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DeCandia AL, Adeduro L, Thacher P, Crosier A, Marinari P, Bortner R, Garelle D, Livieri T, Santymire R, Comizzoli P, Maslanka M, Maldonado JE, Koepfli KP, Muletz-Wolz C, Bornbusch SL. Gut bacterial composition shows sex-specific shifts during breeding season in ex situ managed black-footed ferrets. J Hered 2024; 115:385-398. [PMID: 37886904 DOI: 10.1093/jhered/esad065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 10/28/2023] Open
Abstract
The gut microbiome of mammals engages in a dynamic relationship with the body and contributes to numerous physiological processes integral to overall health. Understanding the factors shaping animal-associated bacterial communities is therefore paramount to the maintenance and management in ex situ wildlife populations. Here, we characterized the gut microbiome of 48 endangered black-footed ferrets (Mustela nigripes) housed at Smithsonian's National Zoo and Conservation Biology Institute (Front Royal, Virginia, USA). We collected longitudinal fecal samples from males and females across two distinct reproductive seasons to consider the role of host sex and reproductive physiology in shaping bacterial communities, as measured using 16S rRNA amplicon sequencing. Within each sex, gut microbial composition differed between breeding and non-breeding seasons, with five bacterial taxa emerging as differentially abundant. Between sexes, female and male microbiomes were similar during non-breeding season but significantly different during breeding season, which may result from sex-specific physiological changes associated with breeding. Finally, we found low overall diversity consistent with other mammalian carnivores alongside high relative abundances of potentially pathogenic microbes such as Clostridium, Escherichia, Paeniclostridium, and (to a lesser degree) Enterococcus-all of which have been associated with gastrointestinal or reproductive distress in mammalian hosts, including black-footed ferrets. We recommend further study of these microbes and possible therapeutic interventions to promote more balanced microbial communities. These results have important implications for ex situ management practices that can improve the gut microbial health and long-term viability of black-footed ferrets.
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Affiliation(s)
- Alexandra L DeCandia
- Biology Department, Georgetown University, Washington, DC, United States
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Laura Adeduro
- Biology Department, Georgetown University, Washington, DC, United States
| | - Piper Thacher
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, United States
| | - Adrienne Crosier
- Center for Animal Care Sciences, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Paul Marinari
- Center for Animal Care Sciences, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Robyn Bortner
- National Black-Footed Ferret Conservation Center, Carr, CO, United States
| | - Della Garelle
- National Black-Footed Ferret Conservation Center, Carr, CO, United States
| | - Travis Livieri
- Prairie Wildlife Research, Stevens Point, WI, United States
| | - Rachel Santymire
- Biology Department, Georgia State University, Atlanta, GA, United States
| | - Pierre Comizzoli
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Michael Maslanka
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, United States
- Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Carly Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
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2
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Garcias-Bonet N, Roik A, Tierney B, García FC, Villela HDM, Dungan AM, Quigley KM, Sweet M, Berg G, Gram L, Bourne DG, Ushijima B, Sogin M, Hoj L, Duarte G, Hirt H, Smalla K, Rosado AS, Carvalho S, Thurber RV, Ziegler M, Mason CE, van Oppen MJH, Voolstra CR, Peixoto RS. Horizon scanning the application of probiotics for wildlife. Trends Microbiol 2024; 32:252-269. [PMID: 37758552 DOI: 10.1016/j.tim.2023.08.012] [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: 05/31/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Bremerhaven, Germany
| | - Braden Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Francisca C García
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena D M Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ashley M Dungan
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kate M Quigley
- Minderoo Foundation, Perth, WA, Australia; James Cook University, Townsville, Australia
| | - Michael Sweet
- Aquatic Research Facility, Nature-based Solutions Research Centre, University of Derby, Derby, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; University of Potsdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Maggie Sogin
- Molecular Cell Biology, University of California, Merced, CA, USA
| | - Lone Hoj
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Gustavo Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; IMPG, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heribert Hirt
- Center for Desert Agriculture (CDA), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; WorldQuant Initiative on Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | | | - Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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3
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Buttimer S, Moura-Campos D, Greenspan SE, Neely WJ, Ferrante L, Toledo LF, Becker CG. Skin microbiome disturbance linked to drought-associated amphibian disease. Ecol Lett 2024; 27:e14372. [PMID: 38288868 DOI: 10.1111/ele.14372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
The onset of global climate change has led to abnormal rainfall patterns, disrupting associations between wildlife and their symbiotic microorganisms. We monitored a population of pumpkin toadlets and their skin bacteria in the Brazilian Atlantic Forest during a drought. Given the recognized ability of some amphibian skin bacteria to inhibit the widespread fungal pathogen Batrachochytrium dendrobatidis (Bd), we investigated links between skin microbiome health, susceptibility to Bd and host mortality during a die-off event. We found that rainfall deficit was an indirect predictor of Bd loads through microbiome disruption, while its direct effect on Bd was weak. The microbiome was characterized by fewer putative Bd-inhibitory bacteria following the drought, which points to a one-month lagged effect of drought on the microbiome that may have increased toadlet susceptibility to Bd. Our study underscores the capacity of rainfall variability to disturb complex host-microbiome interactions and alter wildlife disease dynamics.
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Affiliation(s)
- Shannon Buttimer
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, Center for Infectious Disease Dynamics, Ecology Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Diego Moura-Campos
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Sasha E Greenspan
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Wesley J Neely
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
- Department of Biology, Texas State University, San Marcos, Texas, USA
| | - Lucas Ferrante
- Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Luís Felipe Toledo
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - C Guilherme Becker
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, Center for Infectious Disease Dynamics, Ecology Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
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4
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Alexiev A, Melie T, Martindale R, Delacey C, Quandt CA, McKenzie VJ. Mr. Toad's Wild Fungi: Fungal Isolate Diversity on Colorado Boreal Toads and their Capacity for Pathogen Inhibition. FUNGAL ECOL 2023; 66:101297. [PMID: 38487623 PMCID: PMC10938945 DOI: 10.1016/j.funeco.2023.101297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
The amphibian skin pathogen Batrachochytrium dendrobatidis (Bd) has caused an ongoing biodiversity crisis, including in the locally endangered Colorado boreal toad (Anaxyrus boreas boreas). Although researchers have investigated the bacteria living on amphibian skin and how they interact with Bd, there is less information about fungal community members. This study describes (1) the diversity of culturable fungi from boreal toad skin, (2) which subset of these isolates is Bd-inhibitory, and (3) how Bd affects these isolates' growth and morphology. Most isolates were from the orders Capnodiales, Helotiales, and Pleosporales. Of 16 isolates tested for Bd-inhibition, two from the genus Neobulgaria and three from Pseudeurotium inhibited Bd. Fungal growth in co-culture with Bd varied with weak statistical support for Neobulgaria sp. (isolate BTF_36) and cf Psychrophila (isolate BTF_60) (p-values = 0.076 and 0.092, respectively). Fungal morphology remained unchanged in co-culture with Bd, however, these results could be attributed to low replication per isolate. Nonetheless, two fungal isolates' growth may have been affected by Bd, implying that fungal growth changes in Bd co-culture could be a variable worth measuring in the future (with higher replication). These findings add to the sparse but growing literature on amphibian-associated fungi and suggest further study may uncover the relevance of fungi to amphibian health and Bd infection.
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Affiliation(s)
- Alexandra Alexiev
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
| | - Tina Melie
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
| | - Rachel Martindale
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
| | - Cameron Delacey
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
| | - C. Alisha Quandt
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
| | - Valerie J. McKenzie
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology
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5
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Woodhams DC, McCartney J, Walke JB, Whetstone R. The adaptive microbiome hypothesis and immune interactions in amphibian mucus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 145:104690. [PMID: 37001710 PMCID: PMC10249470 DOI: 10.1016/j.dci.2023.104690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 05/20/2023]
Abstract
The microbiome is known to provide benefits to hosts, including extension of immune function. Amphibians are a powerful immunological model for examining mucosal defenses because of an accessible epithelial mucosome throughout their developmental trajectory, their responsiveness to experimental treatments, and direct interactions with emerging infectious pathogens. We review amphibian skin mucus components and describe the adaptive microbiome as a novel process of disease resilience where competitive microbial interactions couple with host immune responses to select for functions beneficial to the host. We demonstrate microbiome diversity, specificity of function, and mechanisms for memory characteristic of an adaptive immune response. At a time when industrialization has been linked to losses in microbiota important for host health, applications of microbial therapies such as probiotics may contribute to immunotherapeutics and to conservation efforts for species currently threatened by emerging diseases.
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Affiliation(s)
- Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA.
| | - Julia McCartney
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Jenifer B Walke
- Department of Biology, Eastern Washington University, Cheney, WA, 99004-2440, USA
| | - Ross Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
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6
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Rollins-Smith LA, Le Sage EH. Heat stress and amphibian immunity in a time of climate change. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220132. [PMID: 37305907 PMCID: PMC10258666 DOI: 10.1098/rstb.2022.0132] [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: 01/05/2023] [Accepted: 03/28/2023] [Indexed: 06/13/2023] Open
Abstract
As a class of vertebrates, amphibians, are at greater risk for declines or extinctions than any other vertebrate group, including birds and mammals. There are many threats, including habitat destruction, invasive species, overuse by humans, toxic chemicals and emerging diseases. Climate change which brings unpredictable temperature changes and rainfall constitutes an additional threat. Survival of amphibians depends on immune defences functioning well under these combined threats. Here, we review the current state of knowledge of how amphibians respond to some natural stressors, including heat and desiccation stress, and the limited studies of the immune defences under these stressful conditions. In general, the current studies suggest that desiccation and heat stress can activate the hypothalamus pituitary-interrenal axis, with possible suppression of some innate and lymphocyte-mediated responses. Elevated temperatures can alter microbial communities in amphibian skin and gut, resulting in possible dysbiosis that fosters reduced resistance to pathogens. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
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Affiliation(s)
- Louise A. Rollins-Smith
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Emily H. Le Sage
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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7
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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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8
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Adeyemi OD, Tian Y, Khwatenge CN, Grayfer L, Sang Y. Molecular diversity and functional implication of amphibian interferon complex: Remarking immune adaptation in vertebrate evolution. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 140:104624. [PMID: 36586430 DOI: 10.1016/j.dci.2022.104624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Cross-species comparison of vertebrate genomes has unraveled previously unknown complexities of interferon (IFN) systems in amphibian species. Recent genomic curation revealed that amphibian species have evolved expanded repertoires of four types of intron-containing IFN genes akin to those seen in jawed fish, intronless type I IFNs and intron-containing type III IFNs akin to those seen in amniotes, as well as uniquely intronless type III IFNs. This appears to be the case with at least ten analyzed amphibian species; with distinct species encoding diverse repertoires of these respective IFN gene subsets. Amphibians represent a key stage in vertebrate evolution, and in this context offer a unique perspective into the divergent and converged pathways leading to the emergence of distinct IFN families and groups. Recent studies have begun to unravel the roles of amphibian IFNs during these animals' immune responses in general and during their antiviral responses, in particular. However, the pleiotropic potentials of these highly expanded amphibian IFN repertoires warrant further studies. Based on recent reports and our omics analyses using Xenopus models, we posit that amphibian IFN complex may have evolved novel functions, as indicated by their extensive molecular diversity. Here, we provide an overview and an update of the present understanding of the amphibian IFN complex in the context of the evolution of vertebrate immune systems. A greater understanding of the amphibian IFN complex will grant new perspectives on the evolution of vertebrate immunity and may yield new measures by which to counteract the global amphibian declines.
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Affiliation(s)
- Oluwaseun D Adeyemi
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN, USA
| | - Yun Tian
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN, USA
| | - Collins N Khwatenge
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN, USA
| | - Leon Grayfer
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN, USA.
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Alexiev A, Chen MY, Korpita T, Weier AM, McKenzie VJ. Together or Alone: Evaluating the Pathogen Inhibition Potential of Bacterial Cocktails against an Amphibian Pathogen. Microbiol Spectr 2023; 11:e0151822. [PMID: 36719234 PMCID: PMC10100949 DOI: 10.1128/spectrum.01518-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 12/11/2022] [Indexed: 02/01/2023] Open
Abstract
The amphibian fungal skin disease Batrachochytrium dendrobatidis (Bd) has caused major biodiversity losses globally. Several experimental trials have tested the use of Janthinobacterium lividum to reduce mortality due to Bd infections, usually in single-strain amendments. It is well-characterized in terms of its anti-Bd activity mechanisms. However, there are many other microbes that inhibit Bd in vitro, and not all experiments have demonstrated consistent results with J. lividum. We used a series of in vitro assays involving bacterial coculture with Bd lawns, bacterial growth tests in liquid broth, and Bd grown in bacterial cell-free supernatant (CFS) to determine: (i) which skin bacteria isolated from a locally endangered amphibian, namely, the Colorado boreal toad (Anaxyrus boreas boreas), are able to inhibit Bd growth; (ii) whether multistrain combinations are more effective than single-strains; and (iii) the mechanism behind microbe-microbe interactions. Our results indicate that there are some single strain and multistrain probiotics (especially including strains from Pseudomonas, Chryseobacterium, and Microbacterium) that are potentially more Bd-inhibitive than is J. lividum alone and that some combinations may lead to a loss of inhibition, potentially through antagonistic metabolite effects. Additionally, if J. lividum continues being developed as a wild boreal toad probiotic, we should investigate it in combination with Curvibacter CW54D, as they inhibited Bd additively and grew at a higher rate when combined than did either alone. This highlights the fact that combinations of probiotics function in variable and unpredictable ways as well as the importance of considering the potential for interactions among naturally resident host microbiota and probiotic additions. IMPORTANCE Batrachochytrium dendrobatidis (Bd) is a pathogen that infects amphibians globally and is causing a biodiversity crisis. Our research group studies one of the species affected by Bd, namely, the Colorado boreal toad (Anaxyrus boreas boreas). Many researchers focus their studies on one probiotic bacterial isolate called Janthinobacterium lividum, which slows Bd growth in lab cultures and is currently being field tested in Colorado boreal toads. Although promising, J. lividum is not consistently effective across all amphibian individuals or species. For Colorado boreal toads, we addressed whether there are other bacterial strains that also inhibit Bd (potentially better than does J. lividum) and whether we can create two-strain probiotics that function better than do single-strain probiotics. In addition, we evaluate which types of interactions occur between two-strain combinations and what these results mean in the context of adding a probiotic to an existing amphibian skin microbiome.
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Affiliation(s)
- Alexandra Alexiev
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Melissa Y. Chen
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Timothy Korpita
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Andrew M. Weier
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Valerie J. McKenzie
- Department of Ecology & Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
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10
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Vickers E, Kerney R. Screening Salamanders for Symbionts. Methods Mol Biol 2023; 2562:425-442. [PMID: 36272092 DOI: 10.1007/978-1-0716-2659-7_28] [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] [Indexed: 06/16/2023]
Abstract
Microbial symbionts are broadly categorized by their impacts on host fitness: commensals, pathogens, and mutualists. However, recent investigations into the physiological basis of these impacts have revealed nuanced microbial influences on a wide range of host developmental, immunological, and physiological processes, including regeneration. Exploring these impacts begins with knowing which microbes are present. This methodological pipeline contains both targeted assays using PCR and culturing, as well as culture-independent approaches, to survey host salamander tissues for common and unknown microbial symbionts.
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Affiliation(s)
- Elli Vickers
- Gettysburg College, Department of Biology, Gettysburg, PA, USA
| | - Ryan Kerney
- Gettysburg College, Department of Biology, Gettysburg, PA, USA.
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11
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Overgaard Poulsen K, Astono J, Jakobsen RR, Uldbjerg N, Fuglsang J, Nielsen DS, Sundekilde UK. Influence of maternal body mass index on human milk composition and associations to infant metabolism and gut colonisation: MAINHEALTH - a study protocol for an observational birth cohort. BMJ Open 2022; 12:e059552. [PMID: 36323479 PMCID: PMC9639067 DOI: 10.1136/bmjopen-2021-059552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION Human milk provides all macronutrients for growth, bioactive compounds, micro-organisms and immunological components, which potentially interacts with and primes infant growth and, development, immune responses and the gut microbiota of the new-born. Infants with an overweight mother are more likely to become overweight later in life and overweight has been related to the gut microbiome. Therefore, it is important to investigate the mother-milk-infant triad as a biological system and if the maternal weight status influences the human milk composition, infant metabolism and gut microbiome. METHODS AND ANALYSIS This study aims to include 200 mother-infant dyads stratified into one of three body mass index (BMI) categories based on mother's prepregnancy BMI. Multiomics analyses include metabolomics, proteomics, glycomics and microbiomics methods, aiming to characterise human milk from the mothers and further relate the composition to infant gut microbiota and its metabolic impact in the infant. Infant gut microbiota is analysed using 16S sequencing of faeces samples. Nuclear magnetic resonance and mass spectrometry are used for the remaining omics analysis. We investigate whether maternal pre-pregnancy BMI results in a distinct human milk composition that potentially affects the initial priming of the infant's gut environment and metabolism early in life. ETHICS AND DISSEMINATION The Central Denmark Region Committees on Health Research Ethics has approved the protocol (J-nr. 1-10-72-296-18). All participants have before inclusion signed informed consent and deputy informed consent in accordance with the Declaration of Helsinki II. Results will be disseminated to health professionals including paediatricians, research community, nutritional policymakers, industry and finally the public. The scientific community will be informed via peer-reviewed publications and presentations at scientific conferences, the industry will be invited for meetings, and the public will be informed via reports in science magazines and the general press. Data cleared for personal data, will be deposited at public data repositories. TRIAL REGISTRATION NUMBER Danish regional committee of the Central Jutland Region, journal number: 1-10-72-296-18, version 6.Danish Data Protection Agency, journal number: 2016-051-000001, 1304. CLINICALTRIALS gov, identifier: NCT05111990.
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Affiliation(s)
- Katrine Overgaard Poulsen
- Department of Food Science, Aarhus University, Aarhus N, Denmark
- Sino-Danish Centre for Education and Research (SDC), University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Julie Astono
- Department of Food Science, Aarhus University, Aarhus N, Denmark
| | | | - Niels Uldbjerg
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Jens Fuglsang
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus N, Denmark
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12
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Abstract
Temporal changes and transmission patterns in host-associated microbial communities have important implications for host health. The diversity of amphibian skin microbial communities is associated with disease outcome in amphibians exposed to the fungal pathogen Batrachochytrium dendrobatidis (Bd). To successfully develop conservation strategies against Bd, we need a comprehensive understanding of how skin microbes are maintained and transmitted over time within populations. We used 16S rRNA sequence analysis to compare Epipedobates anthonyi frogs housed with one conspecific to frogs housed singly at four time points over the course of 1 year. We found that both α and β diversity of frog skin bacterial communities changed significantly over the course of the experiment. Specifically, we found that bacterial communities of cohabitating frogs became more similar over time. We also observed that some bacterial taxa were differentially abundant between frogs housed singly and frogs housed with a conspecific. These results suggest that conspecific contact may play a role in mediating amphibian skin microbial diversity and that turnover of skin microbial communities can occur across time. Our findings provide rationale for future studies exploring horizontal transmission as a potential mechanism of host-associated microbial maintenance in amphibians.
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Affiliation(s)
- Ariel Kruger
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, USA
| | - Spencer Roth
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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13
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Miao Y, Zhang X, Chen S, Zhou W, Xu D, Shi X, Li J, Tu J, Yuan X, Lv K, Tian G. Identifying cancer tissue-of-origin by a novel machine learning method based on expression quantitative trait loci. Front Oncol 2022; 12:946552. [PMID: 36016607 PMCID: PMC9396384 DOI: 10.3389/fonc.2022.946552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer of unknown primary (CUP) refers to cancer with primary lesion unidentifiable by regular pathological and clinical diagnostic methods. This kind of cancer is extremely difficult to treat, and patients with CUP usually have a very short survival time. Recent studies have suggested that cancer treatment targeting primary lesion will significantly improve the survival of CUP patients. Thus, it is critical to develop accurate yet fast methods to infer the tissue-of-origin (TOO) of CUP. In the past years, there are a few computational methods to infer TOO based on single omics data like gene expression, methylation, somatic mutation, and so on. However, the metastasis of tumor involves the interaction of multiple levels of biological molecules. In this study, we developed a novel computational method to predict TOO of CUP patients by explicitly integrating expression quantitative trait loci (eQTL) into an XGBoost classification model. We trained our model with The Cancer Genome Atlas (TCGA) data involving over 7,000 samples across 20 types of solid tumors. In the 10-fold cross-validation, the prediction accuracy of the model with eQTL was over 0.96, better than that without eQTL. In addition, we also tested our model in an independent data downloaded from Gene Expression Omnibus (GEO) consisting of 87 samples across 4 cancer types. The model also achieved an f1-score of 0.7-1 depending on different cancer types. In summary, eQTL was an important information in inferring cancer TOO and the model might be applied in clinical routine test for CUP patients in the future.
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Affiliation(s)
- Yongchang Miao
- Gastroenterology Center, The Second People’s Hospital of Lianyungang, Lianyungang, China
- Lianyungang Clinical College of Xuzhou Medical University, Lianyungang, China
- The Second People’s Hospital of Lianyungang, Affiliated to Kangda College of Nanjing Medical University, Lianyungang, China
| | - Xueliang Zhang
- Fifth Division of Cancer, Jiamusi Cancer Hospital, Jiamusi, China
| | - Sijie Chen
- Department of Mathematics, Ocean University of China, Qingdao, China
| | - Wenjing Zhou
- Department of Oncology, Hiser Medical Center of Qingdao, Qingdao, China
| | - Dalai Xu
- Gastrointestinal Surgery, The Second People’s Hospital of Lianyungang, Lianyungang, China
| | - Xiaoli Shi
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Jian Li
- Department of Mathematics, Ocean University of China, Qingdao, China
| | - Jinhui Tu
- Department of Mathematics, Ocean University of China, Qingdao, China
| | - Xuelian Yuan
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
| | - Kebo Lv
- Department of Mathematics, Ocean University of China, Qingdao, China
| | - Geng Tian
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
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14
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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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Ahamad N, Gupta S, Parashar D. Using Omics to Study Leprosy, Tuberculosis, and Other Mycobacterial Diseases. Front Cell Infect Microbiol 2022; 12:792617. [PMID: 35281437 PMCID: PMC8908319 DOI: 10.3389/fcimb.2022.792617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 02/01/2022] [Indexed: 12/12/2022] Open
Abstract
Mycobacteria are members of the Actinomycetales order, and they are classified into one family, Mycobacteriaceae. More than 20 mycobacterial species cause disease in humans. The Mycobacterium group, called the Mycobacterium tuberculosis complex (MTBC), has nine closely related species that cause tuberculosis in animals and humans. TB can be detected worldwide and one-fourth of the world's population is contaminated with tuberculosis. According to the WHO, about two million dies from it, and more than nine million people are newly infected with TB each year. Mycobacterium tuberculosis (M. tuberculosis) is the most potential causative agent of tuberculosis and prompts enormous mortality and morbidity worldwide due to the incompletely understood pathogenesis of human tuberculosis. Moreover, modern diagnostic approaches for human tuberculosis are inefficient and have many lacks, while MTBC species can modulate host immune response and escape host immune attacks to sustain in the human body. "Multi-omics" strategies such as genomics, transcriptomics, proteomics, metabolomics, and deep sequencing technologies could be a comprehensive strategy to investigate the pathogenesis of mycobacterial species in humans and offer significant discovery to find out biomarkers at the early stage of disease in the host. Thus, in this review, we attempt to understand an overview of the mission of "omics" approaches in mycobacterial pathogenesis, including tuberculosis, leprosy, and other mycobacterial diseases.
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Affiliation(s)
- Naseem Ahamad
- Department of Oral and Maxillofacial Diagnostic Sciences, College of Dentistry, University of Florida, Gainesville, FL, United States
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, India
| | - Deepak Parashar
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, United States
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Effects of the NF-κB Signaling Pathway Inhibitor BAY11-7082 in the Replication of ASFV. Viruses 2022; 14:v14020297. [PMID: 35215890 PMCID: PMC8877168 DOI: 10.3390/v14020297] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/28/2022] [Indexed: 02/01/2023] Open
Abstract
African swine fever virus (ASFV) mainly infects the monocyte/macrophage lineage of pigs and regulates the production of cytokines that influence host immune responses. Several studies have reported changes in cytokine production after infection with ASFV, but the regulatory mechanisms have not yet been elucidated. Therefore, the aim of this study was to examine the immune response mechanism of ASFV using transcriptomic and proteomic analyses. Through multi-omics joint analysis, it was found that ASFV infection regulates the expression of the host NF-B signal pathway and related cytokines. Additionally, changes in the NF-κB signaling pathway and IL-1β and IL-8 expression in porcine alveolar macrophages (PAMs) infected with ASFV were examined. Results show that ASFV infection activates the NF-κB signaling pathway and up-regulates the expression of IL-1β and IL-8. The NF-κB inhibitor BAY11-7082 inhibited the expression profiles of phospho-NF-κB p65, p-IκB, and MyD88 proteins, and inhibited ASFV-induced NF-κB signaling pathway activation. Additionally, the results show that the NF-κB inhibitor BAY11-7082 can inhibit the replication of ASFV and can inhibit IL-1β and, IL-8 expression. Overall, the findings of this study indicate that ASFV infection activates the NF-κB signaling pathway and up-regulates the expression of IL-1β and IL-8, and inhibits the replication of ASFV by inhibiting the NF-κB signaling pathway and interleukin-1 beta and interleukin-8 production. These findings not only provide new insights into the molecular mechanism of the association between the NF-κB signaling pathway and ASFV infection, but also indicate that the NF-κB signaling pathway is a potential immunomodulatory pathway that controls ASF.
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17
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Abstract
Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.
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18
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Analysis of Nanotoxicity with Integrated Omics and Mechanobiology. NANOMATERIALS 2021; 11:nano11092385. [PMID: 34578701 PMCID: PMC8470953 DOI: 10.3390/nano11092385] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022]
Abstract
Nanoparticles (NPs) in biomedical applications have benefits owing to their small size. However, their intricate and sensitive nature makes an evaluation of the adverse effects of NPs on health necessary and challenging. Since there are limitations to conventional toxicological methods and omics analyses provide a more comprehensive molecular profiling of multifactorial biological systems, omics approaches are necessary to evaluate nanotoxicity. Compared to a single omics layer, integrated omics across multiple omics layers provides more sensitive and comprehensive details on NP-induced toxicity based on network integration analysis. As multi-omics data are heterogeneous and massive, computational methods such as machine learning (ML) have been applied for investigating correlation among each omics. This integration of omics and ML approaches will be helpful for analyzing nanotoxicity. To that end, mechanobiology has been applied for evaluating the biophysical changes in NPs by measuring the traction force and rigidity sensing in NP-treated cells using a sub-elastomeric pillar. Therefore, integrated omics approaches are suitable for elucidating mechanobiological effects exerted by NPs. These technologies will be valuable for expanding the safety evaluations of NPs. Here, we review the integration of omics, ML, and mechanobiology for evaluating nanotoxicity.
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19
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Identifying fungal-host associations in an amphibian host system. PLoS One 2021; 16:e0256328. [PMID: 34411153 PMCID: PMC8376043 DOI: 10.1371/journal.pone.0256328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 08/04/2021] [Indexed: 02/07/2023] Open
Abstract
Host-associated microbes can interact with macro-organisms in a number of ways that affect host health. Few studies of host-associated microbiomes, however, focus on fungi. In addition, it is difficult to discern whether a fungal organism found in or on an ectotherm host is associating with it in a durable, symbiotic interaction versus a transient one, and to what extent the habitat and host share microbes. We seek to identify these host-microbe interactions on an amphibian, the Colorado boreal toad (Anaxyrus boreas boreas). We sequenced the ITS1 region of the fungal community on the skin of wild toads (n = 124) from four sites in the Colorado Rocky Mountains, across its physiologically dynamic developmental life stages. We also sampled the common habitats used by boreal toads: water from their natal wetland and aquatic pond sediment. We then examined diversity patterns within different life stages, between host and habitat, and identified fungal taxa that could be putatively host-associated with toads by using an indicator species analysis on toad versus environmental samples. Host and habitat were strikingly similar, with the exception of toad eggs. Post-hatching toad life stages were distinct in their various fungal diversity measures. We identified eight fungal taxa that were significantly associated with eggs, but no other fungal taxa were associated with other toad life stages compared with their environmental habitat. This suggests that although pre- and post-metamorphic toad life stages differ from each other, the habitat and host fungal communities are so similar that identifying obligate host symbionts is difficult with the techniques used here. This approach does, however, leverage sequence data from host and habitat samples to predict which microbial taxa are host-associated versus transient microbes, thereby condensing a large set of sequence data into a smaller list of potential targets for further consideration.
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20
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Barnes EM, Kutos S, Naghshineh N, Mesko M, You Q, Lewis JD. Assembly of the amphibian microbiome is influenced by the effects of land-use change on environmental reservoirs. Environ Microbiol 2021; 23:4595-4611. [PMID: 34190389 DOI: 10.1111/1462-2920.15653] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 01/04/2023]
Abstract
A growing focus in microbial ecology is understanding how beneficial microbiome function is created and maintained through various assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species in the soil and on amphibian hosts. We compared the microbial communities of Plethodon cinereus salamanders along a land-use gradient in the New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that variation in skin microbial community composition would correlate with changes seen in the soil which functions as the regional species pool. We found that salamanders and soil share many microbial taxa but that these two communities exhibit differences in the relative abundances of the bacterial phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varies with changes in land-use associated factors creating site-specific compositions. By employing a quantitative, null-based assembly model, we identified that dispersal limitation, variable selection, and drift guide assembly of microbes onto their skin, creating high dissimilarity between individuals with likely consequences in disease preventative function.
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Affiliation(s)
- Elle M Barnes
- Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, 10504, USA.,Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Steve Kutos
- Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, 10504, USA.,Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Nina Naghshineh
- Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, 10504, USA.,Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Marissa Mesko
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Qing You
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - J D Lewis
- Louis Calder Center - Biological Field Station, Fordham University, Armonk, NY, 10504, USA.,Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
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Tian Y, De Jesús Andino F, Khwatenge CN, Li J, Robert J, Sang Y. Virus-Targeted Transcriptomic Analyses Implicate Ranaviral Interaction with Host Interferon Response in Frog Virus 3-Infected Frog Tissues. Viruses 2021; 13:v13071325. [PMID: 34372531 PMCID: PMC8309979 DOI: 10.3390/v13071325] [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: 06/04/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022] Open
Abstract
Ranaviruses (Iridoviridae), including Frog Virus 3 (FV3), are large dsDNA viruses that cause devastating infections globally in amphibians, fish, and reptiles, and contribute to catastrophic amphibian declines. FV3’s large genome (~105 kb) contains at least 98 putative open reading frames (ORFs) as annotated in its reference genome. Previous studies have classified these coding genes into temporal classes as immediate early, delayed early, and late viral transcripts based on their sequential expression during FV3 infection. To establish a high-throughput characterization of ranaviral gene expression at the genome scale, we performed a whole transcriptomic analysis (RNA-Seq) using total RNA samples containing both viral and cellular transcripts from FV3-infected Xenopus laevis adult tissues using two FV3 strains, a wild type (FV3-WT) and an ORF64R-deleted recombinant (FV3-∆64R). In samples from the infected intestine, liver, spleen, lung, and especially kidney, an FV3-targeted transcriptomic analysis mapped reads spanning the full-genome coverage at ~10× depth on both positive and negative strands. By contrast, reads were only mapped to partial genomic regions in samples from the infected thymus, skin, and muscle. Extensive analyses validated the expression of almost all of the 98 annotated ORFs and profiled their differential expression in a tissue-, virus-, and temporal class-dependent manner. Further studies identified several putative ORFs that encode hypothetical proteins containing viral mimicking conserved domains found in host interferon (IFN) regulatory factors (IRFs) and IFN receptors. This study provides the first comprehensive genome-wide viral transcriptome profiling during infection and across multiple amphibian host tissues that will serve as an instrumental reference. Our findings imply that Ranaviruses like FV3 have acquired previously unknown molecular mimics, interfering with host IFN signaling during evolution.
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Affiliation(s)
- Yun Tian
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN 37209, USA; (Y.T.); (C.N.K.); (J.L.)
| | - Francisco De Jesús Andino
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Collins N. Khwatenge
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN 37209, USA; (Y.T.); (C.N.K.); (J.L.)
| | - Jiuyi Li
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN 37209, USA; (Y.T.); (C.N.K.); (J.L.)
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA;
- Correspondence: (J.R.); (Y.S.); Tel.: +1-585-275-1722 (J.R.); +615-963-5183 (Y.S.)
| | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN 37209, USA; (Y.T.); (C.N.K.); (J.L.)
- Correspondence: (J.R.); (Y.S.); Tel.: +1-585-275-1722 (J.R.); +615-963-5183 (Y.S.)
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22
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Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2021. [PMID: 33622992 PMCID: PMC7371965 DOI: 10.1007/s12041-020-01225-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease-mediated extinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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Medina D, Greenspan SE, Carvalho T, Becker CG, Toledo LF. Co-infecting pathogen lineages have additive effects on host bacterial communities. FEMS Microbiol Ecol 2021; 97:6134751. [PMID: 33580951 DOI: 10.1093/femsec/fiab030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/11/2021] [Indexed: 01/08/2023] Open
Abstract
Amphibian skin bacteria may confer protection against the fungus Batrachochytrium dendrobatidis (Bd), but responses of skin bacteria to different Bd lineages are poorly understood. The global panzootic lineage (Bd-GPL) has caused amphibian declines and extinctions globally. However, other lineages are enzootic (Bd-Asia-2/Brazil). Increased contact rates between Bd-GPL and enzootic lineages via globalization pose unknown consequences for host-microbiome-pathogen dynamics. We conducted a laboratory experiment and used 16S rRNA amplicon-sequencing to assess: (i) whether two lineages (Bd-Asia-2/Brazil and Bd-GPL) and their recombinant, in single and mixed infections, differentially affect amphibian skin bacteria; (ii) and the changes associated with the transition to laboratory conditions. We determined no clear differences in bacterial diversity among Bd treatments, despite differences in infection intensity. However, we observed an additive effect of mixed infections on bacterial alpha diversity and a potentially antagonistic interaction between Bd genotypes. Additionally, observed changes in community composition suggest a higher ability of Bd-GPL to alter skin bacteria. Lastly, we observed a drastic reduction in bacterial diversity and a change in community structure in laboratory conditions. We provide evidence for complex interactions between Bd genotypes and amphibian skin bacteria during coinfections, and expand on the implications of experimental conditions in ecological studies.
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Affiliation(s)
- Daniel Medina
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Instituto de Biologia, Universidade Estadual de Campinas, R. Monteiro Lobato, 255 - CEP 13083-862, Campinas, São Paulo, Brazil.,Sistema Nacional de Investigación, SENACYT, Building 205, City of Knowledge, Clayton, Panama, Republic of Panama
| | - Sasha E Greenspan
- Department of Biological Sciences, The University of Alabama, 1339 Science and Engineering Complex, Tuscaloosa 35487, Alabama, USA
| | - Tamilie Carvalho
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Instituto de Biologia, Universidade Estadual de Campinas, R. Monteiro Lobato, 255 - CEP 13083-862, Campinas, São Paulo, Brazil
| | - C Guilherme Becker
- Department of Biological Sciences, The University of Alabama, 1339 Science and Engineering Complex, Tuscaloosa 35487, Alabama, USA
| | - Luís Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Instituto de Biologia, Universidade Estadual de Campinas, R. Monteiro Lobato, 255 - CEP 13083-862, Campinas, São Paulo, Brazil
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Abarca JG, Whitfield SM, Zuniga-Chaves I, Alvarado G, Kerby J, Murillo-Cruz C, Pinto-Tomás AA. Genotyping and differential bacterial inhibition of Batrachochytrium dendrobatidis in threatened amphibians in Costa Rica. MICROBIOLOGY-SGM 2021; 167. [PMID: 33529150 DOI: 10.1099/mic.0.001017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Amphibians have declined around the world in recent years, in parallel with the emergence of an epidermal disease called chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd). This disease has been associated with mass mortality in amphibians worldwide, including in Costa Rica, and Bd is considered an important contributor to the disappearance of this group of vertebrates. While many species are susceptible to the disease, others show tolerance and manage to survive infection with the pathogen. We evaluated the pathogen Bd circulating in Costa Rica and the capacity of amphibian skin bacteria to inhibit the growth of the pathogen in vitro. We isolated and characterized - genetically and morphologically - several Bd isolates from areas with declining populations of amphibians. We determined that the circulating chytrid fungus in Costa Rica belongs to the virulent strain Bd-GPL-2, which has been related to massive amphibian deaths worldwide; however, the isolates obtained showed genetic and morphological variation. Furthermore, we isolated epidermal bacteria from 12 amphibian species of surviving populations, some in danger of extinction, and evaluated their inhibitory activity against the collection of chytrid isolates. Through bioassays we confirmed the presence of chytrid-inhibitory bacterial genera in Costa Rican amphibians. However, we observed that the inhibition varied between different isolates of the same bacterial genus, and each bacterial isolation inhibited fungal isolation differently. In total, 14 bacterial isolates belonging to the genera Stenotrophomonas, Streptomyces, Enterobacter, Pseudomonas and Klebsiella showed inhibitory activity against all Bd isolates. Given the observed variation both in the pathogen and in the bacterial inhibition capacity, it is highly relevant to include local isolates and to consider the origin of the microorganisms when performing in vivo infection tests aimed at developing and implementing mitigation strategies for chytridiomycosis.
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Affiliation(s)
- Juan G Abarca
- Laboratorio de Recursos Naturales y Vida Silvestre (LARNAVISI), Escuela de Ciencias Biológicas, Universidad Nacional, Heredia, Costa Rica
| | - Steven M Whitfield
- Conservation and Research Department, Zoo Miami, St, Miami, FL 33177, USA
| | - Ibrahim Zuniga-Chaves
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Pedro, Costa Rica.,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Gilbert Alvarado
- Laboratorio de Patología Experimental y Comparada (LAPECOM), Escuela de Biología, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Jacob Kerby
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, San Pedro, Costa Rica.,Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Pedro, Costa Rica
| | - Adrián A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, San Pedro, Costa Rica.,Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Pedro, Costa Rica.,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
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25
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Deng W, Dittoe DK, Pavilidis HO, Chaney WE, Yang Y, Ricke SC. Current Perspectives and Potential of Probiotics to Limit Foodborne Campylobacter in Poultry. Front Microbiol 2020; 11:583429. [PMID: 33414767 PMCID: PMC7782433 DOI: 10.3389/fmicb.2020.583429] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/03/2020] [Indexed: 01/07/2023] Open
Abstract
Poultry has been one of the major contributors of Campylobacter related human foodborne illness. Numerous interventions have been applied to limit Campylobacter colonization in poultry at the farm level, but other strategies are under investigation to achieve more efficient control. Probiotics are viable microbial cultures that can establish in the gastrointestinal tract (GIT) of the host animal and elicit health and nutrition benefits. In addition, the early establishment of probiotics in the GIT can serve as a barrier to foodborne pathogen colonization. Thus, probiotics are a potential feed additive for reducing and eliminating the colonization of Campylobacter in the GIT of poultry. Screening probiotic candidates is laborious and time-consuming, requiring several tests and validations both in vitro and in vivo. The selected probiotic candidate should possess the desired physiological characteristics and anti-Campylobacter effects. Probiotics that limit Campylobacter colonization in the GIT rely on different mechanistic strategies such as competitive exclusion, antagonism, and immunomodulation. Although numerous research efforts have been made, the application of Campylobacter limiting probiotics used in poultry remains somewhat elusive. This review summarizes current research progress on identifying and developing probiotics against Campylobacter and presenting possible directions for future research efforts.
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Affiliation(s)
- Wenjun Deng
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Dana K. Dittoe
- Center of Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR, United States
| | | | | | - Yichao Yang
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
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26
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Pileggi M, Pileggi SA, Sadowsky MJ. Herbicide bioremediation: from strains to bacterial communities. Heliyon 2020; 6:e05767. [PMID: 33392402 PMCID: PMC7773584 DOI: 10.1016/j.heliyon.2020.e05767] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/23/2020] [Accepted: 12/15/2020] [Indexed: 01/12/2023] Open
Abstract
There is high demand for herbicides based on the necessity to increase crop production to satisfy world-wide demands. Nevertheless, there are negative impacts of herbicide use, manifesting as selection for resistant weeds, production of toxic metabolites from partial degradation of herbicides, changes in soil microbial communities and biogeochemical cycles, alterations in plant nutrition and soil fertility, and persistent environmental contamination. Some herbicides damage non-target microorganisms via directed interference with host metabolism and via oxidative stress mechanisms. For these reasons, it is necessary to identify sustainable, efficient methods to mitigate these environmental liabilities. Before the degradation process can be initiated by microbial enzymes and metabolic pathways, microorganisms need to tolerate the oxidative stresses caused by the herbicides themselves. This can be achieved via a complex system of enzymatic and non-enzymatic antioxidative stress systems. Many of these response systems are not herbicide specific, but rather triggered by a variety of substances. Collectively, these nonspecific response systems enhance the survival and fitness potential of microorganisms. Biodegradation studies and remediation approaches have relied on individually selected strains to effectively remediate herbicides in the environment. Nevertheless, it has been shown that microbial communication systems that modulate social relationships and metabolic pathways inside biofilm structures among microorganisms are complex; therefore, use of isolated strains for xenobiotic degradation needs to be enhanced using a community-based approach with biodegradation pathway integration. Bioremediation efforts can use omics-based technologies to gain a deeper understanding of the molecular complexes of bacterial communities to achieve to more efficient elimination of xenobiotics. With this knowledge, the possibility of altering microbial communities is increased to improve the potential for bioremediation without causing other environmental impacts not anticipated by simpler approaches. The understanding of microbial community dynamics in free-living microbiota and those present in complex communities and in biofilms is paramount to achieving these objectives. It is also essential that non-developed countries, which are major food producers and consumers of pesticides, have access to these techniques to achieve sustainable production, without causing impacts through unknown side effects.
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Affiliation(s)
- Marcos Pileggi
- Laboratory of Environmental Microbiology, Biological Science and Health Institute, Department of Structural and Molecular Biology, and Genetics, State University of Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Sônia A.V. Pileggi
- Laboratory of Environmental Microbiology, Biological Science and Health Institute, Department of Structural and Molecular Biology, and Genetics, State University of Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Michael J. Sadowsky
- The Biotechnology Institute, Department of Soil, Water, and Climate, Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
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Ghosh PN, Brookes LM, Edwards HM, Fisher MC, Jervis P, Kappel D, Sewell TR, Shelton JM, Skelly E, Rhodes JL. Cross-Disciplinary Genomics Approaches to Studying Emerging Fungal Infections. Life (Basel) 2020; 10:E315. [PMID: 33260763 PMCID: PMC7761180 DOI: 10.3390/life10120315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/15/2020] [Accepted: 11/19/2020] [Indexed: 11/16/2022] Open
Abstract
Emerging fungal pathogens pose a serious, global and growing threat to food supply systems, wild ecosystems, and human health. However, historic chronic underinvestment in their research has resulted in a limited understanding of their epidemiology relative to bacterial and viral pathogens. Therefore, the untargeted nature of genomics and, more widely, -omics approaches is particularly attractive in addressing the threats posed by and illuminating the biology of these pathogens. Typically, research into plant, human and wildlife mycoses have been largely separated, with limited dialogue between disciplines. However, many serious mycoses facing the world today have common traits irrespective of host species, such as plastic genomes; wide host ranges; large population sizes and an ability to persist outside the host. These commonalities mean that -omics approaches that have been productively applied in one sphere and may also provide important insights in others, where these approaches may have historically been underutilised. In this review, we consider the advances made with genomics approaches in the fields of plant pathology, human medicine and wildlife health and the progress made in linking genomes to other -omics datatypes and sets; we identify the current barriers to linking -omics approaches and how these are being underutilised in each field; and we consider how and which -omics methodologies it is most crucial to build capacity for in the near future.
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Affiliation(s)
- Pria N. Ghosh
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Lola M. Brookes
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK
- Royal Veterinary College, Hawkshead Lane, North Mymms, Herts AL9 7TA, UK
| | - Hannah M. Edwards
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Phillip Jervis
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Dana Kappel
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Thomas R. Sewell
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Jennifer M.G. Shelton
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
- UK Centre for Ecology & Hydrology, Wallingford OX10 8BB, UK
| | - Emily Skelly
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
| | - Johanna L. Rhodes
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, St Mary’s Campus, Imperial College London, London W2 1PG, UK; (L.M.B.); (H.M.E.); (M.C.F.); (P.J.); (D.K.); (T.R.S.); (J.M.G.S.); (E.S.); (J.L.R.)
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28
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Toward a systematic design of smart probiotics. Curr Opin Biotechnol 2020; 64:199-209. [DOI: 10.1016/j.copbio.2020.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 04/24/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022]
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29
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Kruger A. Frog Skin Microbiota Vary With Host Species and Environment but Not Chytrid Infection. Front Microbiol 2020; 11:1330. [PMID: 32670233 PMCID: PMC7328345 DOI: 10.3389/fmicb.2020.01330] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/25/2020] [Indexed: 01/15/2023] Open
Abstract
Describing the structure and function of the amphibian cutaneous microbiome has gained importance with the spread of Batrachochytrium dendrobatidis (Bd), the fungal pathogen that can cause the skin disease chytridiomycosis. Sampling amphibian skin microbiota is needed to characterize current infection status and to help predict future susceptibility to Bd based on microbial composition since some skin microbes have antifungal capabilities that may confer disease resistance. Here, I use 16S rRNA sequencing to describe the composition and structure of the cutaneous microbiota of six species of amphibians. Frog skin samples were also tested for Bd, and I found 11.8% Bd prevalence among all individuals sampled (n = 76). Frog skin microbiota varied by host species and sampling site, but did not differ among Bd-positive and Bd-negative individuals. These results suggest that bacterial composition reflects host species and the environment, but does not reflect Bd infection among the species sampled here. Of the bacterial OTUs identified using an indicator species analysis as strongly associated with amphibians, significantly more indicator OTUs were putative anti-Bd taxa than would be expected based on the proportion of anti-Bd OTUs among all frog OTUs, suggesting strong associations between host species and anti-Bd OTUs. This relationship may partially explain why some of these frogs are asymptomatic carriers of Bd, but more work is needed to determine the other factors that contribute to interspecific variation in Bd susceptibility. This work provides important insights on inter- and intra-specific variation in microbial community composition, putative function, and disease dynamics in populations of amphibians that appear to be coexisting with Bd.
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Affiliation(s)
- Ariel Kruger
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States
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30
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Rebollar EA, Martínez-Ugalde E, Orta AH. The Amphibian Skin Microbiome and Its Protective Role Against Chytridiomycosis. HERPETOLOGICA 2020. [DOI: 10.1655/0018-0831-76.2.167] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Emanuel Martínez-Ugalde
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
| | - Alberto H. Orta
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
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31
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Rollins-Smith LA. Global Amphibian Declines, Disease, and the Ongoing Battle between Batrachochytrium Fungi and the Immune System. HERPETOLOGICA 2020. [DOI: 10.1655/0018-0831-76.2.178] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Louise A. Rollins-Smith
- Departments of Pathology, Microbiology and Immunology and Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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32
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Bernardo-Cravo AP, Schmeller DS, Chatzinotas A, Vredenburg VT, Loyau A. Environmental Factors and Host Microbiomes Shape Host-Pathogen Dynamics. Trends Parasitol 2020; 36:616-633. [PMID: 32402837 DOI: 10.1016/j.pt.2020.04.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 04/11/2020] [Accepted: 04/11/2020] [Indexed: 12/18/2022]
Abstract
Microorganisms are increasingly recognized as ecosystem-relevant components because they affect the population dynamics of hosts. Functioning at the interface of the host and pathogen, skin and gut microbiomes are vital components of immunity. Recent work reveals a strong influence of biotic and abiotic environmental factors (including the environmental microbiome) on disease dynamics, yet the importance of the host-host microbiome-pathogen-environment interaction has been poorly reflected in theory. We use amphibians and the disease chytridiomycosis caused by the fungal pathogen Batrachochytrium dendrobatidis to show how interactions between host, host microbiome, pathogen, and the environment all affect disease outcome. Our review provides new perspectives that improve our understanding of disease dynamics and ecology by incorporating environmental factors and microbiomes into disease theory.
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Affiliation(s)
- Adriana P Bernardo-Cravo
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France; Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Dirk S Schmeller
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France.
| | - Antonis Chatzinotas
- Helmholtz Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Permoserstrasse 15, 04318, Leipzig, Germany; Leipzig University, Institute of Biology, Johannisallee 21-23, 04103 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Adeline Loyau
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France; Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhütte 2, Stechlin, D-16775, Germany
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Abstract
Discovering that chytrid fungi cause chytridiomycosis in amphibians represented a paradigm shift in our understanding of how emerging infectious diseases contribute to global patterns of biodiversity loss. In this Review we describe how the use of multidisciplinary biological approaches has been essential to pinpointing the origins of amphibian-parasitizing chytrid fungi, including Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans, as well as to timing their emergence, tracking their cycles of expansion and identifying the core mechanisms that underpin their pathogenicity. We discuss the development of the experimental methods and bioinformatics toolkits that have provided a fuller understanding of batrachochytrid biology and informed policy and control measures.
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34
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O’Donnell ST, Ross RP, Stanton C. The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach. Front Microbiol 2020; 10:3084. [PMID: 32047482 PMCID: PMC6997344 DOI: 10.3389/fmicb.2019.03084] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.
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Affiliation(s)
- Shane Thomas O’Donnell
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
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35
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Kruger A. Functional Redundancy of Batrachochytrium dendrobatidis Inhibition in Bacterial Communities Isolated from Lithobates clamitans Skin. MICROBIAL ECOLOGY 2020; 79:231-240. [PMID: 31165187 DOI: 10.1007/s00248-019-01387-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/29/2019] [Indexed: 06/09/2023]
Abstract
The cutaneous microbial community can influence the health of amphibians exposed to Batrachochytrium dendrobatidis (Bd), a fungal pathogen that has contributed to recent amphibian declines. Resistance to Bd in amphibian populations is correlated with the presence of anti-Bd cutaneous microbes, which confer disease resistance by inhibiting Bd growth. I aimed to determine if green frogs (Lithobates clamitans), an abundant and widely distributed species in New Jersey, harbored bacteria that inhibit Bd and whether the presence and identity of these microbes varied among sites. I used in vitro challenge assays to determine if bacteria isolated from green frog skin could inhibit or enhance the growth of Bd. I found that green frogs at all sites harbored anti-Bd bacteria. However, there were differences in Bd inhibition capabilities among bacterial isolates identified as the same operational taxonomic unit (OTU), lending support to the idea that phylogenetic relatedness does not always predict Bd inhibition status. Additionally, anti-Bd bacterial richness did not vary by site, but the composition of anti-Bd bacterial taxa was distinct at each site. This suggests that there is functional redundancy of Bd inhibition across unique communities of anti-Bd symbionts found on frogs at different sites. These findings highlight the need to better elucidate the structure-function relationship of microbiomes and their role in disease resistance.
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Affiliation(s)
- Ariel Kruger
- Graduate Program in Ecology and Evolution, Department of Ecology, Evolution, and Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, 08901, USA.
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Woodhams DC, Rollins-Smith LA, Reinert LK, Lam BA, Harris RN, Briggs CJ, Vredenburg VT, Patel BT, Caprioli RM, Chaurand P, Hunziker P, Bigler L. Probiotics Modulate a Novel Amphibian Skin Defense Peptide That Is Antifungal and Facilitates Growth of Antifungal Bacteria. MICROBIAL ECOLOGY 2020; 79:192-202. [PMID: 31093727 DOI: 10.1007/s00248-019-01385-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Probiotics can ameliorate diseases of humans and wildlife, but the mechanisms remain unclear. Host responses to interventions that change their microbiota are largely uncharacterized. We applied a consortium of four natural antifungal bacteria to the skin of endangered Sierra Nevada yellow-legged frogs, Rana sierrae, before experimental exposure to the pathogenic fungus Batrachochytrium dendrobatidis (Bd). The probiotic microbes did not persist, nor did they protect hosts, and skin peptide sampling indicated immune modulation. We characterized a novel skin defense peptide brevinin-1Ma (FLPILAGLAANLVPKLICSITKKC) that was downregulated by the probiotic treatment. Brevinin-1Ma was tested against a range of amphibian skin cultures and found to inhibit growth of fungal pathogens Bd and B. salamandrivorans, but enhanced the growth of probiotic bacteria including Janthinobacterium lividum, Chryseobacterium ureilyticum, Serratia grimesii, and Pseudomonas sp. While commonly thought of as antimicrobial peptides, here brevinin-1Ma showed promicrobial function, facilitating microbial growth. Thus, skin exposure to probiotic bacterial cultures induced a shift in skin defense peptide profiles that appeared to act as an immune response functioning to regulate the microbiome. In addition to direct microbial antagonism, probiotic-host interactions may be a critical mechanism affecting disease resistance.
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Affiliation(s)
- Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA.
| | - Louise A Rollins-Smith
- Departments of Pathology, Microbiology and Immunology and Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Biological Science, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA
| | - Laura K Reinert
- Departments of Pathology, Microbiology and Immunology and Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Briana A Lam
- Department of Biology, James Madison University, Harrisonburg, VA, 22807, USA
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, VA, 22807, USA
| | - Cheryl J Briggs
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, 93106-9610, USA
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA, 94132-1722, USA
| | - Bhumi T Patel
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center and Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232-8575, USA
| | - Pierre Chaurand
- Department of Chemistry, Université de Montréal, Montreal, QC, H3T 1J4, Canada
| | - Peter Hunziker
- Functional Genomics Center Zurich, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Laurent Bigler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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37
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Campbell LJ, Pawlik AH, Harrison XA. Amphibian ranaviruses in Europe: important directions for future research. Facets (Ott) 2020. [DOI: 10.1139/facets-2020-0007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Ranaviruses are an emerging group of pathogens capable of infecting all cold-blooded vertebrates. In Europe, ranaviruses pose a particularly potent threat to wild amphibian populations. Since the 1980s research on amphibian-infecting ranaviruses in Europe has been growing. The wide distribution of amphibian populations in Europe, the ease with which many are monitored, and the tractable nature of counterpart ex situ experimental systems have provided researchers with a unique opportunity to study many aspects of host–ranavirus interactions in the wild. These characteristics of European amphibian populations will also enable researchers to lead the way as the field of host–ranavirus interactions progresses. In this review, we provide a summary of the current key knowledge regarding amphibian infecting ranaviruses throughout Europe. We then outline important areas of further research and suggest practical ways each could be pursued. We address the study of potential interactions between the amphibian microbiome and ranaviruses, how pollution may exacerbate ranaviral disease either as direct stressors of amphibians or indirect modification of the amphibian microbiome. Finally, we discuss the need for continued surveillance of ranaviral emergence in the face of climate change.
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Affiliation(s)
- Lewis J. Campbell
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Alice H. Pawlik
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Xavier A. Harrison
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall TR10 9FE, UK
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38
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Kang M, Gao J. Integration of Multi-omics Data for Expression Quantitative Trait Loci (eQTL) Analysis and eQTL Epistasis. Methods Mol Biol 2020; 2082:157-171. [PMID: 31849014 DOI: 10.1007/978-1-0716-0026-9_11] [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] [Indexed: 06/10/2023]
Abstract
Expression quantitative trait loci (eQTL) mapping studies identify genetic loci that regulate gene expression. eQTL mapping studies can capture gene regulatory interactions and provide insight into the genetic mechanism of biological systems. Recently, the integration of multi-omics data, such as single-nucleotide polymorphisms (SNPs), copy number variations (CNVs), DNA methylation, and gene expression, plays an important role in elucidating complex biological systems, since biological systems involve a sequence of complex interactions between various biological processes. This chapter introduces multi-omics data that have been used in many eQTL studies and integrative methodologies that incorporate multi-omics data for eQTL studies. Furthermore, we describe a statistical approach that can detect nonlinear causal relationships between eQTLs, called eQTL epistasis, and its importance.
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Affiliation(s)
- Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Jean Gao
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX, USA.
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39
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Gupta P, Robin VV, Dharmarajan G. Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2020; 99:65. [PMID: 33622992 PMCID: PMC7371965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/23/2020] [Accepted: 05/25/2020] [Indexed: 08/23/2024]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease mediated extinctions and wildlife epidemics. We then focus on elucidating how host-parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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Affiliation(s)
- Pooja Gupta
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29801, USA.
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40
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Tian Y, Jennings J, Gong Y, Sang Y. Xenopus Interferon Complex: Inscribing the Amphibiotic Adaption and Species-Specific Pathogenic Pressure in Vertebrate Evolution? Cells 2019; 9:E67. [PMID: 31888074 PMCID: PMC7016992 DOI: 10.3390/cells9010067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/24/2022] Open
Abstract
Several recent studies have revealed previously unknown complexity of the amphibian interferon (IFN) system. Being unique in vertebrate animals, amphibians not only conserve and multiply the fish-like intron-containing IFN genes, but also rapidly evolve amniote-like intronless IFN genes in each tested species. We postulate that the amphibian IFN system confers an essential model to study vertebrate immune evolution in molecular and functional diversity to cope with unprecedented pathophysiological requirement during terrestrial adaption. Studies so far have ascribed a potential role of these IFNs in immune regulation against intracellular pathogens, particularly viruses; however, many knowledge gaps remain elusive. Based on recent reports about IFN's multifunctional properties in regulation of animal physiological and defense responses, we interpret that amphibian IFNs may evolve novel function pertinent to their superior molecular diversity. Such new function revealed by the emerging studies about antifungal and developmental regulation of amphibian IFNs will certainly promote our understanding of immune evolution in vertebrates to address current pathogenic threats causing amphibian decline.
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Affiliation(s)
| | | | | | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN 37209, USA; (Y.T.); (J.J.); (Y.G.)
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41
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Harrison XA, Price SJ, Hopkins K, Leung WTM, Sergeant C, Garner TWJ. Diversity-Stability Dynamics of the Amphibian Skin Microbiome and Susceptibility to a Lethal Viral Pathogen. Front Microbiol 2019; 10:2883. [PMID: 31956320 PMCID: PMC6951417 DOI: 10.3389/fmicb.2019.02883] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/29/2019] [Indexed: 12/20/2022] Open
Abstract
Variation among animals in their host-associated microbial communities is increasingly recognized as a key determinant of important life history traits including growth, metabolism, and resistance to disease. Quantitative estimates of the factors shaping the stability of host microbiomes over time at the individual level in non-model organisms are scarce. Addressing this gap in our knowledge is important, as variation among individuals in microbiome stability may represent temporal gain or loss of key microbial species and functions linked to host health and/or fitness. Here we use controlled experiments to investigate how both heterogeneity in microbial species richness of the environment and exposure to the emerging pathogen Ranavirus influence the structure and temporal dynamics of the skin microbiome in a vertebrate host, the European common frog (Rana temporaria). Our evidence suggests that altering the bacterial species richness of the environment drives divergent temporal microbiome dynamics of the amphibian skin. Exposure to ranavirus effects changes in skin microbiome structure irrespective of total microbial diversity, but individuals with higher pre-exposure skin microbiome diversity appeared to exhibit higher survival. Higher diversity skin microbiomes also appear less stable over time compared to lower diversity microbiomes, but stability of the 100 most abundant ("core") community members was similar irrespective of microbiome richness. Our study highlights the importance of extrinsic factors in determining the stability of host microbiomes over time, which may in turn have important consequences for the stability of host-microbe interactions and microbiome-fitness correlations.
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Affiliation(s)
- Xavier A Harrison
- Institute of Zoology, Zoological Society of London, London, United Kingdom.,Centre for Ecology and Conservation, University of Exeter, Exeter, United Kingdom
| | - Stephen J Price
- Institute of Zoology, Zoological Society of London, London, United Kingdom.,UCL Genetics Institute, University College London, London, United Kingdom
| | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - William T M Leung
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Chris Sergeant
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Trenton W J Garner
- Institute of Zoology, Zoological Society of London, London, United Kingdom
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42
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Hughey MC, Sokol ER, Walke JB, Becker MH, Belden LK. Ecological Correlates of Large-Scale Turnover in the Dominant Members of Pseudacris crucifer Skin Bacterial Communities. MICROBIAL ECOLOGY 2019; 78:832-842. [PMID: 30949751 DOI: 10.1007/s00248-019-01372-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
Animals host a wide diversity of symbiotic microorganisms that contribute important functions to host health, and our knowledge of what drives variation in the composition of these complex communities continues to grow. Microbiome studies at larger spatial scales present opportunities to evaluate the contribution of large-scale factors to variation in the microbiome. We conducted a large-scale field study to assess variation in the bacterial symbiont communities on adult frog skin (Pseudacris crucifer), characterized using 16S rRNA gene amplicon sequencing. We found that skin bacterial communities on frogs were less diverse than, and structurally distinct from, the surrounding habitat. Frog skin was typically dominated by one of two bacterial OTUs: at western sites, a Proteobacteria dominated the community, whereas eastern sites were dominated by an Actinobacteria. Using a metacommunity framework, we then sought to identify factors explaining small- and large-scale variation in community structure-that is, among hosts within a pond, and among ponds spanning the study transect. We focused on the presence of a fungal skin pathogen, Batrachochytrium dendrobatidis (Bd) as one potential driver of variation. We found no direct link between skin bacterial community structure and Bd infection status of individual frog hosts. Differences in pond-level community structure, however, were explained by Bd infection prevalence. Importantly, Bd infection prevalence itself was correlated with numerous other environmental factors; thus, skin bacterial diversity may be influenced by a complex suite of extrinsic factors. Our findings indicate that large-scale factors and processes merit consideration when seeking to understand microbiome diversity.
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Affiliation(s)
- Myra C Hughey
- Biology Department, Vassar College, Poughkeepsie, NY, USA.
- Department of Biological Sciences, Virginia Tech, 4088 Derring Hall, 926 West Campus Drive, Blacksburg, VA, USA.
| | - Eric R Sokol
- Department of Biological Sciences, Virginia Tech, 4088 Derring Hall, 926 West Campus Drive, Blacksburg, VA, USA
- Battelle, National Ecological Observatory Network (NEON), Boulder, CO, USA
- Institute of Arctic and Alpine Research (INSTAAR), University of Colorado Boulder, Boulder, CO, USA
| | - Jenifer B Walke
- Department of Biological Sciences, Virginia Tech, 4088 Derring Hall, 926 West Campus Drive, Blacksburg, VA, USA
- Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Matthew H Becker
- Department of Biological Sciences, Virginia Tech, 4088 Derring Hall, 926 West Campus Drive, Blacksburg, VA, USA
- Department of Biology and Chemistry, Liberty University, Lynchburg, VA, USA
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, 4088 Derring Hall, 926 West Campus Drive, Blacksburg, VA, USA
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43
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Wilkins LGE, Matthews KR, Steel ZL, Nusslé SC, Carlson SM. Population dynamics of
Rana sierrae
at Dusy Basin: influence of non‐native predators, drought, and restoration potential. Ecosphere 2019. [DOI: 10.1002/ecs2.2951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Laetitia G. E. Wilkins
- Department of Environmental Science, Policy & Management University of California, Berkeley Berkeley California USA
- Genome and Biomedical Sciences Facility University of California, Davis Davis California USA
| | | | - Zachary L. Steel
- Department of Environmental Science, Policy & Management University of California, Berkeley Berkeley California USA
- Department of Environmental Science & Policy University of California, Davis Davis California USA
| | - Sébastien C. Nusslé
- Department of Environmental Science, Policy & Management University of California, Berkeley Berkeley California USA
| | - Stephanie M. Carlson
- Department of Environmental Science, Policy & Management University of California, Berkeley Berkeley California USA
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44
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Bass D, Stentiford GD, Wang HC, Koskella B, Tyler CR. The Pathobiome in Animal and Plant Diseases. Trends Ecol Evol 2019; 34:996-1008. [PMID: 31522755 DOI: 10.1016/j.tree.2019.07.012] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/14/2019] [Accepted: 07/23/2019] [Indexed: 12/11/2022]
Abstract
A growing awareness of the diversity and ubiquity of microbes (eukaryotes, prokaryotes, and viruses) associated with larger 'host' organisms has led to the realisation that many diseases thought to be caused by one primary agent are the result of interactions between multiple taxa and the host. Even where a primary agent can be identified, its effect is often moderated by other symbionts. Therefore, the one pathogen-one disease paradigm is shifting towards the pathobiome concept, integrating the interaction of multiple symbionts, host, and environment in a new understanding of disease aetiology. Taxonomically, pathobiomes are variable across host species, ecology, tissue type, and time. Therefore, a more functionally driven understanding of pathobiotic systems is necessary, based on gene expression, metabolic interactions, and ecological processes.
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Affiliation(s)
- David Bass
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe, Weymouth, DT4 8UB, UK; Sustainable Aquaculture Futures, University of Exeter, Exeter, EX4 4QD, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
| | - Grant D Stentiford
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe, Weymouth, DT4 8UB, UK; Sustainable Aquaculture Futures, University of Exeter, Exeter, EX4 4QD, UK
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan; International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Charles R Tyler
- Sustainable Aquaculture Futures, University of Exeter, Exeter, EX4 4QD, UK; Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4HB, UK
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45
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Jiménez RR, Alvarado G, Estrella J, Sommer S. Moving Beyond the Host: Unraveling the Skin Microbiome of Endangered Costa Rican Amphibians. Front Microbiol 2019; 10:2060. [PMID: 31572313 PMCID: PMC6751270 DOI: 10.3389/fmicb.2019.02060] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/21/2019] [Indexed: 01/12/2023] Open
Abstract
Some neotropical amphibians, including a few species in Costa Rica, were presumed to be "extinct" after dramatic population declines in the late 1980s but have been rediscovered in isolated populations. Such populations seem to have evolved a resistance/tolerance to Batrachochytrium dendrobatidis (Bd), a fungal pathogen that causes a deadly skin disease and is considered one of the main drivers of worldwide amphibian declines. The skin microbiome is an important component of the host's innate immune system and is associated with Bd-resistance. However, the way that the bacterial diversity of the skin microbiome confers protection against Bd in surviving species remains unclear. We studied variation in the skin microbiome and the prevalence of putatively anti-Bd bacterial taxa in four co-habiting species in the highlands of the Juan Castro Blanco National Park in Costa Rica using 16S rRNA amplicon sequencing. Lithobates vibicarius, Craugastor escoces, and Isthmohyla rivularis have recently been rediscovered, whereas Isthmohyla pseudopuma has suffered population fluctuations but has never disappeared. To investigate the life stage at which the protective skin microbiome is shaped and when shifts occur in the diversity of putatively anti-Bd bacteria, we studied the skin microbiome of tadpoles, juveniles and adults of L. vibicarius. We show that the skin bacterial composition of sympatric species and hosts with distinct Bd-infection statuses differs at the phyla, family, and genus level. We detected 94 amplicon sequence variants (ASVs) with putative anti-Bd activity pertaining to distinct bacterial taxa, e.g., Pseudomonas spp., Acinetobacter johnsonii, and Stenotrophomonas maltophilia. Bd-uninfected L. vibicarius harbored 79% more putatively anti-Bd ASVs than Bd-infected individuals. Although microbiome composition and structure differed across life stages, the diversity of putative anti-Bd bacteria was similar between pre- and post-metamorphic stages of L. vibicarius. Despite low sample size, our results support the idea that the skin microbiome is dynamic and protects against ongoing Bd presence in endangered species persisting after their presumed extinction. Our study serves as a baseline to understand the microbial patterns in species of high conservation value. Identification of microbial signatures linked to variation in disease susceptibility might, therefore, inform mitigation strategies for combating the global decline of amphibians.
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Affiliation(s)
- Randall R. Jiménez
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Gilbert Alvarado
- Laboratory of Comparative Wildlife Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - Josimar Estrella
- Laboratory of Experimental and Comparative Pathology (LAPECOM), Biology School, University of Costa Rica, San José, Costa Rica
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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46
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Bostanci N, Bao K, Greenwood D, Silbereisen A, Belibasakis GN. Periodontal disease: From the lenses of light microscopy to the specs of proteomics and next-generation sequencing. Adv Clin Chem 2019; 93:263-290. [PMID: 31655732 DOI: 10.1016/bs.acc.2019.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Periodontal disease entails the inflammatory destruction of the tooth supporting (periodontal) tissues as a result of polymicrobial colonization of the tooth surface in the form of biofilms. Extensive data collected over the past decades on this chronic disease demonstrate that its progression is infrequent and episodic, and the susceptibility to it can vary among individuals. Physical assessments of previously occurring damage to periodontal tissues remain the cornerstone of detection and diagnosis, whereas traditionally used diagnostic procedures do neither identify susceptible individuals nor distinguish between disease-active and disease-inactive periodontal sites. Thus, more sensitive and accurate "measurable biological indicators" of periodontal diseases are needed in order to place diagnosis (e.g., the presence or stage) and management of the disease on a more rational less empirical basis. Contemporary "omics" technologies may help unlock the path to this quest. High throughput nucleic acid sequencing technologies have enabled us to examine the taxonomic distribution of microbial communities in oral health and disease, whereas proteomic technologies allowed us to decipher the molecular state of the host in disease, as well as the interactive cross-talk of the host with the microbiome. The newly established field of metaproteomics has enabled the identification of the repertoire of proteins that oral microorganisms use to compete or co-operate with each other. Vast such data is derived from oral biological fluids, including gingival crevicular fluid and saliva, which is progressively completed and catalogued as the analytical technologies and bioinformatics tools progressively advance. This chapter covers the current "omics"-derived knowledge on the microbiome, the host and their "interactome" with regard to periodontal diseases, and addresses challenges and opportunities ahead.
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Affiliation(s)
- Nagihan Bostanci
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Kai Bao
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David Greenwood
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Angelika Silbereisen
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Georgios N Belibasakis
- Section of Periodontology and Dental Prevention, Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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47
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Campbell LJ, Garner TWJ, Hopkins K, Griffiths AGF, Harrison XA. Outbreaks of an Emerging Viral Disease Covary With Differences in the Composition of the Skin Microbiome of a Wild United Kingdom Amphibian. Front Microbiol 2019; 10:1245. [PMID: 31281291 PMCID: PMC6597677 DOI: 10.3389/fmicb.2019.01245] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/20/2019] [Indexed: 12/19/2022] Open
Abstract
There is growing appreciation of the important role of commensal microbes in ensuring the normal function and health of their hosts, including determining how hosts respond to pathogens. A range of infectious diseases are threatening amphibians worldwide, and evidence is accumulating that the host-associated bacteria that comprise the microbiome may be key in mediating interactions between amphibian hosts and infectious pathogens. We used 16S rRNA amplicon sequencing to quantify the skin microbial community structure of over 200 individual wild adult European common frogs (Rana temporaria), from ten populations with contrasting history of the lethal disease ranavirosis, caused by emerging viral pathogens belonging to the genus Ranavirus. All populations had similar species richness irrespective of disease history, but populations that have experienced historical outbreaks of ranavirosis have a distinct skin microbiome structure (beta diversity) when compared to sites where no outbreaks of the disease have occurred. At the individual level, neither age, body length, nor sex of the frog could predict the structure of the skin microbiota. Our data potentially support the hypothesis that variation among individuals in skin microbiome structure drive differences in susceptibility to infection and lethal outbreaks of disease. More generally, our results suggest that population-level processes are more important for driving differences in microbiome structure than variation among individuals within populations in key life history traits such as age and body size.
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Affiliation(s)
- Lewis J Campbell
- Environment and Sustainability Institute, University of Exeter, Penryn, United Kingdom.,Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Trenton W J Garner
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Kevin Hopkins
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | | | - Xavier A Harrison
- Institute of Zoology, Zoological Society of London, London, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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48
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Zhang T, Wang Z, Lv X, Li Y, Zhuang L. High-throughput sequencing reveals the diversity and community structure of rhizosphere fungi of Ferula Sinkiangensis at different soil depths. Sci Rep 2019; 9:6558. [PMID: 31024051 PMCID: PMC6484027 DOI: 10.1038/s41598-019-43110-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/12/2019] [Indexed: 01/09/2023] Open
Abstract
Ferula sinkiangesis is a valuable medicinal plant that has become endangered. Improving the soil habitat of Ferula sinkiangesis can alleviate plant damage. Fungi play an important role in the soil, but current information on the fungal community structure in the habitat of Ferula sinkiangesis and the relationship between soil fungi and abiotic factors remains unclear. In this study, we analyzed the relative abundance of fungal species in the rhizosphere of Ferula sinkiangesis. Spearman correlation analysis showed that the abiotic factor total potassium (TK) significantly explained the alpha diversity of the fungal community. At altitude, available phosphorus (AP), nitrate nitrogen (NN) and TK were significantly associated with the fungal species. In addition, a two-way ANOVA showed that soil depth had no significant effects on the alpha diversity of rhizosphere and non-rhizosphere fungi. Interestingly, linear discriminant effect size (LEfSe) analysis indicated that different biomarkers were present at varying soil depths. These findings may be related to the growth and medicinal properties of Ferula Sinkiangensis.
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Affiliation(s)
- Tao Zhang
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Xinjiang Shihezi, 832003, China
| | - Zhongke Wang
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Xinjiang Shihezi, 832003, China
| | - Xinhua Lv
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Xinjiang Shihezi, 832003, China
| | - Yang Li
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Xinjiang Shihezi, 832003, China
| | - Li Zhuang
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource Utilization, Ministry of Education, Shihezi University, Xinjiang Shihezi, 832003, China.
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49
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Jin Song S, Woodhams DC, Martino C, Allaband C, Mu A, Javorschi-Miller-Montgomery S, Suchodolski JS, Knight R. Engineering the microbiome for animal health and conservation. Exp Biol Med (Maywood) 2019; 244:494-504. [PMID: 30776908 PMCID: PMC6547002 DOI: 10.1177/1535370219830075] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
IMPACT STATEMENT Considering the clear effects of microbiota on important aspects of animal biology and development (including in humans), this topic is timely and broadly appealing, as it compels us to consider the possibilities of altering the microbiome (without antibiotics) to positively affect animal health. In this review, we highlight three general approaches to manipulating the microbiome that have demonstrated success and promise for use in animal health. We also point out knowledge gaps where further inquiry would most benefit the field. Our paper not only provides a short and digestible overview of the current state of application, but also calls for further exploration of the microbial diversity at hand to expand our toolkit, while also leveraging the diversity and flexibility of animal systems to better understand mechanisms of efficacy.
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Affiliation(s)
- Se Jin Song
- Department of Pediatrics, University of California, San Diego, CA 92093, USA
| | - Douglas C Woodhams
- Biology Department, University of Massachusetts Boston, Boston, MA 02125, USA
- Smithsonian Tropical Research Institute, Panama city 0843-03092, Panama
| | - Cameron Martino
- Bioinformatics and Systems Biology Program, University of California, San Diego, CA 92093, USA
| | - Celeste Allaband
- Biomedical Sciences Graduate Program, University of California, San Diego, CA 92093, USA
| | - Andre Mu
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville 3010, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Parkville 3010, Australia
| | - Sandrine Javorschi-Miller-Montgomery
- Department of Bioengineering, University of California, San Diego, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA
| | - Jan S Suchodolski
- Gastrointestinal Laboratory, Texas A&M University, College Station, TX 77843, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA
- Department of Computer Science and Engineering, University of California, San Diego, CA 92093, USA
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Grogan LF, Robert J, Berger L, Skerratt LF, Scheele BC, Castley JG, Newell DA, McCallum HI. Review of the Amphibian Immune Response to Chytridiomycosis, and Future Directions. Front Immunol 2018; 9:2536. [PMID: 30473694 PMCID: PMC6237969 DOI: 10.3389/fimmu.2018.02536] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/15/2018] [Indexed: 12/27/2022] Open
Abstract
The fungal skin disease, chytridiomycosis (caused by Batrachochytrium dendrobatidis and B. salamandrivorans), has caused amphibian declines and extinctions globally since its emergence. Characterizing the host immune response to chytridiomycosis has been a focus of study with the aim of disease mitigation. However, many aspects of the innate and adaptive arms of this response are still poorly understood, likely due to the wide range of species' responses to infection. In this paper we provide an overview of expected immunological responses (with inference based on amphibian and mammalian immunology), together with a synthesis of current knowledge about these responses for the amphibian-chytridiomycosis system. We structure our review around four key immune stages: (1) the naïve immunocompetent state, (2) immune defenses that are always present (constitutive defenses), (3) mechanisms for recognition of a pathogen threat and innate immune defenses, and (4) adaptive immune responses. We also evaluate the current hot topics of immunosuppression and immunopathology in chytridiomycosis, and discuss their respective roles in pathogenesis. Our synthesis reveals that susceptibility to chytridiomycosis is likely to be multifactorial. Susceptible amphibians appear to have ineffective constitutive and innate defenses, and a late-stage response characterized by immunopathology and Bd-induced suppression of lymphocyte responses. Overall, we identify substantial gaps in current knowledge, particularly concerning the entire innate immune response (mechanisms of initial pathogen detection and possible immunoevasion by Bd, degree of activation and efficacy of the innate immune response, the unexpected absence of innate leukocyte infiltration, and the cause and role of late-stage immunopathology in pathogenesis). There are also gaps concerning most of the adaptive immune system (the relative importance of B and T cell responses for pathogen clearance, the capacity and extent of immunological memory, and specific mechanisms of pathogen-induced immunosuppression). Improving our capacity for amphibian immunological research will require selection of an appropriate Bd-susceptible model species, the development of taxon-specific affinity reagents and cell lines for functional assays, and the application of a suite of conventional and emerging immunological methods. Despite current knowledge gaps, immunological research remains a promising avenue for amphibian conservation management.
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Affiliation(s)
- Laura F Grogan
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Nathan, QLD, Australia
| | - Jacques Robert
- University of Rochester Medical Center, Rochester, NY, United States
| | - Lee Berger
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia.,Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Werribee, VIC, Australia
| | - Lee F Skerratt
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia.,Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Werribee, VIC, Australia
| | - Benjamin C Scheele
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia.,Threatened Species Recovery Hub, National Environmental Science Program, Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
| | - J Guy Castley
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Nathan, QLD, Australia
| | - David A Newell
- Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - Hamish I McCallum
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Nathan, QLD, Australia
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