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The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance. ISME JOURNAL 2021; 15:1628-1640. [PMID: 33564111 PMCID: PMC8163836 DOI: 10.1038/s41396-020-00875-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/24/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022]
Abstract
Infectious pathogens can disrupt the microbiome in addition to directly affecting the host. Impacts of disease may be dependent on the ability of the microbiome to recover from such disturbance, yet remarkably little is known about microbiome recovery after disease, particularly in nonhuman animals. We assessed the resilience of the amphibian skin microbial community after disturbance by the pathogen, Batrachochytrium dendrobatidis (Bd). Skin microbial communities of laboratory-reared mountain yellow-legged frogs were tracked through three experimental phases: prior to Bd infection, after Bd infection (disturbance), and after clearing Bd infection (recovery period). Bd infection disturbed microbiome composition and altered the relative abundances of several dominant bacterial taxa. After Bd infection, frogs were treated with an antifungal drug that cleared Bd infection, but this did not lead to recovery of microbiome composition (measured as Unifrac distance) or relative abundances of dominant bacterial groups. These results indicate that Bd infection can lead to an alternate stable state in the microbiome of sensitive amphibians, or that microbiome recovery is extremely slow—in either case resilience is low. Furthermore, antifungal treatment and clearance of Bd infection had the additional effect of reducing microbial community variability, which we hypothesize results from similarity across frogs in the taxa that colonize community vacancies resulting from the removal of Bd. Our results indicate that the skin microbiota of mountain yellow-legged frogs has low resilience following Bd-induced disturbance and is further altered by the process of clearing Bd infection, which may have implications for the conservation of this endangered amphibian.
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52
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Piccinni MZ, Watts JEM, Fourny M, Guille M, Robson SC. The skin microbiome of Xenopus laevis and the effects of husbandry conditions. Anim Microbiome 2021; 3:17. [PMID: 33546771 PMCID: PMC7866774 DOI: 10.1186/s42523-021-00080-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Historically the main source of laboratory Xenopus laevis was the environment. The increase in genetically altered animals and evolving governmental constraints around using wild-caught animals for research has led to the establishment of resource centres that supply animals and reagents worldwide, such as the European Xenopus Resource Centre. In the last decade, centres were encouraged to keep animals in a "low microbial load" or "clean" state, where embryos are surface sterilized before entering the housing system; instead of the conventional, "standard" conditions where frogs and embryos are kept without prior surface treatment. Despite Xenopus laevis having been kept in captivity for almost a century, surprisingly little is known about the frogs as a holobiont and how changing the microbiome may affect resistance to disease. This study examines how the different treatment conditions, "clean" and "standard" husbandry in recirculating housing, affects the skin microbiome of tadpoles and female adults. This is particularly important when considering the potential for poor welfare caused by a change in husbandry method as animals move from resource centres to smaller research colonies. RESULTS We found strong evidence for developmental control of the surface microbiome on Xenopus laevis; adults had extremely similar microbial communities independent of their housing, while both tadpole and environmental microbiome communities were less resilient and showed greater diversity. CONCLUSIONS Our findings suggest that the adult Xenopus laevis microbiome is controlled and selected by the host. This indicates that the surface microbiome of adult Xenopus laevis is stable and defined independently of the environment in which it is housed, suggesting that the use of clean husbandry conditions poses little risk to the skin microbiome when transferring adult frogs to research laboratories. This will have important implications for frog health applicable to Xenopus laevis research centres throughout the world.
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Affiliation(s)
- Maya Z. Piccinni
- grid.4701.20000 0001 0728 6636School of Biological Sciences, University of Portsmouth, Portsmouth, UK
- grid.4701.20000 0001 0728 6636European Xenopus Resource Centre, University of Portsmouth, Portsmouth, UK
| | - Joy E. M. Watts
- grid.4701.20000 0001 0728 6636School of Biological Sciences, University of Portsmouth, Portsmouth, UK
- grid.4701.20000 0001 0728 6636Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK
| | - Marie Fourny
- grid.10400.350000 0001 2108 3034University of Rouen-Normandy, Rouen, France
| | - Matt Guille
- grid.4701.20000 0001 0728 6636School of Biological Sciences, University of Portsmouth, Portsmouth, UK
- grid.4701.20000 0001 0728 6636European Xenopus Resource Centre, University of Portsmouth, Portsmouth, UK
| | - Samuel C. Robson
- grid.4701.20000 0001 0728 6636Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK
- grid.4701.20000 0001 0728 6636School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
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53
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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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54
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Mo X, Cai X, Hui Q, Sun H, Yu R, Bu R, Yan B, Ou Q, Li Q, He S, Jiang C. Whole genome sequencing and metabolomics analyses reveal the biosynthesis of nerol in a multi-stress-tolerant Meyerozyma guilliermondii GXDK6. Microb Cell Fact 2021; 20:4. [PMID: 33413399 PMCID: PMC7789178 DOI: 10.1186/s12934-020-01490-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/30/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Nerol (C10H18O), an acyclic monoterpene, naturally presents in plant essential oils, and is used widely in food, cosmetics and pharmaceuticals as the valuable fragrance. Meanwhile, chemical synthesis is the only strategy for large-scale production of nerol, and the disadvantages of chemical synthesis greatly limit the production and its application. These defects drive the interests of researchers shift to the production of nerol by eco-friendly methods known as biosynthesis methods. However, the main technical bottleneck restricting the biosynthesis of nerol is the lacking of corresponding natural aroma-producing microorganisms. RESULTS In this study, a novel multi-stress-tolerant probiotics Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified by whole genome sequencing and metabolomics technology. GXDK6 showed a broad pH tolerance in the range of 2.5-10.0. The species also showed salt tolerance with up to 12% NaCl and up to 18% of KCl or MgCl2. GXDK6 exhibited heavy-metal Mn2+ tolerance of up to 5494 ppm. GXDK6 could also ferment with a total of 21 kinds of single organic matter as the carbon source, and produce abundant aromatic metabolites. Results from the gas chromatography-mass spectrometry indicated the production of 8-14 types of aromatic metabolites (isopentanol, nerol, geraniol, phenylethanol, isobutanol, etc.) when GXDK6 was fermented up to 72 h with glucose, sucrose, fructose, or xylose as the single carbon source. Among them, nerol was found to be a novel aromatic metabolite from GXDK6 fermentation, and its biosynthesis mechanism had also been further revealed. CONCLUSION A novel aroma-producing M. guilliermondii GXDK6 was identified successfully by whole genome sequencing and metabolomics technology. GXDK6 showed high multi-stress-tolerant properties with acid-base, salty, and heavy-metal environments. The aroma-producing mechanism of nerol in GXDK6 had also been revealed. These findings indicated the aroma-producing M. guilliermondii GXDK6 with multi-stress-tolerant properties has great potential value in the fermentation industry.
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Affiliation(s)
- Xueyan Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Xinghua Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Qinyan Hui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Huijie Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Ran Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Ru Bu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Bing Yan
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai, 536000, China
| | - Qian Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Quanwen Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Sheng He
- Guangxi Birth Defects Prevention and Control Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530033, China.
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai, 536000, China.
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55
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Gust KA, Indest KJ, Lotufo G, Everman SJ, Jung CM, Ballentine ML, Hoke AV, Sowe B, Gautam A, Hammamieh R, Ji Q, Barker ND. Genomic investigations of acute munitions exposures on the health and skin microbiome composition of leopard frog (Rana pipiens) tadpoles. ENVIRONMENTAL RESEARCH 2021; 192:110245. [PMID: 32987006 DOI: 10.1016/j.envres.2020.110245] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
Natural communities of microbes inhabiting amphibian skin, the skin microbiome, are critical to supporting amphibian health and disease resistance. To enable the pro-active health assessment and management of amphibians on Army installations and beyond, we investigated the effects of acute (96h) munitions exposures to Rana pipiens (leopard frog) tadpoles and the associated skin microbiome, integrated with RNAseq-based transcriptomic responses in the tadpole host. Tadpoles were exposed to the legacy munition 2,4,6-trinitrotoluene (TNT), the new insensitive munition (IM) formulation, IMX-101, and the IM constituents nitroguinidine (NQ) and 1-methyl-3-nitroguanidine (MeNQ). The 96h LC50 values and 95% confidence intervals were 2.6 (2.4, 2.8) for ΣTNT and 68.2 (62.9, 73.9) for IMX-101, respectively. The NQ and MeNQ exposures caused no significant impacts on survival in 96h exposures even at maximum exposure levels of 3560 and 5285 mg/L, respectively. However, NQ and MeNQ, as well as TNT and IMX-101 exposures, all elicited changes in the tadpole skin microbiome profile, as evidenced by significantly increased relative proportions of the Proteobacteria with increasing exposure concentrations, and significantly decreased alpha-diversity in the NQ exposure. The potential for direct effects of munitions exposure on the skin microbiome were observed including increased abundance of munitions-tolerant phylogenetic groups, in addition to possible indirect effects on microbial flora where transcriptional responses suggestive of changes in skin mucus-layer properties, antimicrobial peptide production, and innate immune factors were observed in the tadpole host. Additional insights into the tadpole host's transcriptional response to munitions exposures indicated that TNT and IMX-101 exposures significantly enriched transcriptional expression within type-I and type-II xenobiotic metabolism pathways, where dose-responsive increases in expression were observed. Significant enrichment and increased transcriptional expression of heme and iron binding functions in the TNT exposures served as likely indicators of known mechanisms of TNT toxicity including hemolytic anemia and methemoglobinemia. The significant enrichment and dose-responsive decrease in transcriptional expression of cell cycle pathways in the IMX-101 exposures was consistent with previous observations in fish, while significant enrichment of immune-related function in response to NQ exposure were consistent with potential immune suppression at the highest NQ exposure concentration. Finally, the MeNQ exposures elicited significantly decreased transcriptional expression of keratin 16, type I, a gene likely involved in keratinization processes in amphibian skin. Overall, munitions showed the potential to alter tadpole skin microbiome composition and affect transcriptional profiles in the amphibian host, some suggestive of potential impacts on host health and immune status relevant to disease susceptibility.
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Affiliation(s)
- Kurt A Gust
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, USA.
| | - Karl J Indest
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, USA.
| | - Guilherme Lotufo
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, USA.
| | | | - Carina M Jung
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, USA.
| | - Mark L Ballentine
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, USA.
| | - Allison V Hoke
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA; ORISE fellow, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - Bintu Sowe
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA; ORISE fellow, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - Aarti Gautam
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - Qing Ji
- Bennett Aerospace, Cary, NC, USA.
| | - Natalie D Barker
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, USA.
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56
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Towards a food web based control strategy to mitigate an amphibian panzootic in agricultural landscapes. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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57
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Le Sage EH, LaBumbard BC, Reinert LK, Miller BT, Richards-Zawacki CL, Woodhams DC, Rollins-Smith LA. Preparatory immunity: Seasonality of mucosal skin defences and Batrachochytrium infections in Southern leopard frogs. J Anim Ecol 2020; 90:542-554. [PMID: 33179786 DOI: 10.1111/1365-2656.13386] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022]
Abstract
Accurately predicting the impacts of climate change on wildlife health requires a deeper understanding of seasonal rhythms in host-pathogen interactions. The amphibian pathogen, Batrachochytrium dendrobatidis (Bd), exhibits seasonality in incidence; however, the role that biological rhythms in host defences play in defining this pattern remains largely unknown. The aim of this study was to examine whether host immune and microbiome defences against Bd correspond with infection risk and seasonal fluctuations in temperature and humidity. Over the course of a year, five populations of Southern leopard frogs (Rana [Lithobates] sphenocephala) in Tennessee, United States, were surveyed for host immunity, microbiome and pathogen dynamics. Frogs were swabbed for pathogen load and skin bacterial diversity and stimulated to release stored antimicrobial peptides (AMPs). Secretions were analysed to estimate total hydrophobic peptide concentrations, presence of known AMPs and effectiveness of Bd growth inhibition in vitro. The diversity and proportion of bacterial reads with a 99% match to sequences of isolates known to inhibit Bd growth in vitro were used as an estimate of predicted anti-Bd function of the skin microbiome. Batrachochytrium dendrobatidis dynamics followed the expected seasonal fluctuations-peaks in cooler months-which coincided with when host mucosal defences were most potent against Bd. Specifically, the concentration and expression of stored AMPs cycled synchronously with Bd dynamics. Although microbiome changes followed more linear trends over time, the proportion of bacteria that can function to inhibit Bd growth was greatest when risk of Bd infection was highest. We interpret the increase in peptide storage in the fall and the shift to a more anti-Bd microbiome over winter as a preparatory response for subsequent infection risk during the colder periods when AMP synthesis and bacterial growth is slow and pathogen pressure from this cool-adapted fungus is high. Given that a decrease in stored AMP concentrations as temperatures warm in spring likely means greater secretion rates, the subsequent decrease in prevalence suggests seasonality of Bd in this host may be in part regulated by annual immune rhythms, and dominated by the effects of temperature.
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Affiliation(s)
- Emily H Le Sage
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Laura K Reinert
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Brian T Miller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | | | - Doug C Woodhams
- Department of Biology, University of Massachusetts, Boston, MA, USA
| | - Louise A Rollins-Smith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
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58
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Brannelly LA, McCallum HI, Grogan LF, Briggs CJ, Ribas MP, Hollanders M, Sasso T, Familiar López M, Newell DA, Kilpatrick AM. Mechanisms underlying host persistence following amphibian disease emergence determine appropriate management strategies. Ecol Lett 2020; 24:130-148. [PMID: 33067922 DOI: 10.1111/ele.13621] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/18/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022]
Abstract
Emerging infectious diseases have caused many species declines, changes in communities and even extinctions. There are also many species that persist following devastating declines due to disease. The broad mechanisms that enable host persistence following declines include evolution of resistance or tolerance, changes in immunity and behaviour, compensatory recruitment, pathogen attenuation, environmental refugia, density-dependent transmission and changes in community composition. Here we examine the case of chytridiomycosis, the most important wildlife disease of the past century. We review the full breadth of mechanisms allowing host persistence, and synthesise research on host, pathogen, environmental and community factors driving persistence following chytridiomycosis-related declines and overview the current evidence and the information required to support each mechanism. We found that for most species the mechanisms facilitating persistence have not been identified. We illustrate how the mechanisms that drive long-term host population dynamics determine the most effective conservation management strategies. Therefore, understanding mechanisms of host persistence is important because many species continue to be threatened by disease, some of which will require intervention. The conceptual framework we describe is broadly applicable to other novel disease systems.
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Affiliation(s)
- Laura A Brannelly
- Veterinary BioSciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Vic, 3030, Australia
| | - Hamish I McCallum
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Nathan, Qld., 4111, Australia
| | - Laura F Grogan
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Nathan, Qld., 4111, Australia.,Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Cheryl J Briggs
- Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Maria P Ribas
- Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia.,Wildlife Conservation Medicine Research Group, Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Matthijs Hollanders
- Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Thais Sasso
- Environmental Futures Research Institute and School of Environment and Science, Griffith University, Nathan, Qld., 4111, Australia
| | - Mariel Familiar López
- School of Environment and Sciences, Griffith University, Gold Coast, Qld., 4215, Australia
| | - David A Newell
- Forest Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Auston M Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
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59
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Martin H. C, Ibáñez R, Nothias LF, Caraballo-Rodríguez AM, Dorrestein PC, Gutiérrez M. Metabolites from Microbes Isolated from the Skin of the Panamanian Rocket Frog Colostethus panamansis (Anura: Dendrobatidae). Metabolites 2020; 10:E406. [PMID: 33065987 PMCID: PMC7601193 DOI: 10.3390/metabo10100406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 01/02/2023] Open
Abstract
The Panamanian rocket frog Colostethus panamansis (family Dendrobatidae) has been affected by chytridiomycosis, a deadly disease caused by the fungus Batrachochytrium dendrobatidis (Bd). While there are still uninfected frogs, we set out to isolate microbes from anatomically distinct regions in an effort to create a cultivable resource within Panama for potential drug/agricultural/ecological applications that perhaps could also be used as part of a strategy to protect frogs from infections. To understand if there are specific anatomies that should be explored in future applications of this resource, we mapped skin-associated bacteria of C. panamansis and their metabolite production potential by mass spectrometry on a 3D model. Our results indicate that five bacterial families (Enterobacteriaceae, Comamonadaceae, Aeromonadaceae, Staphylococcaceae and Pseudomonadaceae) dominate the cultivable microbes from the skin of C. panamansis. The combination of microbial classification and molecular analysis in relation to the anti-Bd inhibitory databases reveals the resource has future potential for amphibian conservation.
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Affiliation(s)
- Christian Martin H.
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, Panama 0843-01103, Panama;
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur 522510, India
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama 0843-03092, Panama;
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; (L.-F.N.); (A.M.C.-R.); (P.C.D.)
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; (L.-F.N.); (A.M.C.-R.); (P.C.D.)
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; (L.-F.N.); (A.M.C.-R.); (P.C.D.)
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, Panama 0843-01103, Panama;
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60
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Samuelson MM, Pulis EE, Ray C, Arias CR, Samuelson DR, Mattson EE, Solangi M. Analysis of the fecal microbiome in Kemp’s ridley sea turtles Lepidochelys kempii undergoing rehabilitation. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The impact of the intestinal and fecal microbiome on animal health has received considerable attention in recent years and has direct implications for the veterinary and wildlife rehabilitation fields. To examine the effects of rehabilitation on the microbiome in Kemp’s ridley sea turtlesLepidochelys kempii, fecal samples from 30 incidentally captured juveniles were collected during rehabilitation. Samples were analyzed to determine alpha- (α) and beta- (β) diversity as well as the taxonomic abundance of the fecal microbiota during rehabilitation and in response to treatment with antibiotics. The fecal microbial communities of animals housed in rehabilitation for a ‘short-term’ stay (samples collected 0-9 d post-capture) were compared with ‘long-term’ (samples collected 10+ d post-capture) and ‘treated’ groups (samples collected from turtles that had received antibiotic medication). Results of this study indicate that the most dominant phylum in fecal samples wasBacteroidetes(relative abundance, 45.44 ± 5.92% [SD]), followed byFirmicutes(26.62 ± 1.58%),Fusobacteria(19.49 ± 9.07%), andProteobacteria(7.39 ± 1.84%). Similarly, at the family level,Fusobacteriaceae(28.36 ± 17.75%),Tannerellaceae(15.41 ± 10.50%),Bacteroidaceae(14.58 ± 8.48%), andRuminococcaceae(11.49 ± 3.47%) were the most abundant. Our results indicated that both antibiotic-treated and long-term rehabilitated turtles demonstrated a significant decrease in β-diversity when compared to short-term rehabilitated turtles. Our results likewise showed that the length of time turtles spent in rehabilitation was negatively correlated with α- and β-diversity. This study demonstrates the importance of a judicious use of antibiotics during the rehabilitation process and emphasizes the importance of limiting the length of hospital stays for sick and injured sea turtles as much as possible.
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Affiliation(s)
- MM Samuelson
- The Institute for Marine Mammal Studies, Gulfport, MS 39503, USA
- Department of Comparative Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5875, USA
| | - EE Pulis
- The Institute for Marine Mammal Studies, Gulfport, MS 39503, USA
- Math and Science Department, Northern State University, Aberdeen, SD 57401, USA
| | - C Ray
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, AL 36849, USA
- Harry K. Dupree Stuttgart National Aquaculture Research Center, U.S. Department of Agriculture, Stuttgart, AR 72160, USA
| | - CR Arias
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, AL 36849, USA
| | - DR Samuelson
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - EE Mattson
- The Institute for Marine Mammal Studies, Gulfport, MS 39503, USA
| | - M Solangi
- The Institute for Marine Mammal Studies, Gulfport, MS 39503, USA
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Weeks DM, Parris MJ, Brown SP. Recovery and resiliency of skin microbial communities on the southern leopard frog (Lithobates sphenocephalus) following two biotic disturbances. Anim Microbiome 2020; 2:35. [PMID: 33499962 PMCID: PMC7807490 DOI: 10.1186/s42523-020-00053-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 09/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microorganisms have intimate functional relationships with invertebrate and vertebrate taxa, with the potential to drastically impact health outcomes. Perturbations that affect microbial communities residing on animals can lead to dysbiosis, a change in the functional relationship, often associated with disease. Batrachochytrium dendrobatidis (Bd), a fungal pathogen of amphibians, has been responsible for catastrophic amphibian population declines around the globe. Amphibians harbor a diverse cutaneous microbiome, including some members which are known to be antagonistic to Bd (anti-Bd). Anti-Bd microorganisms facilitate the ability of some frog populations to persist in the presence of Bd, where other populations that lack anti-Bd microorganisms have declined. Research suggests disease-antagonistic properties of the microbiome may be a function of microbial community interactions, rather than individual bacterial species. Conservation efforts have identified amphibian-associated bacteria that exhibit anti-fungal properties for use as 'probiotics' on susceptible amphibian populations. Probiotic application, usually with a single bacterial species, may benefit from a greater understanding of amphibian species-specific microbiome responses to disturbances (e.g. dysbiosis vs. recovery). We assessed microbiome responses to two microbial disturbance events over multiple time points. RESULTS Exposing Lithobates sphenocephalus (southern leopard frog) adults to the biopesticidal bacteria Bacillus thuringiensis, followed by exposure to the fungal pathogen Bd, did not have long term impacts on the microbiome. After initial shifts, microbial communities recovered and returned to a state that resembled pre-disturbance. CONCLUSIONS Our results indicate microbial communities on L. sphenocephalus are robust and resistant to permanent shifts from some disturbances. This resiliency of microbial communities may explain why L. sphenocephalus is not experiencing the population declines from Bd that impacts many other species. Conservation efforts may benefit from studies outlining amphibian species-specific microbiome responses to disturbances (e.g. dysbiosis vs. recovery). If microbial communities on a threatened amphibian species are unlikely to recover following a disturbance, additional measures may be implemented to ameliorate the impacts of physical and chemical stressors on host-associated microbial communities.
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Affiliation(s)
- Denita M Weeks
- Department of Biology, Grand Junction, Colorado Mesa University, Grand Junction, CO, 81501, USA.
| | - Matthew J Parris
- Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA
| | - Shawn P Brown
- Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA.,Center for Biodiversity Research, The University of Memphis, Memphis, TN, 38152, USA
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Loudon AH, Kurtz A, Esposito E, Umile TP, Minbiole KPC, Parfrey LW, Sheafor BA. Columbia spotted frogs (Rana luteiventris) have characteristic skin microbiota that may be shaped by cutaneous skin peptides and the environment. FEMS Microbiol Ecol 2020; 96:5894915. [DOI: 10.1093/femsec/fiaa168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/13/2020] [Indexed: 01/20/2023] Open
Abstract
ABSTRACT
Global amphibian declines due to the fungal pathogen Batrachochytrium dendrobatidis (Bd) have led to questions about how amphibians defend themselves against skin diseases. A total of two amphibian defense mechanisms are antimicrobial peptides (AMPs), a component of amphibian innate immune defense and symbiotic skin bacteria, which can act in synergy. We characterized components of these factors in four populations of Columbia spotted frogs (Rana luteiventris) to investigate their role in disease defense. We surveyed the ability of their AMPs to inhibit Bd, skin bacterial community composition, skin metabolite profiles and presence and intensity of Bd infection. We found that AMPs from R. luteiventris inhibited Bd in bioassays, but inhibition did not correlate with Bd intensity on frogs. R. luteiventris had two prevalent and abundant core bacteria: Rhizobacter and Chryseobacterium. Rhizobacter relative abundance was negatively correlated with AMP's ability to inhibit Bd, but was not associated with Bd status itself. There was no relationship between metabolites and Bd. Bacterial communities and Bd differ by location, which suggests a strong environmental influence. R. luteiventris are dominated by consistent core bacteria, but also house transient bacteria that are site specific. Our emergent hypothesis is that host control and environmental factors shape the microbiota on R. luteiventris.
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Affiliation(s)
- A H Loudon
- Department of Zoology and Biodiversity Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
| | - A Kurtz
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
| | - E Esposito
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
| | - T P Umile
- Department of Chemistry, Villanova University, Villanova, Pennsylvania, 19085-1603, USA
| | - K P C Minbiole
- Department of Chemistry, Villanova University, Villanova, Pennsylvania, 19085-1603, USA
| | - L W Parfrey
- Department of Zoology and Biodiversity Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, CA
| | - B A Sheafor
- Biology Department, Carroll College, Helena, Montana, 59625-0002, USA
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Lemieux-Labonté V, Dorville NASY, Willis CKR, Lapointe FJ. Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats ( Eptesicus fuscus) Infected With the Causal Agent of White-Nose Syndrome. Front Microbiol 2020; 11:1776. [PMID: 32793178 PMCID: PMC7390961 DOI: 10.3389/fmicb.2020.01776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/06/2020] [Indexed: 01/01/2023] Open
Abstract
Little is known about skin microbiota in the context of the disease white-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans (Pd), that has caused enormous declines of hibernating North American bats over the past decade. Interestingly, some hibernating species, such as the big brown bat (Eptesicus fuscus), appear resistant to the disease and their skin microbiota could play a role. However, a comprehensive analysis of the skin microbiota of E. fuscus in the context of Pd has not been done. In January 2017, we captured hibernating E. fuscus, sampled their skin microbiota, and inoculated them with Pd or sham inoculum. We allowed the bats to hibernate in the lab under controlled conditions for 11 weeks and then sampled their skin microbiota to test the following hypotheses: (1) Pd infection would not disrupt the skin microbiota of Pd-resistant E. fuscus; and (2) microbial taxa with antifungal properties would be abundant both before and after inoculation with Pd. Using high-throughput 16S rRNA gene sequencing, we discovered that beta diversity of Pd-inoculated bats changed more over time than that of sham-inoculated bats. Still, the most abundant taxa in the community were stable throughout the experiment. Among the most abundant taxa, Pseudomonas and Rhodococcus are known for antifungal potential against Pd and other fungi. Thus, in contrast to hypothesis 1, Pd infection destabilized the skin microbiota but consistent with hypothesis 2, bacteria with known antifungal properties remained abundant and stable on the skin. This study is the first to provide a comprehensive survey of skin microbiota of E. fuscus, suggesting potential associations between the bat skin microbiota and resistance to the Pd infection and WNS. These results set the stage for future studies to characterize microbiota gene expression, better understand mechanisms of resistance to WNS, and help develop conservation strategies.
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Affiliation(s)
| | - Nicole A. S.-Y. Dorville
- Department of Biology, Centre for Forest Interdisciplinary Research, The University of Winnipeg, Winnipeg, MB, Canada
| | - Craig K. R. Willis
- Department of Biology, Centre for Forest Interdisciplinary Research, The University of Winnipeg, Winnipeg, MB, Canada
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Abstract
Soil-borne pathogens cause high losses in crop yields globally. The development of environmentally friendly approaches is urgently needed, but is often constrained by complex interactions between root-associated microbes and pathogens. Here, we demonstrate that the interactions within microbial consortia mediated by iron-scavenging siderophores play an important role in reducing pathogen infection and enhancing plant health. This study provides a promising and novel research direction for dealing with a wide range of microbial infections through iron exploitation, which is important for the colonization and infection of both plant and human hosts by pathogens. Interactions between plant pathogens and root-associated microbes play an important role in determining disease outcomes. While several studies have suggested that steering these interactions may improve plant health, such approaches have remained challenging in practice. Because of low iron availability in most soils, competition for iron via secreted siderophore molecules might influence microbial interaction outcomes. Here, we tested if bacterial interactions mediated by iron-scavenging siderophores can be used to predict the disease suppressiveness of microbial consortia against soilborne Ralstonia solanacearum, a bacterial pathogen in the tomato rhizosphere. Iron availability significantly affected the interactions within inoculated consortia and between the consortia and the pathogen. We observed contrasting effects of siderophores and other nonsiderophore metabolites on the pathogen growth, while the siderophore effects were relatively much stronger. Specifically, disease incidence was reduced in vivo when the inoculated consortia produced siderophores that the pathogen could not use for its own growth. Employing siderophore-mediated interactions to engineer functionally robust microbial inoculants shows promise in protecting plants from soilborne pathogens. IMPORTANCE Soil-borne pathogens cause high losses in crop yields globally. The development of environmentally friendly approaches is urgently needed, but is often constrained by complex interactions between root-associated microbes and pathogens. Here, we demonstrate that the interactions within microbial consortia mediated by iron-scavenging siderophores play an important role in reducing pathogen infection and enhancing plant health. This study provides a promising and novel research direction for dealing with a wide range of microbial infections through iron exploitation, which is important for the colonization and infection of both plant and human hosts by pathogens.
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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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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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67
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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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Chong R, Cheng Y, Hogg CJ, Belov K. Marsupial Gut Microbiome. Front Microbiol 2020; 11:1058. [PMID: 32547513 PMCID: PMC7272691 DOI: 10.3389/fmicb.2020.01058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
The study of the gut microbiome in threatened wildlife species has enormous potential to improve conservation efforts and gain insights into host-microbe coevolution. Threatened species are often housed in captivity, and during this process undergo considerable changes to their gut microbiome. Studying the gut microbiome of captive animals therefore allows identification of dysbiosis and opportunities for improving management practices in captivity and for subsequent translocations. Manipulation of the gut microbiome through methods such as fecal transplant may offer an innovative means of restoring dysbiotic microbiomes in threatened species to provide health benefits. Finally, characterization of the gut microbiome (including the viral components, or virome) provides important baseline health information and may lead to discovery of significant microbial pathogens. Here we summarize our current understanding of microbiomes in Australian marsupial species.
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Affiliation(s)
- Rowena Chong
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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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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Walker DM, Hill AJ, Albecker MA, McCoy MW, Grisnik M, Romer A, Grajal-Puche A, Camp C, Kelehear C, Wooten J, Rheubert J, Graham SP. Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity. MICROBIAL ECOLOGY 2020; 79:985-997. [PMID: 31802185 DOI: 10.1007/s00248-019-01456-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.
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Affiliation(s)
- Donald M Walker
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA.
| | - Aubree J Hill
- Department of Biology, Tennessee Technological University, 1100 N. Dixie Ave, Cookeville, TN, 38505, USA
| | - Molly A Albecker
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Michael W McCoy
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Matthew Grisnik
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA
| | - Alexander Romer
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA
| | - Alejandro Grajal-Puche
- Department of Biology, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, 37132, USA
| | - Carlos Camp
- Department of Biology, Piedmont College, 1021 Central Avenue, Demorest, GA, 30535, USA
| | - Crystal Kelehear
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Ancon, Panama, Republic of Panama
- Department of Biology, Geology and Physical Sciences, Sul Ross State University, Alpine, TX, 79832, USA
| | - Jessica Wooten
- Department of Biology, Piedmont College, 1021 Central Avenue, Demorest, GA, 30535, USA
| | - Justin Rheubert
- Department of Natural Sciences, The University of Findlay, 1000 N. Main St, Findlay, OH, 45840, USA
| | - Sean P Graham
- Department of Biology, Geology and Physical Sciences, Sul Ross State University, Alpine, TX, 79832, USA
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DiRenzo GV, Chen R, Ibsen K, Toothman M, Miller AJ, Gershman A, Mitragotri S, Briggs CJ. Investigating the potential use of an ionic liquid (1-Butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide) as an anti-fungal treatment against the amphibian chytrid fungus, Batrachochytrium dendrobatidis. PLoS One 2020; 15:e0231811. [PMID: 32302369 PMCID: PMC7164615 DOI: 10.1371/journal.pone.0231811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/01/2020] [Indexed: 11/19/2022] Open
Abstract
The disease chytridiomycosis, caused by the pathogenic chytrid fungus, Batrachochytrium dendrobatidis (Bd), has contributed to global amphibian declines. Bd infects the keratinized epidermal tissue in amphibians and causes hyperkeratosis and excessive skin shedding. In individuals of susceptible species, the regulatory function of the amphibian’s skin is disrupted resulting in an electrolyte depletion, osmotic imbalance, and eventually death. Safe and effective treatments for chytridiomycosis are urgently needed to control chytrid fungal infections and stabilize populations of endangered amphibian species in captivity and in the wild. Currently, the most widely used anti-Bd treatment is itraconazole. Preparations of itraconazole formulated for amphibian use has proved effective, but treatment involves short baths over seven to ten days, a process which is logistically challenging, stressful, and causes long-term health effects. Here, we explore a novel anti-fungal therapeutic using a single application of the ionic liquid, 1-Butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide (BMP-NTf2), for the treatment of chytridiomycosis. BMP-NTf2 was found be effective at killing Bd in vitro at low concentrations (1:1000 dilution). We tested BMP-NTf2 in vivo on two amphibian species, one that is relatively tolerant of chytridiomycosis (Pseudacris regilla) and one that is highly susceptible (Dendrobates tinctorius). A toxicity trial revealed a surprising interaction between Bd infection status and the impact of BMP-NTf2 on D. tinctorius survival. Uninfected D. tinctorius tolerated BMP-NTf2 (mean ± SE; 96.01 ± 9.00 μl/g), such that only 1 out of 30 frogs died following treatment (at a dose of 156.95 μL/g), whereas, a lower dose (mean ± SE; 97.45 ± 3.52 μL/g) was not tolerated by Bd-infected D. tinctorius, where 15 of 23 frogs died shortly upon BMP-NTf2 application. Those that tolerated the BMP-NTf2 application did not exhibit Bd clearance. Thus, BMP-NTf2 application, under the conditions tested here, is not a suitable option for clearing Bd infection in D. tinctorius. However, different results were obtained for P. regilla. Two topical applications of BMP-NTf2 on Bd-infected P. regilla (using a lower BMP-NTf2 dose than on D. tinctorius, mean ± SE; 9.42 ± 1.43 μL/g) reduced Bd growth, although the effect was lower than that obtained by daily doses of itracanozole (50% frogs exhibited complete clearance on day 16 vs. 100% for itracanozole). Our findings suggest that BMP-NTf2 has the potential to treat Bd infection, however the effect depends on several parameters. Further optimization of dose and schedule are needed before BMP-NTf2 can be considered as a safe and effective alternative to more conventional antifungal agents, such as itraconazole.
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Affiliation(s)
- Graziella V. DiRenzo
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, CA, United States of America
- * E-mail:
| | - Renwei Chen
- Center for Bioengineering, University of California, Santa Barbara, CA, United States of America
| | - Kelly Ibsen
- Center for Bioengineering, University of California, Santa Barbara, CA, United States of America
- Department of Chemical Engineering, University of California, Santa Barbara, CA, United States of America
- School of Engineering and Applied Sciences, Harvard University Cambridge, Cambridge, MA, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States of America
| | - Mary Toothman
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, CA, United States of America
| | - Abigail J. Miller
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, CA, United States of America
| | - Ariel Gershman
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, CA, United States of America
| | - Samir Mitragotri
- Center for Bioengineering, University of California, Santa Barbara, CA, United States of America
- Department of Chemical Engineering, University of California, Santa Barbara, CA, United States of America
- School of Engineering and Applied Sciences, Harvard University Cambridge, Cambridge, MA, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States of America
| | - Cheryl J. Briggs
- Department of Ecology, Evolution, & Marine Biology, University of California, Santa Barbara, CA, United States of America
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Fletcher QE, Webber QMR, Willis CKR. Modelling the potential efficacy of treatments for white‐nose syndrome in bats. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13619] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Quinn E. Fletcher
- Department of Biology and Centre for Forest Interdisciplinary Research (C‐FIR) University of Winnipeg Winnipeg MB Canada
| | - Quinn M. R. Webber
- Department of Biology and Centre for Forest Interdisciplinary Research (C‐FIR) University of Winnipeg Winnipeg MB Canada
- Cognitive and Behavioural Ecology Interdisciplinary Program Memorial University of Newfoundland St. John's NL Canada
| | - Craig K. R. Willis
- Department of Biology and Centre for Forest Interdisciplinary Research (C‐FIR) University of Winnipeg Winnipeg MB Canada
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73
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Barnhart KL, Bletz MC, LaBumbard BC, Tokash-Peters AG, Gabor CR, Woodhams DC. Batrachochytrium salamandrivorans ELICITS ACUTE STRESS RESPONSE IN SPOTTED SALAMANDERS BUT NOT INFECTION OR MORTALITY. Anim Conserv 2020; 23:533-546. [PMID: 33071596 DOI: 10.1111/acv.12565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The emerging fungal pathogen Batrachochytrium salamandrivorans (Bsal) is a major threat to amphibian species worldwide with potential to infect many species if it invades salamander biodiversity hotspots in the Americas. Bsal can cause the disease chytridiomycosis, and it is important to assess the risk of Bsal-induced chytridiomycosis to species in North America. We evaluated the susceptibility to Bsal of the common and widespread spotted salamander, Ambystoma maculatum, across life history stages and monitored the effect of Bsal exposure on growth rate and response of the stress hormone, corticosterone. We conclude that spotted salamanders appear resistant to Bsal because they showed no indication of disease or infection, and experienced minor effects on growth upon exposure. While we focused on a single population for this study, results were consistent across conditions of exposure including high or repeated doses of Bsal, life-stage at exposure, environmental conditions including two temperatures and two substrates, and promoting pathogen infectivity by conditioning Bsal cultures with thyroid hormone. Exposure to high levels of Bsal elicited an acute but not chronic increase in corticosterone in spotted salamanders, and reduced growth. We hypothesize that the early acute increase in corticosterone facilitated mounting an immune response to the pathogen, perhaps through immunoredistribution to the skin, but further study is needed to determine immune responses to Bsal. These results will contribute to development of appropriate Bsal management plans to conserve species at risk of emerging disease.
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Affiliation(s)
- Kelly L Barnhart
- University of Massachusetts Boston, Department of Biology, 100 William T Morrissey Blvd, Boston, MA 02125
| | - Molly C Bletz
- University of Massachusetts Boston, Department of Biology, 100 William T Morrissey Blvd, Boston, MA 02125
| | - Brandon C LaBumbard
- University of Massachusetts Boston, Department of Biology, 100 William T Morrissey Blvd, Boston, MA 02125
| | - Amanda G Tokash-Peters
- University of Massachusetts Boston, Department of Biology, 100 William T Morrissey Blvd, Boston, MA 02125
| | - Caitlin R Gabor
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666
| | - Douglas C Woodhams
- University of Massachusetts Boston, Department of Biology, 100 William T Morrissey Blvd, Boston, MA 02125
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74
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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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75
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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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76
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Kenison EK, Hernández-Gómez O, Williams RN. A novel bioaugmentation technique effectively increases the skin-associated microbial diversity of captive eastern hellbenders. CONSERVATION PHYSIOLOGY 2020; 8:coaa040. [PMID: 32431814 PMCID: PMC7221235 DOI: 10.1093/conphys/coaa040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 12/01/2019] [Accepted: 04/12/2020] [Indexed: 05/20/2023]
Abstract
Captive environments are maintained in hygienic ways that lack free-flowing microbes found in animals' natural environments. As a result, captive animals often have depauperate host-associated microbial communities compared to conspecifics in the wild and may have increased disease susceptibility and reduced immune function. Eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) have suffered precipitous population declines over the past few decades. To bolster populations, eastern hellbenders are reared in captivity before being translocated to the wild. However, the absence of natural microbial reservoirs within the captive environment diminishes the diversity of skin-associated bacteria on hellbender skin and may negatively influence their ability to defend against pathogenic species once they are released into the wild. To prepare hellbenders for natural bacteria found in riverine environments, we devised a novel bioaugmentation method to increase the diversity of skin microbial communities within a captive setting. We exposed juvenile hellbenders to increasing amounts of river water over 5 weeks before translocating them to the river. We genetically identified and phylogenetically compared bacteria collected from skin swabs and river water for alpha (community richness) and beta (community composition) diversity estimates. We found that hellbenders exposed to undiluted river water in captivity had higher alpha diversity and distinct differentiation in the community composition on their skin, compared to hellbenders only exposed to well water. We also found strong evidence that hellbender skin microbiota is host-specific rather than environmentally driven and is colonized by rare environmental operational taxonomic units in river water. This technique may increase hellbender translocation success as increasing microbial diversity is often correlated with elevated disease resistance. Future work is necessary to refine our methods, investigate the relationship between microbial diversity and hellbender health and understand how this bioaugmentation technique influences hellbenders' survival following translocation from captivity into the wild.
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Affiliation(s)
- Erin K Kenison
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN 47907, USA
- Idaho Fish and Wildlife Office, U.S. Fish and Wildlife Service, 1387 S. Vinnell Way, Boise, ID 83706, USA
- Corresponding author: Idaho Fish and Wildlife Office, U.S. Fish and Wildlife Service, Boise, ID 83706, USA. Tel: (208) 685-6965.
| | - Obed Hernández-Gómez
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN 47907, USA
- Department of Natural Sciences and Mathematics, Dominican University of California, 50 Acacia Ave., San Rafael, CA 94901, USA
| | - Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN 47907, USA
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77
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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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78
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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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79
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Bletz MC, Bunk B, Spröer C, Biwer P, Reiter S, Rabemananjara FCE, Schulz S, Overmann J, Vences M. Amphibian skin-associated Pigmentiphaga: Genome sequence and occurrence across geography and hosts. PLoS One 2019; 14:e0223747. [PMID: 31603945 PMCID: PMC6788695 DOI: 10.1371/journal.pone.0223747] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/29/2019] [Indexed: 11/19/2022] Open
Abstract
The bacterial communities colonizing amphibian skin have been intensively studied due to their interactions with pathogenic chytrid fungi that are causing drastic amphibian population declines. Bacteria of the family Alcaligenaceae, and more specifically of the genus Pigmentiphaga, have been found to be associated specifically to arboreal frogs. Here we analyze their occurrence in a previously assembled global skin microbiome dataset from 205 amphibian species. Pigmentiphaga made up about 5% of the total number of reads in this global dataset. They were mostly found in unrelated arboreal frogs from Madagascar (Mantellidae and Hyperoliidae), but also occurred at low abundances on Neotropical frogs. Based on their 16S sequences, most of the sequences belong to a clade within Pigmentiphaga not assignable to any type strains of the five described species of the genus. One isolate from Madagascar clustered with Pigmentiphaga aceris (>99% sequence similarity on 16S rRNA gene level). Here, we report the full genome sequence of this bacterium which, based on 16S sequences of >97% similarity, has previously been found on human skin, floral nectar, tree sap, stream sediment and soil. Its genome consists of a single circular chromosome with 6,165,255 bp, 5,300 predicted coding sequences, 57 tRNA genes, and three rRNA operons. In comparison with other known Pigmentiphaga genomes it encodes a higher number of genes associated with environmental information processing and cellular processes. Furthermore, it has a biosynthetic gene cluster for a nonribosomal peptide syntethase, and bacteriocin biosynthetic genes can be found, but clusters for β-lactones present in other comparative Pigmentiphaga genomes are lacking.
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Affiliation(s)
- Molly C. Bletz
- Department of Biology, University of Massachusetts Boston, Boston, MA, United States of America
- Zoological Institute, Technische Universitt Braunschweig, Braunschweig, Germany
- * E-mail:
| | - Boyke Bunk
- DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Peter Biwer
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Silke Reiter
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | | | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jörg Overmann
- DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Microbiology Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Miguel Vences
- Zoological Institute, Technische Universitt Braunschweig, Braunschweig, Germany
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80
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Niederle MV, Bosch J, Ale CE, Nader-Macías ME, Aristimuño Ficoseco C, Toledo LF, Valenzuela-Sánchez A, Soto-Azat C, Pasteris SE. Skin-associated lactic acid bacteria from North American bullfrogs as potential control agents of Batrachochytrium dendrobatidis. PLoS One 2019; 14:e0223020. [PMID: 31560707 PMCID: PMC6764794 DOI: 10.1371/journal.pone.0223020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/11/2019] [Indexed: 11/18/2022] Open
Abstract
The fungal pathogen Batrachochytrium dendrobatidis (Bd) is the causative agent of chytridiomycosis and has been a key driver in the catastrophic decline of amphibians globally. While many strategies have been proposed to mitigate Bd outbreaks, few have been successful. In recent years, the use of probiotic formulations that protect an amphibian host by killing or inhibiting Bd have shown promise as an effective chytridiomycosis control strategy. The North American bullfrog (Lithobates catesbeianus) is a common carrier of Bd and harbours a diverse skin microbiota that includes lactic acid bacteria (LAB), a microbial group containing species classified as safe and conferring host benefits. We investigated beneficial/probiotic properties: anti-Bd activity, and adhesion and colonisation characteristics (hydrophobicity, biofilm formation and exopolysaccharide-EPS production) in two confirmed LAB (cLAB-Enterococcus gallinarum CRL 1826, Lactococcus garvieae CRL 1828) and 60 presumptive LAB (pLAB) [together named as LABs] isolated from bullfrog skin.We challenged LABs against eight genetically diverse Bd isolates and found that 32% of the LABs inhibited at least one Bd isolate with varying rates of inhibition. Thus, we established a score of sensitivity from highest (BdGPL AVS7) to lowest (BdGPL C2A) for the studied Bd isolates. We further reveal key factors underlying host adhesion and colonisation of LABs. Specifically, 90.3% of LABs exhibited hydrophilic properties that may promote adhesion to the cutaneous mucus, with the remaining isolates (9.7%) being hydrophobic in nature with a surface polarity compatible with colonisation of acidic, basic or both substrate types. We also found that 59.7% of LABs showed EPS synthesis and 66.1% produced biofilm at different levels: 21% weak, 29% moderate, and 16.1% strong. Together all these properties enhance colonisation of the host surface (mucus or epithelial cells) and may confer protective benefits against Bd through competitive exclusion. Correspondence analysis indicated that biofilm synthesis was LABs specific with high aggregating bacteria correlating with strong biofilm producers, and EPS producers being correlated to negative biofilm producing LABs. We performed Random Amplified Polymorphic DNA (RAPD)-PCR analysis and demonstrated a higher degree of genetic diversity among rod-shaped pLAB than cocci. Based on the LAB genetic analysis and specific probiotic selection criteria that involve beneficial properties, we sequenced 16 pLAB which were identified as Pediococcus pentosaceus, Enterococcus thailandicus, Lactobacillus pentosus/L. plantarum, L. brevis, and L. curvatus. Compatibility assays performed with cLAB and the 16 species described above indicate that all tested LAB can be included in a mixed probiotic formula. Based on our analyses, we suggest that E. gallinarum CRL 1826, L. garvieae CRL 1828, and P. pentosaceus 15 and 18B represent optimal probiotic candidates for Bd control and mitigation.
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Affiliation(s)
- M. V. Niederle
- Instituto Superior de Investigaciones Biológicas (INSIBIO), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Instituto de Biología “Dr. Francisco D. Barbieri”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán, Argentina
| | - J. Bosch
- Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
- Research Unit of Biodiversity (CSIC, UO, PA), Oviedo University—Campus Mieres, Spain
| | - C. E. Ale
- Instituto Superior de Investigaciones Biológicas (INSIBIO), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Instituto de Biología “Dr. Francisco D. Barbieri”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán, Argentina
| | - M. E. Nader-Macías
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Argentina
| | - C. Aristimuño Ficoseco
- Centro de Referencia para Lactobacilos (CERELA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Miguel de Tucumán, Argentina
| | - L. F. Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - A. Valenzuela-Sánchez
- Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Organización No Gubernamental (ONG) Ranita de Darwin, Santiago, Chile
- Organización No Gubernamental (ONG) Ranita de Darwin, Valdivia, Chile
| | - C. Soto-Azat
- Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - S. E. Pasteris
- Instituto Superior de Investigaciones Biológicas (INSIBIO), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Instituto de Biología “Dr. Francisco D. Barbieri”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán, Argentina
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81
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Keiser CN, Wantman T, Rebollar EA, Harris RN. Tadpole body size and behaviour alter the social acquisition of a defensive bacterial symbiont. ROYAL SOCIETY OPEN SCIENCE 2019; 6:191080. [PMID: 31598324 PMCID: PMC6774948 DOI: 10.1098/rsos.191080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/01/2019] [Indexed: 05/29/2023]
Abstract
Individual differences in host phenotypes can generate heterogeneity in the acquisition and transmission of microbes. Although this has become a prominent factor of disease epidemiology, host phenotypic variation might similarly underlie the transmission of microbial symbionts that defend against pathogen infection. Here, we test whether host body size and behaviour influence the social acquisition of a skin bacterium, Janthinobacterium lividum, which in some hosts can confer protection against infection by Batrachochytrium dendrobatidis, the causative agent of the amphibian skin disease chytridiomycosis. We measured body size and boldness (time spent in an open field) of green frog tadpoles and haphazardly constructed groups of six individuals. In some groups, we exposed one individual in each group to J. lividum and, in other groups, we inoculated a patch of aquarium pebbles to J. lividum. After 24 h, we swabbed each individual to estimate the presence of J. lividum on their skin. On average, tadpoles acquired nearly four times more bacteria when housed with an exposed individual compared to those housed with a patch of inoculated substrate. When tadpoles were housed with an exposed group-mate, larger and 'bolder' individuals acquired more bacteria. These data suggest that phenotypically biased acquisition of defensive symbionts might generate biased patterns of mortality from the pathogens against which they protect.
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Affiliation(s)
- Carl N. Keiser
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Trina Wantman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Reid N. Harris
- Amphibian Survival Alliance, London SW7 2HQ, UK
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
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82
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Bates KA, Shelton JMG, Mercier VL, Hopkins KP, Harrison XA, Petrovan SO, Fisher MC. Captivity and Infection by the Fungal Pathogen Batrachochytrium salamandrivorans Perturb the Amphibian Skin Microbiome. Front Microbiol 2019; 10:1834. [PMID: 31507541 PMCID: PMC6716147 DOI: 10.3389/fmicb.2019.01834] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/25/2019] [Indexed: 12/13/2022] Open
Abstract
The emerging fungal pathogen, Batrachochytrium salamandrivorans (Bsal) is responsible for the catastrophic decline of European salamanders and poses a threat to amphibians globally. The amphibian skin microbiome can influence disease outcome for several host-pathogen systems, yet little is known of its role in Bsal infection. In addition, many experimental in-vivo amphibian disease studies to date have relied on specimens that have been kept in captivity for long periods without considering the influence of environment on the microbiome and how this may impact the host response to pathogen exposure. We characterized the impact of captivity and exposure to Bsal on the skin bacterial and fungal communities of two co-occurring European newt species, the smooth newt, Lissotriton vulgaris and the great-crested newt, Triturus cristatus. We show that captivity led to significant losses in bacterial and fungal diversity of amphibian skin, which may be indicative of a decline in microbe-mediated protection. We further demonstrate that in both L. vulgaris and T. cristatus, Bsal infection was associated with changes in the composition of skin bacterial communities with possible negative consequences to host health. Our findings advance current understanding of the role of host-associated microbiota in Bsal infection and highlight important considerations for ex-situ amphibian conservation programmes.
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Affiliation(s)
- Kieran A Bates
- Department of Zoology, University of Oxford, Oxford, United Kingdom.,Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom.,Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Jennifer M G Shelton
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Victoria L Mercier
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Kevin P 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
| | - Silviu O Petrovan
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Froglife, Peterborough, United Kingdom
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
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83
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Becker CG, Bletz MC, Greenspan SE, Rodriguez D, Lambertini C, Jenkinson TS, Guimarães PR, Assis APA, Geffers R, Jarek M, Toledo LF, Vences M, Haddad CFB. Low-load pathogen spillover predicts shifts in skin microbiome and survival of a terrestrial-breeding amphibian. Proc Biol Sci 2019; 286:20191114. [PMID: 31409249 DOI: 10.1098/rspb.2019.1114] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Wildlife disease dynamics are strongly influenced by the structure of host communities and their symbiotic microbiota. Conspicuous amphibian declines associated with the waterborne fungal pathogen Batrachochytrium dendrobatidis (Bd) have been observed in aquatic-breeding frogs globally. However, less attention has been given to cryptic terrestrial-breeding amphibians that have also been declining in tropical regions. By experimentally manipulating multiple tropical amphibian assemblages harbouring natural microbial communities, we tested whether Bd spillover from naturally infected aquatic-breeding frogs could lead to Bd amplification and mortality in our focal terrestrial-breeding host: the pumpkin toadlet Brachycephalus pitanga. We also tested whether the strength of spillover could vary depending on skin bacterial transmission within host assemblages. Terrestrial-breeding toadlets acquired lethal spillover infections from neighbouring aquatic hosts and experienced dramatic but generally non-protective shifts in skin bacterial composition primarily attributable to their Bd infections. By contrast, aquatic-breeding amphibians maintained mild Bd infections and higher survival, with shifts in bacterial microbiomes that were unrelated to Bd infections. Our results indicate that Bd spillover from even mildly infected aquatic-breeding hosts may lead to dysbiosis and mortality in terrestrial-breeding species, underscoring the need to further investigate recent population declines of terrestrial-breeding amphibians in the tropics.
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Affiliation(s)
- C Guilherme Becker
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35847, USA
| | - Molly C Bletz
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Sasha E Greenspan
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35847, USA
| | - David Rodriguez
- Department of Biology, Texas State University, San Marcos, TX 78666, USA
| | - Carolina Lambertini
- Department of Animal Biology, Universidade Estadual de Campinas, Campinas, SP 13083-865, Brazil
| | - Thomas S Jenkinson
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA 94720, USA
| | - Paulo R Guimarães
- Departamento de Ecologia, Universidade de Sao Paulo, Sao Paulo, SP 05508-090, Brazil
| | - Ana Paula A Assis
- Departamento de Ecologia, Universidade de Sao Paulo, Sao Paulo, SP 05508-090, Brazil
| | - Robert Geffers
- Department of Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, LS 38124, Germany
| | - Michael Jarek
- Department of Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, LS 38124, Germany
| | - Luís Felipe Toledo
- Department of Animal Biology, Universidade Estadual de Campinas, Campinas, SP 13083-865, Brazil
| | - Miguel Vences
- Division of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, Braunschweig, LS 38106, Germany
| | - Célio F B Haddad
- Department of Zoology and Aquaculture Center (CAUNESP), Universidade Estadual Paulista, Rio Claro, SP 13506-900, Brazil
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84
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Ellison S, Rovito S, Parra-Olea G, Vásquez-Almazán C, Flechas SV, Bi K, Vredenburg VT. The Influence of Habitat and Phylogeny on the Skin Microbiome of Amphibians in Guatemala and Mexico. MICROBIAL ECOLOGY 2019; 78:257-267. [PMID: 30467714 DOI: 10.1007/s00248-018-1288-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Microbial symbionts are increasingly recognized as playing a critical role in organismal health across a wide range of hosts. Amphibians are unique hosts in that their skin helps to regulate the exchange of water, ions, and gases, and it plays an active role in defense against pathogens through the synthesis of anti-microbial peptides. The microbiome of amphibian skin includes a diverse community of bacteria known to defend against pathogens, including the global pandemic lineage of Batrachochytrium dendrobatidis associated with mass amphibian die-offs. The relative influence of host phylogeny and environment in determining the composition of the amphibian skin microbiome remains poorly understood. We collected skin swabs from montane amphibians in Mexico and Guatemala, focusing on two genera of plethodontid salamanders and one genus of frogs. We used high throughput sequencing to characterize the skin bacterial microbiome and tested the impact of phylogeny and habitat on bacterial diversity. Our results show that phylogenetic history strongly influences the diversity and community structure of the total bacterial microbiome at higher taxonomic levels (between orders), but on lower scales (within genera and species), the effect of habitat predominates. These results add to a growing consensus that habitat exerts a strong effect on microbiome structure and composition, particularly at shallow phylogenetic scales.
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Affiliation(s)
- Silas Ellison
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA, 94132, USA
| | - Sean Rovito
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA.
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Guanajuato, Mexico.
| | - Gabriela Parra-Olea
- Departamento de Zoología, Insituto de Biología, Universidad Nacional Autónoma de México, CP04510, México, DF, Mexico
| | - Carlos Vásquez-Almazán
- Museo de Historia Natural y Escuela de Biología, Universidad de San Carlos, Guatemala, Guatemala
| | - Sandra V Flechas
- Department of Biological Sciences, Universidad de los Andes, AA 4976, Bogotá, Colombia
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences University of California, Berkeley, CA, 94720, USA
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA, 94132, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA
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85
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Greenspan SE, Lyra ML, Migliorini GH, Kersch-Becker MF, Bletz MC, Lisboa CS, Pontes MR, Ribeiro LP, Neely WJ, Rezende F, Romero GQ, Woodhams DC, Haddad CFB, Toledo LF, Becker CG. Arthropod-bacteria interactions influence assembly of aquatic host microbiome and pathogen defense. Proc Biol Sci 2019; 286:20190924. [PMID: 31238845 DOI: 10.1098/rspb.2019.0924] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The host-associated microbiome is vital to host immunity and pathogen defense. In aquatic ecosystems, organisms may interact with environmental bacteria to influence the pool of potential symbionts, but the effects of these interactions on host microbiome assembly and pathogen resistance are unresolved. We used replicated bromeliad microecosystems to test for indirect effects of arthropod-bacteria interactions on host microbiome assembly and pathogen burden, using tadpoles and the fungal amphibian pathogen Batrachochytrium dendrobatidis as a model host-pathogen system. Arthropods influenced host microbiome assembly by altering the pool of environmental bacteria, with arthropod-bacteria interactions specifically reducing host colonization by transient bacteria and promoting antimicrobial components of aquatic bacterial communities. Arthropods also reduced fungal zoospores in the environment, but fungal infection burdens in tadpoles corresponded most closely with arthropod-mediated patterns in microbiome assembly. This result indicates that the cascading effects of arthropods on the maintenance of a protective host microbiome may be more strongly linked to host health than negative effects of arthropods on pools of pathogenic zoospores. Our work reveals tight links between healthy ecosystem dynamics and the functioning of host microbiomes, suggesting that ecosystem disturbances such as loss of arthropods may have downstream effects on host-associated microbial pathogen defenses and host fitness.
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Affiliation(s)
- Sasha E Greenspan
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
| | - Mariana L Lyra
- 2 Department of Zoology and Aquaculture Center (CAUNESP), Universidade Estadual Paulista , Rio Claro , SP 13506-900 , Brazil
| | - Gustavo H Migliorini
- 3 Programa de Pós-graduação em Biologia Animal, Universidade Estadual Paulista 'Júlio de Mesquita Filho' , São José do Rio Preto SP 15054-000 , Brazil
| | - Mônica F Kersch-Becker
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
| | - Molly C Bletz
- 4 Department of Biology, University of Massachusetts Boston , Boston, MA 02125 , USA
| | | | - Mariana R Pontes
- 6 Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil.,8 Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - Luisa P Ribeiro
- 6 Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil.,8 Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - Wesley J Neely
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
| | - Felipe Rezende
- 6 Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - Gustavo Q Romero
- 7 Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas SP 13083-862 , Brazil
| | - Douglas C Woodhams
- 4 Department of Biology, University of Massachusetts Boston , Boston, MA 02125 , USA
| | - Célio F B Haddad
- 2 Department of Zoology and Aquaculture Center (CAUNESP), Universidade Estadual Paulista , Rio Claro , SP 13506-900 , Brazil
| | - Luís Felipe Toledo
- 8 Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal, Universidade Estadual de Campinas , Campinas, SP 13083-862 , Brazil
| | - C Guilherme Becker
- 1 Department of Biological Sciences, The University of Alabama , Tuscaloosa, AL 35487 , USA
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86
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Field trial of a probiotic bacteria to protect bats from white-nose syndrome. Sci Rep 2019; 9:9158. [PMID: 31235813 PMCID: PMC6591354 DOI: 10.1038/s41598-019-45453-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 06/03/2019] [Indexed: 12/30/2022] Open
Abstract
Tools for reducing wildlife disease impacts are needed to conserve biodiversity. White-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans, has caused widespread declines in North American bat populations and threatens several species with extinction. Few tools exist for managers to reduce WNS impacts. We tested the efficacy of a probiotic bacterium, Pseudomonas fluorescens, to reduce impacts of WNS in two simultaneous experiments with caged and free-flying Myotis lucifugus bats at a mine in Wisconsin, USA. In the cage experiment there was no difference in survival between control and P. fluorescens-treated bats. However, body mass, not infection intensity, predicted mortality, suggesting that within-cage disturbance influenced the cage experiment. In the free-flying experiment, where bats were able to avoid conspecific disturbance, infection intensity predicted the date of emergence from the mine. In this experiment treatment with P. fluorescens increased apparent overwinter survival five-fold compared to the control group (from 8.4% to 46.2%) by delaying emergence of bats from the site by approximately 32 days. These results suggest that treatment of bats with P. fluorescens may substantially reduce WNS mortality, and, if used in combination with other interventions, could stop population declines.
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87
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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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88
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Medina D, Hughey MC, Walke JB, Becker MH, Pontarelli K, Sun S, Badgley B, Belden LK. Amphibian skin fungal communities vary across host species and do not correlate with infection by a pathogenic fungus. Environ Microbiol 2019; 21:2905-2920. [PMID: 31087743 DOI: 10.1111/1462-2920.14682] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 05/10/2019] [Accepted: 05/11/2019] [Indexed: 12/26/2022]
Abstract
Amphibian population declines caused by the fungus Batrachochytrium dendrobatidis (Bd) have prompted studies on the bacterial community that resides on amphibian skin. However, studies addressing the fungal portion of these symbiont communities have lagged behind. Using ITS1 amplicon sequencing, we examined the fungal portion of the skin microbiome of temperate and tropical amphibian species currently coexisting with Bd in nature. We assessed cooccurrence patterns between bacterial and fungal OTUs using a subset of samples for which bacterial 16S rRNA gene amplicon data were also available. We determined that fungal communities were dominated by members of the phyla Ascomycota and Basidiomycota, and also by Chytridiomycota in the most aquatic amphibian species. Alpha diversity of the fungal communities differed across host species, and fungal community structure differed across species and regions. However, we did not find a correlation between fungal diversity/community structure and Bd infection, though we did identify significant correlations between Bd and specific OTUs. Moreover, positive bacterial-fungal cooccurrences suggest that positive interactions between these organisms occur in the skin microbiome. Understanding the ecology of amphibian skin fungi, and their interactions with bacteria will complement our knowledge of the factors influencing community assembly and the overall function of these symbiont communities.
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Affiliation(s)
- Daniel Medina
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Myra C Hughey
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Department of Biology, Vassar College, Poughkeepsie, NY, USA
| | - Jenifer B Walke
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Department of Biology, Eastern Washington University, Cheney, WA, USA
| | - Matthew H Becker
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | | | - Shan Sun
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA.,College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Brian Badgley
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Lisa K Belden
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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89
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Frenken T, Agha R, Schmeller DS, van West P, Wolinska J. Biological Concepts for the Control of Aquatic Zoosporic Diseases. Trends Parasitol 2019; 35:571-582. [PMID: 31076352 DOI: 10.1016/j.pt.2019.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/04/2019] [Accepted: 04/06/2019] [Indexed: 12/26/2022]
Abstract
Aquatic zoosporic diseases are threatening global biodiversity and ecosystem services, as well as economic activities. Current means of controlling zoosporic diseases are restricted primarily to chemical treatments, which are usually harmful or likely to be ineffective in the long term. Furthermore, some of these chemicals have been banned due to adverse effects. As a result, there is a need for alternative methods with minimal side-effects on the ecosystem or environment. Here, we integrate existing knowledge of three poorly interconnected areas of disease research - amphibian conservation, aquaculture, and plankton ecology - and arrange it into seven biological concepts to control zoosporic diseases. These strategies may be less harmful and more sustainable than chemical approaches. However, more research is needed before safe application is possible.
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Affiliation(s)
- Thijs Frenken
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.
| | - Ramsy Agha
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Dirk S Schmeller
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, Toulouse, France
| | - Pieter van West
- Aberdeen Oomycete Laboratory, College of Life Sciences and Medicine, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Justyna Wolinska
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institute of Biology, Freie Universität Berlin, Berlin, Germany
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90
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Walker DM, Leys JE, Grisnik M, Grajal-Puche A, Murray CM, Allender MC. Variability in snake skin microbial assemblages across spatial scales and disease states. ISME JOURNAL 2019; 13:2209-2222. [PMID: 31065028 PMCID: PMC6776063 DOI: 10.1038/s41396-019-0416-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 02/07/2023]
Abstract
Understanding how biological patterns translate into functional processes across different scales is a central question in ecology. Within a spatial context, extent is used to describe the overall geographic area of a study, whereas grain describes the overall unit of observation. This study aimed to characterize the snake skin microbiota (grain) and to determine host–microbial assemblage–pathogen effects across spatial extents within the Southern United States. The causative agent of snake fungal disease, Ophidiomyces ophiodiicola, is a fungal pathogen threatening snake populations. We hypothesized that the skin microbial assemblage of snakes differs from its surrounding environment, by host species, spatial scale, season, and in the presence of O. ophiodiicola. We collected snake skin swabs, soil samples, and water samples across six states in the Southern United States (macroscale extent), four Tennessee ecoregions (mesoscale extent), and at multiple sites within each Tennessee ecoregion (microscale extent). These samples were subjected to DNA extraction and quantitative PCR to determine the presence/absence of O. ophiodiicola. High-throughput sequencing was also utilized to characterize the microbial communities. We concluded that the snake skin microbial assemblage was partially distinct from environmental microbial communities. Snake host species was strongly predictive of the skin microbiota at macro-, meso-, and microscale spatial extents; however, the effect was variable across geographic space and season. Lastly, the presence of the fungal pathogen O. ophiodiicola is predictive of skin microbial assemblages across macro- and meso-spatial extents, and particular bacterial taxa associate with O. ophiodiicola pathogen load. Our results highlight the importance of scale regarding wildlife host–pathogen–microbial assemblage interactions.
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Affiliation(s)
- Donald M Walker
- Toxicology and Disease Group, Biology Department, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, USA.
| | - Jacob E Leys
- Department of Biology, Tennessee Technological University, Cookeville, TN, USA
| | - Matthew Grisnik
- Toxicology and Disease Group, Biology Department, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, USA
| | - Alejandro Grajal-Puche
- Toxicology and Disease Group, Biology Department, Middle Tennessee State University, PO Box 60, Murfreesboro, TN, USA
| | | | - Matthew C Allender
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, USA
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91
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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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92
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Martin H C, Ibáñez R, Nothias LF, Boya P CA, Reinert LK, Rollins-Smith LA, Dorrestein PC, Gutiérrez M. Viscosin-like lipopeptides from frog skin bacteria inhibit Aspergillus fumigatus and Batrachochytrium dendrobatidis detected by imaging mass spectrometry and molecular networking. Sci Rep 2019; 9:3019. [PMID: 30816229 PMCID: PMC6395710 DOI: 10.1038/s41598-019-39583-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/22/2019] [Indexed: 12/17/2022] Open
Abstract
Amphibian populations worldwide have declined and in some cases become extinct due to chytridiomycosis, a pandemic disease caused by the fungus Batrachochytrium dendrobatidis; however, some species have survived these fungal epidemics. Previous studies have suggested that the resistance of these species is due to the presence of cutaneous bacteria producing antifungal metabolites. As our understanding of these metabolites is still limited, we assessed the potential of such compounds against human-relevant fungi such as Aspergillus. In this work we isolated 201 bacterial strains from fifteen samples belonging to seven frog species collected in the highlands of Panama and tested them against Aspergillus fumigatus. Among the 29 bacterial isolates that exhibited antifungal activity, Pseudomonas cichorii showed the greatest inhibition. To visualize the distribution of compounds and identify them in the inhibition zone produced by P. cichorii, we employed MALDI imaging mass spectrometry (MALDI IMS) and MS/MS molecular networking. We identified viscosin and massetolides A, F, G and H in the inhibition zone. Furthermore, viscosin was isolated and evaluated in vitro against A. fumigatus and B. dendrobatidis showing MIC values of 62.50 µg/mL and 31.25 µg/mL, respectively. This is the first report of cyclic depsipeptides with antifungal activity isolated from frog cutaneous bacteria.
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Affiliation(s)
- Christian Martin H
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama.,Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama.,Departamento de Zoología, Universidad de Panamá, Panama, Republic of Panama
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Cristopher A Boya P
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama.,Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Laura K Reinert
- Department of Pathology, Microbiology, and Immunology, and Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Louise A Rollins-Smith
- Department of Pathology, Microbiology, and Immunology, and Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama, Republic of Panama.
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93
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Kueneman JG, Bletz MC, McKenzie VJ, Becker CG, Joseph MB, Abarca JG, Archer H, Arellano AL, Bataille A, Becker M, Belden LK, Crottini A, Geffers R, Haddad CFB, Harris RN, Holden WM, Hughey M, Jarek M, Kearns PJ, Kerby JL, Kielgast J, Kurabayashi A, Longo AV, Loudon A, Medina D, Nuñez JJ, Perl RGB, Pinto-Tomás A, Rabemananjara FCE, Rebollar EA, Rodríguez A, Rollins-Smith L, Stevenson R, Tebbe CC, Vargas Asensio G, Waldman B, Walke JB, Whitfield SM, Zamudio KR, Zúñiga Chaves I, Woodhams DC, Vences M. Community richness of amphibian skin bacteria correlates with bioclimate at the global scale. Nat Ecol Evol 2019; 3:381-389. [DOI: 10.1038/s41559-019-0798-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 01/06/2019] [Indexed: 12/15/2022]
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94
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Trevelline BK, Fontaine SS, Hartup BK, Kohl KD. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc Biol Sci 2019; 286:20182448. [PMID: 30963956 PMCID: PMC6364583 DOI: 10.1098/rspb.2018.2448] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022] Open
Abstract
The central aim of conservation biology is to understand and mitigate the effects of human activities on biodiversity. To successfully achieve this objective, researchers must take an interdisciplinary approach that fully considers the effects, both direct and indirect, of anthropogenic disturbances on wildlife physiology and health. A recent surge in research has revealed that host-associated microbiota-the archaeal, bacterial, fungal and viral communities residing on and inside organisms-profoundly influence animal health, and that these microbial communities can be drastically altered by anthropogenic activities. Therefore, conservation practitioners should consider the disruption of host-associated microbial diversity as a serious threat to wildlife populations. Despite the tremendous potential for microbiome research to improve conservation outcomes, few efforts have been made to truly integrate these fields. In this review, we call for the microbial renaissance of conservation biology, where biodiversity of host-associated microbiota is recognized as an essential component of wildlife management practices. Using evidence from the existing literature, we will examine the known effects of anthropogenic activities on the diversity of host-associated microbial communities and integrate approaches for maintaining microbial diversity to successfully achieve conservation objectives.
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Affiliation(s)
- Brian K. Trevelline
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Samantha S. Fontaine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Barry K. Hartup
- Department of Conservation Medicine, International Crane Foundation, Baraboo, WI, USA
- School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - Kevin D. Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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95
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Ellison S, Knapp RA, Sparagon W, Swei A, Vredenburg VT. Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host. Mol Ecol 2018; 28:127-140. [PMID: 30506592 DOI: 10.1111/mec.14964] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 09/28/2018] [Accepted: 10/30/2018] [Indexed: 12/13/2022]
Abstract
The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects the skin of amphibians and has caused severe declines and extinctions of amphibians globally. In this study, we investigate the interaction between Bd and the bacterial skin microbiome of the endangered Sierra Nevada yellow-legged frog, Rana sierrae, using both culture-dependent and culture-independent methods. Samples were collected from two populations of R. sierrae that likely underwent Bd epizootics in the past, but that continue to persist with Bd in an enzootic disease state, and we address the hypothesis that such "persistent" populations are aided by mutualistic skin microbes. Our 16S rRNA metabarcoding data reveal that the skin microbiome of highly infected juvenile frogs is characterized by significantly reduced species richness and evenness, and by strikingly lower variation between individuals, compared to juveniles and adults with lower infection levels. Over 90% of DNA sequences from the skin microbiome of highly infected frogs were derived from bacteria in a single order, Burkholderiales, compared to just 54% in frogs with lower infection levels. In a culture-dependent Bd inhibition assay, the bacterial metabolites we evaluated all inhibited the growth of Bd. Together, these results illustrate the disruptive effects of Bd infection on host skin microbial community structure and dynamics, and suggest possible avenues for the development of anti-Bd probiotic treatments.
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Affiliation(s)
- Silas Ellison
- Department of Biology, San Francisco State University, San Francisco, California
| | - Roland A Knapp
- Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, California
| | - Wesley Sparagon
- Department of Biology, Whitman College, Walla Walla, Washington
| | - Andrea Swei
- Department of Biology, San Francisco State University, San Francisco, California
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, California.,Museum of Vertebrate Zoology, University of California, Berkeley, California
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96
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Seyedmousavi S, Bosco SDMG, de Hoog S, Ebel F, Elad D, Gomes RR, Jacobsen ID, Jensen HE, Martel A, Mignon B, Pasmans F, Piecková E, Rodrigues AM, Singh K, Vicente VA, Wibbelt G, Wiederhold NP, Guillot J. Fungal infections in animals: a patchwork of different situations. Med Mycol 2018. [PMID: 29538732 DOI: 10.1093/mmy/myx104] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The importance of fungal infections in both human and animals has increased over the last decades. This article represents an overview of the different categories of fungal infections that can be encountered in animals originating from environmental sources without transmission to humans. In addition, the endemic infections with indirect transmission from the environment, the zoophilic fungal pathogens with near-direct transmission, the zoonotic fungi that can be directly transmitted from animals to humans, mycotoxicoses and antifungal resistance in animals will also be discussed. Opportunistic mycoses are responsible for a wide range of diseases from localized infections to fatal disseminated diseases, such as aspergillosis, mucormycosis, candidiasis, cryptococcosis and infections caused by melanized fungi. The amphibian fungal disease chytridiomycosis and the Bat White-nose syndrome are due to obligatory fungal pathogens. Zoonotic agents are naturally transmitted from vertebrate animals to humans and vice versa. The list of zoonotic fungal agents is limited but some species, like Microsporum canis and Sporothrix brasiliensis from cats, have a strong public health impact. Mycotoxins are defined as the chemicals of fungal origin being toxic for warm-blooded vertebrates. Intoxications by aflatoxins and ochratoxins represent a threat for both human and animal health. Resistance to antifungals can occur in different animal species that receive these drugs, although the true epidemiology of resistance in animals is unknown, and options to treat infections caused by resistant infections are limited.
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Affiliation(s)
- Seyedmojtaba Seyedmousavi
- Molecular Microbiology Section, Laboratory of Clinical Microbiology and Immunology (LCMI), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sandra de M G Bosco
- Department of Microbiology and Immunology, Institute of Biosciences-UNESP Univ Estadual Paulista Botucatu, São Paulo, Brazil
| | - Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, and Center of Expertise in Mycology of Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Frank Ebel
- Institut für Infektionsmedizin und Zoonosen, Munich, Germany
| | - Daniel Elad
- Department of Clinical Bacteriology and Mycology, Kimron Veterinary Institute, Veterinary Services, Ministry of Agriculture, Beit Dagan, Israel
| | - Renata R Gomes
- Microbiology, Parasitology and Pathology Graduate Programme, Curitiba Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Ilse D Jacobsen
- Research Group Microbial Immunology, Hans Knöll Institute, Jena, Germany
| | | | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases. Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bernard Mignon
- Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, FARAH (Fundamental and Applied Research for Animals & Health), University of Liège, Liège, Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases. Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Elena Piecková
- Faculty of Medicine, Slovak Medical University, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovakia
| | - Anderson Messias Rodrigues
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo, Brazil
| | - Karuna Singh
- Department of Zoology, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, India
| | - Vania A Vicente
- Research Group Microbial Immunology, Hans Knöll Institute, Jena, Germany
| | - Gudrun Wibbelt
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Nathan P Wiederhold
- Fungus Testing Laboratory, Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Jacques Guillot
- Department of Parasitology, Mycology and Dermatology, EA Dynamyc UPEC, EnvA, Ecole nationale vétérinaire d'Alfort, Maisons-Alfort, France
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97
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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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98
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Flechas SV, Acosta-González A, Escobar LA, Kueneman JG, Sánchez-Quitian ZA, Parra-Giraldo CM, Rollins-Smith LA, Reinert LK, Vredenburg VT, Amézquita A, Woodhams DC. Microbiota and skin defense peptides may facilitate coexistence of two sympatric Andean frog species with a lethal pathogen. ISME JOURNAL 2018; 13:361-373. [PMID: 30254321 DOI: 10.1038/s41396-018-0284-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/21/2018] [Accepted: 08/23/2018] [Indexed: 12/13/2022]
Abstract
Management of hyper-virulent generalist pathogens is an emergent global challenge, yet for most disease systems we lack a basic understanding as to why some host species suffer mass mortalities, while others resist epizootics. We studied two sympatric species of frogs from the Colombian Andes, which coexist with the amphibian pathogen Batrachochytrium dendrobatidis (Bd), to understand why some species did not succumb to the infection. We found high Bd prevalence in juveniles for both species, yet infection intensities remained low. We also found that bacterial community composition and host defense peptides are specific to amphibian life stages. We detected abundant Bd-inhibitory skin bacteria across life stages and Bd-inhibitory defense peptides post-metamorphosis in both species. Bd-inhibitory bacteria were proportionally more abundant in adults of both species than in earlier developmental stages. We tested for activity of peptides against the skin microbiota and found that in general peptides did not negatively affect bacterial growth and in some instances facilitated growth. Our results suggest that symbiotic bacteria and antimicrobial peptides may be co-selected for, and that together they contribute to the ability of Andean amphibian species to coexist with the global pandemic lineage of Bd.
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Affiliation(s)
- Sandra V Flechas
- Department of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia. .,Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia.
| | | | - Laura A Escobar
- Department of Microbiology, Faculty of Sciences, Pontificia Universidad Javeriana, Bogotá, AA 56710, Colombia
| | - Jordan G Kueneman
- Biology Department, University of Massachusetts Boston, Boston, MA, 02125, USA.,Smithsonian Tropical Research Institute, Panama, Apartado 0843-03092, Republic of Panama
| | - Zilpa Adriana Sánchez-Quitian
- Department of Microbiology, Faculty of Sciences, Pontificia Universidad Javeriana, Bogotá, AA 56710, Colombia.,Environmental Management Group, Department of Biology and Microbiology, Universidad de Boyacá, Tunja, 150000003, Colombia
| | - Claudia M Parra-Giraldo
- Department of Microbiology, Faculty of Sciences, Pontificia Universidad Javeriana, Bogotá, AA 56710, Colombia
| | - Louise A Rollins-Smith
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, School of Medicine, Nashville, TN, 37232, USA
| | - Laura K Reinert
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, School of Medicine, Nashville, TN, 37232, USA
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA, 94132-1722, USA
| | - Adolfo Amézquita
- Department of Biological Sciences, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Douglas C Woodhams
- Biology Department, University of Massachusetts Boston, Boston, MA, 02125, USA.,Smithsonian Tropical Research Institute, Panama, Apartado 0843-03092, Republic of Panama
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99
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Lüddecke T, Schulz S, Steinfartz S, Vences M. A salamander’s toxic arsenal: review of skin poison diversity and function in true salamanders, genus Salamandra. Naturwissenschaften 2018; 105:56. [DOI: 10.1007/s00114-018-1579-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/03/2018] [Accepted: 08/05/2018] [Indexed: 12/16/2022]
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100
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Bletz MC, Kelly M, Sabino-Pinto J, Bales E, Van Praet S, Bert W, Boyen F, Vences M, Steinfartz S, Pasmans F, Martel A. Disruption of skin microbiota contributes to salamander disease. Proc Biol Sci 2018; 285:rspb.2018.0758. [PMID: 30135150 DOI: 10.1098/rspb.2018.0758] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/27/2018] [Indexed: 12/15/2022] Open
Abstract
Escalating occurrences of emerging infectious diseases underscore the importance of understanding microbiome-pathogen interactions. The amphibian cutaneous microbiome is widely studied for its potential to mitigate disease-mediated amphibian declines. Other microbial interactions in this system, however, have been largely neglected in the context of disease outbreaks. European fire salamanders have suffered dramatic population crashes as a result of the newly emerged Batrachochytrium salamandrivorans (Bsal). In this paper, we investigate microbial interactions on multiple fronts within this system. We show that wild, healthy fire salamanders maintain complex skin microbiotas containing Bsal-inhibitory members, but these community are present at a remarkably low abundance. Through experimentation, we show that increasing bacterial densities of Bsal-inhibiting bacteria via daily addition slowed disease progression in fire salamanders. Additionally, we find that experimental-Bsal infection elicited subtle changes in the skin microbiome, with selected opportunistic bacteria increasing in relative abundance resulting in septicemic events that coincide with extensive destruction of the epidermis. These results suggest that fire salamander skin, in natural settings, maintains bacterial communities at numbers too low to confer sufficient protection against Bsal, and, in fact, the native skin microbiota can constitute a source of opportunistic bacterial pathogens that contribute to pathogenesis. By shedding light on the complex interaction between the microbiome and a lethal pathogen, these data put the interplay between skin microbiomes and a wildlife disease into a new perspective.
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Affiliation(s)
- Molly C Bletz
- Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA .,Zoological Institute, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Moira Kelly
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Joana Sabino-Pinto
- Zoological Institute, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Emma Bales
- Zoological Institute, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Sarah Van Praet
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Wim Bert
- Department of Biology, Nematology Research Unit, Faculty of Science, Ghent University, 9000 Ghent, Belgium
| | - Filip Boyen
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Sebastian Steinfartz
- Zoological Institute, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
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