmental changes in cold seeps.
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Affiliation(s)
- Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
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21
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Michl K, Kanasugi M, Förster A, Wuggenig R, Issifu S, Hrynkiewicz K, Emmerling C, David C, Dumont B, Mårtensson LMD, Rasche F, Berg G, Cernava T. The microbiome of a perennial cereal differs from annual winter wheat only in the root endosphere. ISME COMMUNICATIONS 2025; 5:ycae165. [PMID: 39936170 PMCID: PMC11812607 DOI: 10.1093/ismeco/ycae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 11/08/2024] [Accepted: 12/19/2024] [Indexed: 02/13/2025]
Abstract
The intensification of agriculture has led to environmental degradation, including the loss of biodiversity. This has prompted interest in perennial grain cropping systems to address and mitigate some of these negative impacts. In order to determine if perennial grain cultivation promotes a higher microbial diversity, we assessed the endophytic microbiota of a perennial grain crop (intermediate wheatgrass, Thinopyrum intermedium L.) in comparison to its annual counterpart, wheat (Triticum aestivum L.). The study covered three sampling sites in a pan-European gradient (Sweden, Belgium, and France), two plant genotypes, three plant compartments (roots, stems, and leaves), and two sampling time points. We observed that the host genotype effect was mainly evident in the belowground compartment, and only to a lesser extent in the aboveground tissues, with a similar pattern at all three sampling sites. Moreover, intermediate wheatgrass roots harbored a different bacterial community composition and higher diversity and richness compared to their annual counterparts. The root bacterial diversity was influenced by not only several soil chemical parameters, such as the carbon:nitrogen ratio, but also soil microbial parameters, such as soil respiration and dehydrogenase activity. Consistent findings across time and space suggest stable mechanisms in microbiota assembly associated with perennial grain cropping, underscoring their potential role in supporting biodiversity within sustainable agricultural systems.
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Affiliation(s)
- Kristina Michl
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Makoto Kanasugi
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun 87-100, Poland
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg 15374, Germany
| | - Alena Förster
- Department of Soil Science, Faculty of Regional and Environmental Sciences, University of Trier, Trier 54286, Germany
| | - Regina Wuggenig
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
| | - Sulemana Issifu
- Department of Agronomy in the Tropics and Subtropics, Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart 70593, Germany
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun 87-100, Poland
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg 15374, Germany
| | - Christoph Emmerling
- Department of Soil Science, Faculty of Regional and Environmental Sciences, University of Trier, Trier 54286, Germany
| | - Christophe David
- Agroecology and Environment Research Unit, ISARA,Lyon 69364, France
| | - Benjamin Dumont
- University of Liege - Gembloux Agro-Bio Tech, Plant Sciences Axis, Crop Science lab., Gembloux 5030, Belgium
| | | | - Frank Rasche
- Department of Agronomy in the Tropics and Subtropics, Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart 70593, Germany
- International Institute of Tropical Agriculture, P.O. Box 30772-00100, Nairobi, Kenya
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
- Leibniz-Institute for Agricultural Engineering and Bioeconomy Potsdam, Potsdam 14469, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz 8010, Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO171BJ, United Kingdom
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22
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DeCandia AL, Lu J, Hamblen EE, Brenner LJ, King JL, Gagorik CN, Schamel JT, Baker SS, Ferrara FJ, Booker M, Bridges A, Carrasco C, vonHoldt BM, Koepfli KP, Maldonado JE. Phylosymbiosis and Elevated Cancer Risk in Genetically Depauperate Channel Island Foxes. Mol Ecol 2025; 34:e17610. [PMID: 39655703 DOI: 10.1111/mec.17610] [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: 08/13/2024] [Revised: 11/08/2024] [Accepted: 11/26/2024] [Indexed: 01/07/2025]
Abstract
Examination of the host-associated microbiome in wildlife can provide critical insights into the eco-evolutionary factors driving species diversification and response to disease. This is particularly relevant for isolated populations lacking genomic variation, a phenomenon that is increasingly common as human activities create habitat 'islands' for wildlife. Here, we characterised the gut and otic microbial communities of one such species: Channel Island foxes (Urocyon littoralis). The gut microbiome provided evidence of phylosymbiosis by reflecting the host phylogeny, geographic proximity, history of island colonisation and contemporary ecological differences, whereas the otic microbiome primarily reflected geography and disease. Santa Catalina Island foxes are uniquely predisposed to ceruminous gland tumours following infection with Otodectes cynotis ear mites, while San Clemente and San Nicolas Island foxes exhibit ear mite infections without evidence of tumours. Comparative analyses of otic microbiomes revealed that mite-infected Santa Catalina and San Clemente Island foxes exhibited reduced bacterial diversity, skewed abundance towards the opportunistic pathogen Staphylococcus pseudintermedius and disrupted microbial community networks. However, Santa Catalina Island foxes uniquely harboured Fusobacterium and Prevotella bacteria as potential keystone taxa. These bacteria have previously been associated with colorectal cancer and may predispose Santa Catalina Island foxes to an elevated cancer risk. In contrast, mite-infected San Nicolas Island foxes maintained high bacterial diversity and robust microbial community networks, suggesting that they harbour more resilient microbiomes. Considered together, our results highlight the diverse eco-evolutionary factors influencing commensal microbial communities and their hosts and underscore how the microbiome can contribute to disease outcomes.
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Affiliation(s)
- Alexandra L DeCandia
- Department of Biology, Georgetown University, Washington, DC, USA
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Jasmine Lu
- Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | | | | | - Julie L King
- Catalina Island Conservancy, Avalon, California, USA
- Santa Clara Valley Habitat Agency, Morgan Hill, California, USA
| | - Calypso N Gagorik
- Department of Biology, Northern Arizona University, Flagstaff, Arizona, USA
| | | | | | - Francesca J Ferrara
- Environmental Division - Environmental Planning and Conservation Branch, Naval Base Ventura County, Point Mugu, California, USA
| | - Melissa Booker
- Environmental Division, Naval Base Coronado, San Diego, California, USA
| | - Andrew Bridges
- Institute for Wildlife Studies, San Diego, California, USA
| | - Cesar Carrasco
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Bridgett M vonHoldt
- Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, Virginia, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
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23
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Bathia J, Miklós M, Gyulai I, Fraune S, Tökölyi J. Environmental microbial reservoir influences the bacterial communities associated with Hydra oligactis. Sci Rep 2024; 14:32167. [PMID: 39741169 PMCID: PMC11688501 DOI: 10.1038/s41598-024-82944-0] [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: 08/08/2024] [Accepted: 12/10/2024] [Indexed: 01/02/2025] Open
Abstract
The objective to study the influence of microbiome on host fitness is frequently constrained by spatial and temporal variability of microbial communities. In particular, the environment serves as a dynamic reservoir of microbes that provides potential colonizers for animal microbiomes. In this study, we analyzed the microbiome of Hydra oligactis and corresponding water samples from 15 Hungarian lakes to reveal the contribution of environmental microbiota on host microbiome. Correlation analyses and neutral modeling revealed that differences in Hydra microbiota are associated with differences in environmental microbiota. To further investigate the influence of environmental bacterial community on the host microbiome, field-collected Hydra polyps from three populations were cultured in native water or foreign water. Our results show that lake water bacteria significantly contribute to Hydra microbial communities, but the compositional profile remained stable when cultured in different water sources. Longitudinal analysis of the in vitro experiment revealed a site-specific change in microbiome that correlated with the source water quality. Taken together, our findings demonstrate that while freshwater serves as a critical microbial reservoir, Hydra microbial communities exhibit remarkable resilience to environmental changes maintaining stability despite potential invasion. This dual approach highlights the complex interplay between environmental reservoirs and host microbiome integrity.
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Affiliation(s)
- Jay Bathia
- Institute of Zoology and Organismic Interactions, Heinrich-Heine University, Düsseldorf, Germany.
| | - Máté Miklós
- Institute of Evolution, HUN-REN Centre for Ecological Research, Budapest, Hungary
- Centre for Eco-Epidemiology, National Laboratory for Health Security, Budapest, Hungary
| | - István Gyulai
- National Laboratory for Water Science and Water Security, Department of Hydrobiology, University of Debrecen, Debrecen, Hungary
| | - Sebastian Fraune
- Institute of Zoology and Organismic Interactions, Heinrich-Heine University, Düsseldorf, Germany
| | - Jácint Tökölyi
- MTA-DE "Momentum" Ecology, Evolution & Developmental Biology Research Group, Dept. of Evolutionary Zoology, University of Debrecen, Debrecen, Hungary.
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24
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Zou Y, Zou Q, Yang H, Han C. Investigation of Intestinal Microbes of Five Zokor Species Based on 16S rRNA Sequences. Microorganisms 2024; 13:27. [PMID: 39858794 PMCID: PMC11767591 DOI: 10.3390/microorganisms13010027] [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: 11/26/2024] [Revised: 12/21/2024] [Accepted: 12/24/2024] [Indexed: 01/27/2025] Open
Abstract
Zokor is a group of subterranean rodents that are adapted to underground life and feed on plant roots. Here, we investigated the intestinal microbes of five zokor species (Eospalax cansus, Eospalax rothschildi, Eospalax smithi, Myospalax aspalax, and Myospalax psilurus) using 16S amplicon technology combined with bioinformatics. Microbial composition analysis showed similar intestinal microbes but different proportions among five zokor species, and their dominant bacteria corresponded to those of herbivores. To visualize the relationships among samples, PCoA and PERMANOVA tests showed that the intestinal microbes of zokors are largely clustered by host species, but less so by genetics and geographical location. To find microbes that differ among species, LefSe analysis identified Lactobacillus, Muribaculaceae, Lachnospiraceae_NK4A136_group, unclassified_f_Christensenellaceae, and Desulfovibrio as biomarkers for E. cansus, E. rothschildi, E. smithi, M. aspalax, and M. psilurus, respectively. PICRUSt metagenome predictions revealed enriched microbial genes for carbohydrate and amino acid metabolism in E. cansus and E. smithi, and for cofactor and vitamin metabolism as well as glycan biosynthesis and metabolism in E. rothschildi, M. aspalax, and M. psilurus. Our results demonstrated differences in the microbial composition and functions among five zokor species, potentially related to host genetics, and host ecology including dietary habits and habitat environment. These works would provide new insight into understanding how subterranean zokors adapt to their habitats by regulating intestinal microbes.
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Affiliation(s)
- Yao Zou
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China; (Y.Z.); (Q.Z.)
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, Northwest Agriculture and Forestry University, Yangling 712100, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Quan Zou
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China; (Y.Z.); (Q.Z.)
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Yang
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China; (Y.Z.); (Q.Z.)
| | - Chongxuan Han
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, Northwest Agriculture and Forestry University, Yangling 712100, China
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25
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Leasi F, Eckert EM, Norenburg JL, Thomas WK, Sevigny JL, Hall JA, Wirshing HH, Fontaneto D. Microbiota Associated With Ototyphlonemertes Species (Nemertea, Hoplonemertea, Monostilifera, Ototyphlonemertidae) Reveal Evidence of Phylosymbiosis. Ecol Evol 2024; 14:e70471. [PMID: 39629175 PMCID: PMC11612514 DOI: 10.1002/ece3.70471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/01/2024] [Accepted: 10/03/2024] [Indexed: 12/07/2024] Open
Abstract
Phylosymbiosis, the association between the phylogenetic relatedness of hosts and the composition of their microbial communities, is a widespread phenomenon in diverse animal taxa. However, the generality of the existence of such a pattern has been questioned in many animals across the tree of life, including small-sized aquatic invertebrates. This study aims to investigate the microbial communities associated with poorly known marine interstitial nemerteans to uncover their microbiota diversity and assess the occurrence of phylosymbiosis. Specimens from various Central American sites were analyzed using morphology-based taxonomy and molecular techniques targeting the host 18S rRNA gene whereas their microbial association was analyzed by targeting the prokaryotic 16S rRNA gene. Phylogenetic and statistical analyses were conducted to examine the potential effects of host nemertean taxa and sampling locations on the host-associated microbial communities. The results provide compelling evidence of phylosymbiosis in meiofaunal nemertean species, highlighting the significant impact of host genetic relatedness on microbiome diversity in small-sized animals. This finding supports previous studies that demonstrate how certain nemertean species harbor distinct microbial communities with functional and ecological implications. Given the remarkable diversity of meiofaunal animals-spanning numerous phyla with varying lifestyles and co-existing in the same habitat-combined with advancements in multi-omics approaches, there is a promising opportunity to deepen our understanding of the evolutionary and ecological interactions between hosts and their microbiota throughout the animal tree of life.
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Affiliation(s)
- Francesca Leasi
- Department of Biology, Geology, and Environmental ScienceUniversity of Tennessee at ChattanoogaChattanoogaTennesseeUSA
| | - Ester M. Eckert
- National Research Council of Italy (CNR), water Research Institute (IRSA)Molecular Ecology Group (MEG)Verbania PallanzaItaly
| | - Jon L. Norenburg
- National Museum of Natural HistorySmithsonian InstitutionWashington, DCUSA
| | - W. Kelley Thomas
- Hubbard Center for Genome StudiesUniversity of New HampshireDurhamNew HampshireUSA
| | - Joseph L. Sevigny
- Hubbard Center for Genome StudiesUniversity of New HampshireDurhamNew HampshireUSA
| | - Jeffrey A. Hall
- Hubbard Center for Genome StudiesUniversity of New HampshireDurhamNew HampshireUSA
| | - Herman H. Wirshing
- National Museum of Natural HistorySmithsonian InstitutionWashington, DCUSA
| | - Diego Fontaneto
- National Research Council of Italy (CNR), water Research Institute (IRSA)Molecular Ecology Group (MEG)Verbania PallanzaItaly
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26
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Ouwehand J, Peijnenburg WJGM, Vijver MG. Microbial function matters: Microbiome-aware nano-ecotoxicology needs functional endpoints besides compositional data. CHEMOSPHERE 2024; 369:143905. [PMID: 39643017 DOI: 10.1016/j.chemosphere.2024.143905] [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: 11/04/2024] [Revised: 12/03/2024] [Accepted: 12/03/2024] [Indexed: 12/09/2024]
Abstract
The microbiome provides an active barrier to the external environment and aids in the metabolism of the host. Nanomaterials are known to interact with this microbiome host plane. Given the recent advances in techniques to study the microbiome, there has been a vast increase in studies trying to find causality in host response via the microbiome in nano-ecotoxicology. Our review integrates the latest advancements in understanding the microbiome's role in elucidating host health related to nanomaterial exposure, thereby explicitly emphasizing the gap between compositional and functional studies. Both the techniques used to interfere and the current understanding of microbiome-host relationships in nano-ecotoxicology are discussed. To further highlight the functional side of the microbiome, we performed an explorative meta-analysis to bridge the gap between top-down and bottom-up studies. This review gives a perspective on generalising microbiome-aware nano-ecotoxicology and discusses methodologies to enhance the interpretation of nanomaterial or chemical exposure to host-microbiome interactions. The current study discloses that correlations built on compositional data are not a good proxy for host outcome and more in-depth analysis coupled with functional analysis should be explored more in microbiome-aware nano-ecotoxicology.
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Affiliation(s)
- Jesse Ouwehand
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, Leiden, 2300, RA, the Netherlands.
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, Leiden, 2300, RA, the Netherlands; National Institute of Public Health and the Environment (RIVM), P.O. Box 1, Bilthoven, the Netherlands
| | - Martina G Vijver
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, Leiden, 2300, RA, the Netherlands
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27
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Ferreira SCM, Jarquín-Díaz VH, Planillo A, Ďureje Ľ, Martincová I, Kramer-Schadt S, Forslund-Startceva SK, Heitlinger E. Eco-evolutionary dynamics of host-microbiome interactions in a natural population of closely related mouse subspecies and their hybrids. Proc Biol Sci 2024; 291:20241970. [PMID: 39689880 DOI: 10.1098/rspb.2024.1970] [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: 06/19/2024] [Revised: 11/01/2024] [Accepted: 11/08/2024] [Indexed: 12/19/2024] Open
Abstract
Closely related host species share similar symbionts, but the effects of host genetic admixture and environmental conditions on these communities remain largely unknown. We investigated the influence of host genetic admixture and environmental factors on the intestinal prokaryotic and eukaryotic communities (fungi, parasites) of two house mouse subspecies (Mus musculus domesticus and M. m. musculus) and their hybrids in two settings: (i) wild-caught mice from the European hybrid zone and (ii) wild-derived inbred mice in a controlled laboratory environment before and during a community perturbation (infection). In wild-caught mice, environmental factors strongly predicted the overall microbiome composition. Subspecies' genetic distance significantly influenced the overall microbiome composition, and each component (bacteria, parasites and fungi). While hybridization had a weak effect, it significantly impacted fungal composition. We observed similar patterns in wild-derived mice, where genetic distances and hybridization influenced microbiome composition, with fungi being more stable to infection-induced perturbations than other microbiome components. Subspecies' genetic distance has a stronger and consistent effect across microbiome components than differences in expected heterozygosity among hybrids, suggesting that host divergence and host filtering play a key role in microbiome divergence, influenced by environmental factors. Our findings offer new insights into the eco-evolutionary processes shaping host-microbiome interactions.
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Affiliation(s)
- Susana C M Ferreira
- Division of Computational Systems Biology, Center for Microbiology and Ecological Systems Science, University of Vienna, Djerassipl. 1, Vienna 1030, Austria
- Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin (HU). Philippstr. 13 Haus 14, Berlin 10115, Germany
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstraße 1, Vienna A-1160, Austria
| | - Víctor Hugo Jarquín-Díaz
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, Berlin 13125, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC). Robert-Rössle-Str. 10, Berlin 13125, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz Institute for Zoo and Wildlife Research (IZW). Alfred-Kowalke-Straße 17, Berlin 10315, Germany
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Aimara Planillo
- Department of Ecological Dynamics, Leibniz Institute for Zoo and Wildlife Research (IZW). Alfred-Kowalke-Straße 17, Berlin 10315, Germany
| | - Ľudovít Ďureje
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Iva Martincová
- Research Facility Studenec, Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Stephanie Kramer-Schadt
- Department of Ecological Dynamics, Leibniz Institute for Zoo and Wildlife Research (IZW). Alfred-Kowalke-Straße 17, Berlin 10315, Germany
- Institute of Ecology, Chair of Planning-related Animal Ecology, Technische Universität Berlin (TUB), Rothenburgstr. 12, Berlin 12165, Germany
| | - Sofia K Forslund-Startceva
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, Berlin 13125, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC). Robert-Rössle-Str. 10, Berlin 13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Emanuel Heitlinger
- Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin (HU). Philippstr. 13 Haus 14, Berlin 10115, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz Institute for Zoo and Wildlife Research (IZW). Alfred-Kowalke-Straße 17, Berlin 10315, Germany
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28
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Pereira H, Chakarov N, Caspers BA, Gilles M, Jones W, Mijoro T, Zefania S, Székely T, Krüger O, Hoffman JI. The gut microbiota of three avian species living in sympatry. BMC Ecol Evol 2024; 24:144. [PMID: 39574002 PMCID: PMC11580620 DOI: 10.1186/s12862-024-02329-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 11/06/2024] [Indexed: 11/24/2024] Open
Abstract
BACKGROUND Evolutionary divergence and genetic variation are often linked to differences in microbial community structure and diversity. While environmental factors and diet heavily influence gut microbial communities, host species contributions are harder to quantify. Closely related species living in sympatry provide a unique opportunity to investigate species differences without the confounding effects of habitat and dietary variation. We therefore compared and contrasted the gut microbiota of three sympatric plover species: the widespread Kittlitz's and white-fronted plovers (Anarhynchus pecuarius and A. marginatus) and the endemic and vulnerable Madagascar plover (A. thoracicus). RESULTS We found no significant differences in the beta diversity (composition) of the gut microbiota of the three species. However, A. thoracicus exhibited higher intraspecific compositional similarity (i.e. lower pairwise distances) than the other two species; this pattern was especially pronounced among juveniles. By contrast, microbial alpha diversity varied significantly among the species, being highest in A. pecuarius, intermediate in A. marginatus and lowest in A. thoracicus. This pattern was again stronger among juveniles. Geographical distance did not significantly affect the composition of the gut microbiota, but genetic relatedness did. CONCLUSION While patterns of microbial diversity varied across species, the lack of compositional differences suggests that habitat and diet likely exert a strong influence on the gut microbiota of plovers. This may be enhanced by their precocial, ground-dwelling nature, which could facilitate the horizontal transmission of microbes from the environment. We hypothesise that gut microbiota diversity in plovers primarily reflects the ecological pool of microbiota, which is subsequently modified by host-specific factors including genetics. The reduced microbial and genetic diversity of the endemic A. thoracicus may hinder its ability to adapt to environmental changes, highlighting the need for increased conservation efforts for this vulnerable species.
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Grants
- 316099922 Deutsche Forschungsgemeinschaft
- 316099922 Deutsche Forschungsgemeinschaft
- 316099922 Deutsche Forschungsgemeinschaft
- 316099922 Deutsche Forschungsgemeinschaft
- 316099922 Deutsche Forschungsgemeinschaft
- 316099922 Deutsche Forschungsgemeinschaft
- 316099922 Deutsche Forschungsgemeinschaft
- 316099922 Deutsche Forschungsgemeinschaft
- 316099922 Deutsche Forschungsgemeinschaft
- 316099922 Deutsche Forschungsgemeinschaft
- 396780709 Deutsche Forschungsgemeinschaft,
- 396780709 Deutsche Forschungsgemeinschaft,
- 396780709 Deutsche Forschungsgemeinschaft,
- 396780709 Deutsche Forschungsgemeinschaft,
- 396780709 Deutsche Forschungsgemeinschaft,
- 396780709 Deutsche Forschungsgemeinschaft,
- 396780709 Deutsche Forschungsgemeinschaft,
- 396780709 Deutsche Forschungsgemeinschaft,
- 396780709 Deutsche Forschungsgemeinschaft,
- 396780709 Deutsche Forschungsgemeinschaft,
- Universität Bielefeld (3146)
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Affiliation(s)
- Hugo Pereira
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany.
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, Bielefeld, 33615, Germany
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, Bielefeld, 33615, Germany
| | - Marc Gilles
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany
| | - William Jones
- Institut Supérieur de Technologie de Menabe, Université of Toliara & Morondava, Toliara, 601, Madagascar
| | - Tafitasoa Mijoro
- HUN-REN-Debrecen University Reproductive Strategies Research Group, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Sama Zefania
- HUN-REN-Debrecen University Reproductive Strategies Research Group, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Tamás Székely
- Institut Supérieur de Technologie de Menabe, Université of Toliara & Morondava, Toliara, 601, Madagascar
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, Bielefeld, 33615, Germany
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany
- Department of Evolutionary Population Genetics, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, Bielefeld, 33615, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Universitätsstraße 25, Bielefeld, 33615, Germany
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Neu AT, Torchin ME, Allen EE, Roy K. Microbiome divergence of marine gastropod species separated by the Isthmus of Panama. Appl Environ Microbiol 2024; 90:e0100324. [PMID: 39480095 PMCID: PMC11614449 DOI: 10.1128/aem.01003-24] [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: 05/28/2024] [Accepted: 07/22/2024] [Indexed: 11/02/2024] Open
Abstract
The rise of the Isthmus of Panama separated the populations of many marine organisms, which then diverged into new geminate sister species currently living in the Eastern Pacific Ocean and the Caribbean Sea. However, we know very little about how such evolutionary divergences of host species have shaped the compositions of their microbiomes. Here, we compared the microbiomes of whole-body and shell-surface samples of geminate species of marine gastropods in the genera Cerithium and Cerithideopsis to those of congeneric outgroups. Our results suggest that the effects of ~3 million years of separation and isolation on microbiome composition varied among host genera and between sample types within the same hosts. In the whole-body samples, microbiome compositions of geminate species pairs tended to be similar, likely due to host filtering, although the strength of this relationship varied among the two groups and across similarity metrics. Shell-surface microbiomes show contrasting patterns, with co-divergence between the host taxa and a small number of microbial clades evident in Cerithideopsis but not Cerithium. These results suggest that (i) isolation of host populations after the rise of the Isthmus of Panama affected microbiomes of geminate hosts in a complex and host-specific manner, and (ii) host-associated microbial taxa respond differently to vicariance events than the hosts themselves.IMPORTANCEWhile considerable work has been done on evolutionary divergences of marine species in response to the rise of the Isthmus of Panama, which separated two previously connected oceans, how this event shaped the microbiomes of these marine hosts remains poorly known. Using whole-body and shell-surface microbiomes of closely related gastropod species from opposite sides of the Isthmus, we show that divergences of microbial taxa after the formation of the Isthmus are often not concordant with those of their gastropod hosts. Our results show that evolutionary responses of marine gastropod-associated microbiomes to major environmental perturbations are complex and are shaped more by local environments than host evolutionary history.
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Affiliation(s)
- Alexander T. Neu
- Department of Ecology,
Behavior and Evolution, School of Biological Sciences, University of
California San Diego, La
Jolla, California, USA
- Smithsonian Tropical
Research Institute, Ancon,
Balboa, Panama
| | - Mark E. Torchin
- Smithsonian Tropical
Research Institute, Ancon,
Balboa, Panama
| | - Eric E. Allen
- Department of
Molecular Biology, School of Biological Sciences, University of
California San Diego, La
Jolla, California, USA
- Marine Biology
Research Division, Scripps Institution of Oceanography, University of
California San Diego, La
Jolla, California, USA
| | - Kaustuv Roy
- Department of Ecology,
Behavior and Evolution, School of Biological Sciences, University of
California San Diego, La
Jolla, California, USA
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30
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Prioux C, Ferrier-Pages C, Deter J, Tignat-Perrier R, Guilbert A, Ballesta L, Allemand D, van de Water JAJM. Insights into the occurrence of phylosymbiosis and co-phylogeny in the holobionts of octocorals from the Mediterranean Sea and Red Sea. Anim Microbiome 2024; 6:62. [PMID: 39497183 PMCID: PMC11533408 DOI: 10.1186/s42523-024-00351-2] [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: 07/22/2024] [Accepted: 10/24/2024] [Indexed: 11/06/2024] Open
Abstract
BACKGROUND Corals are the foundational species of coral reefs and coralligenous ecosystems. Their success has been linked to symbioses with microorganisms, and a coral host and its symbionts are therefore considered a single entity, called the holobiont. This suggests that there may be evolutionary links between corals and their microbiomes. While there is evidence of phylosymbiosis in scleractinian hexacorals, little is known about the holobionts of Alcyonacean octocorals. RESULTS 16S rRNA gene amplicon sequencing revealed differences in the diversity and composition of bacterial communities associated with octocorals collected from the mesophotic zones of the Mediterranean and Red Seas. The low diversity and consistent dominance of Endozoicomonadaceae and/or Spirochaetaceae in the bacterial communities of Mediterranean octocorals suggest that these corals may have a shared evolutionary history with their microbiota. Phylosymbiotic signals were indeed detected and cophylogeny in associations between several bacterial strains, particularly those belonging to Endozoicomonadaceae or Spirochaetaceae, and coral species were identified. Conversely, phylosymbiotic patterns were not evident in Red Sea octocorals, likely due to the high bacterial taxonomic diversity in their microbiota, but cophylogeny in associations between certain coral and bacterial species was observed. Noteworthy were the associations with Endozoicomonadaceae, suggesting a plausible evolutionary link that warrants further investigations to uncover potential underlying patterns. CONCLUSIONS Overall, our findings emphasize the importance of Endozoicomonadaceae and Spirochaetaceae in coral symbiosis and the significance of exploring host-microbiome interactions in mesophotic ecosystems for a comprehensive understanding of coral-microbiome evolutionary history.
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Affiliation(s)
- C Prioux
- Unité de Recherche Sur La Biologie des Coraux Précieux CSM - CHANEL, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, MC, Principality of Monaco
- Coral Ecophysiology Team, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, MC, Principality of Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, MC, Principality of Monaco
| | - C Ferrier-Pages
- Coral Ecophysiology Team, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, MC, Principality of Monaco.
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, MC, Principality of Monaco.
| | - J Deter
- Andromède Océanologie, 7 place Cassan-Carnon plage, 34130, Mauguio, France
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Place Eugène Bataillon, 34095, Montpellier, France
| | - R Tignat-Perrier
- Unité de Recherche Sur La Biologie des Coraux Précieux CSM - CHANEL, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, MC, Principality of Monaco
- Coral Ecophysiology Team, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, MC, Principality of Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, MC, Principality of Monaco
| | - A Guilbert
- Andromède Océanologie, 7 place Cassan-Carnon plage, 34130, Mauguio, France
| | - L Ballesta
- Andromède Océanologie, 7 place Cassan-Carnon plage, 34130, Mauguio, France
| | - D Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, MC, Principality of Monaco
| | - J A J M van de Water
- Unité de Recherche Sur La Biologie des Coraux Précieux CSM - CHANEL, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, MC, Principality of Monaco.
- Coral Ecophysiology Team, Centre Scientifique de Monaco, 8 Quai Antoine 1er, 98000, Monaco, MC, Principality of Monaco.
- Department of Estuarine Delta Systems, Royal Netherlands Institute for Sea Research, Korringaweg 7, 4401 NT, Yerseke, The Netherlands.
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31
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Magura T, Mizser S, Horváth R, Tóth M, Lövei GL. Urbanization impoverishes taxonomic but not functional diversity of the gut microbiota in a forest specialist ground beetle, Carabus convexus. Sci Rep 2024; 14:25546. [PMID: 39461984 PMCID: PMC11513054 DOI: 10.1038/s41598-024-75864-6] [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: 08/08/2024] [Accepted: 10/08/2024] [Indexed: 10/28/2024] Open
Abstract
Symbiotic microorganisms living in the digestive tracts of invertebrates can be crucial in host-symbiont interactions, as they play fundamental roles in important biological processes. Urbanization-related habitat alteration and disturbance, however, considerably affect the environment of host insects, from which their gut microbiota is derived. Still, relatively few studies, all on flying insects, have assessed the impact of urbanization on the gut microbiota of insects. Here, we compared the gut bacterial microbiota in rural and urban individuals of a flightless ground beetle, Carabus convexus, using next generation sequencing. Across the 48 gut samples we identified 1163 different bacterial operational taxonomic units (OTUs), forming significantly different gut bacterial communities in rural versus urban beetles. The taxonomic diversity of the gut bacterial microbiota expressed by the Hill numbers was significantly higher in rural than urban individuals, as well as in rural males vs. females. Smaller differences were found in functional diversity, assessed by the Rao's quadratic entropy which was marginally significantly higher in urban than rural beetles.
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Affiliation(s)
- Tibor Magura
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Egyetem Sq. 1, Debrecen, 4032, Hungary.
- HUN-REN-UD Anthropocene Ecology Research Group, Egyetem Sq. 1, Debrecen, 4032, Hungary.
| | - Szabolcs Mizser
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Egyetem Sq. 1, Debrecen, 4032, Hungary
| | - Roland Horváth
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Egyetem Sq. 1, Debrecen, 4032, Hungary
- HUN-REN-UD Anthropocene Ecology Research Group, Egyetem Sq. 1, Debrecen, 4032, Hungary
| | - Mária Tóth
- Department of Ecology, Faculty of Science and Technology, University of Debrecen, Egyetem Sq. 1, Debrecen, 4032, Hungary
- HUN-REN-UD Anthropocene Ecology Research Group, Egyetem Sq. 1, Debrecen, 4032, Hungary
| | - Gábor L Lövei
- HUN-REN-UD Anthropocene Ecology Research Group, Egyetem Sq. 1, Debrecen, 4032, Hungary
- Department of Agroecology, Flakkebjerg Research Centre, Aarhus University, 4200, Slagelse, Denmark
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32
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Delleuze M, Schwob G, Orlando J, Gerard K, Saucède T, Brickle P, Poulin E, Cabrol L. Habitat specificity modulates the bacterial biogeographic patterns in the Southern Ocean. FEMS Microbiol Ecol 2024; 100:fiae134. [PMID: 39363207 PMCID: PMC11523047 DOI: 10.1093/femsec/fiae134] [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: 09/06/2024] [Accepted: 10/02/2024] [Indexed: 10/05/2024] Open
Abstract
Conceptual biogeographic frameworks have proposed that the relative contribution of environmental and geographical factors on microbial distribution depends on several characteristics of the habitat (e.g. environmental heterogeneity, species diversity, and proportion of specialist/generalist taxa), all of them defining the degree of habitat specificity, but few experimental demonstrations exist. Here, we aimed to determine the effect of habitat specificity on bacterial biogeographic patterns and assembly processes in benthic coastal ecosystems of the Southern Ocean (Patagonia, Falkland/Malvinas, Kerguelen, South Georgia, and King George Islands), using 16S rRNA gene metabarcoding. The gradient of habitat specificity resulted from a 'natural experimental design' provided by the Abatus sea urchin model, from the sediment (least specific habitat) to the intestinal tissue (most specific habitat). The phylogenetic composition of the bacterial communities showed a clear differentiation by site, driven by a similar contribution of geographic and environmental distances. However, the strength of this biogeographic pattern decreased with increasing habitat specificity: sediment communities showed stronger geographic and environmental divergence compared to gut tissue. The proportion of stochastic and deterministic processes contributing to bacterial assembly varied according to the geographic scale and the habitat specificity level. For instance, an increased contribution of dispersal limitation was observed in gut tissue habitat. Our results underscore the importance of considering different habitats with contrasting levels of specificity to better understand bacterial biogeography and assembly processes over oceanographic scales.
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Affiliation(s)
- Mélanie Delleuze
- Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
- Marine Biology Lab, CP160/15, Université Libre de Bruxelles (ULB), Brussels 1050, Belgium
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago 7800003, Chile
| | - Guillaume Schwob
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago 7800003, Chile
| | - Julieta Orlando
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago 7800003, Chile
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Karin Gerard
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago 7800003, Chile
- Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Punta Arenas 6210427, Chile
- Cape Horn Investigation Center, Puerto Williams 6350054, Chile
| | - Thomas Saucède
- Biogéosciences, UMR CNRS 6282, Université de Bourgogne, 21000 Dijon, France
| | - Paul Brickle
- South Atlantic Environmental Research Institute, Port Stanley FIQQ 1ZZ, Falkland Islands
- School of Biological Sciences (Zoology), University of Aberdeen, Aberdeen AB24 3FX, Scotland, United Kingdom
| | - Elie Poulin
- Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago 7800003, Chile
| | - Léa Cabrol
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago 7800003, Chile
- Aix-Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (M.I.O.) UM 110, 13009 Marseille, France
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Han CJ, Huang JP, Chiang MR, Jean OSM, Nand N, Etebari K, Shelomi M. The hindgut microbiota of coconut rhinoceros beetles ( Oryctes rhinoceros) in relation to their geographical populations. Appl Environ Microbiol 2024; 90:e0098724. [PMID: 39311575 PMCID: PMC11497824 DOI: 10.1128/aem.00987-24] [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: 05/21/2024] [Accepted: 08/22/2024] [Indexed: 10/25/2024] Open
Abstract
The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a palm tree pest capable of rapidly expanding its population in new territories. Previous studies identified a digestive symbiosis between CRB and its gut microbes. However, no research compared the genetic variation of CRBs with their hindgut microbiota on a global scale. This study aims to investigate the genetic divergence of CRB and the compositional variation of CRB's microbiota across different geographical locations, and explore the association between them and their predicted functional profiles and environmental data. The research reveals a distinct and consistent microbial community within local populations, but it varies across different geographical populations. The microbial functional profiles linked to the production of digestive enzymes, including cellulases and ligninases, are nonetheless globally conserved. This suggests that CRBs employ specific mechanisms to select and maintain microbes with functional benefits, contributing to host adaptability, stress tolerance, and fitness. The CRB microbial communities did not appear to recapitulate the genetic variation of their hosts. Rather than depend on obligate symbionts, CRBs seem to establish similar digestive associations with whatever environmentally acquired microbes are available wherever they are, aiding them in successfully establishing after invading a new location.IMPORTANCECoconut rhinoceros beetles (CRBs) are notorious pests on Arecaceae plants, posing destructive threats to countries highly reliant on coconut, oil palm, and date palm as economic crops. In the last century, CRBs have rapidly expanded their presence to territories that were once free of these beetles. The United States, for instance, has officially designated CRBs as invasive and alien pests. Given their remarkable ability to swiftly adapt to new environments, their gut microbes may play a crucial role in this process. While the microbiota of CRBs vary depending on geographical location, these beetles consistently exhibit a functionally identical digestive association with locally acquired microbes. This underscores the significance of CRB-microbe association in shaping the adaptive strategies of this agricultural pest.
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Affiliation(s)
- Chiao-Jung Han
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Min-Rou Chiang
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | | | - Nitesh Nand
- Plant Health Laboratory, The Pacific Community, Suva, Fiji
| | - Kayvan Etebari
- Faculty of Science, School of Agriculture and Food Sustainability, The University of Queensland, Gatton, Australia
| | - Matan Shelomi
- Department of Entomology, National Taiwan University, Taipei, Taiwan
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34
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Silvaraju S, Zhang QH, Kittelmann S, Puniamoorthy N. Genetics, age, and diet influence gut bacterial communities and performance of black soldier fly larvae (Hermetia illucens). Anim Microbiome 2024; 6:56. [PMID: 39407272 PMCID: PMC11481748 DOI: 10.1186/s42523-024-00340-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Accepted: 09/16/2024] [Indexed: 10/19/2024] Open
Abstract
BACKGROUND The gut microbiota of black soldier fly larvae (BSFL, Hermetia illucens) play a crucial role in recycling various organic waste streams. This capability is linked to the presence of a potential common core microbiota in BSFL. However, subjective thresholds for defining core taxa and the difficulty of separating genetic and environmental influences have prevented a clear consensus in the literature. We analysed the gut bacterial communities of two genetically distinct BSF lines (wild type (WT) and lab-adapted line (LD)) raised on ten different diets based on common agricultural by-products and food waste in Southeast Asia. RESULTS High-throughput 16S rRNA gene sequencing revealed that gut bacterial communities were significantly influenced by genetics (p = 0.001), diet (plant/meat-dominated; p = 0.001), larval age (p = 0.001), and the interactions between all three (p = 0.002). This led us to investigate both common core taxa and lineage-specific core taxa. At a strict > 97% prevalence threshold, four core taxa were identified: Providencia_A_732258, an unclassified genus within the family Enterococcaceae, Morganella, and Enterococcus_H_360604. A relaxed threshold (> 80% prevalence) extended the core to include other potential common core taxa such as Klebsiella, Proteus, and Scrofimicrobium. Our data suggest that Proteus, Scrofimicrobium, Corynebacterium, Vagococcus_B, Lysinibacillus_304693 (all LD), and Paenibacillus_J_366884 (WT) are lineage-specific rather than members of a common core (> 90% prevalence in either LD or WT, with prevalence significantly different between lines (p ≤ 0.05)). Positive correlations were observed between several core genera and larval performance in LD, typical of a highly optimized lab-adapted line. Interestingly, only members of the genus Providencia appeared to play a crucial role in most aspects of larval performance in both genetic lineages. CONCLUSION Our study demonstrates that the gut microbiota of BSFL is influenced by genetic factors, diet composition, larval age, and their interactions. We identified a distinct lineage-specific core microbiota, emphasizing genetic background's role. Future studies should apply a standardized high prevalence threshold of at least > 90% unless there is a valid reason for relaxation or sample exclusion. The consistent association of Providencia spp. with larval performance across both genetic lines highlights their crucial role in the BSFL gut ecosystem.
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Affiliation(s)
- Shaktheeshwari Silvaraju
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
- Wilmar International Limited, 28 Biopolis Road, Singapore, 138568, Singapore
| | - Qi-Hui Zhang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Sandra Kittelmann
- Wilmar International Limited, 28 Biopolis Road, Singapore, 138568, Singapore.
| | - Nalini Puniamoorthy
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
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35
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Degregori S, Schiettekatte NMD, Casey JM, Brandl SJ, Mercière A, Amato KR, Mazel F, Parravicini V, Barber PH. Host diet drives gut microbiome convergence between coral reef fishes and mammals. Mol Ecol 2024; 33:e17520. [PMID: 39205506 DOI: 10.1111/mec.17520] [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: 01/24/2024] [Revised: 06/05/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Animal gut microbiomes are critical to host physiology and fitness. The gut microbiomes of fishes-the most abundant and diverse vertebrate clade-have received little attention relative to other clades. Coral reef fishes, in particular, make up a wide range of evolutionary histories and feeding ecologies that are likely associated with gut microbiome diversity. The repeated evolution of herbivory in fishes and mammals also allows us to examine microbiome similarity in relationship to diet across the entire vertebrate tree of life. Here, we generate a large coral reef fish gut microbiome dataset (n = 499 samples, 19 species) and combine it with a diverse aggregation of public microbiome data (n = 447) to show that host diet drives significant convergence between coral reef fish and mammalian gut microbiomes. We demonstrate that this similarity is largely driven by carnivory and herbivory and that herbivorous and carnivorous hosts exhibit distinct microbial compositions across fish and mammals. We also show that fish and mammal gut microbiomes share prominent microbial taxa, including Ruminoccocus spp. and Akkermansia spp., and predicted metabolic pathways. Despite the major evolutionary and ecological differences between fishes and mammals, our results reveal that their gut microbiomes undergo similar dietary selective pressures. Thus, diet, in addition to phylosymbiosis must be considered even when comparing the gut microbiomes of distantly related hosts.
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Affiliation(s)
- Samuel Degregori
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | | | - Jordan M Casey
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, USA
| | - Simon J Brandl
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, USA
| | - Alexandre Mercière
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Florent Mazel
- Department of Ecology and Evolution and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Valeriano Parravicini
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
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36
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Wang W, Song W, Majzoub ME, Feng X, Xu B, Tao J, Zhu Y, Li Z, Qian PY, Webster NS, Thomas T, Fan L. Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont. Nat Commun 2024; 15:8205. [PMID: 39294150 PMCID: PMC11410982 DOI: 10.1038/s41467-024-52464-6] [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: 10/31/2023] [Accepted: 09/07/2024] [Indexed: 09/20/2024] Open
Abstract
Holobionts are highly organized assemblages of eukaryotic hosts, cellular microbial symbionts, and viruses, whose interactions and evolution involve complex biological processes. It is largely unknown which specific determinants drive similarity or individuality in genetic diversity between holobionts. Here, we combine short- and long-read sequencing and DNA-proximity-linkage technologies to investigate intraspecific diversity of the microbiomes, including host-resolved viruses, in individuals of a model marine sponge. We find strong impacts of the sponge host and the cellular hosts of viruses on strain-level organization of the holobiont, whereas substantial overlap in nucleotide diversity between holobionts suggests frequent exchanges of microbial cells and viruses at intrastrain level in the local sponge population. Immune-evasive arms races likely restricted virus-host co-evolution at the intrastrain level, generated holobiont-specific genome variations, and linked virus-host genetics through recombination. Our work shows that a decoupling of strain- and intrastrain-level interactions is a key factor in the genetic diversification of holobionts.
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Affiliation(s)
- Wenxiu Wang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Weizhi Song
- Center for Marine Science and Innovation, University of New South Wales, Sydney, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Marwan E Majzoub
- Center for Marine Science and Innovation, University of New South Wales, Sydney, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Xiaoyuan Feng
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Bu Xu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jianchang Tao
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yuanqing Zhu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Minhang, Shanghai, China
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
| | - Nicole S Webster
- The Australian Antarctic Division, Kingston, Tasmania, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Torsten Thomas
- Center for Marine Science and Innovation, University of New South Wales, Sydney, New South Wales, Australia.
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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Cullen NP, Ashman TL. Hyperaccumulation of nickel but not selenium drives floral microbiome differentiation: A study with six species of Brassicaceae. AMERICAN JOURNAL OF BOTANY 2024; 111:e16382. [PMID: 39148360 DOI: 10.1002/ajb2.16382] [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: 09/25/2023] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 08/17/2024]
Abstract
PREMISE Intraspecific variation in flower microbiome composition can mediate pollination and reproduction, and so understanding the community assembly processes driving this variation is critical. Yet the relative importance of trait-based host filtering and dispersal in shaping among-species variation in floral microbiomes remains unknown. METHODS Within two clades of Brassicaceae, we compared diversity and composition of floral microbiomes in natural populations of focal nickel and selenium hyperaccumulator species and two of their non-accumulating relatives. We assessed the relative strengths of floral elemental composition, plant phylogenetic distance (host filtering), and geography (dispersal) in driving floral microbiome composition. RESULTS Species in the nickel hyperaccumulator clade had strongly divergent floral microbiomes, the most of that variation driven by floral elemental composition, followed by geographic distance between plant populations and, lastly, phylogenetic distance. Conversely, within the selenium hyperaccumulator clade, floral microbiome divergence was much lower among the species and elemental composition, geography, and plant phylogeny were far weaker determinants of microbiome variation. CONCLUSIONS Our results show that the strength of elemental hyperaccumulation's effect on floral microbiomes differs substantially among plant clades, possibly due to variation in elements as selective filters or in long-distance dispersal probability in different habitats.
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Affiliation(s)
- Nevin P Cullen
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, 15260, Pennsylvania, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, 15260, Pennsylvania, USA
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Lipowska MM, Sadowska ET, Kohl KD, Koteja P. Experimental Evolution of a Mammalian Holobiont? Genetic and Maternal Effects on the Cecal Microbiome in Bank Voles Selectively Bred for Herbivorous Capability. ECOLOGICAL AND EVOLUTIONARY PHYSIOLOGY 2024; 97:274-291. [PMID: 39680902 DOI: 10.1086/732781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2024]
Abstract
AbstractMammalian herbivory represents a complex adaptation requiring evolutionary changes across all levels of biological organization, from molecules to morphology to behavior. Explaining the evolution of such complex traits represents a major challenge in biology, as it is simultaneously muddled and enlightened by a growing awareness of the crucial role of symbiotic associations in shaping organismal adaptations. The concept of hologenomic evolution includes the partnered unit of the holobiont, the host with its microbiome, as a selection unit that may undergo adaptation. Here, we test some of the assumptions underlying the concept of hologenomic evolution using a unique experimental evolution model: lines of the bank vole (Myodes [=Clethrionomys] glareolus) selected for increased ability to cope with a low-quality herbivorous diet and unselected control lines. Results from a complex nature-nurture design, in which we combined cross-fostering between the selected and control lines with dietary treatment, showed that the herbivorous voles harbored a cecal microbiome with altered membership and structure and changed abundances of several phyla and genera regardless of the origin of their foster mothers. Although the differences were small, they were statistically significant and partially robust to changes in diet and housing conditions. Microbial characteristics also correlated with selection-related traits at the level of individual variation. Thus, the results support the hypothesis that selection on a host performance trait leads to genetic changes in the host that promote the maintenance of a beneficial microbiome. Such a result is consistent with some of the assumptions underlying the concept of hologenomic evolution.
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39
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Zhang S, Zhang H, Zhang C, Wang G, Shi C, Li Z, Gao F, Cui Y, Li M, Yang G. Composition and evolutionary characterization of the gut microbiota in pigs. Int Microbiol 2024; 27:993-1008. [PMID: 37982990 PMCID: PMC11300507 DOI: 10.1007/s10123-023-00449-8] [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: 09/10/2022] [Revised: 10/28/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
The intestinal microbiota plays significant role in the physiology and functioning of host organisms. However, there is limited knowledge of the composition and evolution of microbiota-host relationships from wild ancestors to modern domesticated species. In this study, the 16S rRNA gene V3-V4 in the intestinal contents of different pig breeds was analyzed and was compared using high-throughput sequencing. This identified 18 323 amplicon sequence variants, of which the Firmicutes and Actinobacteria phyla and Bifidobacterium and Allobaculum genera were most prevalent in wild pigs (WP). In contrast, Proteobacteria and Firmicutes predominated in Chinese Shanxi Black pigs (CSB), while Firmicutes were the most prevalent phylum in Large White pigs (LW) and Iberian pigs (IB), followed by Bacteroidetes in IB and Proteobacteria in LW. At the genus level, Shigella and Lactobacillus were most prevalent in CSB and LW, while Actinobacillus and Sarcina predominated in IB. Differential gene expression together with phylogenetic and functional analyses indicated significant differences in the relative abundance of microbial taxa between different pig breeds. Although many microbial taxa were common to both wild and domestic pigs, significant diversification was observed in bacterial genes that potentially influence host phenotypic traits. Overall, these findings suggested that both the composition and functions of the microbiota were closely associated with domestication and the evolutionary changes in the host. The members of the microbial communities were vertically transmitted in pigs, with evidence of co-evolution of both the hosts and their intestinal microbial communities. These results enhance our understanding and appreciation of the complex interactions between intestinal microbes and hosts and highlight the importance of applying this knowledge in agricultural and microbiological research.
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Affiliation(s)
- Shuhong Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Huan Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Cheng Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guan Wang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Chuanxing Shi
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Zhiqiang Li
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Fengyi Gao
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Yanyan Cui
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Guangli Yang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China.
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Gilbert SF. Inter-kingdom communication and the sympoietic way of life. Front Cell Dev Biol 2024; 12:1427798. [PMID: 39071805 PMCID: PMC11275584 DOI: 10.3389/fcell.2024.1427798] [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: 05/04/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024] Open
Abstract
Organisms are now seen as holobionts, consortia of several species that interact metabolically such that they sustain and scaffold each other's existence and propagation. Sympoiesis, the development of the symbiotic relationships that form holobionts, is critical for our understanding the origins and maintenance of biodiversity. Rather than being the read-out of a single genome, development has been found to be sympoietic, based on multigenomic interactions between zygote-derived cells and symbiotic microbes. These symbiotic and sympoietic interactions are predicated on the ability of cells from different kingdoms of life (e.g., bacteria and animals) to communicate with one another and to have their chemical signals interpreted in a manner that facilitates development. Sympoiesis, the creation of an entity by the interactions of other entities, is commonly seen in embryogenesis (e.g., the creation of lenses and retinas through the interaction of brain and epidermal compartments). In holobiont sympoiesis, interactions between partners of different domains of life interact to form organs and biofilms, wherein each of these domains acts as the environment for the other. If evolution is forged by changes in development, and if symbionts are routinely involved in our development, then changes in sympoiesis can constitute an important factor in evolution.
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Affiliation(s)
- Scott F. Gilbert
- Department of Biology, Swarthmore College, Swarthmore, PA, United States
- Evolutionary Phenomics Group, Biotechnology Institute, University of Helsinki, Helsinki, Finland
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41
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Williams SE, Varliero G, Lurgi M, Stach JE, Race PR, Curnow P. Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001478. [PMID: 39073401 PMCID: PMC11286294 DOI: 10.1099/mic.0.001478] [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: 02/23/2024] [Accepted: 07/01/2024] [Indexed: 07/30/2024]
Abstract
Sponges (phylum Porifera) harbour specific microbial communities that drive the ecology and evolution of the host. Understanding the structure and dynamics of these communities is emerging as a primary focus in marine microbial ecology research. Much of the work to date has focused on sponges from warm and shallow coastal waters, while sponges from the deep ocean remain less well studied. Here, we present a metataxonomic analysis of the microbial consortia associated with 23 individual deep-sea sponges. We identify a high abundance of archaea relative to bacteria across these communities, with certain sponge microbiomes comprising more than 90 % archaea. Specifically, the archaeal family Nitrosopumilaceae is prolific, comprising over 99 % of all archaeal reads. Our analysis revealed that sponge microbial communities reflect the host sponge phylogeny, indicating a key role for host taxonomy in defining microbiome composition. Our work confirms the contribution of both evolutionary and environmental processes to the composition of microbial communities in deep-sea sponges.
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Affiliation(s)
- Sam E. Williams
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs., Lyngby, Denmark
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Miguel Lurgi
- Department of Biosciences, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - James E.M. Stach
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul R. Race
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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Radaelli E, Palladino G, Nanetti E, Scicchitano D, Rampelli S, Airoldi S, Candela M, Marangi M. Meta-analysis of the Cetacea gut microbiome: Diversity, co-evolution, and interaction with the anthropogenic pathobiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172943. [PMID: 38714258 DOI: 10.1016/j.scitotenv.2024.172943] [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: 02/27/2024] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 05/09/2024]
Abstract
Despite their critical roles in marine ecosystems, only few studies have addressed the gut microbiome (GM) of cetaceans in a comprehensive way. Being long-living apex predators with a carnivorous diet but evolved from herbivorous ancestors, cetaceans are an ideal model for studying GM-host evolutionary drivers of symbiosis and represent a valuable proxy of overall marine ecosystem health. Here, we investigated the GM of eight different cetacean species, including both Odontocetes (toothed whales) and Mysticetes (baleen whales), by means of 16S rRNA-targeted amplicon sequencing. We collected faecal samples from free-ranging cetaceans circulating within the Pelagos Sanctuary (North-western Mediterranean Sea) and we also included publicly available cetacean gut microbiome sequences. Overall, we show a clear GM trajectory related to host phylogeny and taxonomy (i.e., phylosymbiosis), with remarkable GM variations which may reflect adaptations to different diets between baleen and toothed whales. While most samples were found to be infected by protozoan parasites of potential anthropic origin, we report that this phenomenon did not lead to severe GM dysbiosis. This study underlines the importance of both host phylogeny and diet in shaping the GM of cetaceans, highlighting the role of neutral processes as well as environmental factors in the establishment of this GM-host symbiosis. Furthermore, the presence of potentially human-derived protozoan parasites in faeces of free-ranging cetaceans emphasizes the importance of these animals as bioindicators of anthropic impact on marine ecosystems.
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Affiliation(s)
- Elena Radaelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1, 61032, Fano, Italy
| | - Giorgia Palladino
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1, 61032, Fano, Italy
| | - Enrico Nanetti
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1, 61032, Fano, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1, 61032, Fano, Italy
| | - Sabina Airoldi
- Tethys Research Institute, Viale G.B. Gadio 2, 20121 Milano, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1, 61032, Fano, Italy.
| | - Marianna Marangi
- Department of Clinical and Experimental Medicine, University of Foggia, Viale Luigi Pinto, 71122 Foggia, Italy.
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Holt JR, Cavichiolli de Oliveira N, Medina RF, Malacrinò A, Lindsey ARI. Insect-microbe interactions and their influence on organisms and ecosystems. Ecol Evol 2024; 14:e11699. [PMID: 39041011 PMCID: PMC11260886 DOI: 10.1002/ece3.11699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/14/2024] [Accepted: 06/21/2024] [Indexed: 07/24/2024] Open
Abstract
Microorganisms are important associates of insect and arthropod species. Insect-associated microbes, including bacteria, fungi, and viruses, can drastically impact host physiology, ecology, and fitness, while many microbes still have no known role. Over the past decade, we have increased our knowledge of the taxonomic composition and functional roles of insect-associated microbiomes and viromes. There has been a more recent shift toward examining the complexity of microbial communities, including how they vary in response to different factors (e.g., host genome, microbial strain, environment, and time), and the consequences of this variation for the host and the wider ecological community. We provide an overview of insect-microbe interactions, the variety of associated microbial functions, and the evolutionary ecology of these relationships. We explore the influence of the environment and the interactive effects of insects and their microbiomes across trophic levels. Additionally, we discuss the potential for subsequent synergistic and reciprocal impacts on the associated microbiomes, ecological interactions, and communities. Lastly, we discuss some potential avenues for the future of insect-microbe interactions that include the modification of existing microbial symbionts as well as the construction of synthetic microbial communities.
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Affiliation(s)
| | | | - Raul F. Medina
- Department of EntomologyTexas A&M University, Minnie Bell Heep CenterCollege StationTexasUSA
| | - Antonino Malacrinò
- Department of AgricultureUniversità Degli Studi Mediterranea di Reggio CalabriaReggio CalabriaItaly
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44
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Buschi E, Dell’Anno A, Tangherlini M, Candela M, Rampelli S, Turroni S, Palladino G, Esposito E, Martire ML, Musco L, Stefanni S, Munari C, Fiori J, Danovaro R, Corinaldesi C. Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome. SCIENCE ADVANCES 2024; 10:eadk9117. [PMID: 38905343 PMCID: PMC11192080 DOI: 10.1126/sciadv.adk9117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications.
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Affiliation(s)
- Emanuela Buschi
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn,” Fano Marine Centre, Fano, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Fano Marine Center, the Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Erika Esposito
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luigi Musco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica “Anton Dohrn,” Villa Comunale, Napoli, Italy
| | - Cristina Munari
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Jessica Fiori
- Department of Chemistry “G. Ciamician” Alma Mater Studiorum, University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italia
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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Anka IZ, Uren Webster TM, Berbel-Filho WM, Hitchings M, Overland B, Weller S, Garcia de Leaniz C, Consuegra S. Microbiome and epigenetic variation in wild fish with low genetic diversity. Nat Commun 2024; 15:4725. [PMID: 38830879 PMCID: PMC11148108 DOI: 10.1038/s41467-024-49162-8] [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: 05/11/2023] [Accepted: 05/23/2024] [Indexed: 06/05/2024] Open
Abstract
Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity.
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Affiliation(s)
- Ishrat Z Anka
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
- Department of Aquaculture, Chattogram Veterinary and Animal Sciences University, Chattogram, 4225, Bangladesh
| | - Tamsyn M Uren Webster
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Waldir M Berbel-Filho
- Department of Biology, University of Oklahoma, Norman, OK, 73019, USA
- Department of Biology, University of West Florida, Pensacola, FL, USA
| | - Matthew Hitchings
- Institute of Life Science, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Benjamin Overland
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Sarah Weller
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Carlos Garcia de Leaniz
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
- Marine Research Centre (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Sofia Consuegra
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK.
- Grupo de Biotecnología Acuática, Departamento de Biotecnología y Acuicultura, Instituto de Investigacións Mariñas, IIM-CSIC, Vigo, Spain.
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Abraham JO, Lin B, Miller AE, Henry LP, Demmel MY, Warungu R, Mwangi M, Lobura PM, Pallares LF, Ayroles JF, Pringle RM, Rubenstein DI. Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi). Mol Ecol 2024; 33:e17370. [PMID: 38682799 DOI: 10.1111/mec.17370] [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: 09/08/2023] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
Abstract
The composition of mammalian gut microbiomes is highly conserved within species, yet the mechanisms by which microbiome composition is transmitted and maintained within lineages of wild animals remain unclear. Mutually compatible hypotheses exist, including that microbiome fidelity results from inherited dietary habits, shared environmental exposure, morphophysiological filtering and/or maternal effects. Interspecific hybrids are a promising system in which to interrogate the determinants of microbiome composition because hybrids can decouple traits and processes that are otherwise co-inherited in their parent species. We used a population of free-living hybrid zebras (Equus quagga × grevyi) in Kenya to evaluate the roles of these four mechanisms in regulating microbiome composition. We analysed faecal DNA for both the trnL-P6 and the 16S rRNA V4 region to characterize the diets and microbiomes of the hybrid zebra and of their parent species, plains zebra (E. quagga) and Grevy's zebra (E. grevyi). We found that both diet and microbiome composition clustered by species, and that hybrid diets and microbiomes were largely nested within those of the maternal species, plains zebra. Hybrid microbiomes were less variable than those of either parent species where they co-occurred. Diet and microbiome composition were strongly correlated, although the strength of this correlation varied between species. These patterns are most consistent with the maternal-effects hypothesis, somewhat consistent with the diet hypothesis, and largely inconsistent with the environmental-sourcing and morphophysiological-filtering hypotheses. Maternal transmittance likely operates in conjunction with inherited feeding habits to conserve microbiome composition within species.
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Affiliation(s)
- Joel O Abraham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Bing Lin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- School of Public and International Affairs, Princeton University, Princeton, New Jersey, USA
| | - Audrey E Miller
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Lucas P Henry
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Department of Biology, New York University, New York City, New York, USA
| | - Margaret Y Demmel
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Section of Ecology, Behavior and Evolution, University of California San Diego, San Diego, California, USA
| | | | | | | | - Luisa F Pallares
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Julien F Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Robert M Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel I Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Mpala Research Conservancy, Laikipia County, Kenya
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Tsang CTT, Hui TKL, Chung NM, Yuen WT, Tsang LM. Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification. Mol Ecol 2024; 33:e17377. [PMID: 38713089 DOI: 10.1111/mec.17377] [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: 09/13/2023] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/08/2024]
Abstract
The acquisition of microbial symbionts enables animals to rapidly adapt to and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness and success of their hosts. However, the dynamics of host-microbe interactions and their evolutionary implications remain largely underexplored in marine invertebrates. Crabs of the family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants of mangrove forests and are considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed to have been facilitated by symbiotic gut microbes, enabling successful colonization of intertidal and terrestrial environments. To investigate the patterns and mechanisms shaping the microbial communities and the role of microbes in the evolution of Sesarmidae, we characterized and compared the gut microbiome compositions across 43 crab species from Sesarmidae and other mangrove-associated families using 16S metabarcoding. We found that the gut microbiome assemblages in crabs are primarily determined by host identity, with a secondary influence from environmental factors such as microhabitat and sampling location, and to a lesser extent influenced by biological factors such as sex and gut region. While patterns of phylosymbiosis (i.e. when microbial community relationships recapitulate the phylogeny of their hosts) were consistently observed in all beta-diversity metrics analysed, the strength of phylosymbiosis varied across crab families. This suggests that the bacterial assemblages in each family were differentially shaped by different degrees of host filtering and/or other evolutionary processes. Notably, Sesarmidae displayed signals of cophylogeny with its core gut bacterial genera, which likely play crucial functional roles in their hosts by providing lignocellulolytic enzymes, essential amino acids, and fatty acids supplementation. Our results support the hypothesis of microbial contribution to herbivory and terrestrialization in mangrove crabs, highlighting the tight association and codiversification of the crab holobiont.
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Affiliation(s)
- Chandlar Tsz To Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Tom Kwok Lun Hui
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nga Man Chung
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wing Tan Yuen
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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48
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Li F, Lin Y, Yang C, Yan Y, Hao R, Mkuye R, Deng Y. Effects of titanium dioxide nanoparticle exposure on the gut microbiota of pearl oyster (Pinctada fucata martensii). Comp Biochem Physiol C Toxicol Pharmacol 2024; 280:109906. [PMID: 38522712 DOI: 10.1016/j.cbpc.2024.109906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/05/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
With the advancement of nanotechnology and the growing utilization of nanomaterials, titanium dioxide (TiO2) has been released into aquatic environments, posing potential ecotoxicological risks to aquatic organisms. In this study, the toxicological effects of TiO2 nanoparticles were investigated on the intestinal health of pearl oyster (Pinctada fucata martensii). The pearl oysters were subjected to a 14-day exposure to 5-mg/L TiO2 nanoparticle, followed by a 7-day recovery period. Subsequently, the intestinal tissues were analyzed using 16S rDNA high-throughput sequencing. The results from LEfSe analysis revealed that TiO2 nanoparticle increased the susceptibility of pearl oysters to potential pathogenic bacteria infections. Additionally, the TiO2 nanoparticles led to alterations in the abundance of microbial communities in the gut of pearl oysters. Notable changes included a decrease in the relative abundance of Phaeobacter and Nautella, and an increase in the Actinobacteria, which could potentially impact the immune function of pearl oysters. The abundance of Firmicutes and Bacteroidetes, as well as the expression of genes related to energy metabolism (AMPK, PK, SCS-1, SCS-2, SCS-3), were down-regulated, suggesting that TiO2 nanoparticles exposure may affect the digestive and energy metabolic functions of pearl oysters. Furthermore, the short-term recovery of seven days did not fully restore these levels to normal. These findings provide crucial insights and serve as an important reference for understanding the toxic effects of TiO2 nanoparticles on bivalves.
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Affiliation(s)
- Fengfeng Li
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yujing Lin
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Chuangye Yang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang 524088, China.
| | - Yilong Yan
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ruijuan Hao
- Development and Research Center for Biological Marine Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang 524088, China
| | - Robert Mkuye
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yuewen Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang 524088, China; Pearl Research Institute, Guangdong Ocean University, Zhanjiang, China
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49
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Härer A, Frazier CJ, Rennison DJ. Host ecotype and rearing environment are the main drivers of threespine stickleback gut microbiota diversity in a naturalistic experiment. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240649. [PMID: 39100190 PMCID: PMC11296155 DOI: 10.1098/rsos.240649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/01/2024] [Indexed: 08/06/2024]
Abstract
Host-microbiota interactions play a critical role in the hosts' biology, and thus, it is crucial to elucidate the mechanisms that shape gut microbial communities. We leveraged threespine stickleback fish (Gasterosteus aculeatus) as a model system to investigate the contribution of host and environmental factors to gut microbiota variation. These fish offer a unique opportunity for experiments in naturalistic conditions; we reared benthic and limnetic ecotypes from three different lakes in experimental ponds, allowing us to assess the relative effects of shared environment (pond), geographic origin (lake-of-origin), trophic ecology and genetics (ecotype) and biological sex on gut microbiota α- and β-diversity. Host ecotype had the strongest influence on α-diversity, with benthic fish exhibiting higher diversity than limnetic fish, followed by the rearing environment. β-diversity was primarily shaped by rearing environment, followed by host ecotype, indicating that environmental factors play a crucial role in determining gut microbiota composition. Furthermore, numerous bacterial orders were differentially abundant across ponds, underlining the substantial contribution of environmental factors to gut microbiota variation. Our study illustrates the complex interplay between environmental and host ecological or genetic factors in shaping the stickleback gut microbiota and highlights the value of experiments conducted under naturalistic conditions for understanding gut microbiota dynamics.
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Affiliation(s)
- Andreas Härer
- School of Biological Sciences, Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, CA, USA
| | - Christine J. Frazier
- School of Biological Sciences, Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, CA, USA
| | - Diana J. Rennison
- School of Biological Sciences, Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, CA, USA
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50
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Baiz MD, Wood AW, Toews DPL. Association between the gut microbiome and carotenoid plumage phenotype in an avian hybrid zone. Proc Biol Sci 2024; 291:20240238. [PMID: 38628125 PMCID: PMC11022011 DOI: 10.1098/rspb.2024.0238] [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: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Vertebrates host complex microbiomes that impact their physiology. In many taxa, including colourful wood-warblers, gut microbiome similarity decreases with evolutionary distance. This may suggest that as host populations diverge, so do their microbiomes, because of either tight coevolutionary dynamics, or differential environmental influences, or both. Hybridization is common in wood-warblers, but the effects of evolutionary divergence on the microbiome during secondary contact are unclear. Here, we analyse gut microbiomes in two geographically disjunct hybrid zones between blue-winged warblers (Vermivora cyanoptera) and golden-winged warblers (Vermivora chrysoptera). We performed 16S faecal metabarcoding to identify species-specific bacteria and test the hypothesis that host admixture is associated with gut microbiome disruption. Species identity explained a small amount of variation between microbiomes in only one hybrid zone. Co-occurrence of species-specific bacteria was rare for admixed individuals, yet microbiome richness was similar among admixed and parental individuals. Unexpectedly, we found several bacteria that were more abundant among admixed individuals with a broader deposition of carotenoid-based plumage pigments. These bacteria are predicted to encode carotenoid biosynthesis genes, suggesting birds may take advantage of pigments produced by their gut microbiomes. Thus, host admixture may facilitate beneficial symbiotic interactions which contribute to plumage ornaments that function in sexual selection.
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Affiliation(s)
- Marcella D. Baiz
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Andrew W. Wood
- Department of Biology, Pennylvania State University, University Park, PA 16802, USA
| | - David P. L. Toews
- Department of Biology, Pennylvania State University, University Park, PA 16802, USA
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