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Rowley AF, Baker-Austin C, Boerlage AS, Caillon C, Davies CE, Duperret L, Martin SAM, Mitta G, Pernet F, Pratoomyot J, Shields JD, Shinn AP, Songsungthong W, Srijuntongsiri G, Sritunyalucksana K, Vidal-Dupiol J, Uren Webster TM, Taengchaiyaphum S, Wongwaradechkul R, Coates CJ. Diseases of marine fish and shellfish in an age of rapid climate change. iScience 2024; 27:110838. [PMID: 39318536 PMCID: PMC11420459 DOI: 10.1016/j.isci.2024.110838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024] Open
Abstract
A recurring trend in evidence scrutinized over the past few decades is that disease outbreaks will become more frequent, intense, and widespread on land and in water, due to climate change. Pathogens and the diseases they inflict represent a major constraint on seafood production and yield, and by extension, food security. The risk(s) for fish and shellfish from disease is a function of pathogen characteristics, biological species identity, and the ambient environmental conditions. A changing climate can adversely influence the host and environment, while augmenting pathogen characteristics simultaneously, thereby favoring disease outbreaks. Herein, we use a series of case studies covering some of the world's most cultured aquatic species (e.g., salmonids, penaeid shrimp, and oysters), and the pathogens (viral, fungal, bacterial, and parasitic) that afflict them, to illustrate the magnitude of disease-related problems linked to climate change.
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Affiliation(s)
- Andrew F Rowley
- Biosciences, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, Wales, UK
| | | | - Annette S Boerlage
- Centre for Epidemiology and Planetary Health (CEPH), SRUC School of Veterinary Medicine, Inverness, Scotland, UK
| | - Coline Caillon
- Université of Brest, Ifremer, CNRS, IRD, LEMAR, Plouzané, France
| | - Charlotte E Davies
- Biosciences, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, Wales, UK
| | - Léo Duperret
- IHPE, Université of Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, Montpellier, France
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland, UK
| | - Guillaume Mitta
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Tahiti, French Polynesia
| | - Fabrice Pernet
- Université of Brest, Ifremer, CNRS, IRD, LEMAR, Plouzané, France
| | - Jarunan Pratoomyot
- Institute of Marine Science, Burapha University, Chonburi 20131, Thailand
| | - Jeffrey D Shields
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA 23062, USA
| | - Andrew P Shinn
- INVE Aquaculture (Thailand), 471 Bond Street, Bangpood, Pakkred, Nonthaburi 11120, Thailand
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Warangkhana Songsungthong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Bangkok 10400, Thailand
| | - Gun Srijuntongsiri
- School of Information, Computer, and Communication Technology, Sirindhorn International Institute of Technology, Thammasat University, Pathum Thani, Thailand
| | - Kallaya Sritunyalucksana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Bangkok 10400, Thailand
| | - Jeremie Vidal-Dupiol
- IHPE, Université of Montpellier, CNRS, Ifremer, University Perpignan Via Domitia, Montpellier, France
| | - Tamsyn M Uren Webster
- Biosciences, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, Wales, UK
| | - Suparat Taengchaiyaphum
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Bangkok 10400, Thailand
| | | | - Christopher J Coates
- Biosciences, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, Wales, UK
- Zoology and Ryan Institute, School of Natural Sciences, University of Galway, H91 TK33 Galway, Ireland
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Zhang X, Jiang C, Xu S, Zheng X, Liu X, Wang J, Wu W, Wang C, Zhuang X. Microbiome and network analysis reveal potential mechanisms underlying Carassius auratus diseases: The interactions between critical environmental and microbial factors. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122485. [PMID: 39278018 DOI: 10.1016/j.jenvman.2024.122485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 08/09/2024] [Accepted: 09/10/2024] [Indexed: 09/17/2024]
Abstract
Despite the rapid development of research on aquatic environment microbiota, limited attention has been paid to exploring the complex interactions between microbial communities and aquatic environments. Particularly, the mechanisms underlying fish diseases based on such dynamic interactions remain unknown. This study aimed to address the gap by conducting microbiome and co-occurrence network analyses on the typical freshwater aquaculture systems. High-throughput 16S rRNA gene sequencing results revealed significant differences in the microbiota between the disease and healthy groups. Notably, disease mortality varied consistently with the gradient of relative abundance of Proteobacteria (intestine, R2 = 0.46, p < 0.05) and Cyanobacteria (gill, R2 = 0.67, p < 0.01), indicating their potential use as diagnostic criteria. Furthermore, the elevated hepatosomatic index, NO3-N, COD and TC (sediment) were directly correlated with diseases (r > 0.54, p < 0.01). Mean concentrations of NO3-N, COD and TC were elevated by 78.87%, 25.63% and 44.2%, respectively, in ponds where diseases occurred. Quantitative analysis (qPCR) revealed that Aeromonas sobria infected hosts through a potential pathway of "sediment (4.4 × 105 copy number/g)-water (1.1 × 103 copy number/mL)-intestine (1.2 × 106 copy number/g)". Similarly, the potential route for Aeromonas veronii was sediment (4.9 × 106 copy number/g) to gill (5.1 × 105 copy number/g). Additionally, the complexity of microbial networks in the intestine, water, and sediment was significantly lower in the disease group, although no similar phenomenon was observed in the gill microbial network. In summary, these findings reveal that elevated concentrations of crucial environmental factors disrupt the linkages within microbiota, fostering the growth of opportunistic bacteria capable of colonizing fish gut or gills. This offers new insights into potential mechanisms by which environmental factors cause disease in fish.
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Affiliation(s)
- Xupo Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cancan Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shengjun Xu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Yangtze River Delta Research Center for Eco-Environmental Sciences, China Key Laboratory of Environmental Biotechnology, Yiwu, 322000, China.
| | - Xiaoxu Zheng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxuan Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Jinglin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenzheng Wu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cong Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuliang Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
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Leveau JHJ. Re-Envisioning the Plant Disease Triangle: Full Integration of the Host Microbiota and a Focal Pivot to Health Outcomes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:31-47. [PMID: 38684078 DOI: 10.1146/annurev-phyto-121423-042021] [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: 05/02/2024]
Abstract
The disease triangle is a structurally simple but conceptually rich model that is used in plant pathology and other fields of study to explain infectious disease as an outcome of the three-way relationship between a host, a pathogen, and their environment. It also serves as a guide for finding solutions to treat, predict, and prevent such diseases. With the omics-driven, evidence-based realization that the abundance and activity of a pathogen are impacted by proximity to and interaction with a diverse multitude of other microorganisms colonizing the same host, the disease triangle evolved into a tetrahedron shape, which features an added fourth dimension representing the host-associated microbiota. Another variant of the disease triangle emerged from the recently formulated pathobiome paradigm, which deviates from the classical "one pathogen" etiology of infectious disease in favor of a scenario in which disease represents a conditional outcome of complex interactions between and among a host, its microbiota (including microbes with pathogenic potential), and the environment. The result is a version of the original disease triangle where "pathogen" is substituted with "microbiota." Here, as part of a careful and concise review of the origin, history, and usage of the disease triangle, I propose a next step in its evolution, which is to replace the word "disease" in the center of the host-microbiota-environment triad with the word "health." This triangle highlights health as a desirable outcome (rather than disease as an unwanted state) and as an emergent property of host-microbiota-environment interactions. Applied to the discipline of plant pathology, the health triangle offers an expanded range of targets and approaches for the diagnosis, prediction, restoration, and maintenance of plant health outcomes. Its applications are not restricted to infectious diseases only, and its underlying framework is more inclusive of all microbial contributions to plant well-being, including those by mycorrhizal fungi and nitrogen-fixing bacteria, for which there never was a proper place in the plant disease triangle. The plant health triangle also may have an edge as an education and communication tool to convey and stress the importance of healthy plants and their associated microbiota to a broader public and stakeholdership.
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Affiliation(s)
- Johan H J Leveau
- Department of Plant Pathology, University of California, Davis, California, USA;
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Marcianò D, Kappel L, Ullah SF, Srivastava V. From glycans to green biotechnology: exploring cell wall dynamics and phytobiota impact in plant glycopathology. Crit Rev Biotechnol 2024:1-19. [PMID: 39004515 DOI: 10.1080/07388551.2024.2370341] [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: 03/06/2024] [Accepted: 06/06/2024] [Indexed: 07/16/2024]
Abstract
Filamentous plant pathogens, including fungi and oomycetes, pose significant threats to cultivated crops, impacting agricultural productivity, quality and sustainability. Traditionally, disease control heavily relied on fungicides, but concerns about their negative impacts motivated stakeholders and government agencies to seek alternative solutions. Biocontrol agents (BCAs) have been developed as promising alternatives to minimize fungicide use. However, BCAs often exhibit inconsistent performances, undermining their efficacy as plant protection alternatives. The eukaryotic cell wall of plants and filamentous pathogens contributes significantly to their interaction with the environment and competitors. This highly adaptable and modular carbohydrate armor serves as the primary interface for communication, and the intricate interplay within this compartment is often mediated by carbohydrate-active enzymes (CAZymes) responsible for cell wall degradation and remodeling. These processes play a crucial role in the pathogenesis of plant diseases and contribute significantly to establishing both beneficial and detrimental microbiota. This review explores the interplay between cell wall dynamics and glycan interactions in the phytobiome scenario, providing holistic insights for efficiently exploiting microbial traits potentially involved in plant disease mitigation. Within this framework, the incorporation of glycobiology-related functional traits into the resident phytobiome can significantly enhance the plant's resilience to biotic stresses. Therefore, in the rational engineering of future beneficial consortia, it is imperative to recognize and leverage the understanding of cell wall interactions and the role of the glycome as an essential tool for the effective management of plant diseases.
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Affiliation(s)
- Demetrio Marcianò
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy
| | - Lisa Kappel
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
| | - Sadia Fida Ullah
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
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Zhu W, Chang L, Zhang M, Chen Q, Sui L, Shen C, Jiang J. Microbial diversity in mountain-dwelling amphibians: The combined effects of host and climatic factors. iScience 2024; 27:109907. [PMID: 38812552 PMCID: PMC11135016 DOI: 10.1016/j.isci.2024.109907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/30/2023] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Comprehending the determinants of host-associated microbiota is pivotal in microbial ecology. Yet, the links between climatic factors and variations in host-associated microbiota necessitate further clarification. Mountain-dwelling amphibians, with limited dispersal abilities, serve as valuable models for addressing these questions. Our study, using 126 amphibian-associated microbial samples (64 gut and 62 skin) and 101 environmental microbial samples (51 soil and 50 water) from the eastern Tibetan Plateau, revealed host factors as primary drivers of the variations in host-associated microbiota. However, climatic factors contributed to additional variations in gut microbial beta-diversity and skin microbial function. Water microbiota were identified as a significant contributor to the amphibian-associated microbiomes, with their climate-driven variations mediating an indirect association between the variations in climatic factors and host-associated microbiota. These findings extend our understanding of the assembly of host-associated microbiota in amphibians, emphasizing the significance of microbiota in evaluating the impact of climate change on animals.
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Affiliation(s)
- Wei Zhu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Liming Chang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Meihua Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Qiheng Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Sui
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Shen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Romero-Contreras YJ, González-Serrano F, Bello-López E, Formey D, Aragón W, Cevallos MÁ, Rebollar EA, Serrano M. Bacteria from the skin of amphibians promote growth of Arabidopsis thaliana and Solanum lycopersicum by modifying hormone-related transcriptome response. PLANT MOLECULAR BIOLOGY 2024; 114:39. [PMID: 38615069 PMCID: PMC11016013 DOI: 10.1007/s11103-024-01444-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/11/2024] [Indexed: 04/15/2024]
Abstract
Plants and microorganisms establish beneficial associations that can improve their development and growth. Recently, it has been demonstrated that bacteria isolated from the skin of amphibians can contribute to plant growth and defense. However, the molecular mechanisms involved in the beneficial effect for the host are still unclear. In this work, we explored whether bacteria isolated from three tropical frogs species can contribute to plant growth. After a wide screening, we identified three bacterial strains with high biostimulant potential, capable of modifying the root structure of Arabidopsis thaliana plants. In addition, applying individual bacterial cultures to Solanum lycopersicum plants induced an increase in their growth. To understand the effect that these microorganisms have over the host plant, we analysed the transcriptomic profile of A. thaliana during the interaction with the C32I bacterium, demonstrating that the presence of the bacteria elicits a transcriptional response associated to plant hormone biosynthesis. Our results show that amphibian skin bacteria can function as biostimulants to improve agricultural crops growth and development by modifying the plant transcriptomic responses.
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Affiliation(s)
- Yordan J Romero-Contreras
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
- Programa de Doctorado en Ciencias Biomédicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
| | | | - Elena Bello-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Wendy Aragón
- Instituto de Biociencias, Universidad Autónoma de Chiapas, Blvd. Príncipe Akishino s/n, 30798, Tapachula, Chiapas, Mexico
| | - Miguel Ángel Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
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Zhu Q, Qi S, Guo D, Li C, Su M, Wang J, Li Z, Yang D, Sun H, Wang X, Wang M, Wu H, Yu S, Bai W, Zhang Y, Yang X, Jiang L, Liu J, Zhao Y, Xing X, Shi D, Feng L, Sun D. A survey of fecal virome and bacterial community of the diarrhea-affected cattle in northeast China reveals novel disease-associated ecological risk factors. mSystems 2024; 9:e0084223. [PMID: 38108282 PMCID: PMC10804951 DOI: 10.1128/msystems.00842-23] [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: 08/10/2023] [Accepted: 11/06/2023] [Indexed: 12/19/2023] Open
Abstract
Limited information on the virome and bacterial community hampers our ability to discern systemic ecological risk factors that cause cattle diarrhea, which has become a pressing issue in the control of disease. A total of 110 viruses, 1,011 bacterial genera, and 322 complete viral genomes were identified from 70 sequencing samples mixed with 1,120 fecal samples from 58 farms in northeast China. For the diarrheic samples, the identified virome and bacterial community varied in terms of composition, abundance, diversity, and geographic distribution in relation to different disease-associated ecological factors; the abundance of identified viruses and bacteria was significantly correlated with the host factors of clinical status, cattle type, and age, and with environmental factors such as aquaculture model and geographical location (P < 0.05); a significant interaction occurred between viruses and viruses, bacteria and bacteria, as well as between bacteria and viruses (P < 0.05). The abundance of SMB53, Butyrivibrio, Facklamia, Trichococcus, and Turicibacter was significantly correlated with the health status of cattle (P < 0.05). The proportion of BRV, BCoV, BKV, BToV, BoNoV, BoNeV, BoAstV, BEV, BoPV, and BVDV in 1,120 fecal samples varied from 1.61% to 12.05%. A series of significant correlations were observed between the prevalence of individual viruses and the disease-associated ecological factors. A genome-based phylogenetic analysis revealed high variability of 10 bovine enteric viruses. The bovine hungarovirus was initially identified in both dairy and beef cattle in China. This study elucidates the fecal virome and bacterial community signatures of cattle affected by diarrhea, and reveals novel disease-associated ecological risk factors, including cattle type, cattle age, aquaculture model, and geographical location.IMPORTANCEThe lack of data on the virome and bacterial community restricts our capability to recognize ecological risk factors for bovine diarrhea disease, thereby hindering our overall comprehension of the disease's cause. In this study, we found that, for the diarrheal samples, the identified virome and bacterial community varied in terms of composition, abundance, diversity, configuration, and geographic distribution in relation to different disease-associated ecological factors. A series of significant correlations were observed between the prevalence of individual viruses and the disease-associated ecological factors. Our study aims to uncover novel ecological risk factors of bovine diarrheal disease by examining the pathogenic microorganism-host-environment disease ecology, thereby providing a new perspective on the control of bovine diarrheal diseases.
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Affiliation(s)
- Qinghe Zhu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shanshan Qi
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Donghua Guo
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Chunqiu Li
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Mingjun Su
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jianfa Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zijian Li
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Dan Yang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Haibo Sun
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiaoran Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Meijiao Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Haoyang Wu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shiping Yu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wenfei Bai
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yongchen Zhang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xu Yang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Limin Jiang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jiaying Liu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yingying Zhao
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiaoxu Xing
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Da Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Dongbo Sun
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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8
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Sakda P, Xiang X, Song Z, Wu Y, Zhou L. Impact of Season on Intestinal Bacterial Communities and Pathogenic Diversity in Two Captive Duck Species. Animals (Basel) 2023; 13:3879. [PMID: 38136916 PMCID: PMC10740475 DOI: 10.3390/ani13243879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Vertebrates and their gut bacteria interact in complex and mutually beneficial ways. The intestinal microbial composition is influenced by several external influences. In addition to food, the abiotic elements of the environment, such as temperature, humidity, and seasonal fluctuation are also important determinants. Fecal samples were collected from two captive duck species, Baikal teal (Sibirionetta formosa) and common teal (Anas crecca) across four seasons (summer, autumn, winter, and spring). These ducks were consistently fed the same diet throughout the entire experiment. High throughput sequencing (Illumina Mi-seq) was employed to analyze the V4-V5 region of the 16sRNA gene. The dominant phyla in all seasons were Proteobacteria and Firmicutes. Interestingly, the alpha diversity was higher in winter for both species. The NMDS, PCoA, and ANOSIM analysis showed the distinct clustering of bacterial composition between different seasons, while no significant differences were discovered between duck species within the same season. In addition, LefSe analysis demonstrated specific biomarkers in different seasons, with the highest number revealed in winter. The co-occurrence network analysis also showed that during winter, the network illustrated a more intricate structure with the greatest number of nodes and edges. However, this study identified ten potentially pathogenic bacterial species, which showed significantly enhanced diversity and abundance throughout the summer. Overall, our results revealed that season mainly regulated the intestinal bacterial community composition and pathogenic bacteria of captive ducks under the instant diet. This study provides an important new understanding of the seasonal variations in captive wild ducks' intestinal bacterial community structure. The information available here may be essential data for preventing and controlling infections caused by pathogenic bacteria in captive waterbirds.
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Affiliation(s)
- Patthanan Sakda
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
| | - Xingjia Xiang
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
| | - Zhongqiao Song
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
| | - Yuannuo Wu
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
| | - Lizhi Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
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9
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Neely WJ, Martins RA, Mendonça da Silva CM, Ferreira da Silva T, Fleck LE, Whetstone RD, Woodhams DC, Cook WH, Prist PR, Valiati VH, Greenspan SE, Tozetti AM, Earley RL, Becker CG. Linking microbiome and stress hormone responses in wild tropical treefrogs across continuous and fragmented forests. Commun Biol 2023; 6:1261. [PMID: 38087051 PMCID: PMC10716138 DOI: 10.1038/s42003-023-05600-9] [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: 07/26/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
The amphibian skin microbiome is an important component of anti-pathogen defense, but the impact of environmental change on the link between microbiome composition and host stress remains unclear. In this study, we used radiotelemetry and host translocation to track microbiome composition and function, pathogen infection, and host stress over time across natural movement paths for the forest-associated treefrog, Boana faber. We found a negative correlation between cortisol levels and putative microbiome function for frogs translocated to forest fragments, indicating strong integration of host stress response and anti-pathogen potential of the microbiome. Additionally, we observed a capacity for resilience (resistance to structural change and functional loss) in the amphibian skin microbiome, with maintenance of putative pathogen-inhibitory function despite major temporal shifts in microbiome composition. Although microbiome community composition did not return to baseline during the study period, the rate of microbiome change indicated that forest fragmentation had more pronounced effects on microbiome composition than translocation alone. Our findings reveal associations between stress hormones and host microbiome defenses, with implications for resilience of amphibians and their associated microbes facing accelerated tropical deforestation.
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Affiliation(s)
- Wesley J Neely
- Department of Biology, The University of Alabama, Tuscaloosa, AL, 35487, USA.
- Department of Biology, Texas State University, San Marcos, TX, 78666, USA.
| | - Renato A Martins
- Department of Biology, and Center for Infectious Disease Dynamics, One Health Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Camila M Mendonça da Silva
- Programa de Pos‑Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022‑750, Brazil
| | - Tainá Ferreira da Silva
- Programa de Pos‑Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022‑750, Brazil
| | - Lucas E Fleck
- Programa de Pos‑Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022‑750, Brazil
| | - Ross D Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - W Harrison Cook
- Department of Biology, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Paula R Prist
- EcoHealth Alliance, 520 Eight Avenue, Suite 1200, New York, NY, 10018, USA
| | - Victor H Valiati
- Programa de Pos‑Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022‑750, Brazil
| | - Sasha E Greenspan
- Department of Biology, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Alexandro M Tozetti
- Programa de Pos‑Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022‑750, Brazil
| | - Ryan L Earley
- Department of Biology, The University of Alabama, Tuscaloosa, AL, 35487, USA
| | - C Guilherme Becker
- Department of Biology, and Center for Infectious Disease Dynamics, One Health Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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10
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Sun D, Herath J, Zhou S, Ellepola G, Meegaskumbura M. Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts. ISME COMMUNICATIONS 2023; 3:123. [PMID: 37993728 PMCID: PMC10665332 DOI: 10.1038/s43705-023-00332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Amphibian skin harbors microorganisms that are associated with the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, one of the most significant wildlife diseases known. This pathogen originated in Asia, where diverse Bd lineages exist; hence, native amphibian hosts have co-existed with Bd over long time periods. Determining the nuances of this co-existence is crucial for understanding the prevalence and spread of Bd from a microbial context. However, associations of Bd with the natural skin microbiome remain poorly understood for Asian hosts, especially in relation to skin-associated fungi. We used 16 S rRNA and fungal internal transcribed spacer (ITS) gene sequencing to characterize the skin microbiome of four native Asian amphibian species and examined the relationships between Bd infection and their skin bacterial and fungal communities; we also analyzed the correlates of the putative anti-Bd bacteria. We show that both skin bacterial and fungal community structure and composition had significant associations with infection status (Bd presence/absence) and infection intensity (frequency of Bd sequence reads). We also found that the putative anti-Bd bacterial richness was correlated with Bd infection status and infection intensity, and observed that the relative abundance of anti-Bd bacteria roughly correspond with changes in both Bd prevalence and mean infection intensity in populations. Additionally, the microbial co-occurrence network of infected frogs was significantly different from that of uninfected frogs that were characterized by more keystone nodes (connectors) and larger proportions in correlations between bacteria, suggesting stronger inter-module bacterial interactions. These results indicate that the mutual effects between Bd and skin-associated microbiome, including the interplay between bacteria and fungi, might vary with Bd infection in susceptible amphibian species. This knowledge will help in understanding the dynamics of Bd from a microbial perspective, potentially contributing to mitigate chytridiomycosis in other regions of the world.
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Affiliation(s)
- Dan Sun
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Jayampathi Herath
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- School of Biomedical Sciences, International Institute of Health Sciences (IIHS), No 704 Negombo Rd, Welisara, 71722, Sri Lanka
| | - Shipeng Zhou
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Gajaba Ellepola
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- Department of Zoology, Faculty of Science, University of Peradeniya, Peradeniya, KY20400, Sri Lanka
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China.
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11
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Lamine I, Chahouri A, Moukrim A, Ait Alla A. The impact of climate change and pollution on trematode-bivalve dynamics. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106130. [PMID: 37625953 DOI: 10.1016/j.marenvres.2023.106130] [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: 04/13/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
Coastal ecosystems and their marine populations are increasingly threatened by global environmental changes. Bivalves have emerged as crucial bioindicators within these ecosystems, offering valuable insights into biodiversity and overall ecosystem health. In particular, bivalves serve as hosts to trematode parasites, making them a focal point of study. Trematodes, with their life cycles intricately linked to external factors, provide excellent indicators of environmental changes and exhibit a unique ability to accumulate pollutants beyond ambient levels. Thus, they act as living sentinels, reflecting the ecological condition of their habitats. This paper presents a comprehensive review of recent research on the use of bivalve species as hosts for trematodes, examining the interactions between these organisms. The study also investigates the combined impact of trematode infections and other pollutants on bivalve molluscs. Trematode infections have multifaceted consequences for bivalve species, influencing various aspects of their physiology and behavior, including population-wide mortality. Furthermore, the coexistence of trematode infections and other sources of pollution compromises host resistance, disrupts parasite transmission, and reduces the abundance of intermediate hosts for complex-living parasites. The accumulation process of these parasites is influenced not only by external factors but also by host physiology. Consequently, the implications of climate change and environmental factors, such as temperature, salinity, and ocean acidification, are critical considerations. In summary, the intricate relationship between bivalves, trematode parasites, and their surrounding environment provides valuable insights into the health and sustainability of coastal ecosystems. A comprehensive understanding of these interactions, along with the influence of climate change and environmental parameters, is essential for effective management and conservation strategies aimed at preserving these delicate ecosystems and the diverse array of species that rely on them.
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Affiliation(s)
- Imane Lamine
- Laboratory of Aquatic Systems: Marine and Continental Ecosystems, Department of Biology, Faculty of Sciences, Ibn Zohr University, BP 8106, Agadir, Morocco.
| | - Abir Chahouri
- Laboratory of Aquatic Systems: Marine and Continental Ecosystems, Department of Biology, Faculty of Sciences, Ibn Zohr University, BP 8106, Agadir, Morocco
| | | | - Aicha Ait Alla
- Laboratory of Aquatic Systems: Marine and Continental Ecosystems, Department of Biology, Faculty of Sciences, Ibn Zohr University, BP 8106, Agadir, Morocco
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12
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Schmit KJ, Garcia P, Sciortino A, Aho VTE, Pardo Rodriguez B, Thomas MH, Gérardy JJ, Bastero Acha I, Halder R, Cialini C, Heurtaux T, Ostahi I, Busi SB, Grandmougin L, Lowndes T, Singh Y, Martens EC, Mittelbronn M, Buttini M, Wilmes P. Fiber deprivation and microbiome-borne curli shift gut bacterial populations and accelerate disease in a mouse model of Parkinson's disease. Cell Rep 2023; 42:113071. [PMID: 37676767 PMCID: PMC10548091 DOI: 10.1016/j.celrep.2023.113071] [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: 07/29/2022] [Revised: 07/01/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023] Open
Abstract
Parkinson's disease (PD) is a neurological disorder characterized by motor dysfunction, dopaminergic neuron loss, and alpha-synuclein (αSyn) inclusions. Many PD risk factors are known, but those affecting disease progression are not. Lifestyle and microbial dysbiosis are candidates in this context. Diet-driven gut dysbiosis and reduced barrier function may increase exposure of enteric neurons to toxins. Here, we study whether fiber deprivation and exposure to bacterial curli, a protein cross-seeding with αSyn, individually or together, exacerbate disease in the enteric and central nervous systems of a transgenic PD mouse model. We analyze the gut microbiome, motor behavior, and gastrointestinal and brain pathologies. We find that diet and bacterial curli alter the microbiome and exacerbate motor performance, as well as intestinal and brain pathologies, but to different extents. Our results shed important insights on how diet and microbiome-borne insults modulate PD progression via the gut-brain axis and have implications for lifestyle management of PD.
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Affiliation(s)
- Kristopher J Schmit
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Institute for Medical Genetics and Applied Genomics, Hospital University Tubingen, 72076 Tubingen, Germany; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg.
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Alessia Sciortino
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Velma T E Aho
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Beatriz Pardo Rodriguez
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Mélanie H Thomas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Jean-Jacques Gérardy
- Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg; National Center of Pathology, Laboratoire National de Santé, 3555 Dudelange, Luxembourg
| | - Irati Bastero Acha
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Camille Cialini
- Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg; Department of Cancer Research, Luxembourg Institute of Health, 1526 Luxembourg, Luxembourg
| | - Tony Heurtaux
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg; Department of Life Sciences and Medicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Irina Ostahi
- National Center of Pathology, Laboratoire National de Santé, 3555 Dudelange, Luxembourg
| | - Susheel B Busi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Léa Grandmougin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Tuesday Lowndes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg
| | - Yogesh Singh
- Institute for Medical Genetics and Applied Genomics, Hospital University Tubingen, 72076 Tubingen, Germany
| | - Eric C Martens
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg; National Center of Pathology, Laboratoire National de Santé, 3555 Dudelange, Luxembourg; Department of Cancer Research, Luxembourg Institute of Health, 1526 Luxembourg, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Luxembourg Center of Neuropathology, 3555 Dudelange, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg.
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13
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Murphy KM, Le SM, Wilson AE, Warner DA. The Microbiome as a Maternal Effect: A Systematic Review on Vertical Transmission of Microbiota. Integr Comp Biol 2023; 63:597-609. [PMID: 37218690 DOI: 10.1093/icb/icad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/24/2023] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
The microbiome is an interactive and fluctuating community of microbes that colonize and develop across surfaces, including those associated with organismal hosts. A growing number of studies exploring how microbiomes vary in ecologically relevant contexts have recognized the importance of microbiomes in affecting organismal evolution. Thus, identifying the source and mechanism for microbial colonization in a host will provide insight into adaptation and other evolutionary processes. Vertical transmission of microbiota is hypothesized to be a source of variation in offspring phenotypes with important ecological and evolutionary implications. However, the life-history traits that govern vertical transmission are largely unexplored in the ecological literature. To increase research attention to this knowledge gap, we conducted a systematic review to address the following questions: (1) How often is vertical transmission assessed as a contributor to offspring microbiome colonization and development? (2) Do studies have the capacity to address how maternal transmission of microbes affects the offspring phenotype? (3) How do studies vary based on taxonomy and life history of the study organism, as well as the experimental, molecular, and statistical methods employed? Extensive literature searches reveal that many studies examining vertical transmission of microbiomes fail to collect whole microbiome samples from both maternal and offspring sources, particularly for oviparous vertebrates. Additionally, studies should sample functional diversity of microbes to provide a better understanding of mechanisms that influence host phenotypes rather than solely taxonomic variation. An ideal microbiome study incorporates host factors, microbe-microbe interactions, and environmental factors. As evolutionary biologists continue to merge microbiome science and ecology, examining vertical transmission of microbes across taxa can provide inferences on causal links between microbiome variation and phenotypic evolution.
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Affiliation(s)
- Kaitlyn M Murphy
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Samantha M Le
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Alan E Wilson
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Daniel A Warner
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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14
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Siomko SA, Greenspan SE, Barnett KM, Neely WJ, Chtarbanova S, Woodhams DC, McMahon TA, Becker CG. Selection of an anti-pathogen skin microbiome following prophylaxis treatment in an amphibian model system. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220126. [PMID: 37305917 PMCID: PMC10258671 DOI: 10.1098/rstb.2022.0126] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/03/2022] [Indexed: 06/13/2023] Open
Abstract
With emerging diseases on the rise, there is an urgent need to identify and understand novel mechanisms of prophylactic protection in vertebrate hosts. Inducing resistance against emerging pathogens through prophylaxis is an ideal management strategy that may impact pathogens and their host-associated microbiome. The host microbiome is recognized as a critical component of immunity, but the effects of prophylactic inoculation on the microbiome are unknown. In this study, we investigate the effects of prophylaxis on host microbiome composition, focusing on the selection of anti-pathogenic microbes contributing to host acquired immunity in a model host-fungal disease system, amphibian chytridiomycosis. We inoculated larval Pseudacris regilla against the fungal pathogen Batrachochytrium dendrobatidis (Bd) with a Bd metabolite-based prophylactic. Increased prophylactic concentration and exposure duration were associated with significant increases in proportions of putatively Bd-inhibitory host-associated bacterial taxa, indicating a protective prophylactic-induced shift towards microbiome members that are antagonistic to Bd. Our findings are in accordance with the adaptive microbiome hypothesis, where exposure to a pathogen alters the microbiome to better cope with subsequent pathogen encounters. Our study advances research on the temporal dynamics of microbiome memory and the role of prophylaxis-induced shifts in microbiomes contributing to prophylaxis effectiveness. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
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Affiliation(s)
- Samantha A. Siomko
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Sasha E. Greenspan
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - K. M. Barnett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Wesley J. Neely
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | | | - Douglas C. Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Taegan A. McMahon
- Department of Biology, Connecticut College, New London, CT 06320, USA
| | - C. Guilherme Becker
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, One Health Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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15
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Hughey MC, Warne R, Dulmage A, Reeve RE, Curtis GH, Whitfield K, Schock DM, Crespi E. Diet- and salinity-induced modifications of the gut microbiota are associated with differential physiological responses to ranavirus infection in Rana sylvatica. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220121. [PMID: 37305908 PMCID: PMC10258663 DOI: 10.1098/rstb.2022.0121] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/26/2023] [Indexed: 06/13/2023] Open
Abstract
Greater knowledge of how host-microbiome interactions vary with anthropogenic environmental change and influence pathogenic infections is needed to better understand stress-mediated disease outcomes. We investigated how increasing salinization in freshwaters (e.g. due to road de-icing salt runoff) and associated increases in growth of nutritional algae influenced gut bacterial assembly, host physiology and responses to ranavirus exposure in larval wood frogs (Rana sylvatica). Elevating salinity and supplementing a basic larval diet with algae increased larval growth and also increased ranavirus loads. However, larvae given algae did not exhibit elevated kidney corticosterone levels, accelerated development or weight loss post-infection, whereas larvae fed a basic diet did. Thus, algal supplementation reversed a potentially maladaptive stress response to infection observed in prior studies in this system. Algae supplementation also reduced gut bacterial diversity. Notably, we observed higher relative abundances of Firmicutes in treatments with algae-a pattern consistent with increased growth and fat deposition in mammals-that may contribute to the diminished stress responses to infection via regulation of host metabolism and endocrine function. Our study informs mechanistic hypotheses about the role of microbiome mediation of host responses to infection that can be tested in future experiments in this host-pathogen system. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
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Affiliation(s)
- Myra C. Hughey
- Department of Biology, Vassar College, Poughkeepsie, NY 12604, USA
| | - Robin Warne
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
| | - Alexa Dulmage
- School of Biological Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | - Robyn E. Reeve
- School of Biological Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | - Grace H. Curtis
- School of Biological Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | - Kourtnie Whitfield
- School of Biological Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | | | - Erica Crespi
- School of Biological Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
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16
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Assis VR, Robert J, Titon SCM. Introduction to the special issue Amphibian immunity: stress, disease and ecoimmunology. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220117. [PMID: 37305915 PMCID: PMC10258669 DOI: 10.1098/rstb.2022.0117] [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: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Amphibian populations have been declining worldwide, with global climate changes and infectious diseases being among the primary causes of this scenario. Infectious diseases are among the primary drivers of amphibian declines, including ranavirosis and chytridiomycosis, which have gained more attention lately. While some amphibian populations are led to extinction, others are disease-resistant. Although the host's immune system plays a major role in disease resistance, little is known about the immune mechanisms underlying amphibian disease resistance and host-pathogen interactions. As ectotherms, amphibians are directly subjected to changes in temperature and rainfall, which modulate stress-related physiology, including immunity and pathogen physiology associated with diseases. In this sense, the contexts of stress, disease and ecoimmunology are essential for a better understanding of amphibian immunity. This issue brings details about the ontogeny of the amphibian immune system, including crucial aspects of innate and adaptive immunity and how ontogeny can influence amphibian disease resistance. In addition, the papers in the issue demonstrate an integrated view of the amphibian immune system associated with the influence of stress on immune-endocrine interactions. The collective body of research presented herein can provide valuable insights into the mechanisms underlying disease outcomes in natural populations, particularly in the context of changing environmental conditions. These findings may ultimately enhance our ability to forecast effective conservation strategies for amphibian populations. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
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Affiliation(s)
- Vania Regina Assis
- Departamento de Fisiologia, Instituto de Biociências, Universidade de São Paulo, 05508-900 São Paulo, Brazil
- College of Public Health, University of South Florida, Tampa, FL 33612-9415, USA
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA
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Tang T, Wang F, Fang G, Mao T, Guo J, Kuang H, Sun G, Guo X, Duan Y, You J. Coptischinensis Franch root rot infection disrupts microecological balance of rhizosphere soil and endophytic microbiomes. Front Microbiol 2023; 14:1180368. [PMID: 37303806 PMCID: PMC10248259 DOI: 10.3389/fmicb.2023.1180368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/21/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction The ecological balance of the plant microbiome, as a barrier against pathogens, is very important for host health. Coptis chinensis is one of the important medicinal plants in China. In recent years, Illumina Miseq high-throughput sequencing technology was frequently used to analyze root rot pathogens and the effects of root rot on rhizosphere microorganisms of C. chinensis. But the effects of root rot infection on rhizosphere microecological balance of C. chinensis have received little attention. Methods In this study, Illumina Miseq high-throughput sequencing technology was applied to analyze the impact on microbial composition and diversity of C. chinensis by root rot. Results The results showed that root rot infection had significant impact on bacterial α-diversity in rhizome samples, but had no significant effect on that in leaf samples and rhizosphere soil samples, while root rot infection exhibited significant impact on the fungal α-diversity in leaf samples and rhizosphere soil samples, and no significant impact on that in rhizome samples. PCoA analysis showed that the root rot infection had a greater impact on the fungal community structure in the rhizosphere soil, rhizome, and leaf samples of C. chinensis than on the bacterial community structure. Root rot infection destroyed the microecological balance of the original microbiomes in the rhizosphere soil, rhizome, and leaf samples of C. chinensis, which may also be one of the reasons for the serious root rot of C. chinensis. Discussion In conclusion, our findings suggested that root rot infection with C. chinensis disrupts microecological balance of rhizosphere soil and endophytic microbiomes. The results of this study can provide theoretical basis for the prevention and control of C. chinensis root rot by microecological regulation.
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Affiliation(s)
- Tao Tang
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Fanfan Wang
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Guobin Fang
- Hubei Provincial Plant Protection Station, Wuhan, China
| | - Ting Mao
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
| | - Jie Guo
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Hui Kuang
- Hubei Provincial Plant Protection Station, Wuhan, China
| | | | - Xiaoliang Guo
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
| | - Yuanyuan Duan
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Jingmao You
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
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18
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Chai L, Wang H, Li X, Wang H. Comparison of the characteristics of gut microbiota response to lead in Bufo gargarizans tadpole at different developmental stages. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:20907-20922. [PMID: 36261638 DOI: 10.1007/s11356-022-23671-9] [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: 06/08/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
In amphibians, lead (Pb) exposure could alter the composition and structure of gut microbiota, but changes involving microbiota of several successive phases following Pb exposure have been less studied. In the present study, we compared the effects of Pb exposure on morphological parameters and gut microbiota of Bufo gargarizans at Gosner stage (Gs) 33, Gs36, and Gs42. Our results showed that total length (TL), snout-vent length (SVL), and body wet weight (TW) of B. gargarizans at Gs33, as well as TL and SVL at Gs42, were significantly increased after Pb exposure. In addition, high-throughput sequencing analysis indicated that gut microbiota has distinct responses to Pb exposure at different developmental stages. The diversity of gut microbiota was significantly reduced under Pb exposure at Gs33, while it was significantly increased at Gs42. In terms of community composition, Spirochaetota, Armatimonadota, and Patescibacteria appeared in the control groups at Gs42, but not after Pb treatment. Furthermore, functional prediction indicated that the relative abundance of metabolism pathway was significantly decreased at Gs33 and Gs36, and significantly increased at Gs42. Our results fill an important knowledge gap and provide comparative information on the gut microbiota of tadpoles at different developmental stages following Pb exposure.
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Affiliation(s)
- Lihong Chai
- School of Water and Environment, Chang'an University, Xi'an, 710054, China
- Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710062, China
| | - Hemei Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Xinyi Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Hongyuan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
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19
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Runge P, Ventura F, Kemen E, Stam R. Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis. MICROBIAL ECOLOGY 2023; 85:168-183. [PMID: 35041070 PMCID: PMC9849306 DOI: 10.1007/s00248-021-01947-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.
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Affiliation(s)
- Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Köln, Germany
| | - Freddy Ventura
- Plant Pathology and Bacteriology, International Potato Centre, Avenida La Molina 1895, La Molina, Lima, Peru
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Remco Stam
- Chair of Phytopathology, TUM School of Life Science, Emil-Ramann-Str. 2, 85354, Freising-Weihenstephan, Germany.
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20
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de Angeli Dutra D, Salloum PM, Poulin R. Vector microbiome: will global climate change affect vector competence and pathogen transmission? Parasitol Res 2023; 122:11-17. [PMID: 36401142 DOI: 10.1007/s00436-022-07734-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/14/2022] [Indexed: 11/21/2022]
Abstract
Vector-borne diseases are among the greatest causes of human suffering globally. Several studies have linked climate change and increasing temperature with rises in vector abundance, and in the incidence and geographical distribution of diseases. The microbiome of vectors can have profound effects on how efficiently a vector sustains pathogen development and transmission. Growing evidence indicates that the composition of vectors' gut microbiome might change with shifts in temperature. Nonetheless, due to a lack of studies on vector microbiome turnover under a changing climate, the consequences for vector-borne disease incidence are still unknown. Here, we argue that climate change effects on vector competence are still poorly understood and the expected increase in vector-borne disease transmission might not follow a relationship as simple and straightforward as past research has suggested. Furthermore, we pose questions that are yet to be answered to enhance our current understanding of the effect of climate change on vector microbiomes, competence, and, ultimately, vector-borne diseases transmission.
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Affiliation(s)
| | | | - Robert Poulin
- Department of Zoology, University of Otago, PO Box 56, Dunedin, New Zealand
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21
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Greenspan SE, Peloso P, Fuentes-González JA, Bletz M, Lyra ML, Machado IF, Martins RA, Medina D, Moura-Campos D, Neely WJ, Preuss J, Sturaro MJ, Vaz RI, Navas CA, Toledo LF, Tozetti AM, Vences M, Woodhams DC, Haddad CFB, Pienaar J, Becker CG. Low microbiome diversity in threatened amphibians from two biodiversity hotspots. Anim Microbiome 2022; 4:69. [PMID: 36582011 PMCID: PMC9801548 DOI: 10.1186/s42523-022-00220-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
Microbial diversity positively influences community resilience of the host microbiome. However, extinction risk factors such as habitat specialization, narrow environmental tolerances, and exposure to anthropogenic disturbance may homogenize host-associated microbial communities critical for stress responses including disease defense. In a dataset containing 43 threatened and 90 non-threatened amphibian species across two biodiversity hotspots (Brazil's Atlantic Forest and Madagascar), we found that threatened host species carried lower skin bacterial diversity, after accounting for key environmental and host factors. The consistency of our findings across continents suggests the broad scale at which low bacteriome diversity may compromise pathogen defenses in species already burdened with the threat of extinction.
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Affiliation(s)
- Sasha E. Greenspan
- grid.411015.00000 0001 0727 7545Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Pedro Peloso
- grid.452671.30000 0001 2175 1274Programa de Pós Gradução em Zoologia, Universidade Federal do Pará/Museu Paraense Emílio Goeldi, Belém, Pará 66077-530 Brazil ,Instituto Boitatá de Etnobiologia e Conservação da Fauna, Goiânia, Goiás 74085-480 Brazil
| | - Jesualdo A. Fuentes-González
- grid.65456.340000 0001 2110 1845The Department of Biology and the Institute of Environment, Florida International University, Miami, FL 33199 USA
| | - Molly Bletz
- grid.266685.90000 0004 0386 3207Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Mariana L. Lyra
- grid.410543.70000 0001 2188 478XDepartment of Biodiversity and Aquaculture Center (CAUNESP), Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900 Brazil
| | - Ibere F. Machado
- Instituto Boitatá de Etnobiologia e Conservação da Fauna, Goiânia, Goiás 74085-480 Brazil
| | - Renato A. Martins
- grid.411247.50000 0001 2163 588XPrograma de Pós-Graduação em Conservação da Fauna, Universidade Federal de São Carlos, São Carlos, São Paulo 13565-905 Brazil
| | - Daniel Medina
- Sistema Nacional de Investigación, SENACYT; City of Knowledge, Clayton, Panama, Republic of Panama ,grid.29857.310000 0001 2097 4281Department of Biology, The Pennsylvania State University, University Park, PA 16803 USA
| | - Diego Moura-Campos
- grid.411087.b0000 0001 0723 2494Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862 Brazil ,grid.1001.00000 0001 2180 7477Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, 2601 Australia
| | - Wesley J. Neely
- grid.411015.00000 0001 0727 7545Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Jackson Preuss
- grid.412292.e0000 0004 0417 7532Departamento de Ciências da Vida, Universidade do Oeste de Santa Catarina, São Miguel Do Oeste, Santa Catarina 89900-000 Brazil
| | - Marcelo J. Sturaro
- grid.411249.b0000 0001 0514 7202Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Diadema, São Paulo 09972-270 Brazil
| | - Renata I. Vaz
- grid.11899.380000 0004 1937 0722Departamento de Fisiologia Geral, Instituto de Biociencias, Universidade de São Paulo, São Paulo, São Paulo 05508-090 Brazil
| | - Carlos A. Navas
- grid.11899.380000 0004 1937 0722Departamento de Fisiologia Geral, Instituto de Biociencias, Universidade de São Paulo, São Paulo, São Paulo 05508-090 Brazil
| | - Luís Felipe Toledo
- grid.411087.b0000 0001 0723 2494Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862 Brazil
| | - Alexandro M. Tozetti
- grid.412302.60000 0001 1882 7290Programa de Pos-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, Rio Grande Do Sul 93022-750 Brazil
| | - Miguel Vences
- grid.6738.a0000 0001 1090 0254Zoological Institute, Braunschweig University of Technology, Mendelssohnstr. 4, Brunswick, Germany
| | - Douglas C. Woodhams
- grid.266685.90000 0004 0386 3207Department of Biology, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Célio F. B. Haddad
- grid.410543.70000 0001 2188 478XDepartment of Biodiversity and Aquaculture Center (CAUNESP), Universidade Estadual Paulista, Rio Claro, São Paulo 13506-900 Brazil
| | - Jason Pienaar
- grid.65456.340000 0001 2110 1845The Department of Biology and the Institute of Environment, Florida International University, Miami, FL 33199 USA
| | - C. Guilherme Becker
- grid.29857.310000 0001 2097 4281Department of Biology, The Pennsylvania State University, University Park, PA 16803 USA
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22
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Schmeller DS, Urbach D, Bates K, Catalan J, Cogălniceanu D, Fisher MC, Friesen J, Füreder L, Gaube V, Haver M, Jacobsen D, Le Roux G, Lin YP, Loyau A, Machate O, Mayer A, Palomo I, Plutzar C, Sentenac H, Sommaruga R, Tiberti R, Ripple WJ. Scientists' warning of threats to mountains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158611. [PMID: 36087665 DOI: 10.1016/j.scitotenv.2022.158611] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/04/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
Mountains are an essential component of the global life-support system. They are characterized by a rugged, heterogenous landscape with rapidly changing environmental conditions providing myriad ecological niches over relatively small spatial scales. Although montane species are well adapted to life at extremes, they are highly vulnerable to human derived ecosystem threats. Here we build on the manifesto 'World Scientists' Warning to Humanity', issued by the Alliance of World Scientists, to outline the major threats to mountain ecosystems. We highlight climate change as the greatest threat to mountain ecosystems, which are more impacted than their lowland counterparts. We further discuss the cascade of "knock-on" effects of climate change such as increased UV radiation, altered hydrological cycles, and altered pollution profiles; highlighting the biological and socio-economic consequences. Finally, we present how intensified use of mountains leads to overexploitation and abstraction of water, driving changes in carbon stock, reducing biodiversity, and impacting ecosystem functioning. These perturbations can provide opportunities for invasive species, parasites and pathogens to colonize these fragile habitats, driving further changes and losses of micro- and macro-biodiversity, as well further impacting ecosystem services. Ultimately, imbalances in the normal functioning of mountain ecosystems will lead to changes in vital biological, biochemical, and chemical processes, critically reducing ecosystem health with widespread repercussions for animal and human wellbeing. Developing tools in species/habitat conservation and future restoration is therefore essential if we are to effectively mitigate against the declining health of mountains.
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Affiliation(s)
| | - Davnah Urbach
- Global Mountain Biodiversity Assessment, Institute of Plant Sciences, University of Bern, Bern, Switzerland.
| | - Kieran Bates
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK; Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.
| | - Jordi Catalan
- CREAF Campus UAB, Edifici C, Cerdanyola Del Valles, Spain; CSIC, Campus UAB, Cerdanyola Del Valles, Spain.
| | - Dan Cogălniceanu
- Ovidius University Constanţa, Faculty of Natural Sciences and Agricultural Sciences, Al. Universităţii 1, 900470 Constanţa, Romania
| | - Matthew C Fisher
- MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK.
| | - Jan Friesen
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Leopold Füreder
- Department of Ecology, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria.
| | - Veronika Gaube
- University of Natural Resources and Life Sciences, Vienna, Department of Economics and Social Sciences, Institute of Social Ecology (SEC), Schottenfeldgasse 29, Austria.
| | - Marilen Haver
- LEFE, Université de Toulouse, INPT, UPS, Toulouse, France.
| | - Dean Jacobsen
- Freshwater Biological Section, Dept. Biology, University of Copenhagen, Denmark.
| | - Gael Le Roux
- LEFE, Université de Toulouse, INPT, UPS, Toulouse, France.
| | - Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan.
| | - Adeline Loyau
- LEFE, Université de Toulouse, INPT, UPS, Toulouse, France.
| | - Oliver Machate
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Andreas Mayer
- University of Natural Resources and Life Sciences, Vienna, Department of Economics and Social Sciences, Institute of Social Ecology (SEC), Schottenfeldgasse 29, Austria.
| | - Ignacio Palomo
- Univ. Grenoble-Alpes, IRD, CNRS, Grenoble INP*, IGE, 38000 Grenoble, France.
| | - Christoph Plutzar
- University of Natural Resources and Life Sciences, Vienna, Department of Economics and Social Sciences, Institute of Social Ecology (SEC), Schottenfeldgasse 29, Austria.
| | - Hugo Sentenac
- LEFE, Université de Toulouse, INPT, UPS, Toulouse, France.
| | - Ruben Sommaruga
- Department of Ecology, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria.
| | - Rocco Tiberti
- Department of Earth and Environmental Sciences - DSTA, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy.
| | - William J Ripple
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA.
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23
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Bates KA, Friesen J, Loyau A, Butler H, Vredenburg VT, Laufer J, Chatzinotas A, Schmeller DS. Environmental and Anthropogenic Factors Shape the Skin Bacterial Communities of a Semi-Arid Amphibian Species. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02130-5. [PMID: 36445401 DOI: 10.1007/s00248-022-02130-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
The amphibian skin microbiome is important in maintaining host health, but is vulnerable to perturbation from changes in biotic and abiotic conditions. Anthropogenic habitat disturbance and emerging infectious diseases are both potential disrupters of the skin microbiome, in addition to being major drivers of amphibian decline globally. We investigated how host environment (hydrology, habitat disturbance), pathogen presence, and host biology (life stage) impact the skin microbiome of wild Dhofar toads (Duttaphrynus dhufarensis) in Oman. We detected ranavirus (but not Batrachochytrium dendrobatidis) across all sampling sites, constituting the first report of this pathogen in Oman, with reduced prevalence in disturbed sites. We show that skin microbiome beta diversity is driven by host life stage, water source, and habitat disturbance, but not ranavirus infection. Finally, although trends in bacterial diversity and differential abundance were evident in disturbed versus undisturbed sites, bacterial co-occurrence patterns determined through network analyses revealed high site specificity. Our results therefore provide support for amphibian skin microbiome diversity and taxa abundance being associated with habitat disturbance, with bacterial co-occurrence (and likely broader aspects of microbial community ecology) being largely site specific.
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Affiliation(s)
- K A Bates
- Department of Zoology, University of Oxford, Oxford, UK.
| | - J Friesen
- Centre for Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - A Loyau
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, INPT, UPS, Toulouse, France
| | - H Butler
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - V T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - J Laufer
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - A Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - D S Schmeller
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, INPT, UPS, Toulouse, France
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24
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Tazerji SS, Nardini R, Safdar M, Shehata AA, Duarte PM. An Overview of Anthropogenic Actions as Drivers for Emerging and Re-Emerging Zoonotic Diseases. Pathogens 2022; 11:1376. [PMID: 36422627 PMCID: PMC9692567 DOI: 10.3390/pathogens11111376] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/05/2022] [Accepted: 11/15/2022] [Indexed: 08/05/2023] Open
Abstract
Population growth and industrialization have led to a race for greater food and supply productivity. As a result, the occupation and population of forest areas, contact with wildlife and their respective parasites and vectors, the trafficking and consumption of wildlife, the pollution of water sources, and the accumulation of waste occur more frequently. Concurrently, the agricultural and livestock production for human consumption has accelerated, often in a disorderly way, leading to the deforestation of areas that are essential for the planet's climatic and ecological balance. The effects of human actions on other ecosystems such as the marine ecosystem cause equally serious damage, such as the pollution of this habitat, and the reduction of the supply of fish and other animals, causing the coastal population to move to the continent. The sum of these factors leads to an increase in the demands such as housing, basic sanitation, and medical assistance, making these populations underserved and vulnerable to the effects of global warming and to the emergence of emerging and re-emerging diseases. In this article, we discuss the anthropic actions such as climate changes, urbanization, deforestation, the trafficking and eating of wild animals, as well as unsustainable agricultural intensification which are drivers for emerging and re-emerging of zoonotic pathogens such as viral (Ebola virus, hantaviruses, Hendravirus, Nipah virus, rabies, and severe acute respiratory syndrome coronavirus disease-2), bacterial (leptospirosis, Lyme borreliosis, and tuberculosis), parasitic (leishmaniasis) and fungal pathogens, which pose a substantial threat to the global community. Finally, we shed light on the urgent demand for the implementation of the One Health concept as a collaborative global approach to raise awareness and educate people about the science behind and the battle against zoonotic pathogens to mitigate the threat for both humans and animals.
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Affiliation(s)
- Sina Salajegheh Tazerji
- Department of Clinical Science, Faculty of Veterinary Medicine, Science and Research Branch, Islamic Azad University, Tehran P.O. Box. 1477893855, Iran
- Young Researchers and Elites Club Science and Research Branch, Islamic Azad University; Tehran P.O. Box. 1477893855, Iran
| | - Roberto Nardini
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy
| | - Muhammad Safdar
- Department of Breeding and Genetics, Cholistan University of Veterinary & Animal Sciences, Bahawalpur 63100, Pakistan
| | - Awad A. Shehata
- Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32897, Egypt
- Research and Development Section, PerNaturam GmbH, 56290 Gödenroth, Germany
- Prophy-Institute for Applied Prophylaxis, 59159 Bönen, Germany
| | - Phelipe Magalhães Duarte
- Postgraduate Program in Animal Bioscience, Federal Rural University of Pernambuco (UFRPE), Recife, Pernambuco 52171-900, Brazil
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25
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Cevallos MA, Basanta MD, Bello-López E, Escobedo-Muñoz AS, González-Serrano FM, Nemec A, Romero-Contreras YJ, Serrano M, Rebollar EA. Genomic characterization of antifungal Acinetobacter bacteria isolated from the skin of the frogs Agalychnis callidryas and Craugastor fitzingeri. FEMS Microbiol Ecol 2022; 98:6775075. [PMID: 36288213 DOI: 10.1093/femsec/fiac126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/09/2022] [Accepted: 10/24/2022] [Indexed: 01/21/2023] Open
Abstract
Chytridiomycosis, a lethal fungal disease caused by Batrachochytrium dendrobatidis (Bd), is responsible for population declines and extinctions of amphibians worldwide. However, not all amphibian species are equally susceptible to the disease; some species persist in Bd enzootic regions with no population reductions. Recently, it has been shown that the amphibian skin microbiome plays a crucial role in the defense against Bd. Numerous bacterial isolates with the capacity to inhibit the growth of Batrachochytrium fungi have been isolated from the skin of amphibians. Here, we characterized eight Acinetobacter bacteria isolated from the frogs Agalychnis callidryas and Craugastor fitzingeri at the genomic level. A total of five isolates belonged to Acinetobacter pittii,Acinetobacter radioresistens, or Acinetobactermodestus, and three were not identified as any of the known species, suggesting they are members of new species. We showed that seven isolates inhibited the growth of Bd and that all eight isolates inhibited the growth of the phytopathogen fungus Botrytis cinerea. Finally, we identified the biosynthetic gene clusters that could be involved in the antifungal activity of these isolates. Our results suggest that the frog skin microbiome includes Acinetobacter isolates that are new to science and have broad antifungal functions, perhaps driven by distinct genetic mechanisms.
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Affiliation(s)
- M A Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - M D Basanta
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México.,Department of Biology, University of Nevada Reno, 1664 N Virgina St, Reno, NV 89557, United States
| | - E Bello-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - A S Escobedo-Muñoz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - F M González-Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - A Nemec
- Laboratory of Bacterial Genetics, Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, 100 00 Prague 10, Czechia.,Department of Medical Microbiology, Second Faculty of Medicine, Charles University, and Motol University Hospital, V Úvalu 84, 150 06 Prague 5, Czechia
| | - Y J Romero-Contreras
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - M Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - E A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
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Neely WJ, Greenspan SE, Stahl LM, Heraghty SD, Marshall VM, Atkinson CL, Becker CG. Habitat Disturbance Linked with Host Microbiome Dispersion and Bd Dynamics in Temperate Amphibians. MICROBIAL ECOLOGY 2022; 84:901-910. [PMID: 34671826 DOI: 10.1007/s00248-021-01897-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Anthropogenic habitat disturbances can dramatically alter ecological community interactions, including host-pathogen dynamics. Recent work has highlighted the potential for habitat disturbances to alter host-associated microbial communities, but the associations between anthropogenic disturbance, host microbiomes, and pathogens are unresolved. Amphibian skin microbial communities are particularly responsive to factors like temperature, physiochemistry, pathogen infection, and environmental microbial reservoirs. Through a field survey on wild populations of Acris crepitans (Hylidae) and Lithobates catesbeianus (Ranidae), we assessed the effects of habitat disturbance and connectivity on environmental bacterial reservoirs, Batrachochytrium dendrobatidis (Bd) infection, and skin microbiome composition. We found higher measures of microbiome dispersion (a measure of community variability) in A. crepitans from more disturbed ponds, supporting the hypothesis that disturbance increases stochasticity in biological communities. We also found that habitat disturbance limited microbiome similarity between locations for both species, suggesting greater isolation of bacterial assemblages in more disturbed areas. Higher disturbance was associated with lower Bd prevalence for A. crepitans, which could signify suboptimal microclimates for Bd in disturbed habitats. Combined, our findings show that reduced microbiome stability stemming from habitat disturbance could compromise population health, even in the absence of pathogenic infection.
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Affiliation(s)
- Wesley J Neely
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA.
| | - Sasha E Greenspan
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - Leigha M Stahl
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - Sam D Heraghty
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - Vanessa M Marshall
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - Carla L Atkinson
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - C Guilherme Becker
- Department of Biology, The University of Alabama, 1301 Sciences and Engineering Complex, 300 Hackberry Ln, Tuscaloosa, AL, 35487, USA
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27
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Schmeller DS, Cheng T, Shelton J, Lin CF, Chan-Alvarado A, Bernardo-Cravo A, Zoccarato L, Ding TS, Lin YP, Swei A, Fisher MC, Vredenburg VT, Loyau A. Environment is associated with chytrid infection and skin microbiome richness on an amphibian rich island (Taiwan). Sci Rep 2022; 12:16456. [PMID: 36180528 PMCID: PMC9525630 DOI: 10.1038/s41598-022-20547-3] [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: 12/20/2021] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
Growing evidence suggests that the origins of the panzootic amphibian pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are in Asia. In Taiwan, an island hotspot of high amphibian diversity, no amphibian mass mortality events linked to Bd or Bsal have been reported. We conducted a multi-year study across this subtropical island, sampling 2517 individuals from 30 species at 34 field sites, between 2010 and 2017, and including 171 museum samples collected between 1981 and 2009. We analyzed the skin microbiome of 153 samples (6 species) from 2017 in order to assess any association between the amphibian skin microbiome and the probability of infection amongst different host species. We did not detect Bsal in our samples, but found widespread infection by Bd across central and northern Taiwan, both taxonomically and spatially. Museum samples show that Bd has been present in Taiwan since at least 1990. Host species, geography (elevation), climatic conditions and microbial richness were all associated with the prevalence of infection. Host life-history traits, skin microbiome composition and phylogeny were associated with lower prevalence of infection for high altitude species. Overall, we observed low prevalence and burden of infection in host populations, suggesting that Bd is enzootic in Taiwan where it causes subclinical infections. While amphibian species in Taiwan are currently threatened by habitat loss, our study indicates that Bd is in an endemic equilibrium with the populations and species we investigated. However, ongoing surveillance of the infection is warranted, as changing environmental conditions may disturb the currently stable equilibrium.
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Affiliation(s)
- Dirk S Schmeller
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, INPT, UPS, Toulouse, France
| | - Tina Cheng
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
- Bat Conservation International, Washington, DC, USA
| | - Jennifer Shelton
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | - Chun-Fu Lin
- Zoology Division, Endemic Species Research Institute, Jiji, Nantou, Taiwan, ROC
| | - Alan Chan-Alvarado
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Adriana Bernardo-Cravo
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, INPT, UPS, Toulouse, France
| | - Luca Zoccarato
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhütte 2, 16775, Stechlin, Germany
| | - Tzung-Su Ding
- School of Forestry and Resource Conservation, National Taiwan University, Taipei City, 106, Taiwan, ROC
| | - Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan, ROC
| | - Andrea Swei
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Adeline Loyau
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, INPT, UPS, Toulouse, France.
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhütte 2, 16775, Stechlin, Germany.
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Pitarch A, Diéguez-Uribeondo J, Martín-Torrijos L, Sergio F, Blanco G. Fungal signatures of oral disease reflect environmental degradation in a facultative avian scavenger. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155397. [PMID: 35460785 DOI: 10.1016/j.scitotenv.2022.155397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Degradation of natural ecosystems increases the risk of infections in wildlife due to microbiota dysbiosis. However, little is known about its influence on the development of fungal communities in predators and facultative avian scavengers. We evaluated the incidence of oral disease in wild nestling black kites (Milvus migrans) under contrasting environmental degradation conditions, and explored their oral fungal patterns using molecular methods and multivariate analysis. Oral lesions were found in 36.8% of the 38 nestlings examined in an anthropogenically altered habitat (southeastern Madrid, Spain), but in none of the 105 nestlings examined in a well-conserved natural area (Doñana National Park, Spain). In a subsample of 48 black kites, the composition of the oral fungal community differed among symptomatic nestlings from Madrid (SM) and asymptomatic nestlings from Madrid (AM) and Doñana (AD). Opportunistic fungal pathogens (e.g., Fusarium incarnatum-equiseti species complex, Mucor spp., Rhizopus oryzae) were more prevalent in SM and AM than in AD. Hierarchical clustering and principal component analyses revealed that fungal patterns were distinct between both study areas, and that anthropogenic and natural environmental factors had a greater impact on them than oral disease. Fungal signatures associated with anthropogenic and natural stresses harbored some taxa that could be used to flag oral infection (F. incarnatum-equiseti species complex and Alternaria), indicate environmental degradation (Alternaria) or provide protective benefits in degraded environments (Trichoderma, Epicoccum nigrum and Sordaria). Co-occurrence associations between potentially beneficial and pathogenic fungi were typical of AM and AD, hinting at a possible role in host health. This study shows that early-life exposure to highly degraded environments induces a shift towards a higher prevalence of pathogenic species in the oral cavity of black kites, favoring oral disease. Furthermore, our findings suggest potential ecological applications of the monitoring of oral mycobiome as a bioindication of oral disease and environmental degradation.
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Affiliation(s)
- Aida Pitarch
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid (UCM) and Ramón y Cajal Institute of Health Research (IRYCIS), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain; Teaching Unit of Microbiology and Parasitology, Faculty of Optics and Optometry, Complutense University of Madrid (UCM), Arcos de Jalón, 118, 28037 Madrid, Spain.
| | | | - Laura Martín-Torrijos
- Department of Mycology, Real Jardín Botánico-CSIC, Plaza Murillo 2, 28014 Madrid, Spain
| | - Fabrizio Sergio
- Department of Conservation Biology, Estacion Biologica de Doñana-CSIC, Americo Vespucio 26, 41092 Sevilla, Spain
| | - Guillermo Blanco
- Department of Evolutionary Ecology, Museo Nacional de Ciencias Naturales-CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain
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29
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Rajarajan A, Wolinska J, Walser JC, Mäder M, Spaak P. Infection by a eukaryotic gut parasite in wild Daphnia sp. associates with a distinct bacterial community. FEMS Microbiol Ecol 2022; 98:6677393. [PMID: 36026529 PMCID: PMC9869925 DOI: 10.1093/femsec/fiac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/04/2022] [Accepted: 08/23/2022] [Indexed: 01/26/2023] Open
Abstract
Host-associated bacterial communities play an important role in host fitness and resistance to diseases. Yet, few studies have investigated tripartite interaction between a host, parasite and host-associated bacterial communities in natural settings. Here, we use 16S rRNA gene amplicon sequencing to compare gut- and body- bacterial communities of wild water fleas belonging to the Daphnia longispina complex, between uninfected hosts and those infected with the common and virulent eukaryotic gut parasite Caullerya mesnili (Family: Ichthyosporea). We report community-level changes in host-associated bacteria with the presence of the parasite infection; namely decreased alpha diversity and increased beta diversity at the site of infection, i.e. host gut (but not host body). We also report decreased abundance of bacterial taxa proposed elsewhere to be beneficial for the host, and an appearance of taxa specifically associated with infected hosts. Our study highlights the host-microbiota-infection link in a natural system and raises questions about the role of host-associated microbiota in natural disease epidemics as well as the functional roles of bacteria specifically associated with infected hosts.
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Affiliation(s)
- Amruta Rajarajan
- Corresponding author: Office BU-G09, Überlandstrasse 133, 8600 Dübendorf, Zürich, Switzerland. E-mail: and
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany,Department of Biology, Chemistry, Pharmacy, Institut für Biologie, Freie Universität Berlin (FU), 14195 Berlin, Germany
| | - Jean-Claude Walser
- Department of Environmental systems science (D-USYS), Genetic Diversity Centre (GDC), Federal Institute of Technology (ETH) Zürich, 8092, Zürich, Switzerland
| | - Minea Mäder
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Zürich, Switzerland
| | - Piet Spaak
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Zürich, Switzerland
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30
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Obregon D, Wu-Chuang A, Cabezas-Cruz A. Editorial: Insights into the relationships between host and vector microbiota, host health and response to disease. Front Vet Sci 2022; 9:1002247. [PMID: 36051536 PMCID: PMC9427026 DOI: 10.3389/fvets.2022.1002247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Dasiel Obregon
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
- *Correspondence: Dasiel Obregon
| | - Alejandra Wu-Chuang
- ANSES, INRAE, UMR BIPAR, Laboratoire de Santé Animale, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, UMR BIPAR, Laboratoire de Santé Animale, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
- Alejandro Cabezas-Cruz
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31
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Schmid DW, Fackelmann G, Wasimuddin, Rakotondranary J, Ratovonamana YR, Montero BK, Ganzhorn JU, Sommer S. A framework for testing the impact of co-infections on host gut microbiomes. Anim Microbiome 2022; 4:48. [PMID: 35945629 PMCID: PMC9361228 DOI: 10.1186/s42523-022-00198-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 07/26/2022] [Indexed: 02/07/2023] Open
Abstract
Parasitic infections disturb gut microbial communities beyond their natural range of variation, possibly leading to dysbiosis. Yet it remains underappreciated that most infections are accompanied by one or more co-infections and their collective impact is largely unexplored. Here we developed a framework illustrating changes to the host gut microbiome following single infections, and build on it by describing the neutral, synergistic or antagonistic impacts on microbial α- and ß-diversity expected from co-infections. We tested the framework on microbiome data from a non-human primate population co-infected with helminths and Adenovirus, and matched patterns reported in published studies to the introduced framework. In this case study, α-diversity of co-infected Malagasy mouse lemurs (Microcebus griseorufus) did not differ in comparison with that of singly infected or uninfected individuals, even though community composition captured with ß-diversity metrices changed significantly. Explicitly, we record stochastic changes in dispersion, a sign of dysbiosis, following the Anna-Karenina principle rather than deterministic shifts in the microbial gut community. From the literature review and our case study, neutral and synergistic impacts emerged as common outcomes from co-infections, wherein both shifts and dispersion of microbial communities following co-infections were often more severe than after a single infection alone, but microbial α-diversity was not universally altered. Important functions of the microbiome may also suffer from such heavily altered, though no less species-rich microbial community. Lastly, we pose the hypothesis that the reshuffling of host-associated microbial communities due to the impact of various, often coinciding parasitic infections may become a source of novel or zoonotic diseases.
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A balanced gut microbiota is essential to maintain health in captive sika deer. Appl Microbiol Biotechnol 2022; 106:5659-5674. [PMID: 35922588 DOI: 10.1007/s00253-022-12111-w] [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: 06/16/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/02/2022]
Abstract
Certain animals harbor a high proportion of pathogens, particular the zoonotic pathogens, in their gut microbiome but are usually asymptomic; however, their carried pathogens may seriously threaten the public health. By understanding how the microbiome overcomes the negative effects of pathogens to maintain host health, we can develop novel solutions to control animal-mediated pathogen transmission including identification and application of beneficial microbes. Here, we analyzed the gut microbiota of 10 asymptomic captive sika deer individuals by full-length 16S rDNA sequencing. Twenty-nine known pathogens capable of infecting humans were identified, and the accumulated proportions of the identified pathogens were highly variable among individuals (2.33 to 39.94%). The relative abundances of several beneficial bacteria, including Lactobacillus and Bifidobacterium, were found to be positively correlated with the relative abundances of accumulated pathogens. Whole-genome metagenomic analysis revealed that the beneficial- and pathogenic-associated functions, such as genes involved in the synthesis of short chain fatty acids and virulence factors, were also positively correlated in the microbiome, indicating that the beneficial and pathogenic functions were maintained at a relatively balanced ratio. Furthermore, the bacteriophages that target the identified pathogens were found to be positively correlated with the pathogenic content in the microbiome. Several high-quality genomes of beneficial bacteria affiliated with Lactobacillus and Bifidobacterium and bacteriophages were recovered from the metagenomic data. Overall, this study provides novel insights into the interplay between beneficial and pathogenic content to ensure maintenance of a healthy gut microbiome, and also contributes to discovery of novel beneficial microbes and functions that control pathogens. KEY POINTS: • Certain asymptomic captive sika deer individuals harbor relatively high amounts of zoonotic pathogens. • The beneficial microbes and the beneficial functions are balanced with the pathogenic contents in the gut microbiome. • Several high-quality genomes of beneficial bacteria and bacteriophages are recovered by metagenomics.
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New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True? J Fungi (Basel) 2022; 8:jof8070737. [PMID: 35887492 PMCID: PMC9320658 DOI: 10.3390/jof8070737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as "What's in my soil?", to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported.
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Machate O, Schmeller DS, Loyau A, Paschke A, Krauss M, Carmona E, Schulze T, Moyer A, Lutz K, Brack W. Complex chemical cocktail, containing insecticides diazinon and permethrin, drives acute toxicity to crustaceans in mountain lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154456. [PMID: 35283126 DOI: 10.1016/j.scitotenv.2022.154456] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Mountain lakes have long been perceived as pristine environments. However, atmospheric deposition of persistent organic pollutants (POPs) have been shown to expose these sensitive ecosystems to chemical pollution. Little is known on how this pollution impacts aquatic ecosystems at high altitudes. We combined passive sampling with liquid and gas chromatography high resolution mass spectrometry (LC- and GC-HRMS) to screen the water of eight lakes in three different regions of the French Pyrenees. In total, we screened for 479 organic chemicals including POPs, polycyclic aromatic hydrocarbons (PAHs), legacy and current-use pesticides, biocides, and musk fragrances. We detected a complex cocktail of 151 individual chemicals and used their toxic unit summation (ΣTU) to assess toxicity for crustaceans and algae. While risks for algae never reached chronic risks, this was always the case for crustaceans. Acute toxic risk thresholds for crustaceans were even exceeded in several of our sites. At sites with acute toxic risk levels (> 0.1 ΣTU) crustaceans were completely absent or showed a low abundance. We conclude that crustaceans were at least partly impacted by the high toxic risks driven by the insecticides diazinon and permethrin. These drugs are widely used to protect livestock from blue tongue disease transmitted by sucking insects, suggesting free roaming livestock as local source. Our results provide important evidence on toxic chemical pollution in relatively remote mountain areas, with important consequences for aquatic mountain ecosystems.
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Affiliation(s)
- Oliver Machate
- Helmholtz Centre for Environmental Research - UFZ, Department of Effect Directed Analysis, Permoserstrasse 15, 04318 Leipzig, Germany; University of Leipzig, Department of Biology, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Dirk S Schmeller
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UPS), Toulouse, France.
| | - Adeline Loyau
- Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UPS), Toulouse, France; Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhütte 2, Stechlin D-16775, Germany.
| | - Albrecht Paschke
- Helmholtz Centre for Environmental Research - UFZ, Department of Ecological Chemistry, Permoserstrasse 15, 04318 Leipzig, Germany.
| | - Martin Krauss
- Helmholtz Centre for Environmental Research - UFZ, Department of Effect Directed Analysis, Permoserstrasse 15, 04318 Leipzig, Germany.
| | - Eric Carmona
- Helmholtz Centre for Environmental Research - UFZ, Department of Effect Directed Analysis, Permoserstrasse 15, 04318 Leipzig, Germany.
| | - Tobias Schulze
- Helmholtz Centre for Environmental Research - UFZ, Department of Effect Directed Analysis, Permoserstrasse 15, 04318 Leipzig, Germany.
| | - Alessandra Moyer
- Department of Biology, San Francisco State University, San Francisco, CA 94132-1722, United States of America
| | - Kurt Lutz
- Department of Biology, San Francisco State University, San Francisco, CA 94132-1722, United States of America
| | - Werner Brack
- Helmholtz Centre for Environmental Research - UFZ, Department of Effect Directed Analysis, Permoserstrasse 15, 04318 Leipzig, Germany; Goethe University Frankfurt, Department of Evolutionary Ecology and Environmental Toxicology, Max-von-Laue-Strasse, 13, 60438 Frankfurt am Main, Germany.
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35
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Basanta MD, Rebollar EA, García-Castillo MG, Parra Olea G. Comparative Analysis of Skin Bacterial Diversity and Its Potential Antifungal Function Between Desert and Pine Forest Populations of Boreal Toads Anaxyrus boreas. MICROBIAL ECOLOGY 2022; 84:257-266. [PMID: 34427721 DOI: 10.1007/s00248-021-01845-1] [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: 04/12/2021] [Accepted: 08/14/2021] [Indexed: 06/13/2023]
Abstract
The skin microbiome in amphibians has gained a lot of attention as some of its members play a protective role against pathogens such as the fungus Batrachochytrium dendrobatidis (Bd). The composition of skin bacterial communities has been suggested as one of the factors explaining differences in susceptibility to Bd among amphibian species and populations. The boreal toad Anaxyrus boreas is known to be susceptible to Bd, and severe population declines in its southeastern range have been documented. However, throughout A. boreas distribution, populations present differences in susceptibility to Bd infections which may be associated with differences in skin microbial diversity. This study compared the skin bacterial diversity and Bd infection levels of A. boreas in one desert population and one pine forest population from Baja California, Mexico. We found that desert and pine forest toad populations exhibit differences in skin bacterial community structure but show similar Bd infection levels. Using a predictive method, we found that the abundance of bacteria with potential Bd-inhibitory properties differed between uninfected and infected individuals but not between populations. Our data suggest that several bacteria in the skin community may be offering protection from Bd infections in these A. boreas populations. This study provides foundational evidence for future studies seeking to understand the skin-microbial variation among boreal toads' populations and its relation with Bd susceptibility.
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Affiliation(s)
- M Delia Basanta
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mirna G García-Castillo
- Universidad Politécnica de Huatusco, Huatusco, Veracruz, México
- Facultad de Ciencias Biológicas y Agropecuarias Región: Orizaba-Córdoba, Universidad Veracruzana, Amatlán de Los Reyes, Veracruz, México
| | - Gabriela Parra Olea
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México.
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Poulin R, Jorge F, Salloum PM. Inter-individual variation in parasite manipulation of host phenotype: A role for parasite microbiomes? J Anim Ecol 2022; 92:807-812. [PMID: 35748637 DOI: 10.1111/1365-2656.13764] [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: 04/21/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022]
Abstract
Alterations in host phenotype induced by metazoan parasites are widespread in nature, yet the underlying mechanisms and the sources of intraspecific variation in the extent of those alterations remain poorly understood. In light of the microbiome revolution sweeping through ecology and evolutionary biology, we hypothesise that the composition of symbiotic microbial communities living within individual parasites influences the nature and extent of their effect on host phenotype. The interests of both the parasite and its symbionts are aligned through the latter's vertical transmission, favouring joint contributions to the manipulation of host phenotype. Our hypothesis can explain the variation in the extent to which parasites alter host phenotype, as microbiome composition varies among individual parasites. We propose two non-exclusive approaches to test the hypothesis, furthering the integration of microbiomes into studies of host-parasite interactions.
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Affiliation(s)
- Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Fátima Jorge
- Otago Micro and Nano Imaging, Electron Microscopy Unit, University of Otago, Dunedin, New Zealand
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Hase K. Microflora Influence: The Aquatic Environment Changes Grouping Risk and Development Speed of Toad Tadpoles. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.917067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In addition to habitat loss and fragmentation, behavioral traits and the deterioration of water environments also contribute to the local extinction of amphibians. Abundant microflora in urban ponds may cause fatal diseases, whereas symbiotic bacteria may protect the host from pathogens; these effects may vary with group size. In this study, I monitored the growth of Japanese common toad (Bufo japonicus) larvae in Tokyo using three different group sizes: 1 (solitary), 2 (pair), and 15. Although there was no genetic bias in the major histocompatibility complex (MHC) class II genes or microsatellite loci to the survival of the larvae, the mortality risk of the larvae reared in pond water was higher than that of those reared in tap water. According to the survival analysis, the risk was more significant when the group size was 15. This result would be unwelcomed for the B. japonicus tadpoles, which have habits of social aggregation. Furthermore, larval metamorphosis took longer to complete in pond than tap water without any difference in body length or mass. These findings provide fundamental insight into the impact of the aquatic environment and the effect of the group size on animal health and conservation.
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García-Sánchez JC, Arredondo-Centeno J, Segovia-Ramírez MG, Tenorio Olvera AM, Parra-Olea G, Vredenburg VT, Rovito SM. Factors Influencing Bacterial and Fungal Skin Communities of Montane Salamanders of Central Mexico. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02049-x. [PMID: 35705744 DOI: 10.1007/s00248-022-02049-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Host microbial communities are increasingly seen as an important component of host health. In amphibians, the first land vertebrates that are threatened by a fungal skin disease globally, our understanding of the factors influencing the microbiome of amphibian skin remains incomplete because recent studies have focused almost exclusively on bacteria, and little information exists on fungal communities associated with wild amphibian species. In this study, we describe the effects of host phylogeny, climate, geographic distance, and infection with a fungal pathogen on the composition and structure of bacterial and fungal communities in seven tropical salamander species that occur in the Trans-Mexican Volcanic Belt of Central Mexico. We find that host phylogenetic relatedness is correlated with bacterial community composition while a composite climatic variable of temperature seasonality and precipitation is significantly associated with fungal community composition. We also estimated co-occurrence networks for bacterial and fungal taxa and found differences in the degree of connectivity and the distribution of negative associations between the two networks. Our results suggest that different factors may be responsible for structuring the bacterial and fungal communities of amphibian skin and that the inclusion of fungi in future studies could shed light on important functional interactions within the microbiome.
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Affiliation(s)
- Julio César García-Sánchez
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - José Arredondo-Centeno
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
- Instituto Tecnológico Superior de Irapuato, Irapuato, Guanajuato, México
| | - María Guadalupe Segovia-Ramírez
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Ariadna Marcela Tenorio Olvera
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
- Instituto Tecnológico Superior de Irapuato, Irapuato, Guanajuato, México
| | - Gabriela Parra-Olea
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Sean M Rovito
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México.
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Ma Z(S, Zhang YP. Ecology of Human Medical Enterprises: From Disease Ecology of Zoonoses, Cancer Ecology Through to Medical Ecology of Human Microbiomes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.879130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In nature, the interaction between pathogens and their hosts is only one of a handful of interaction relationships between species, including parasitism, predation, competition, symbiosis, commensalism, and among others. From a non-anthropocentric view, parasitism has relatively fewer essential differences from the other relationships; but from an anthropocentric view, parasitism and predation against humans and their well-beings and belongings are frequently related to heinous diseases. Specifically, treating (managing) diseases of humans, crops and forests, pets, livestock, and wildlife constitute the so-termed medical enterprises (sciences and technologies) humans endeavor in biomedicine and clinical medicine, veterinary, plant protection, and wildlife conservation. In recent years, the significance of ecological science to medicines has received rising attentions, and the emergence and pandemic of COVID-19 appear accelerating the trend. The facts that diseases are simply one of the fundamental ecological relationships in nature, and the study of the relationships between species and their environment is a core mission of ecology highlight the critical importance of ecological science. Nevertheless, current studies on the ecology of medical enterprises are highly fragmented. Here, we (i) conceptually overview the fields of disease ecology of wildlife, cancer ecology and evolution, medical ecology of human microbiome-associated diseases and infectious diseases, and integrated pest management of crops and forests, across major medical enterprises. (ii) Explore the necessity and feasibility for a unified medical ecology that spans biomedicine, clinical medicine, veterinary, crop (forest and wildlife) protection, and biodiversity conservation. (iii) Suggest that a unified medical ecology of human diseases is both necessary and feasible, but laissez-faire terminologies in other human medical enterprises may be preferred. (iv) Suggest that the evo-eco paradigm for cancer research can play a similar role of evo-devo in evolutionary developmental biology. (v) Summarized 40 key ecological principles/theories in current disease-, cancer-, and medical-ecology literatures. (vi) Identified key cross-disciplinary discovery fields for medical/disease ecology in coming decade including bioinformatics and computational ecology, single cell ecology, theoretical ecology, complexity science, and the integrated studies of ecology and evolution. Finally, deep understanding of medical ecology is of obvious importance for the safety of human beings and perhaps for all living things on the planet.
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Martins RA, Greenspan SE, Medina D, Buttimer S, Marshall VM, Neely WJ, Siomko S, Lyra ML, Haddad CFB, São-Pedro V, Becker CG. Signatures of functional bacteriome structure in a tropical direct-developing amphibian species. Anim Microbiome 2022; 4:40. [PMID: 35672870 PMCID: PMC9172097 DOI: 10.1186/s42523-022-00188-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Host microbiomes may differ under the same environmental conditions and these differences may influence susceptibility to infection. Amphibians are ideal for comparing microbiomes in the context of disease defense because hundreds of species face infection with the skin-invading microbe Batrachochytrium dendrobatidis (Bd), and species richness of host communities, including their skin bacteria (bacteriome), may be exceptionally high. We conducted a landscape-scale Bd survey of six co-occurring amphibian species in Brazil’s Atlantic Forest. To test the bacteriome as a driver of differential Bd prevalence, we compared bacteriome composition and co-occurrence network structure among the six focal host species.
Results
Intensive sampling yielded divergent Bd prevalence in two ecologically similar terrestrial-breeding species, a group with historically low Bd resistance. Specifically, we detected the highest Bd prevalence in Ischnocnema henselii but no Bd detections in Haddadus binotatus. Haddadus binotatus carried the highest bacteriome alpha and common core diversity, and a modular network partitioned by negative co-occurrences, characteristics associated with community stability and competitive interactions that could inhibit Bd colonization.
Conclusions
Our findings suggest that community structure of the bacteriome might drive Bd resistance in H. binotatus, which could guide microbiome manipulation as a conservation strategy to protect diverse radiations of direct-developing species from Bd-induced population collapses.
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Fleischer R, Schmid DW, Uddin W, Brändel SD, Rasche A, Corman VM, Drosten C, Tschapka M, Sommer S. Interaction between MHC diversity and constitution, gut microbiota and Astrovirus infections in a neotropical bat. Mol Ecol 2022; 31:3342-3359. [PMID: 35510794 DOI: 10.1111/mec.16491] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 11/28/2022]
Abstract
Astroviruses (AstVs) infect numerous mammalian species including reservoirs such as bats. Peptides encoded by the genes of the highly polymorphic Major Histocompatibility Complex (MHC) form the first line of host defence against pathogens. Aside from direct involvement in mounting adaptive immune responses, MHC class II genes are hypothesized to regulate gut commensal diversity and shape the production of immune-modulatory substances by microbes, indirectly affecting host susceptibility. Despite initial empirical evidence for the link between host MHC and the microbiota, associations among these factors remain largely unknown. To fill this gap, we examined MHC allelic diversity and constitution, the gut bacterial community and abundance pattern of a wild population of the neotropical bat (Artibeus jamaicensis) challenged by AstV infections. First, we show an age-dependent relationship between the host MHC class II diversity and constitution and the gut microbiota in AstV uninfected bats. Crucially, these associations changed in AstV infected bats. Additionally, we identify changes in abundance of specific bacterial taxa linked to the presence of certain MHC supertypes and AstV infection. We suggest changes in the microbiota to be either a result of AstV infection or the MHC-mediated modulation of microbial communities. The latter could subsequently affect microbe-mediated immunity and resistance against AstV infection. Our results underscore that the reciprocal nature of host immune genetics, gut microbial diversity and pathogen infection requires attention, which is particularly important given its repercussions for disease susceptibility and severity in wild animal populations with a history of zoonotic spillover and frequent human contact.
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Affiliation(s)
- Ramona Fleischer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Dominik Werner Schmid
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Wasim Uddin
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Stefan Dominik Brändel
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany.,Smithsonian Tropical Research Institute, Ancon, Panama
| | - Andrea Rasche
- Smithsonian Tropical Research Institute, Ancon, Panama.,Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Chariteplatz 1, 10117, Berlin, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Chariteplatz 1, 10117, Berlin, Germany.,German Centre for Infection Research (DZIF), associated partner Charité, Chariteplatz 1, 10117, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Chariteplatz 1, 10117, Berlin, Germany.,German Centre for Infection Research (DZIF), associated partner Charité, Chariteplatz 1, 10117, Berlin, Germany
| | - Marco Tschapka
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany.,Smithsonian Tropical Research Institute, Ancon, Panama
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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Inhibitory Bacterial Diversity and Mucosome Function Differentiate Susceptibility of Appalachian Salamanders to Chytrid Fungal Infection. Appl Environ Microbiol 2022; 88:e0181821. [PMID: 35348389 PMCID: PMC9040618 DOI: 10.1128/aem.01818-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Mucosal defenses are crucial in animals for protection against pathogens and predators. Host defense peptides (antimicrobial peptides, AMPs) as well as skin-associated microbes are key components of mucosal immunity, particularly in amphibians. We integrate microbiology, molecular biology, network-thinking, and proteomics to understand how host and microbially derived products on amphibian skin (referred to as the mucosome) serve as pathogen defenses. We studied defense mechanisms against chytrid pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), in four salamander species with different Batrachochytrium susceptibilities. Bd infection was quantified using qPCR, mucosome function (i.e., ability to kill Bd or Bsal zoospores in vitro), skin bacterial communities using 16S rRNA gene amplicon sequencing, and the role of Bd-inhibitory bacteria in microbial networks across all species. We explored the presence of candidate-AMPs in eastern newts and red-backed salamanders. Eastern newts had the highest Bd prevalence and mucosome function, while red-back salamanders had the lowest Bd prevalence and mucosome function, and two-lined salamanders and seal salamanders were intermediates. Salamanders with highest Bd infection intensity showed greater mucosome function. Bd infection prevalence significantly decreased as putative Bd-inhibitory bacterial richness and relative abundance increased on hosts. In co-occurrence networks, some putative Bd-inhibitory bacteria were found as hub-taxa, with red-backs having the highest proportion of protective hubs and positive associations related to putative Bd-inhibitory hub bacteria. We found more AMP candidates on salamanders with lower Bd susceptibility. These findings suggest that salamanders possess distinct innate mechanisms that affect chytrid fungi. IMPORTANCE How host mucosal defenses interact, and influence disease outcome is critical in understanding host defenses against pathogens. A more detailed understanding is needed of the interactions between the host and the functioning of its mucosal defenses in pathogen defense. This study investigates the variability of chytrid susceptibility in salamanders and the innate defenses each species possesses to mediate pathogens, thus advancing the knowledge toward a deeper understanding of the microbial ecology of skin-associated bacteria and contributing to the development of bioaugmentation strategies to mediate pathogen infection and disease. This study improves the understanding of complex immune defense mechanisms in salamanders and highlights the potential role of the mucosome to reduce the probability of Bd disease development and that putative protective bacteria may reduce likelihood of Bd infecting skin.
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Haver M, Le Roux G, Friesen J, Loyau A, Vredenburg VT, Schmeller DS. The role of abiotic variables in an emerging global amphibian fungal disease in mountains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152735. [PMID: 34974000 DOI: 10.1016/j.scitotenv.2021.152735] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
The emergence of the chytridiomycete fungal pathogen Batrachochytrium dendrobatidis (Bd), causing the disease chytridiomycosis, has caused collapse of amphibian communities in numerous mountain systems. The health of amphibians and of mountain freshwater habitats they inhabit is also threatened by ongoing changes in environmental and anthropogenic factors such as climate, hydrology, and pollution. Climate change is causing more extreme climatic events, shifts in ice occurrence, and changes in the timing of snowmelt and pollutant deposition cycles. All of these factors impact both pathogen and host, and disease dynamics. Here we review abiotic variables, known to control Bd occurrence and chytridiomycosis severity, and discuss how climate change may modify them. We propose two main categories of abiotic variables that may alter Bd distribution, persistence, and physiology: 1) climate and hydrology (temperature, precipitation, hydrology, ultraviolet radiation (UVR); and, 2) water chemistry (pH, salinity, pollution). For both categories, we identify topics for further research. More studies on the relationship between global change, pollution and pathogens in complex landscapes, such as mountains, are needed to allow for accurate risk assessments for freshwater ecosystems and resulting impacts on wildlife and human health. Our review emphasizes the importance of using data of higher spatiotemporal resolution and uniform abiotic metrics in order to better compare study outcomes. Fine-scale temperature variability, especially of water temperature, variability of moisture conditions and water levels, snow, ice and runoff dynamics should be assessed as abiotic variables shaping the mountain habitat of pathogen and host. A better understanding of hydroclimate and water chemistry variables, as co-factors in disease, will increase our understanding of chytridiomycosis dynamics.
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Affiliation(s)
- Marilen Haver
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UPS), Toulouse, France.
| | - Gaël Le Roux
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UPS), Toulouse, France
| | - Jan Friesen
- Environmental and Biotechnology Centre, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Adeline Loyau
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UPS), Toulouse, France; Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhütte 2, Stechlin D-16775, Germany
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, CA 94132, USA
| | - Dirk S Schmeller
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UPS), Toulouse, France
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Palmieri F, Koutsokera A, Bernasconi E, Junier P, von Garnier C, Ubags N. Recent Advances in Fungal Infections: From Lung Ecology to Therapeutic Strategies With a Focus on Aspergillus spp. Front Med (Lausanne) 2022; 9:832510. [PMID: 35386908 PMCID: PMC8977413 DOI: 10.3389/fmed.2022.832510] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Fungal infections are estimated to be the main cause of death for more than 1.5 million people worldwide annually. However, fungal pathogenicity has been largely neglected. This is notably the case for pulmonary fungal infections, which are difficult to diagnose and to treat. We are currently facing a global emergence of antifungal resistance, which decreases the chances of survival for affected patients. New therapeutic approaches are therefore needed to face these life-threatening fungal infections. In this review, we will provide a general overview on respiratory fungal infections, with a focus on fungi of the genus Aspergillus. Next, the immunological and microbiological mechanisms of fungal pathogenesis will be discussed. The role of the respiratory mycobiota and its interactions with the bacterial microbiota on lung fungal infections will be presented from an ecological perspective. Finally, we will focus on existing and future innovative approaches for the treatment of respiratory fungal infections.
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Affiliation(s)
- Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- *Correspondence: Fabio Palmieri,
| | - Angela Koutsokera
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Eric Bernasconi
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Christophe von Garnier
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Niki Ubags
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
- Niki Ubags,
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45
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Panthee B, Gyawali S, Panthee P, Techato K. Environmental and Human Microbiome for Health. Life (Basel) 2022; 12:life12030456. [PMID: 35330207 PMCID: PMC8949289 DOI: 10.3390/life12030456] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 12/13/2022] Open
Abstract
Microorganisms are an essential part of life on the earth and can exist in association with virtually any living thing. The environmental microbiome is much more diverse than the human microbiome. It is reported that most microbes existing in the environment are difficult to culture in the laboratory. Whereas both pathogenic and beneficial microbes may be prevailing in the environment, the human body can have three categories of microbes- beneficial, pathogenic, and opportunistic pathogenic. With at least 10-fold more cells than human cells, microbes as normal flora are critical for human survival. The microbes present in the human body play a crucial role in maintaining human health, and the environmental microbiome influences the human microbiome makeup. The interaction between the environmental and human microbiome highly influences human health, however it is poorly understood. In addition, as an established infection is associated with health-seeking behavior, a large number of studies have focused on the transmission and dynamics of infectious microorganisms than the noninfectious or beneficial ones. This review will summarize how the interaction between the environmental and human microbiome affects human health and identify approaches that might be beneficial for humans to improve health by being exposed to the natural environment.
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Affiliation(s)
- Bimala Panthee
- Faculty of Environmental Management, Prince of Songkla University, Songkhla 90112, Thailand;
- Sustainable Study and Research Institute, Kathmandu 44600, Nepal;
- Correspondence: (B.P.); (K.T.)
| | - Saroj Gyawali
- Faculty of Environmental Management, Prince of Songkla University, Songkhla 90112, Thailand;
- Sustainable Study and Research Institute, Kathmandu 44600, Nepal;
| | | | - Kuaanan Techato
- Faculty of Environmental Management, Prince of Songkla University, Songkhla 90112, Thailand;
- Correspondence: (B.P.); (K.T.)
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Akbar S, Gu L, Sun Y, Zhang L, Lyu K, Huang Y, Yang Z. Understanding host-microbiome-environment interactions: Insights from Daphnia as a model organism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152093. [PMID: 34863741 DOI: 10.1016/j.scitotenv.2021.152093] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/21/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
Microbes perform a variety of vital functions that are essential for healthy ecosystems, ranging from nutrient recycling, antibiotic production and waste decomposition. In many animals, microbes become an integral part by establishing diverse communities collectively termed as "microbiome/s". Microbiomes defend their hosts against pathogens and provide essential nutrients necessary for their growth and reproduction. The microbiome is a polygenic trait that is dependent on host genotype and environmental variables. However, the alteration of microbiomes by stressful condition and their recovery is still poorly understood. Despite rapid growth in host-associated microbiome studies, very little is known about how they can shape ecological processes. Here, we review current knowledge on the microbiome of Daphnia, its role in fitness, alteration by different stressors, and the ecological and evolutionary aspects of host microbiome interactions. We further discuss how variation in Daphnia physiology, life history traits, and microbiome interactive responses to biotic and abiotic factors could impact patterns of microbial diversity in the total environment, which drives ecosystem function in many freshwater environments. Our literature review provides evidence that microbiome is essential for Daphnia growth, reproduction and tolerance against stressors. Though the core and flexible microbiome of Daphnia is still debatable, it is clear that the Daphnia microbiome is highly dependent on interactions among host genotype, diet and the environment. Different environmental factors alter the microbiome composition and diversity of Daphnia and reduce their fitness. These interactions could have important implications in shaping microbial patterns and their recycling as Daphnia are keystone species in freshwater ecosystem. This review provides a framework for studying these complex relationships to gain a better understanding of the ecological and evolutionary roles of the microbiome.
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Affiliation(s)
- Siddiq Akbar
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Lei Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Yunfei Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Lu Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Kai Lyu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Yuan Huang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Zhou Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China.
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47
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Basanta MD, Rebollar EA, García-Castillo MG, Rosenblum EB, Byrne AQ, Piovia-Scott J, Parra-Olea G. Genetic variation of Batrachochytrium dendrobatidis is linked to skin bacterial diversity in the Pacific treefrog Hyliola regilla (hypochondriaca). Environ Microbiol 2021; 24:494-506. [PMID: 34959256 DOI: 10.1111/1462-2920.15861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022]
Abstract
Symbiotic bacterial communities are crucial to combating infections and contribute to host health. The amphibian skin microbiome plays an important role in protecting their hosts against pathogens such as Batrachochytrium dendrobatidis (Bd), one of the causative agents of chytridiomycosis, which is responsible for dramatic amphibian population declines worldwide. Although symbiotic skin bacteria are known to inhibit Bd growth, an understanding of the relationship between Bd genetic variability, environmental conditions, and skin bacterial communities is limited. Therefore, we examined the associations between Bd infection load, Bd genetic diversity and skin bacterial communities in five populations of Hyliola regilla (hypochondriaca) from environmentally contrasting sites in Baja California, Mexico. We observed differences in Bd genetics and infection load among sites and environments. Genetic analysis of Bd isolates revealed patterns of spatial structure corresponding to the five sites sampled. Amphibian skin bacterial diversity and community structure differed among environments and sites. Bacterial community composition was correlated with Bd genetic differences and infection load, with specific bacterial taxa enriched on infected and un-infected frogs. Our results indicate that skin-associated bacteria and Bd strains likely interact on the host skin, with consequences for microbial community structure and Bd infection intensity.
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Affiliation(s)
- María Delia Basanta
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico.,Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, AP 70-153, C.P. 04510, Mexico.,Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Mirna G García-Castillo
- Universidad Politécnica de Huatusco, Huatusco, Veracruz, Mexico.,Universidad Veracruzana, Facultad de Ciencias Biológicas y Agropecuarias Región: Orizaba-Córdoba, Amatlán de los Reyes, Veracruz, Mexico
| | - Erica Bree Rosenblum
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Allison Q Byrne
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Jonah Piovia-Scott
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
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48
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Cowgill M, Zink AG, Sparagon W, Yap TA, Sulaeman H, Koo MS, Vredenburg VT. Social Behavior, Community Composition, Pathogen Strain, and Host Symbionts Influence Fungal Disease Dynamics in Salamanders. Front Vet Sci 2021; 8:742288. [PMID: 34938792 PMCID: PMC8687744 DOI: 10.3389/fvets.2021.742288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
The emerging fungal pathogen, Batrachochytrium dendrobatidis (Bd), which can cause a fatal disease called chytridiomycosis, is implicated in the collapse of hundreds of host amphibian species. We describe chytridiomycosis dynamics in two co-occurring terrestrial salamander species, the Santa Lucia Mountains slender salamander, Batrachoseps luciae, and the arboreal salamander, Aneides lugubris. We (1) conduct a retrospective Bd-infection survey of specimens collected over the last century, (2) estimate present-day Bd infections in wild populations, (3) use generalized linear models (GLM) to identify biotic and abiotic correlates of infection risk, (4) investigate susceptibility of hosts exposed to Bd in laboratory trials, and (5) examine the ability of host skin bacteria to inhibit Bd in culture. Our historical survey of 2,866 specimens revealed that for most of the early 20th century (~1920–1969), Bd was not detected in either species. By the 1990s the proportion of infected specimens was 29 and 17% (B. luciae and A. lugubris, respectively), and in the 2010s it was 10 and 17%. This was similar to the number of infected samples from contemporary populations (2014–2015) at 10 and 18%. We found that both hosts experience signs of chytridiomycosis and suffered high Bd-caused mortality (88 and 71% for B. luciae and A. lugubris, respectively). Our GLM revealed that Bd-infection probability was positively correlated with intraspecific group size and proximity to heterospecifics but not to abiotic factors such as precipitation, minimum temperature, maximum temperature, mean temperature, and elevation, or to the size of the hosts. Finally, we found that both host species contain symbiotic skin-bacteria that inhibit growth of Bd in laboratory trials. Our results provide new evidence consistent with other studies showing a relatively recent Bd invasion of amphibian host populations in western North America and suggest that the spread of the pathogen may be enabled both through conspecific and heterospecific host interactions. Our results suggest that wildlife disease studies should assess host-pathogen dynamics that consider the interactions and effects of multiple hosts, as well as the historical context of pathogen invasion, establishment, and epizootic to enzootic transitions to better understand and predict disease dynamics.
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Affiliation(s)
- Mae Cowgill
- Department of Biology, San Francisco State University, San Francisco, CA, United States
| | - Andrew G Zink
- Department of Biology, San Francisco State University, San Francisco, CA, United States
| | - Wesley Sparagon
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, UUniversity of Hawai'i at Mānoa, HI, United States
| | - Tiffany A Yap
- Center for Biological Diversity, Oakland, CA, United States
| | - Hasan Sulaeman
- Department of Biology, San Francisco State University, San Francisco, CA, United States
| | - Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA, United States.,Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
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49
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Koo MS, Vredenburg VT, Deck JB, Olson DH, Ronnenberg KL, Wake DB. Tracking, Synthesizing, and Sharing Global Batrachochytrium Data at AmphibianDisease.org. Front Vet Sci 2021; 8:728232. [PMID: 34692807 PMCID: PMC8527349 DOI: 10.3389/fvets.2021.728232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Emerging infectious diseases have been especially devastating to amphibians, the most endangered class of vertebrates. For amphibians, the greatest disease threat is chytridiomycosis, caused by one of two chytridiomycete fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). Research over the last two decades has shown that susceptibility to this disease varies greatly with respect to a suite of host and pathogen factors such as phylogeny, geography (including abiotic factors), host community composition, and historical exposure to pathogens; yet, despite a growing body of research, a comprehensive understanding of global chytridiomycosis incidence remains elusive. In a large collaborative effort, Bd-Maps was launched in 2007 to increase multidisciplinary investigations and understanding using compiled global Bd occurrence data (Bsal was not discovered until 2013). As its database functions aged and became unsustainable, we sought to address critical needs utilizing new technologies to meet the challenges of aggregating data to facilitate research on both Bd and Bsal. Here, we introduce an advanced central online repository to archive, aggregate, and share Bd and Bsal data collected from around the world. The Amphibian Disease Portal (https://amphibiandisease.org) addresses several critical community needs while also helping to build basic biological knowledge of chytridiomycosis. This portal could be useful for other amphibian diseases and could also be replicated for uses with other wildlife diseases. We show how the Amphibian Disease Portal provides: (1) a new repository for the legacy Bd-Maps data; (2) a repository for sample-level data to archive datasets and host published data with permanent DOIs; (3) a flexible framework to adapt to advances in field, laboratory, and informatics technologies; and (4) a global aggregation of Bd and Bsal infection data to enable and accelerate research and conservation. The new framework for this project is built using biodiversity informatics best practices and metadata standards to ensure scientific reproducibility and linkages across other biological and biodiversity repositories.
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Affiliation(s)
- Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
| | - Vance T Vredenburg
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States.,Department of Biology, San Francisco State University, San Francisco, CA, United States
| | - John B Deck
- Berkeley Natural History Museums, University of California, Berkeley, Berkeley, CA, United States
| | - Deanna H Olson
- US Department of Agriculture, Forest Service, Pacific Northwest Research Station, Corvallis, OR, United States
| | - Kathryn L Ronnenberg
- US Department of Agriculture, Forest Service, Pacific Northwest Research Station, Corvallis, OR, United States
| | - David B Wake
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
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50
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Sentenac H, Loyau A, Leflaive J, Schmeller DS. The significance of biofilms to human, animal, plant and ecosystem health. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hugo Sentenac
- Laboratoire Ecologie Fonctionnelle et Environnement UMR 5245 Université de Toulouse CNRS INPT UPS Castanet‐Tolosan Cedex France
| | - Adeline Loyau
- Laboratoire Ecologie Fonctionnelle et Environnement UMR 5245 Université de Toulouse CNRS INPT UPS Castanet‐Tolosan Cedex France
- Department of Experimental Limnology Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin Germany
| | - Joséphine Leflaive
- Laboratoire Ecologie Fonctionnelle et Environnement UMR 5245 Université de Toulouse CNRS INPT UPS Castanet‐Tolosan Cedex France
| | - Dirk S. Schmeller
- Laboratoire Ecologie Fonctionnelle et Environnement UMR 5245 Université de Toulouse CNRS INPT UPS Castanet‐Tolosan Cedex France
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