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Jiang H, Lv M, He T, Xie M, Zhao Z, He J, Luo S, Guo Y, Chen J. Effects of ex situ conservation on commensal bacteria of crocodile lizard and conservation implications. Vet Q 2025; 45:1-14. [PMID: 39930789 PMCID: PMC11816626 DOI: 10.1080/01652176.2025.2463704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2024] [Revised: 01/07/2025] [Accepted: 02/02/2025] [Indexed: 02/14/2025] Open
Abstract
Ex situ conservation is an important wildlife conservation strategy, but endangered wildlife in captivity often exhibit high disease rates. Commensal microorganisms are vital for homeostasis, immunity, and linked to diseases. This study analyzed the structure, assembly, variations of the symbiotic microbiota of the endangered crocodile lizard, and their relationship with environment, as well as the effects of captivity on them, to explore why captive reptiles face high dermatosis rates. Results showed that the reptile's microbiota significantly differ from that of its habitat, demonstrating niche specificity. While species richness among organs showed no significant differences, microbial diversity varied considerably. Skin microbiota showed no site-specific clustering. The assembly of skin, oral, and intestinal bacterial communities was dominated by homogeneous selection. The gut and oral bacterial networks were resilient to disturbances, while the skin bacterial network was sensitive. Captivity primarily affected the skin microbiota, reducing its diversity and stability, thereby increasing disease risk, and these effects were not solely attributable to environmental changes. These findings suggested that skin microbial changes in captive reptiles may be responsible for their increased susceptibility to dermatosis in ex situ conservation. This study underscored the importance of understanding reptile-associated microbes for effective conservation strategies and offers potential solutions.
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Affiliation(s)
- Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Mei Lv
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tengfei He
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Mujiao Xie
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhiwen Zhao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jiasong He
- Guangxi Daguishan Crocodile Lizard National Nature Reserve, Hezhou, China
| | - Shuyi Luo
- Guangxi Daguishan Crocodile Lizard National Nature Reserve, Hezhou, China
| | - Yide Guo
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
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Salazar J, González J, Riofrío R, Siavichay F, Carrera M, Mogrovejo A, Barrera-Galicia G, Valdez-Tenezaca A. MALDI-TOF Mass Spectrometry Characterization of Culturable Microbiota Associated with the Skin of Amphibians from the Southern Andes Mountains of Ecuador. MICROBIAL ECOLOGY 2025; 88:47. [PMID: 40402178 PMCID: PMC12098423 DOI: 10.1007/s00248-025-02555-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2025] [Accepted: 05/13/2025] [Indexed: 05/23/2025]
Abstract
Ecuador is recognized for having a high diversity of anuran species, which are distributed mainly south of the Andes mountains. However, due to their geographic location and accessibility, there are few studies related to the culturable microbiota of these amphibians in this region. The objective of this study was to explore the bacterial and fungal biodiversity present on the skin of wild anuran species in the southern Andes of Ecuador and to observe whether geographical barriers in the region could increase the variability of the culturable microbiota through MALDI-TOF mass spectrometry. This analysis revealed the presence of 29 bacterial taxa and 9 fungal taxa, consisting mainly of: Pseudomonas chlororaphis (28%), Acinetobacter iwoffii (14%), Pseudomonas fluorescens (14%), and Hortaea werneckii (26.4%), Fusarium solani (20.5%), Syncephalastrum spp. (20.5%), respectively. Diversity varied across the five sampling locations, with geographic location proving to be a significant driver of diversity. Some of the most abundant bacterial and fungal genera have important associations with skin diseases in wildlife and humans. This work represents a glimpse into the complex biodiversity of bacteria and fungi that inhabit the skin substrate, and further studies will be needed to better understand bacterial and fungal biodiversity with potential implications for establishing conservation strategies, along with the development of necessary animal protection measures.
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Affiliation(s)
- J Salazar
- Laboratorio de Ecología Microbiana y Principios Activos, Centro de Investigación Innovación y Transferencia de Tecnología CIITT, Universidad Católica de Cuenca, Vía a Biblín, Ricaurte, Cuenca, 010108, Ecuador.
- Grupo de Investigación Geociencia Ambiente y Recursos Naturales (GARN), Cuenca, 010108, Ecuador.
| | - J González
- Laboratorio de Ecología Microbiana y Principios Activos, Centro de Investigación Innovación y Transferencia de Tecnología CIITT, Universidad Católica de Cuenca, Vía a Biblín, Ricaurte, Cuenca, 010108, Ecuador
- Laboratorio de Entomología Agrícola Fitosanitario, Universidad Católica de Cuenca, Cuenca, 010101, Ecuador
| | - R Riofrío
- Laboratorio de Ecología Microbiana y Principios Activos, Centro de Investigación Innovación y Transferencia de Tecnología CIITT, Universidad Católica de Cuenca, Vía a Biblín, Ricaurte, Cuenca, 010108, Ecuador
| | - F Siavichay
- Centro de Conservación de Anfibios, Bioparque AMARU, Cuenca, 010109, Ecuador
| | - M Carrera
- Laboratorio de Ecología Microbiana y Principios Activos, Centro de Investigación Innovación y Transferencia de Tecnología CIITT, Universidad Católica de Cuenca, Vía a Biblín, Ricaurte, Cuenca, 010108, Ecuador
| | - A Mogrovejo
- Laboratorio de Ecología Microbiana y Principios Activos, Centro de Investigación Innovación y Transferencia de Tecnología CIITT, Universidad Católica de Cuenca, Vía a Biblín, Ricaurte, Cuenca, 010108, Ecuador
| | - G Barrera-Galicia
- Laboratorio de Microbiología Ambiental, Unidad Académica de Ciencias Químicas, Universidad de Zacatecas, Campus Siglo XXI, Carretera Zacatecas-Guadalajara Km 6, La Escondida, Zacatecas, 98160, México
| | - A Valdez-Tenezaca
- Laboratorio de Ecología Microbiana y Principios Activos, Centro de Investigación Innovación y Transferencia de Tecnología CIITT, Universidad Católica de Cuenca, Vía a Biblín, Ricaurte, Cuenca, 010108, Ecuador.
- Laboratorio de Patología Frutal, Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Campus Talca, Av. Lircay S/N, 360000, Talca, Chile.
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Ghose SL, Eisen JA. Skin microbiomes of frogs vary among body regions, revealing differences that reflect known patterns of chytrid infection. Front Microbiol 2025; 16:1579231. [PMID: 40432964 PMCID: PMC12106533 DOI: 10.3389/fmicb.2025.1579231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Accepted: 04/22/2025] [Indexed: 05/29/2025] Open
Abstract
Introduction The amphibian skin microbiome is an important line of defense against pathogens including the deadly chytrid fungus, Batrachochytrium dendrobatidis (Bd). Bd is known to preferentially infect ventral skin surfaces and feet of host amphibians, often leaving dorsal surfaces like the back uninfected. Within-individual variation in infection distribution across the skin, therefore, may relate to differences in microbiomes among skin regions. However, microbiome heterogeneity within amphibian individuals remains poorly characterized. Methods We utilized 16S rRNA gene amplicon sequencing to compare microbiomes of 10 body regions from nine captive Rana sierrae individuals and their tank environments. These individuals were naive to Bd, allowing us to assess whether microbiomes differed among body regions prior to any impacts that may be caused by infection. Results We found that frog skin and tank environments harbored distinct microbial communities. On frog skin, the bacterial families Burkholderiaceae (phylum Proteobacteria) and Rubritaleaceae (phylum Verrucomicrobia) were dominant, driven in large part by relative abundances of undescribed members of these families that were significantly higher on frogs than in their environment. Within individuals, we detected differences between microbiomes of body regions where Bd infection would be expected compared to regions that infrequently experience infection. Notably, putative Bd-inhibitory relative abundance was significantly higher on body regions where Bd infection is often localized. Discussion These findings suggest that microbiomes in certain skin regions may be predisposed for interactions with Bd. Further, our results highlight the importance of considering intraindividual heterogeneities, which could provide insights relevant to predicting localized interactions with pathogens.
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Affiliation(s)
- Sonia L. Ghose
- Genome Center, University of California, Davis, Davis, CA, United States
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, United States
| | - Jonathan A. Eisen
- Genome Center, University of California, Davis, Davis, CA, United States
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, United States
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States
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Madison JD, Osborne OG, Ellison A, Garvey Griffith CN, Gentry L, Gross H, Gratwicke B, Grayfer L, Muletz-Wolz CR. Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression. Infect Immun 2025; 93:e0056924. [PMID: 40172536 PMCID: PMC12070741 DOI: 10.1128/iai.00569-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 03/05/2025] [Indexed: 04/04/2025] Open
Abstract
Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.
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Affiliation(s)
- Joseph D. Madison
- Center for Conservation Genomics, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, USA
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, USA
- Department of Biology, Xavier University of Louisiana, New Orleans, Louisiana, USA
| | - Owen G. Osborne
- School of Environmental and Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Amy Ellison
- School of Environmental and Natural Sciences, Bangor University, Bangor, United Kingdom
| | | | - Lindsey Gentry
- Center for Conservation Genomics, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen, Tübingen, Germany
| | - Brian Gratwicke
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Leon Grayfer
- Department of Biology, George Washington University, Washington, DC, USA
| | - Carly R. Muletz-Wolz
- Center for Conservation Genomics, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, USA
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Longo AV, Solano-Iguaran JJ, Valenzuela-Sánchez A, Alvarado-Rybak M, Azat C, Bacigalupe LD. Blurred Lines Between Determinism and Stochasticity in an Amphibian Phylosymbiosis Under Pathogen Infection. Mol Ecol 2025; 34:e17741. [PMID: 40119548 DOI: 10.1111/mec.17741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 03/09/2025] [Accepted: 03/11/2025] [Indexed: 03/24/2025]
Abstract
Selection, dispersal and drift jointly contribute to generating variation in microbial composition within and between hosts, habitats and ecosystems. However, we have limited examples of how these processes interact as hosts and their microbes turn over across latitudinal gradients of biodiversity and climate. To bridge this gap, we assembled an extensive dataset of 580 skin bacteriomes from 22 amphibian species distributed across a 10° latitudinal range in Chile. Amphibians are susceptible to the fungal pathogen Batrachochytrium dendrobatidis (Bd), which infects their skin, potentially leading to changes in the normal skin microbiome (i.e., dysbiosis). Using comparative methods, accounting for pathogen infection and implementing resampling schemes, we found evidence of phylosymbiosis, characterised by more similar bacterial communities in closely related amphibian species. We also compared how neutral processes affected the assembly of skin bacteria by focusing on two widespread species from our dataset: the Chilean four-eyed frog (Pleurodema thaul) and Darwin's frog (Rhinoderma darwinii). Neutral models revealed that dispersal and chance largely facilitated the occurrence of ~90% of skin bacteria in both species. Deterministic processes (e.g., phylosymbiosis, active recruitment of microbes, microbe-microbe interactions) explained the remaining fraction of the bacteriomes. Amphibian species accounted for 21%-32% of the variance found in non-neutral bacterial taxa, whereas the interaction with Bd carried a weaker but still significant effect. Our findings provide evidence from ectotherms that most of their skin bacteria are subject to dispersal and chance, yet contemporary and historical contingencies leave strong signatures in their microbiomes even at large geographical scales.
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Affiliation(s)
- Ana V Longo
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | | | | | - Mario Alvarado-Rybak
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Universidad de Las Américas, Santiago, Chile
| | - Claudio Azat
- One Health Institute, Life Sciences Faculty, Universidad Andres Bello, Santiago, Chile
| | - Leonardo D Bacigalupe
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
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Kouete MT, Longo AV, Byrne AQ, Echalle SN, Rosenblum EB, Blackburn DC. Host and environmental factors drive prevalence of the pathogen Batrachochytrium dendrobatidis in Central African amphibians. Sci Rep 2025; 15:14908. [PMID: 40295564 PMCID: PMC12037773 DOI: 10.1038/s41598-025-97367-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Accepted: 04/03/2025] [Indexed: 04/30/2025] Open
Abstract
The spread of the fungal pathogen Batrachochytrium dendrobatidis (Bd) presents an escalating threat to amphibian populations globally, including in continental Africa. Focusing on Cameroon in Central Africa, we combined data from previous studies with newly sampled archived specimens and contemporary samples to investigate the emergence and dynamics of Bd, and to assess the risks it poses to local amphibian species. We find that Bd was already present in the early 1900s, with a prevalence averaging 54% (39-66, 95% CI), with the earliest record in 1905 in southern Cameroon-the earliest detection in Africa. The first detection in the mountains, which coincided with declining frog populations, occurred after 2009 and may be linked to BdCAPE, the sole lineage identified in the highlands. For the first time, we detected BdGPL in the country and confirmed that BdCAPE remains the dominant lineage. Pathogen dynamics and prevalence were strongly influenced by host factors, including taxonomic identity and ecology, and environmental variables such as precipitation and isothermality, which are likely to change with extreme weather events in the future. Our findings underscore the urgent need to address the dual threats of Bd and climate change, which together jeopardize the survival of amphibian populations in Cameroon.
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Affiliation(s)
- Marcel T Kouete
- Department of Natural History, Division of Herpetology, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, USA.
| | - Ana V Longo
- Department of Biology, College of Liberal Arts & Sciences, University of Florida, Gainesville, FL, USA
| | - Allison Q Byrne
- Department of Environmental Science, Policy, & Management, University of California Berkeley, Berkeley, CA, USA
| | | | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, & Management, University of California Berkeley, Berkeley, CA, USA
| | - David C Blackburn
- Department of Natural History, Division of Herpetology, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
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WAN B, CHEN G, POON ESK, FUNG HS, LAU A, SIN SYW. Environmental factors and host sex influence the skin microbiota structure of Hong Kong newt (Paramesotriton hongkongensis) in a coldspot of chytridiomycosis in subtropical East Asia. Integr Zool 2025; 20:236-255. [PMID: 38872359 PMCID: PMC11897979 DOI: 10.1111/1749-4877.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Chytridiomycosis, an infectious skin disease caused by the chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans, poses a significant threat to amphibian biodiversity worldwide. Antifungal bacteria found on the skin of chytrid-resistant amphibians could potentially provide defense against chytridiomycosis and lower mortality rates among resistant individuals. The Hong Kong newt (Paramesotriton hongkongensis) is native to East Asia, a region suspected to be the origin of chytrids, and has exhibited asymptomatic infection, suggesting a long-term coexistence with the chytrids. Therefore, the skin microbiota of this resistant species warrant investigation, along with other factors that can affect the microbiota. Among the 149 newts sampled in their natural habitats in Hong Kong, China, putative antifungal bacteria were found in all individuals. There were 314 amplicon sequence variants distributed over 25 genera of putative antifungal bacteria; abundant ones included Acinetobacter, Flavobacterium, and Novosphingobium spp. The skin microbiota compositions were strongly influenced by the inter-site geographical distances. Despite inter-site differences, we identified some core skin microbes across sites that could be vital to P. hongkongensis. The dominant cores included the family Comamonadaceae, family Chitinophagaceae, and class Betaproteobacteria. Moreover, habitat elevation and host sex also exhibited significant effects on skin microbiota compositions. The antifungal bacteria found on these newts offer an important resource for conservation against chytridiomycosis, such as developing probiotic treatments for susceptible species.
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Affiliation(s)
- Bowen WAN
- School of Biological SciencesThe University of Hong KongHong KongChina
| | - Guoling CHEN
- School of Biological SciencesThe University of Hong KongHong KongChina
| | | | - Hon Shing FUNG
- School of Biological SciencesThe University of Hong KongHong KongChina
| | - Anthony LAU
- Science UnitLingnan UniversityHong KongChina
| | - Simon Yung Wa SIN
- School of Biological SciencesThe University of Hong KongHong KongChina
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Ghose SL, Eisen JA. Skin microbiomes of frogs vary among individuals and body regions, revealing differences that reflect known patterns of chytrid infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.05.636728. [PMID: 39975414 PMCID: PMC11839087 DOI: 10.1101/2025.02.05.636728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
The amphibian skin microbiome is an important line of defense against pathogens including the deadly chytrid fungus, Batrachochytrium dendrobatidis (Bd). Intra-species variation in disease susceptibility and intra-individual variation in infection distribution across the skin, therefore, may relate to differences in skin microbiomes. However, characterization of microbiome variation within and among amphibian individuals is needed. We utilized 16S rRNA gene amplicon sequencing to compare microbiomes of ten body regions from nine captive R. sierrae individuals and their tank environments. While frogs harbored distinct microbial communities compared to their tank environments, tank identity was associated with more variation in frog microbiomes than individual frog identity. Within individuals, we detected differences between microbiomes of body regions where Bd infection would be expected compared to regions that infrequently experience infection. Notably, the bacterial families Burkholderiaceae (phylum Proteobacteria) and Rubritaleaceae (phylum Verrucomicrobia) were dominant on frog skin, and the relative abundances of undescribed members of these families were important to describing differences among and within individuals. Two undescribed Burkholderiaceae taxa were found to be putatively Bd-inhibitory, and both showed higher relative abundance on body regions where Bd infection is often localized. These findings highlight the importance of considering intrapopulation and intraindividual heterogeneities, which could provide insights relevant to predicting localized interactions with pathogens.
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Affiliation(s)
- Sonia L. Ghose
- Genome Center, University of California, Davis, CA, USA
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Jonathan A. Eisen
- Genome Center, University of California, Davis, CA, USA
- Department of Evolution and Ecology, University of California, Davis, CA, USA
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
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9
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Novotny L, Powers CM, Royal SM, Preston AK, Hendrix GK, Sola MF. Chytridiomycosis in a colony of hellbenders Cryptobranchus alleganiensis. JOURNAL OF AQUATIC ANIMAL HEALTH 2024; 36:303-309. [PMID: 39620492 PMCID: PMC11685054 DOI: 10.1002/aah.10231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 06/20/2024] [Accepted: 07/15/2024] [Indexed: 01/01/2025]
Abstract
OBJECTIVE The hellbender Cryptobranchus alleganiensis is a fully aquatic, long-lived, and state endangered salamander endemic to the eastern and central United States. Chytridiomycosis is a fungal skin disease of salamanders that can be caused by either Batrachochytrium dendrobatidis (Bd) or by recently described B. salamandrivorans. B. salamandrivorans is responsible for massive mortality of salamanders in Europe but, to date, has not been reported in the United States, in contrast to Bd. Common signs of Bd infection in salamanders are excessive skin shedding; cutaneous discoloration; mainly in ventral parts of the abdomen and thighs; and eventually death as a result of osmotic imbalance. METHODS Eastern hellbenders C. a. alleganiensis in the Aquaculture Research Laboratory at Purdue University experienced 33% mortality. Three of the deceased animals were autopsied, and samples for histopathology, microbiology, and Taqman quantitative polymerase chain reaction were taken. RESULT Autopsy revealed an abundant, thick, yellow to green mucoid material on the surface of the skin, mainly on the tail and flanks. Histopathology of the skin samples revealed infection with chytrid fungus consistent with chytridiomycosis. Taqman quantitative polymerase chain reaction confirmed presence of Bd, and bacterial culture confirmed co-infection with Aeromonas hydrophila. Infected hellbenders were treated with ciprofloxacin, itraconazole, and ceftazidime. CONCLUSION The chytridiomycosis outbreak was most likely caused by sudden environmental stress due to filtration failure and secondary bacterial infection. The surviving animals have not shown any clinical signs of chytridiomycosis for more than 1 year after the treatment and were released the wild river system.
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Affiliation(s)
- L. Novotny
- Department of Comparative Pathobiology, College of Veterinary MedicinePurdue UniversityWest LafayetteIndianaUSA
| | - C. M. Powers
- Department of Comparative Pathobiology, College of Veterinary MedicinePurdue UniversityWest LafayetteIndianaUSA
| | - S. M. Royal
- Aquaculture Research Laboratory, Purdue UniversityWest LafayetteIndianaUSA
| | - A. K. Preston
- Amphibian Disease Laboratory, Disease InvestigationsCenter for Conservation Research, San Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
| | - G. K. Hendrix
- Department of Comparative Pathobiology, College of Veterinary MedicinePurdue UniversityWest LafayetteIndianaUSA
| | - M. F. Sola
- Department of Comparative Pathobiology, College of Veterinary MedicinePurdue UniversityWest LafayetteIndianaUSA
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Su R, Chen F, Zhang X, Qin Y, Zhang Y, Zhang W. Immune defense adaptation of Strauchbufo raddei population in heavy metal polluted area: Insights from developmental and environmental perspectives. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 371:123126. [PMID: 39500166 DOI: 10.1016/j.jenvman.2024.123126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 10/14/2024] [Accepted: 10/27/2024] [Indexed: 11/28/2024]
Abstract
The adjustment of immune defense mechanisms is a crucial aspect of biological adaptation to stressful environments. Amphibians, with their unique metamorphic process, experience distinct life stages and exhibit diverse immune defense components. While previous studies have focused on specific immune changes during particular life stages under stress, this research addresses a critical gap by exploring the adaptive immune defense strategies of Strauchbufo raddei in heavy metal-polluted environments. We conducted laboratory experiments, exposing offspring from both polluted and unpolluted areas to control and heavy metal treatments, while continuously monitoring changes in immune components during key metamorphic stages. Notably, we examined the role of the skin microbiome, a crucial but often overlooked barrier against pathogens. The results indicated that individuals from polluted areas exhibited some tolerance to heavy metal exposure, though overall immune function remained diminished. During metamorphosis, when immune defenses are most vulnerable, the skin microbiome rapidly enriched beneficial bacteria, preventing pathogenic colonization and playing a pivotal role in maintaining immune defense in contaminated environments. Moreover, our research highlights energy allocation strategies involving corticosterone and body fat content, enabling populations to maintain development despite immune compromise. The immune adaptations observed may be fixed through genetic assimilation, suggesting a rapid evolutionary response to environmental stress. However, this reduces phenotypic plasticity, making populations more vulnerable to future environmental changes. This study provides key insights into the survival strategies of amphibian populations in heavy metal-contaminated areas, laying the foundation for future research on molecular and evolutionary adaptations.
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Affiliation(s)
- Rui Su
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Fanrui Chen
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Xueying Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Yuting Qin
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Yingmei Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
| | - Wenya Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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Lemieux-Labonté V, Pathmanathan JS, Terrat Y, Tromas N, Simard A, Haase CG, Lausen CL, Willis CKR, Lapointe FJ. Pseudogymnoascus destructans invasion stage impacts the skin microbial functions of highly vulnerable Myotis lucifugus. FEMS Microbiol Ecol 2024; 100:fiae138. [PMID: 39400741 PMCID: PMC11523048 DOI: 10.1093/femsec/fiae138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 06/06/2024] [Accepted: 10/11/2024] [Indexed: 10/15/2024] Open
Abstract
The role of the skin microbiome in resistance and susceptibility of wildlife to fungal pathogens has been examined from a taxonomic perspective but skin microbial function, in the context of fungal infection, has yet to be studied. Our objective was to understand effects of a bat fungal pathogen site infection status and course of invasion on skin microbial function. We sampled seven hibernating colonies of Myotis lucifugus covering three-time points over the course of Pseudogymnoascus destructans (Pd) invasion and white nose syndrome (pre-invasion, epidemic, and established). Our results support three new hypotheses about Pd and skin functional microbiome: (1) there is an important effect of Pd invasion stage, especially at the epidemic stage; (2) disruption by the fungus at the epidemic stage could decrease anti-fungal functions with potential negative effects on the microbiome and bat health; (3) the collection site might have a larger influence on microbiomes at the pre-invasion stage rather than at epidemic and established stages. Future studies with larger sample sizes and using meta-omics approaches will help confirm these hypotheses, and determine the influence of the microbiome on wildlife survival to fungal disease.
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Affiliation(s)
| | - Jananan S Pathmanathan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, Paris, 75005, France
| | - Yves Terrat
- Département de sciences biologiques, Université de Montréal, Montréal, Québec, H2V 0B3, Canada
| | - Nicolas Tromas
- Département de sciences biologiques, Université de Montréal, Montréal, Québec, H2V 0B3, Canada
| | - Anouk Simard
- Ministère de l’Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs, Québec, G1R 5V7, Canada
| | - Catherine G Haase
- Department of Biology, Austin Peay State University, Clarksville, TN, 37044, United States
| | - Cori L Lausen
- Wildlife Conservation Society Canada, Kaslo, British-Columbia, V0G 1M0, Canada
| | - Craig K R Willis
- Department of Biology and Centre for Forest Interdisciplinary Research, University of Winnipeg, Winnipeg, Manitoba, R3B 2E9, Canada
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12
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Chapman PA, Hudson D, Morgan XC, Beck CW. The role of family and environment in determining the skin bacterial communities of captive aquatic frogs, Xenopus laevis. FEMS Microbiol Ecol 2024; 100:fiae131. [PMID: 39317670 PMCID: PMC11503959 DOI: 10.1093/femsec/fiae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 09/11/2024] [Accepted: 09/23/2024] [Indexed: 09/26/2024] Open
Abstract
Skin microbes play an important role in amphibian tissue regeneration. Xenopus spp. (African clawed frogs) are well-established model organisms, and standard husbandry protocols, including use of antibiotics, may affect experimental outcomes by altering bacterial assemblages. It is therefore essential to improve knowledge of Xenopus bacterial community characteristics and inheritance. We undertook bacterial 16S rRNA gene sequencing and source tracking of a captive Xenopus laevis colony, including various life stages and environmental samples across multiple aquarium systems. Tank environments supported the most complex bacterial communities, while egg jelly bacteria were the most diverse of frog life stages; tadpole bacterial communities were relatively simple. Rhizobium (Proteobacteria) and Chryseobacterium (Bacteroidota) were dominant in tadpoles, whereas Chryseobacterium, Vogesella (Proteobacteria), and Acinetobacter (Proteobacteria) were common in females. Tadpoles received approximately two-thirds of their bacteria via vertical transmission, though 23 genera were differentially abundant between females and tadpoles. Female frog skin appears to select for specific taxa, and while tadpoles inherit a proportion of their skin bacteria from females via the egg, they support a distinct and less diverse community. The outcomes of this study suggest the impacts of breaking the bacterial transmission chain with antibiotic treatment should be considered when raising tadpoles for experimental purposes.
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Affiliation(s)
- Phoebe A Chapman
- Department of Zoology, University of Otago, Dunedin, 9016, New Zealand
| | - Daniel Hudson
- Department of Zoology, University of Otago, Dunedin, 9016, New Zealand
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, United States
| | - Caroline W Beck
- Department of Zoology, University of Otago, Dunedin, 9016, New Zealand
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13
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Yánez Galarza JK, Riascos-Flores L, Naranjo-Briceño L, Carrera-Gonzalez A, Ortega-Andrade HM. Molecular detection of Batrachochytrium dendrobatidis (Chytridiomycota) and culturable skin bacteria associated with three critically endangered species of Atelopus (Anura: Bufonidae) in Ecuador. PeerJ 2024; 12:e18317. [PMID: 39465153 PMCID: PMC11512805 DOI: 10.7717/peerj.18317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/24/2024] [Indexed: 10/29/2024] Open
Abstract
Chytridiomycosis is a fungal disease responsible for massive amphibian die-offs worldwide, caused by the fungus Batrachochytrium dendrobatidis (Bd). Potential symbiotic relationships between frogs and the bacteria residing on their skin-referred to as skin-bacteria-may inhibit Bd growth, aiding in resistance to this lethal disease. This research had three main objectives: (1) to detect the presence of Bd in native populations of Atelopus balios, A. bomolochos, and A. nanay in the central Andes and coastal southern regions of Ecuador; (2) to identify the culturable skin-bacteria; and (3) to analyze differences among the bacterial communities in the three Atelopus species studied. Skin swabs were collected from two populations of A. balios (107-203 m a.s.l.) and one population each of A. bomolochos and A. nanay (3,064-3,800 m a.s.l.). These swabs served two purposes: first, to detect Bd using conventional PCR; and second, to isolate culturable bacteria, which were characterized through DNA sequencing, molecular phylogeny, and community composition similarity analysis (Jaccard index). Results showed that Bd was present in all species, with positive Bd PCR amplification found in 11 of the 12 sampled amphibians. The culturable skin-bacteria were classified into 10 genera: Pseudomonas (31.4%), Stenotrophomonas (14.3%), Acinetobacter (11.4%), Serratia (11.4%), Aeromonas (5.7%), Brucella (5.7%), Klebsiella (5.7%), Microbacterium (5.7%), Rhodococcus (5.7%), and Lelliottia (2.9%). The Jaccard index revealed that bacterial genera were least similar in A. bomolochos and A. balios (J = 0.10), while the highest similarity at the genus level was between A. bomolochos and A. nanay (J = 0.33). At the clade-species level, only A. bomolochos and A. nanay show common bacteria (J = 0.13). Culturable bacterial communities of specimens diagnosed as Bd positive (n = 10) or Bd negative (n = 1) share a J value of 0.1 at genus and 0.04 at species-clade level. The prevalence of Bd and the composition of cutaneous bacteria could be influenced by Bd reservoirs, Atelopus biology, and intrinsic environmental conditions. This research contributes to understanding the relationship between endangered Andean species and Bd, and explores the potential use of native skin-bacteria as biocontrol agents against Bd.
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Affiliation(s)
- Jomira K. Yánez Galarza
- Ingeniería en Biotecnología, Facultad de Ciencias de la Vida, Universidad Regional Amazónica Ikiam, Tena, Napo, Ecuador
- Grupo de Investigación en Biogeografía y Ecología Espacial (BioGeoE2), Universidad Regional Amazónica Ikiam, Tena, Napo, Ecuador
| | - Lenin Riascos-Flores
- Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Gent University, Gent, Belgium
- Research Institute for Nature and Forest, Brussels, Belgium
| | - Leopoldo Naranjo-Briceño
- Ingeniería en Biotecnología, Facultad de Ciencias de la Vida, Universidad Regional Amazónica Ikiam, Tena, Napo, Ecuador
- Biotech Lab, Spora Biotech, Santiago, Región Metropolitana, Chile
| | - Andrea Carrera-Gonzalez
- Ingeniería en Biotecnología, Facultad de Ciencias de la Vida, Universidad Regional Amazónica Ikiam, Tena, Napo, Ecuador
- Grupo de Investigación en Biogeografía y Ecología Espacial (BioGeoE2), Universidad Regional Amazónica Ikiam, Tena, Napo, Ecuador
| | - H. Mauricio Ortega-Andrade
- Grupo de Investigación en Biogeografía y Ecología Espacial (BioGeoE2), Universidad Regional Amazónica Ikiam, Tena, Napo, Ecuador
- Herpetology Division, Instituto Nacional de Biodiversidad (INABIO), Quito, Pichincha, Ecuador
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14
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Loyau A, Bouchali R, Sentenac H, Schmeller DS. The commensal skin microbiome of amphibian mountain populations and its association with the pathogen Batrachochytrium dendrobatidis. Environ Microbiol 2024; 26:e16699. [PMID: 39374928 DOI: 10.1111/1462-2920.16699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 08/22/2024] [Indexed: 10/09/2024]
Abstract
Microbial assemblages naturally living on the skin are an integral part of immunity. In amphibians, this skin microbiota may hold a mitigation solution against the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes the panzootic disease chytridiomycosis. We used 16S rRNA gene metabarcoding to test the adaptive microbiome hypothesis. We compared the community composition, richness, and putative Bd-inhibitory function of the skin microbiome of three amphibian host species in the Pyrenees, as well as three species in Taiwan, in both Bd-positive and negative mountain populations. In both geographical regions, the amphibian host species played a decisive role in shaping the microbial assemblage and putative anti-Bd properties. In the Pyrenees, the species most susceptible to chytridiomycosis, Alytes obstetricans, had the lowest relative abundances of putative protective bacteria. In Bd-positive and negative sites, individuals had different skin microbiomes, with all anuran species showing increased relative abundances of potential anti-Bd bacteria, while the Taiwanese caudata Hynobius sonani showed the opposite pattern. Our results suggest that, in response to exposure to the pathogen, the skin microbiota shifted to a defensive state with increased anti-Bd function, which may contribute to promoting disease resistance, as proposed by the adaptive microbiome hypothesis.
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Affiliation(s)
- Adeline Loyau
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3-Paul Sabatier (UT3), Toulouse, France
| | - Rayan Bouchali
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3-Paul Sabatier (UT3), Toulouse, France
| | - Hugo Sentenac
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3-Paul Sabatier (UT3), Toulouse, France
| | - Dirk S Schmeller
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3-Paul Sabatier (UT3), Toulouse, France
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15
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Lu Y, Ren H, Li Z, Leng H, Li A, Dai W, Huang L, Feng J, Sun K. Microbiota diversity and anti- Pseudogymnoascus destructans bacteria isolated from Myotis pilosus skin during late hibernation. Appl Environ Microbiol 2024; 90:e0069324. [PMID: 39058040 PMCID: PMC11337810 DOI: 10.1128/aem.00693-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Symbiotic microorganisms that reside on the host skin serve as the primary defense against pathogens in vertebrates. Specifically, the skin microbiome of bats may play a crucial role in providing resistance against Pseudogymnoascus destructans (Pd), the pathogen causing white-nose syndrome. However, the epidermis symbiotic microbiome and its specific role in resisting Pd in highly resistant bats in Asia are still not well understood. In this study, we collected and characterized skin microbiota samples of 19 Myotis pilosus in China and explored the differences between Pd-positive and negative individuals. We identified inhibitory effects of these bacteria through cultivation methods. Our results revealed that the Simpson diversity index of the skin microbiota for positive individuals was significantly lower than that of negative individuals, and the relative abundance of Pseudomonas was significantly higher in positive bats. Regardless of whether individuals were positive or negative for Pd, the relative abundance of potentially antifungal genera in skin microbiota was high. Moreover, we successfully isolated 165 microbes from bat skin and 41 isolates from positive individuals able to inhibit Pd growth compared to only 12 isolates from negative individuals. A total of 10 genera of Pd-inhibiting bacteria were screened, among which the genera Algoriella, Glutamicibacter, and Psychrobacter were newly discovered as Pd-inhibiting genera. These Pd-inhibiting bacteria metabolized a variety of volatile compounds, including dimethyl trisulfide, dimethyl disulfide, propylene sulfide, 2-undecanone, and 2-nonanone, which were able to completely inhibit Pd growth at low concentrations.IMPORTANCERecently, white-nose syndrome has caused the deaths of millions of hibernating bats, even threatening some with regional extinction. Bats in China with high resistance to Pseudogymnoascus destructans can provide a powerful reference for studying the management of white-nose syndrome and understanding the bats against the pathogen's intrinsic mechanisms. This study sheds light on the crucial role of host symbiotic skin microorganisms in resistance to pathogenic fungi and highlights the potential for harnessing natural defense mechanisms for the prevention and treatment of white-nose syndrome. In addition, this may also provide promising candidates for the development of bioinsecticides and fungicides that offer new avenues for addressing fungal diseases in wildlife and agricultural environments.
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Affiliation(s)
- Yaping Lu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Huilan Ren
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Zhongle Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Aoqiang Li
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Long Huang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
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16
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Haghani NB, Lampe RH, Samuel BS, Chalasani SH, Matty MA. Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection. Microbiol Spectr 2024; 12:e0016924. [PMID: 38980017 PMCID: PMC11302229 DOI: 10.1128/spectrum.00169-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The C. elegans cuticular surface serves as a barrier and first point of contact with their microbial environments. In this study, we identify microbes from C. elegans natural habitats that associate with its cuticle, constituting a simple "skin microbiome." We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the C. elegans surface. Furthermore, we conduct 16S rRNA gene sequencing studies to identify relative shifts in the proportion of mCeMbio bacteria upon surface-sterilization, implying distinct skin- and gut-microbiomes. We find that some strains of bacteria, including Enterobacter sp. JUb101, are primarily found on the nematode skin, while others like Stenotrophomonas indicatrix JUb19 and Ochrobactrum vermis MYb71 are predominantly found in the animal's gut. Finally, we show that this skin microbiome promotes host cuticle integrity in harsh environments. Together, we identify a skin microbiome for the well-studied nematode model and propose its value in conferring host fitness advantages in naturalized contexts. IMPORTANCE The genetic model organism C. elegans has recently emerged as a tool for understanding host-microbiome interactions. Nearly all of these studies either focus on pathogenic or gut-resident microbes. Little is known about the existence of native, nonpathogenic skin microbes or their function. We demonstrate that members of a modified C. elegans model microbiome, mCeMbio, can adhere to the animal's cuticle and confer protection from noxious environments. We combine a novel micro-swab tool, the first 16S microbial sequencing data from relatively unperturbed C. elegans, and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wild C. elegans skin microbiomes and use C. elegans as a model for skin research.
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Affiliation(s)
- Nadia B. Haghani
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
- University of California San Diego, La Jolla, California, USA
| | - Robert H. Lampe
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Buck S. Samuel
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Sreekanth H. Chalasani
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
- University of California San Diego, La Jolla, California, USA
| | - Molly A. Matty
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
- Biology, University of Portland, Portland, Oregon, USA
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17
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Li JD, Gao YY, Stevens EJ, King KC. Dual stressors of infection and warming can destabilize host microbiomes. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230069. [PMID: 38497264 PMCID: PMC10945407 DOI: 10.1098/rstb.2023.0069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/02/2024] [Indexed: 03/19/2024] Open
Abstract
Climate change is causing extreme heating events and intensifying infectious disease outbreaks. Animals harbour microbial communities, which are vital for their survival and fitness under stressful conditions. Understanding how microbiome structures change in response to infection and warming may be important for forecasting host performance under global change. Here, we evaluated alterations in the microbiomes of several wild Caenorhabditis elegans isolates spanning a range of latitudes, upon warming temperatures and infection by the parasite Leucobacter musarum. Using 16S rRNA sequencing, we found that microbiome diversity decreased, and dispersion increased over time, with the former being more prominent in uninfected adults and the latter aggravated by infection. Infection reduced dominance of specific microbial taxa, and increased microbiome dispersion, indicating destabilizing effects on host microbial communities. Exposing infected hosts to warming did not have an additive destabilizing effect on their microbiomes. Moreover, warming during pre-adult development alleviated the destabilizing effects of infection on host microbiomes. These results revealed an opposing interaction between biotic and abiotic factors on microbiome structure. Lastly, we showed that increased microbiome dispersion might be associated with decreased variability in microbial species interaction strength. Overall, these findings improve our understanding of animal microbiome dynamics amidst concurrent climate change and epidemics. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- J. D. Li
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
| | - Y. Y. Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, People's Republic of China
- School of Ecology and Nature Conservation, Beijing Forestry University, 35 Tsinghua East Road, Beijing 100083, People's Republic of China
| | - E. J. Stevens
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
| | - K. C. King
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
- Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
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18
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Cordeiro IF, Lemes CGDC, Sanchez AB, da Silva AK, de Paula CH, de Matos RC, Ribeiro DF, de Matos JP, Garcia CCM, Beirão M, Becker CG, Pires MRS, Moreira LM. Amphibian tolerance to arsenic: microbiome-mediated insights. Sci Rep 2024; 14:10193. [PMID: 38702361 PMCID: PMC11068734 DOI: 10.1038/s41598-024-60879-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Amphibians are often recognized as bioindicators of healthy ecosystems. The persistence of amphibian populations in heavily contaminated environments provides an excellent opportunity to investigate rapid vertebrate adaptations to harmful contaminants. Using a combination of culture-based challenge assays and a skin permeability assay, we tested whether the skin-associated microbiota may confer adaptive tolerance to tropical amphibians in regions heavily contaminated with arsenic, thus supporting the adaptive microbiome principle and immune interactions of the amphibian mucus. At lower arsenic concentrations (1 and 5 mM As3+), we found a significantly higher number of bacterial isolates tolerant to arsenic from amphibians sampled at an arsenic contaminated region (TES) than from amphibians sampled at an arsenic free region (JN). Strikingly, none of the bacterial isolates from our arsenic free region tolerated high concentrations of arsenic. In our skin permeability experiment, where we tested whether a subset of arsenic-tolerant bacterial isolates could reduce skin permeability to arsenic, we found that isolates known to tolerate high concentrations of arsenic significantly reduced amphibian skin permeability to this metalloid. This pattern did not hold true for bacterial isolates with low arsenic tolerance. Our results describe a pattern of environmental selection of arsenic-tolerant skin bacteria capable of protecting amphibians from intoxication, which helps explain the persistence of amphibian populations in water bodies heavily contaminated with arsenic.
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Affiliation(s)
- Isabella Ferreira Cordeiro
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | | | - Angélica Bianchini Sanchez
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Ana Karla da Silva
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Camila Henriques de Paula
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Rosilene Cristina de Matos
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Dilson Fagundes Ribeiro
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Jéssica Pereira de Matos
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Camila Carrião Machado Garcia
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
- Laboratório de Genômica e Interação Bactérias-Ambiente, Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Marina Beirão
- Departamento de Biodiversidade Evolução e Meio Ambiente, Instituto de Ciências Biológicas, Universidade Federal de Ouro Preto, Belo Horizonte, MG, 31270-901, Brazil
| | - C Guilherme Becker
- Department of Biology, One Health Microbiome Center, Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Maria Rita Silvério Pires
- Departamento de Biodiversidade Evolução e Meio Ambiente, Instituto de Ciências Biológicas, Universidade Federal de Ouro Preto, Belo Horizonte, MG, 31270-901, Brazil
| | - Leandro Marcio Moreira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil.
- Laboratório de Genômica e Interação Bactérias-Ambiente, Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil.
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19
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Vargas-Gastélum L, Romer AS, Ghotbi M, Dallas JW, Alexander NR, Moe KC, McPhail KL, Neuhaus GF, Shadmani L, Spatafora JW, Stajich JE, Tabima JF, Walker DM. Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria. mSphere 2024; 9:e0047523. [PMID: 38349154 PMCID: PMC10964425 DOI: 10.1128/msphere.00475-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/10/2024] [Indexed: 03/27/2024] Open
Abstract
Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, lizards, and salamanders are structured by the host taxonomy and that Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus operational taxonomic units present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity support a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides.IMPORTANCEThis work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.
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Affiliation(s)
- Lluvia Vargas-Gastélum
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Alexander S. Romer
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Marjan Ghotbi
- Research Division 3, Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jason W. Dallas
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - N. Reed Alexander
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Kylie C. Moe
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - George F. Neuhaus
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Leila Shadmani
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Javier F. Tabima
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Donald M. Walker
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
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20
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Kamel M, Aleya S, Alsubih M, Aleya L. Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases. J Pers Med 2024; 14:217. [PMID: 38392650 PMCID: PMC10890469 DOI: 10.3390/jpm14020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.
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Affiliation(s)
- Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 11221, Egypt
| | - Sami Aleya
- Faculty of Medecine, Université de Bourgogne Franche-Comté, Hauts-du-Chazal, 25030 Besançon, France;
| | - Majed Alsubih
- Department of Civil Engineering, King Khalid University, Guraiger, Abha 62529, Saudi Arabia;
| | - Lotfi Aleya
- Laboratoire de Chrono-Environnement, Université de Bourgogne Franche-Comté, UMR CNRS 6249, La Bouloie, 25030 Besançon, France;
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21
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Dosi A, Meziti A, Tounta E, Koemtzopoulos K, Komnenou A, Dendrinos P, Kormas K. Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation. Microbiol Spectr 2024; 12:e0280523. [PMID: 38084980 PMCID: PMC10783143 DOI: 10.1128/spectrum.02805-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (Monachus monachus), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal's conservation practices through its microbiome.
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Affiliation(s)
- Aggeliki Dosi
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Eleni Tounta
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Kimon Koemtzopoulos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Anastasia Komnenou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis Dendrinos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
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22
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Zhao W, Bu X, Zhou W, Zeng Q, Qin T, Wu S, Li W, Zou H, Li M, Wang G. Interactions between Balantidium ctenopharyngodoni and microbiota reveal its low pathogenicity in the hindgut of grass carp. BMC Microbiol 2024; 24:7. [PMID: 38172646 PMCID: PMC10762984 DOI: 10.1186/s12866-023-03154-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Hosts, parasites, and microbiota interact with each other, forming a complex ecosystem. Alterations to the microbial structure have been observed in various enteric parasitic infections (e.g. parasitic protists and helminths). Interestingly, some parasites are associated with healthy gut microbiota linked to the intestinal eubiosis state. So the changes in bacteria and metabolites induced by parasite infection may offer benefits to the host, including protection from other parasitesand promotion of intestinal health. The only ciliate known to inhabit the hindgut of grass carp, Balantidium ctenopharyngodoni, does not cause obvious damage to the intestinal mucosa. To date, its impact on intestinal microbiota composition remains unknown. In this study, we investigated the microbial composition in the hindgut of grass carp infected with B. ctenopharyngodoni, as well as the changes of metabolites in intestinal contents resulting from infection. RESULTS Colonization by B. ctenopharyngodoni was associated with an increase in bacterial diversity, a higher relative abundance of Clostridium, and a lower abundance of Enterobacteriaceae. The family Aeromonadaceae and the genus Citrobacter had significantly lower relative abundance in infected fish. Additionally, grass carp infected with B. ctenopharyngodoni exhibited a significant increase in creatine content in the hindgut. This suggested that the presence of B. ctenopharyngodoni may improve intestinal health through changes in microbiota and metabolites. CONCLUSIONS We found that grass carp infected with B. ctenopharyngodoni exhibit a healthy microbiota with an increased bacterial diversity. The results suggested that B. ctenopharyngodoni reshaped the composition of hindgut microbiota similarly to other protists with low pathogenicity. The shifts in the microbiota and metabolites during the colonization and proliferation of B. ctenopharyngodoni indicated that it may provide positive effects in the hindgut of grass carp.
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Affiliation(s)
- Weishan Zhao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xialian Bu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weitian Zhou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingwen Zeng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tian Qin
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shangong Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wenxiang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Hong Zou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ming Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Guitang Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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23
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Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Rebollar EA. Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent. Microb Genom 2024; 10:001181. [PMID: 38240649 PMCID: PMC10868611 DOI: 10.1099/mgen.0.001181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.
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Affiliation(s)
| | - Víctor Ávila-Akerberg
- Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | | | - Eria A. Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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24
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Ange-Stark M, Parise KL, Cheng TL, Hoyt JR, Langwig KE, Frick WF, Kilpatrick AM, Gillece J, MacManes MD, Foster JT. White-nose syndrome restructures bat skin microbiomes. Microbiol Spectr 2023; 11:e0271523. [PMID: 37888992 PMCID: PMC10714735 DOI: 10.1128/spectrum.02715-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/13/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Inherent complexities in the composition of microbiomes can often preclude investigations of microbe-associated diseases. Instead of single organisms being associated with disease, community characteristics may be more relevant. Longitudinal microbiome studies of the same individual bats as pathogens arrive and infect a population are the ideal experiment but remain logistically challenging; therefore, investigations like our approach that are able to correlate invasive pathogens to alterations within a microbiome may be the next best alternative. The results of this study potentially suggest that microbiome-host interactions may determine the likelihood of infection. However, the contrasting relationship between Pd and the bacterial microbiomes of Myotis lucifugus and Perimyotis subflavus indicate that we are just beginning to understand how the bat microbiome interacts with a fungal invader such as Pd.
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Affiliation(s)
- Meghan Ange-Stark
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Katy L. Parise
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Tina L. Cheng
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA
- Bat Conservation International, Austin, Texas, USA
| | - Joseph R. Hoyt
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Kate E. Langwig
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Winifred F. Frick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA
- Bat Conservation International, Austin, Texas, USA
| | - A. Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA
| | - John Gillece
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Matthew D. MacManes
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Jeffrey T. Foster
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
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25
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Campos PM, Lucid MK, Ehlers S, Walke JB. Low-level pathogen infection and geographic location correlate with the skin microbiomes of Columbia spotted frogs ( Rana luteiventris) in a montane landscape. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 6:100213. [PMID: 38187998 PMCID: PMC10770434 DOI: 10.1016/j.crmicr.2023.100213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
The skin microbiome of amphibians can influence host susceptibility towards the fungal pathogen Batrachochytrium dendrobatidis (Bd), while simultaneously having the potential to be altered by Bd. Severe Bd infections are known to alter the amphibian skin microbiome; however, little is known about microbiome interactions in amphibians with low infection intensity. In addition to disease dynamics, environmental factors may influence the microbiome. To test for patterns in bacterial diversity based on pathogen infection and environmental factors, 399 Columbia spotted frogs (Rana luteiventris) were sampled throughout northern Idaho and northeastern Washington across two years. Bd prevalence and intensity were measured in 376 frogs, revealing a prevalence of 69%, but generally low infection intensity (Mean = 127 Bd zoospore equivalents among infected frogs). Skin bacterial communities were characterized in 92 frogs using 16S rRNA gene amplicon sequencing. Our results indicated correlations of decreasing Shannon diversity and evenness as infection intensity increased. Latitude was correlated with bacterial richness and Faith's Phylogenetic Diversity measures, indicating increased diversity in northern locations. Beta diversity (UniFrac) analyses revealed that skin microbiomes were distinct between infected and uninfected frogs, and infection intensity had a significant effect on microbiome composition. Site explained the majority of microbiome variation (weighted UniFrac: 57.5%), suggesting a combination of local habitat conditions explain variation, as only small proportions of variation could be explained by year, month, temperature, elevation, and latitude individually. Bacterial genera with potential for Bd-inhibitory properties were found with differential relative abundance in infected and uninfected frogs, with higher Stenotrophomonas and lower Pseudomonas relative abundance observed in infected frogs. Further study may indicate if Bd inhibition by members of the skin microbiome is an influence behind the low infection intensities observed and whether low Bd infection intensities are capable of altering skin microbiome composition.
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Affiliation(s)
- Philip M. Campos
- Department of Biology, Eastern Washington University, 1175 Washington St., Cheney, WA 99004, USA
| | - Michael K. Lucid
- Idaho Department of Fish and Game, 2885 Kathleen Ave., Coeur d'Alene, ID 83815, USA
- Selkirk Wildlife Science, LLC, PO Box 733, Sandpoint, ID 83864, USA
| | - Shannon Ehlers
- Idaho Department of Fish and Game, 2885 Kathleen Ave., Coeur d'Alene, ID 83815, USA
- U.S. Fish and Wildlife Service, 287 Westside Rd., Bonners Ferry, ID 83805, USA
| | - Jenifer B. Walke
- Department of Biology, Eastern Washington University, 1175 Washington St., Cheney, WA 99004, USA
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26
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Sun D, Herath J, Zhou S, Ellepola G, Meegaskumbura M. Associations of Batrachochytrium dendrobatidis with skin bacteria and fungi on Asian amphibian hosts. ISME COMMUNICATIONS 2023; 3:123. [PMID: 37993728 PMCID: PMC10665332 DOI: 10.1038/s43705-023-00332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Amphibian skin harbors microorganisms that are associated with the fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes chytridiomycosis, one of the most significant wildlife diseases known. This pathogen originated in Asia, where diverse Bd lineages exist; hence, native amphibian hosts have co-existed with Bd over long time periods. Determining the nuances of this co-existence is crucial for understanding the prevalence and spread of Bd from a microbial context. However, associations of Bd with the natural skin microbiome remain poorly understood for Asian hosts, especially in relation to skin-associated fungi. We used 16 S rRNA and fungal internal transcribed spacer (ITS) gene sequencing to characterize the skin microbiome of four native Asian amphibian species and examined the relationships between Bd infection and their skin bacterial and fungal communities; we also analyzed the correlates of the putative anti-Bd bacteria. We show that both skin bacterial and fungal community structure and composition had significant associations with infection status (Bd presence/absence) and infection intensity (frequency of Bd sequence reads). We also found that the putative anti-Bd bacterial richness was correlated with Bd infection status and infection intensity, and observed that the relative abundance of anti-Bd bacteria roughly correspond with changes in both Bd prevalence and mean infection intensity in populations. Additionally, the microbial co-occurrence network of infected frogs was significantly different from that of uninfected frogs that were characterized by more keystone nodes (connectors) and larger proportions in correlations between bacteria, suggesting stronger inter-module bacterial interactions. These results indicate that the mutual effects between Bd and skin-associated microbiome, including the interplay between bacteria and fungi, might vary with Bd infection in susceptible amphibian species. This knowledge will help in understanding the dynamics of Bd from a microbial perspective, potentially contributing to mitigate chytridiomycosis in other regions of the world.
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Affiliation(s)
- Dan Sun
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Jayampathi Herath
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- School of Biomedical Sciences, International Institute of Health Sciences (IIHS), No 704 Negombo Rd, Welisara, 71722, Sri Lanka
| | - Shipeng Zhou
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
| | - Gajaba Ellepola
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China
- Department of Zoology, Faculty of Science, University of Peradeniya, Peradeniya, KY20400, Sri Lanka
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory for Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, 530000, People's Republic of China.
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27
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Robak MJ, Saenz V, de Cortie E, Richards-Zawacki CL. Effects of temperature on the interaction between amphibian skin bacteria and Batrachochytrium dendrobatidis. Front Microbiol 2023; 14:1253482. [PMID: 37942072 PMCID: PMC10628663 DOI: 10.3389/fmicb.2023.1253482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023] Open
Abstract
Symbiotic relationships between animals and microbes are important for a range of functions, from digestion to protection from pathogens. However, the impact of temperature variation on these animal-microbe interactions remains poorly understood. Amphibians have experienced population declines and even extinctions on a global scale due to chytridiomycosis, a disease caused by chytrid fungi in the genus Batrachochytrium. Variation in susceptibility to this disease exists within and among host species. While the mechanisms generating differences in host susceptibility remain elusive, differences in immune system components, as well as variation in host and environmental temperatures, have been associated with this variation. The symbiotic cutaneous bacteria of amphibians are another potential cause for variation in susceptibility to chytridiomycosis, with some bacterial species producing antifungal metabolites that prevent the growth of Bd. The growth of both Bd and bacteria are affected by temperature, and thus we hypothesized that amphibian skin bacteria may be more effective at preventing Bd growth at certain temperatures. To test this, we collected bacteria from the skins of frogs, harvested the metabolites they produced when grown at three different temperatures, and then grew Bd in the presence of those metabolites under those same three temperatures in a three-by-three fully crossed design. We found that both the temperature at which cutaneous bacteria were grown (and metabolites produced) as well as the temperature at which Bd is grown can impact the ability of cutaneous bacteria to inhibit the growth of Bd. While some bacterial isolates showed the ability to inhibit Bd growth across multiple temperature treatments, no isolate was found to be inhibitive across all combinations of bacterial incubation or Bd challenge temperatures, suggesting that temperature affects both the metabolites produced and the effectiveness of those metabolites against the Bd pathogen. These findings move us closer to a mechanistic understanding of why chytridiomycosis outbreaks and related amphibian declines are often limited to certain climates and seasons.
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Affiliation(s)
- Matthew J. Robak
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, United States
| | - Veronica Saenz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biology, The Pennsylvania State University, State College, PA, United States
| | - Esmee de Cortie
- Falk School of Sustainability and Environment, Chatham University, Pittsburgh, PA, United States
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28
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Hartmann AM, McGrath-Blaser SE, Colón-Piñeiro Z, Longo AV. Ontogeny drives shifts in skin bacterial communities in facultatively paedomorphic salamanders. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001399. [PMID: 37815535 PMCID: PMC10634365 DOI: 10.1099/mic.0.001399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/02/2023] [Indexed: 10/11/2023]
Abstract
Microbiomes are major determinants of host growth, development and survival. In amphibians, host-associated bacteria in the skin can inhibit pathogen infection, but many processes can influence the structure and composition of the community. Here we quantified the shifts in skin-associated bacteria across developmental stages in the striped newt (Notophthalmus perstriatus), a threatened salamander species with a complex life history and vulnerable to infection by the amphibian chytrid fungus Batrachochytrium dendrobatidis and ranavirus. Our analyses show that pre-metamorphic larval and paedomorphic stages share similar bacterial compositions, and that the changes in the microbiome coincided with physiological restructuring during metamorphosis. Newts undergoing metamorphosis exhibited microbiome compositions that were intermediate between paedomorphic and post-metamorphic stages, further supporting the idea that metamorphosis is a major driver of host-associated microbes in amphibians. We did not find support for infection-related disruption of the microbiome, though infection replicates were small for each respective life stage.
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Affiliation(s)
- Arik M. Hartmann
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | | | | | - Ana V. Longo
- Department of Biology, University of Florida, Gainesville, Florida, USA
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29
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Villatoro-Castañeda M, Forsburg ZR, Ortiz W, Fritts SR, Gabor CR, Carlos-Shanley C. Exposure to Roundup and Antibiotics Alters Gut Microbial Communities, Growth, and Behavior in Rana berlandieri Tadpoles. BIOLOGY 2023; 12:1171. [PMID: 37759571 PMCID: PMC10525943 DOI: 10.3390/biology12091171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023]
Abstract
The gut microbiome is important for digestion, host fitness, and defense against pathogens, which provides a tool for host health assessment. Amphibians and their microbiomes are highly susceptible to pollutants including antibiotics. We explored the role of an unmanipulated gut microbiome on tadpole fitness and phenotype by comparing tadpoles of Rana berlandieri in a control group (1) with tadpoles exposed to: (2) Roundup® (glyphosate active ingredient), (3) antibiotic cocktail (enrofloxacin, sulfamethazine, trimethoprim, streptomycin, and penicillin), and (4) a combination of Roundup and antibiotics. Tadpoles in the antibiotic and combination treatments had the smallest dorsal body area and were the least active compared to control and Roundup-exposed tadpoles, which were less active than control tadpoles. The gut microbial community significantly changed across treatments at the alpha, beta, and core bacterial levels. However, we did not find significant differences between the antibiotic- and combination-exposed tadpoles, suggesting that antibiotic alone was enough to suppress growth, change behavior, and alter the gut microbiome composition. Here, we demonstrate that the gut microbial communities of tadpoles are sensitive to environmental pollutants, namely Roundup and antibiotics, which may have consequences for host phenotype and fitness via altered behavior and growth.
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Affiliation(s)
- Melissa Villatoro-Castañeda
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
| | - Zachery R. Forsburg
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
- Archbold Biological Station, 123 Main Dr., Venus, FL 33960, USA
| | - Whitney Ortiz
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
- Department of Molecular Microbiology and Immunology, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
| | - Sarah R. Fritts
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
| | - Caitlin R. Gabor
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
| | - Camila Carlos-Shanley
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX 78666, USA; (M.V.-C.); (Z.R.F.); (W.O.); (S.R.F.); (C.C.-S.)
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Ujszegi J, Boros Z, Fodor A, Vajna B, Hettyey A. Metabolites of Xenorhabdus bacteria are potent candidates for mitigating amphibian chytridiomycosis. AMB Express 2023; 13:88. [PMID: 37615904 PMCID: PMC10449739 DOI: 10.1186/s13568-023-01585-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/20/2023] [Indexed: 08/25/2023] Open
Abstract
Chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), has caused extreme losses in amphibian biodiversity. Finding bacteria that produce metabolites with antifungal properties may turn out to be invaluable in the fight against this devastating disease. The entomopathogenic bacteria, Xenorhabdus szentirmaii and X. budapestensis produce secondary metabolites that are effective against a wide range of fungal plant pathogens. To assess whether they may also be effective against Bd, we extracted cell-free culture media (CFCM) from liquid cultures of X. szentirmaii and X. budapestensis and tested their ability to inhibit Bd growth in vitro. As a second step, using juvenile common toads (Bufo bufo) experimentally infected with Bd we also tested the in vivo antifungal efficacy of X. szentirmaii CFCM diluted to 2 and 10% (v/v), while also assessing possible malign side effects on amphibians. Results of the in vitro experiment documented highly effective growth inhibition by CFCMs of both Xenorhabdus species. The in vivo experiment showed that treatment with CFCM of X. szentirmaii applied at a dilution of 10% resulted in infection intensities reduced by ca. 73% compared to controls and to juvenile toads treated with CFCM applied at a dilution of 2%. At the same time, we detected no negative side effects of treatment with CFCM on toad survival and development. Our results clearly support the idea that metabolites of X. szentirmaii, and perhaps of several other Xenorhabdus species as well, may prove highly useful for the treatment of Bd infected amphibians.
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Affiliation(s)
- János Ujszegi
- Department of Evolutionary Ecology, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Budapest, Hungary.
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, Hungary.
| | - Zsófia Boros
- Department of Evolutionary Ecology, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - András Fodor
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Balázs Vajna
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Attila Hettyey
- Department of Evolutionary Ecology, Plant Protection Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, Hungary
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31
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Woodhams DC, McCartney J, Walke JB, Whetstone R. The adaptive microbiome hypothesis and immune interactions in amphibian mucus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 145:104690. [PMID: 37001710 PMCID: PMC10249470 DOI: 10.1016/j.dci.2023.104690] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 05/20/2023]
Abstract
The microbiome is known to provide benefits to hosts, including extension of immune function. Amphibians are a powerful immunological model for examining mucosal defenses because of an accessible epithelial mucosome throughout their developmental trajectory, their responsiveness to experimental treatments, and direct interactions with emerging infectious pathogens. We review amphibian skin mucus components and describe the adaptive microbiome as a novel process of disease resilience where competitive microbial interactions couple with host immune responses to select for functions beneficial to the host. We demonstrate microbiome diversity, specificity of function, and mechanisms for memory characteristic of an adaptive immune response. At a time when industrialization has been linked to losses in microbiota important for host health, applications of microbial therapies such as probiotics may contribute to immunotherapeutics and to conservation efforts for species currently threatened by emerging diseases.
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Affiliation(s)
- Douglas C Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA.
| | - Julia McCartney
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Jenifer B Walke
- Department of Biology, Eastern Washington University, Cheney, WA, 99004-2440, USA
| | - Ross Whetstone
- Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA
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32
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Siomko SA, Greenspan SE, Barnett KM, Neely WJ, Chtarbanova S, Woodhams DC, McMahon TA, Becker CG. Selection of an anti-pathogen skin microbiome following prophylaxis treatment in an amphibian model system. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220126. [PMID: 37305917 PMCID: PMC10258671 DOI: 10.1098/rstb.2022.0126] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/03/2022] [Indexed: 06/13/2023] Open
Abstract
With emerging diseases on the rise, there is an urgent need to identify and understand novel mechanisms of prophylactic protection in vertebrate hosts. Inducing resistance against emerging pathogens through prophylaxis is an ideal management strategy that may impact pathogens and their host-associated microbiome. The host microbiome is recognized as a critical component of immunity, but the effects of prophylactic inoculation on the microbiome are unknown. In this study, we investigate the effects of prophylaxis on host microbiome composition, focusing on the selection of anti-pathogenic microbes contributing to host acquired immunity in a model host-fungal disease system, amphibian chytridiomycosis. We inoculated larval Pseudacris regilla against the fungal pathogen Batrachochytrium dendrobatidis (Bd) with a Bd metabolite-based prophylactic. Increased prophylactic concentration and exposure duration were associated with significant increases in proportions of putatively Bd-inhibitory host-associated bacterial taxa, indicating a protective prophylactic-induced shift towards microbiome members that are antagonistic to Bd. Our findings are in accordance with the adaptive microbiome hypothesis, where exposure to a pathogen alters the microbiome to better cope with subsequent pathogen encounters. Our study advances research on the temporal dynamics of microbiome memory and the role of prophylaxis-induced shifts in microbiomes contributing to prophylaxis effectiveness. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
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Affiliation(s)
- Samantha A. Siomko
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Sasha E. Greenspan
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - K. M. Barnett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Wesley J. Neely
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | | | - Douglas C. Woodhams
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Taegan A. McMahon
- Department of Biology, Connecticut College, New London, CT 06320, USA
| | - C. Guilherme Becker
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, One Health Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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Gajewski Z, Johnson LR, Medina D, Crainer WW, Nagy CM, Belden LK. Skin bacterial community differences among three species of co-occurring Ranid frogs. PeerJ 2023; 11:e15556. [PMID: 37465150 PMCID: PMC10351513 DOI: 10.7717/peerj.15556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/23/2023] [Indexed: 07/20/2023] Open
Abstract
Skin microbial communities are an essential part of host health and can play a role in mitigating disease. Host and environmental factors can shape and alter these microbial communities and, therefore, we need to understand to what extent these factors influence microbial communities and how this can impact disease dynamics. Microbial communities have been studied in amphibian systems due to skin microbial communities providing some resistance to the amphibian chytrid fungus, Batrachochytrium dendrobatidis. However, we are only starting to understand how host and environmental factors shape these communities for amphibians. In this study, we examined whether amphibian skin bacterial communities differ among host species, host infection status, host developmental stage, and host habitat. We collected skin swabs from tadpoles and adults of three Ranid frog species (Lithobates spp.) at the Mianus River Gorge Preserve in Bedford, New York, USA, and used 16S rRNA gene amplicon sequencing to determine bacterial community composition. Our analysis suggests amphibian skin bacterial communities change across host developmental stages, as has been documented previously. Additionally, we found that skin bacterial communities differed among Ranid species, with skin communities on the host species captured in streams or bogs differing from the communities of the species captured on land. Thus, habitat use of different species may drive differences in host-associated microbial communities for closely-related host species.
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Affiliation(s)
- Zachary Gajewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
| | - Leah R. Johnson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
- Department of Statistics, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
| | - Daniel Medina
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
| | - William W. Crainer
- Department of Animal Sciences, Cornell University, Ithaca, New York, United States
| | | | - Lisa K. Belden
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
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West AG, Digby A, Taylor MW, Kākāpō Recovery Team, Kākāpō Aspergillosis Research Consortium. The mycobiota of faeces from the critically endangered kākāpō and associated nest litter. NEW ZEALAND JOURNAL OF ZOOLOGY 2023. [DOI: 10.1080/03014223.2023.2170428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Annie G. West
- Te Kura Mātauranga Koiora School of Biological Sciences, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
| | - Andrew Digby
- Te Papa Atawhai Department of Conservation, Kākāpō Recovery Programme, Invercargill, New Zealand
| | - Michael W. Taylor
- Te Kura Mātauranga Koiora School of Biological Sciences, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
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Kaganer AW, Ossiboff RJ, Keith NI, Schuler KL, Comizzoli P, Hare MP, Fleischer RC, Gratwicke B, Bunting EM. Immune priming prior to pathogen exposure sheds light on the relationship between host, microbiome and pathogen in disease. ROYAL SOCIETY OPEN SCIENCE 2023; 10:220810. [PMID: 36756057 PMCID: PMC9890126 DOI: 10.1098/rsos.220810] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Dynamic interactions between host, pathogen and host-associated microbiome dictate infection outcomes. Pathogens including Batrachochytrium dendrobatidis (Bd) threaten global biodiversity, but conservation efforts are hindered by limited understanding of amphibian host, Bd and microbiome interactions. We conducted a vaccination and infection experiment using Eastern hellbender salamanders (Cryptobranchus alleganiensis alleganiensis) challenged with Bd to observe infection, skin microbial communities and gene expression of host skin, pathogen and microbiome throughout the experiment. Most animals survived high Bd loads regardless of their vaccination status and vaccination did not affect pathogen load, but host gene expression differed based on vaccination. Oral vaccination (exposure to killed Bd) stimulated immune gene upregulation while topically and sham-vaccinated animals did not significantly upregulate immune genes. In early infection, topically vaccinated animals upregulated immune genes but orally and sham-vaccinated animals downregulated immune genes. Bd increased pathogenicity-associated gene expression in late infection when Bd loads were highest. The microbiome was altered by Bd, but there was no correlation between anti-Bd microbe abundance or richness and pathogen burden. Our observations suggest that hellbenders initially generate a vigorous immune response to Bd, which is ineffective at controlling disease and is subsequently modulated. Interactions with antifungal skin microbiota did not influence disease progression.
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Affiliation(s)
- Alyssa W. Kaganer
- Department of Natural Resources and the Environment, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
| | - Robert J. Ossiboff
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Nicole I. Keith
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Biology Department, Hamilton College, Clinton, NY, 13323, USA
| | - Krysten L. Schuler
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Pierre Comizzoli
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Matthew P. Hare
- Department of Natural Resources and the Environment, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Robert C. Fleischer
- Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Brian Gratwicke
- Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, 22630, USA
| | - Elizabeth M. Bunting
- Cornell Wildlife Health Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, 14853, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
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Su R, Zhang S, Zhang X, Wang S, Zhang W. Neglected skin-associated microbial communities: a unique immune defense strategy of Bufo raddei under environmental heavy metal pollution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:22330-22342. [PMID: 36284045 DOI: 10.1007/s11356-022-23803-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Amphibians defend against pathogens using skin microbial communities, in addition to innate and adaptive immunity. Despite skin microbial communities play a key role in the immune function of amphibians, few studies have focused on the changes in its composition and function. In the present study, we identified the variation in adaptive immunity, as well as the corresponding changes in skin microbiome of Bufo raddei living in a heavy metal polluted area. The adaptive immunity of B. raddei in heavy metal polluted area was significantly lower than that in relatively unpolluted area. Further, different skin bacterial communities were found in the two areas. In the heavy metal polluted area, Actinobacteria and Microbacterium were the dominant bacteria in the skin microbiome of B. raddei, which showed broad-spectrum antibacterial activity. Besides, the antibiotic synthesis was also increased in metabolic pathways. The present study suggested that the adaptive immunity of B. raddei was weakened under long-term heavy metal stress. However, the toads increased the abundance of bacteriostatic bacteria by regulating the composition of skin microbiome, which released a large number of bacteriostatic metabolites and enhanced the host resistance to external pathogens in turn.
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Affiliation(s)
- Rui Su
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Sheng Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xueying Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Shengnan Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wenya Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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Goodwin KB, Hutchinson JD, Gompert Z. Spatiotemporal and ontogenetic variation, microbial selection, and predicted Bd-inhibitory function in the skin-associated microbiome of a Rocky Mountain amphibian. Front Microbiol 2022; 13:1020329. [PMID: 36583053 PMCID: PMC9792605 DOI: 10.3389/fmicb.2022.1020329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Host-associated microbiomes play important roles in host health and pathogen defense. In amphibians, the skin-associated microbiota can contribute to innate immunity with potential implications for disease management. Few studies have examined season-long temporal variation in the amphibian skin-associated microbiome, and the interactions between bacteria and fungi on amphibian skin remain poorly understood. We characterize season-long temporal variation in the skin-associated microbiome of the western tiger salamander (Ambystoma mavortium) for both bacteria and fungi between sites and across salamander life stages. Two hundred seven skin-associated microbiome samples were collected from salamanders at two Rocky Mountain lakes throughout the summer and fall of 2018, and 127 additional microbiome samples were collected from lake water and lake substrate. We used 16S rRNA and ITS amplicon sequencing with Bayesian Dirichlet-multinomial regression to estimate the relative abundances of bacterial and fungal taxa, test for differential abundance, examine microbial selection, and derive alpha diversity. We predicted the ability of bacterial communities to inhibit the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), a cutaneous fungal pathogen, using stochastic character mapping and a database of Bd-inhibitory bacterial isolates. For both bacteria and fungi, we observed variation in community composition through time, between sites, and with salamander age and life stage. We further found that temporal trends in community composition were specific to each combination of salamander age, life stage, and lake. We found salamander skin to be selective for microbes, with many taxa disproportionately represented relative to the environment. Salamander skin appeared to select for predicted Bd-inhibitory bacteria, and we found a negative relationship between the relative abundances of predicted Bd-inhibitory bacteria and Bd. We hope these findings will assist in the conservation of amphibian species threatened by chytridiomycosis and other emerging diseases.
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Affiliation(s)
- Kenen B. Goodwin
- Department of Watershed Sciences, Utah State University, Logan, UT, United States
- Department of Wildland Resources, Utah State University, Logan, UT, United States
| | - Jaren D. Hutchinson
- Department of Wildland Resources, Utah State University, Logan, UT, United States
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, UT, United States
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Martínez-Ugalde E, Ávila-Akerberg V, González Martínez TM, Vázquez Trejo M, Zavala Hernández D, Anaya-Morales SL, Rebollar EA. The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection. Anim Microbiome 2022; 4:63. [PMID: 36503640 PMCID: PMC9743558 DOI: 10.1186/s42523-022-00215-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/16/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome. RESULTS We found that the skin bacterial communities of the axolotl A. altamirani are largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although relative abundance of particular bacteria were correlated with Bd infection intensity. CONCLUSIONS Our work shows that metamorphosis is a crucial process that shapes skin bacterial communities and that axolotls under different developmental stages respond differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).
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Affiliation(s)
| | - Víctor Ávila-Akerberg
- Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico
| | | | | | | | - Sara Lucia Anaya-Morales
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
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Adams AJ, Bushell J, Grasso RL. To treat or not to treat? Experimental pathogen exposure, treatment, and release of a threatened amphibian. Ecosphere 2022. [DOI: 10.1002/ecs2.4294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Andrea J. Adams
- Resources Management and Science Division Yosemite National Park El Portal California USA
- Earth Research Institute University of California Santa Barbara California USA
| | | | - Robert L. Grasso
- Resources Management and Science Division Yosemite National Park El Portal California USA
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40
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Bates KA, Friesen J, Loyau A, Butler H, Vredenburg VT, Laufer J, Chatzinotas A, Schmeller DS. Environmental and Anthropogenic Factors Shape the Skin Bacterial Communities of a Semi-Arid Amphibian Species. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02130-5. [PMID: 36445401 DOI: 10.1007/s00248-022-02130-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
The amphibian skin microbiome is important in maintaining host health, but is vulnerable to perturbation from changes in biotic and abiotic conditions. Anthropogenic habitat disturbance and emerging infectious diseases are both potential disrupters of the skin microbiome, in addition to being major drivers of amphibian decline globally. We investigated how host environment (hydrology, habitat disturbance), pathogen presence, and host biology (life stage) impact the skin microbiome of wild Dhofar toads (Duttaphrynus dhufarensis) in Oman. We detected ranavirus (but not Batrachochytrium dendrobatidis) across all sampling sites, constituting the first report of this pathogen in Oman, with reduced prevalence in disturbed sites. We show that skin microbiome beta diversity is driven by host life stage, water source, and habitat disturbance, but not ranavirus infection. Finally, although trends in bacterial diversity and differential abundance were evident in disturbed versus undisturbed sites, bacterial co-occurrence patterns determined through network analyses revealed high site specificity. Our results therefore provide support for amphibian skin microbiome diversity and taxa abundance being associated with habitat disturbance, with bacterial co-occurrence (and likely broader aspects of microbial community ecology) being largely site specific.
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Affiliation(s)
- K A Bates
- Department of Zoology, University of Oxford, Oxford, UK.
| | - J Friesen
- Centre for Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - A Loyau
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Stechlin, Germany
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, INPT, UPS, Toulouse, France
| | - H Butler
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - V T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - J Laufer
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - A Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - D S Schmeller
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, INPT, UPS, Toulouse, France
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Nie P, Feng J. Global niche and range shifts of Batrachochytrium dendrobatidis, a highly virulent amphibian-killing fungus. Fungal Biol 2022; 126:809-816. [PMID: 36517148 DOI: 10.1016/j.funbio.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 01/07/2023]
Abstract
Batrachochytrium dendrobatidis (Bd) is one of the world's most invasive species, and is responsible for chytridiomycosis, an emerging infectious disease that has caused huge losses of global amphibian biodiversity. Few studies have investigated invasive Bd's niche and range relative to those of native Bd. In the present study, we applied niche and range dynamic models to investigate global niche and range dynamics between native and invasive Bd. Invasive Bd occupied wider and different niche positions than did native Bd. Additionally, invasive Bd was observed in hotter, colder, wetter, drier, and more labile climatic conditions. Contrast to most relevant studies presuming Bd's niche remaining stable, we found that invasive Bd rejected niche conservatism hypotheses, suggesting its high lability in niche, and huge invasion potential. Bd's niche non-conservatism may result in range lability, and small niche expansions could induce large increases in range. Niche shifts may therefore be a more sensitive indicator of invasion than are range shifts. Our findings indicate that Bd is a high-risk invasive fungus not only due to its high infection and mortality rates, but also due to its high niche and range lability, which enhance its ability to adapt to novel climatic conditions. Therefore, invasive Bd should be a high-priority focus species in strategizing against biological invasions.
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Affiliation(s)
- Peixiao Nie
- Department of Life Science and Agronomy, Dali University, Dali, 671003, China
| | - Jianmeng Feng
- Department of Life Science and Agronomy, Dali University, Dali, 671003, China.
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42
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Ophidiomyces ophidiicola detection and infection: a global review on a potential threat to the world’s snake populations. EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-022-01612-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractOphidiomyces ophidiicola (Oo) is one of the most relevant fungal pathogens for snakes. It is the etiological agent of ophidiomycosis, an emerging disease causing dysecdysis, skin abnormalities, crusting cutaneous lesions, and ulcerations. Despite this major tegumentary “tropism”, Oo infection can be systemic and it is capable of inducing visceral lesions. Moreover, ophidiomycosis may lead to abnormalities of reproductive physiology, hunting behavior, and thermoregulation, thus increasing the risks of sublethal effects and predation on affected snakes. Oo seems horizontally transmitted and can induce postnatal mortality. This article reviews published data on Oo detection and infection in all snake species in countries around the world and categorizes these data using new classification parameters. The presence of this fungus has been recorded in 11 states (considering the USA as a whole); however, in four states, the mycosis has only been reported in snakes held in captivity. Detection and/or infection of Oo has been ascertained in 62 snake species, divided into nine families. The taxa have been categorized with diagnostic criteria in order to report, for each species, the highest rank of categorization resulting from all cases. Therefore, 20 species have been included within the class “Ophidiomycosis and Oo shedder”, 11 within “Ophidiomycosis”, 16 in “Apparent ophidiomycosis”, and 15 within “Ophidiomyces ophidiicola present”. We also discuss the significance and limits of case classifications and Oo’s impact on wild populations, and we suggest methods for preliminary surveillance. Standardized methods, interdisciplinary studies, and cooperation between various research institutions may facilitate further Oo screening studies, elucidate the unclear aspects of the disease, and protect ophidiofauna from this emerging threat at the global level.
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Schmeller DS, Cheng T, Shelton J, Lin CF, Chan-Alvarado A, Bernardo-Cravo A, Zoccarato L, Ding TS, Lin YP, Swei A, Fisher MC, Vredenburg VT, Loyau A. Environment is associated with chytrid infection and skin microbiome richness on an amphibian rich island (Taiwan). Sci Rep 2022; 12:16456. [PMID: 36180528 PMCID: PMC9525630 DOI: 10.1038/s41598-022-20547-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
Growing evidence suggests that the origins of the panzootic amphibian pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are in Asia. In Taiwan, an island hotspot of high amphibian diversity, no amphibian mass mortality events linked to Bd or Bsal have been reported. We conducted a multi-year study across this subtropical island, sampling 2517 individuals from 30 species at 34 field sites, between 2010 and 2017, and including 171 museum samples collected between 1981 and 2009. We analyzed the skin microbiome of 153 samples (6 species) from 2017 in order to assess any association between the amphibian skin microbiome and the probability of infection amongst different host species. We did not detect Bsal in our samples, but found widespread infection by Bd across central and northern Taiwan, both taxonomically and spatially. Museum samples show that Bd has been present in Taiwan since at least 1990. Host species, geography (elevation), climatic conditions and microbial richness were all associated with the prevalence of infection. Host life-history traits, skin microbiome composition and phylogeny were associated with lower prevalence of infection for high altitude species. Overall, we observed low prevalence and burden of infection in host populations, suggesting that Bd is enzootic in Taiwan where it causes subclinical infections. While amphibian species in Taiwan are currently threatened by habitat loss, our study indicates that Bd is in an endemic equilibrium with the populations and species we investigated. However, ongoing surveillance of the infection is warranted, as changing environmental conditions may disturb the currently stable equilibrium.
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Affiliation(s)
- Dirk S Schmeller
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, INPT, UPS, Toulouse, France
| | - Tina Cheng
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
- Bat Conservation International, Washington, DC, USA
| | - Jennifer Shelton
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | - Chun-Fu Lin
- Zoology Division, Endemic Species Research Institute, Jiji, Nantou, Taiwan, ROC
| | - Alan Chan-Alvarado
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Adriana Bernardo-Cravo
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, INPT, UPS, Toulouse, France
| | - Luca Zoccarato
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhütte 2, 16775, Stechlin, Germany
| | - Tzung-Su Ding
- School of Forestry and Resource Conservation, National Taiwan University, Taipei City, 106, Taiwan, ROC
| | - Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan, ROC
| | - Andrea Swei
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Adeline Loyau
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, INPT, UPS, Toulouse, France.
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhütte 2, 16775, Stechlin, Germany.
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Salazar-Hamm PS, Montoya KN, Montoya L, Cook K, Liphardt S, Taylor JW, Cook JA, Natvig DO. Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:996574. [PMID: 37746221 PMCID: PMC10512277 DOI: 10.3389/ffunb.2022.996574] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/24/2022] [Indexed: 09/26/2023]
Abstract
Human lung mycobiome studies typically sample bronchoalveolar lavage or sputum, potentially overlooking fungi embedded in tissues. Employing ultra-frozen lung tissues from biorepositories, we obtained fungal ribosomal RNA ITS2 sequences from 199 small mammals across 39 species. We documented diverse fungi, including common environmental fungi such as Penicillium and Aspergillus, associates of the human mycobiome such as Malassezia and Candida, and others specifically adapted for lungs (Coccidioides, Blastomyces, and Pneumocystis). Pneumocystis sequences were detected in 83% of the samples and generally exhibited phylogenetic congruence with hosts. Among sequences from diverse opportunistic pathogens in the Onygenales, species of Coccidioides occurred in 12% of samples and species of Blastomyces in 85% of samples. Coccidioides sequences occurred in 14 mammalian species. The presence of neither Coccidioides nor Aspergillus fumigatus correlated with substantial shifts in the overall mycobiome, although there was some indication that fungal communities might be influenced by high levels of A. fumigatus. Although members of the Onygenales were common in lung samples (92%), they are not common in environmental surveys. Our results indicate that Pneumocystis and certain Onygenales are common commensal members of the lung mycobiome. These results provide new insights into the biology of lung-inhabiting fungi and flag small mammals as potential reservoirs for emerging fungal pathogens.
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Affiliation(s)
| | - Kyana N. Montoya
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Liliam Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Kel Cook
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Schuyler Liphardt
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Joseph A. Cook
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, United States
| | - Donald O. Natvig
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
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45
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Snelders NC, Rovenich H, Thomma BPHJ. Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom. FEMS Microbiol Rev 2022; 46:fuac022. [PMID: 35604874 PMCID: PMC9438471 DOI: 10.1093/femsre/fuac022] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Fungi are well-known decomposers of organic matter that thrive in virtually any environment on Earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review, we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals but also beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.
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Affiliation(s)
- Nick C Snelders
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Hanna Rovenich
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
| | - Bart P H J Thomma
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
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46
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Rajarajan A, Wolinska J, Walser JC, Mäder M, Spaak P. Infection by a eukaryotic gut parasite in wild Daphnia sp. associates with a distinct bacterial community. FEMS Microbiol Ecol 2022; 98:6677393. [PMID: 36026529 PMCID: PMC9869925 DOI: 10.1093/femsec/fiac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/04/2022] [Accepted: 08/23/2022] [Indexed: 01/26/2023] Open
Abstract
Host-associated bacterial communities play an important role in host fitness and resistance to diseases. Yet, few studies have investigated tripartite interaction between a host, parasite and host-associated bacterial communities in natural settings. Here, we use 16S rRNA gene amplicon sequencing to compare gut- and body- bacterial communities of wild water fleas belonging to the Daphnia longispina complex, between uninfected hosts and those infected with the common and virulent eukaryotic gut parasite Caullerya mesnili (Family: Ichthyosporea). We report community-level changes in host-associated bacteria with the presence of the parasite infection; namely decreased alpha diversity and increased beta diversity at the site of infection, i.e. host gut (but not host body). We also report decreased abundance of bacterial taxa proposed elsewhere to be beneficial for the host, and an appearance of taxa specifically associated with infected hosts. Our study highlights the host-microbiota-infection link in a natural system and raises questions about the role of host-associated microbiota in natural disease epidemics as well as the functional roles of bacteria specifically associated with infected hosts.
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Affiliation(s)
- Amruta Rajarajan
- Corresponding author: Office BU-G09, Überlandstrasse 133, 8600 Dübendorf, Zürich, Switzerland. E-mail: and
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany,Department of Biology, Chemistry, Pharmacy, Institut für Biologie, Freie Universität Berlin (FU), 14195 Berlin, Germany
| | - Jean-Claude Walser
- Department of Environmental systems science (D-USYS), Genetic Diversity Centre (GDC), Federal Institute of Technology (ETH) Zürich, 8092, Zürich, Switzerland
| | - Minea Mäder
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Zürich, Switzerland
| | - Piet Spaak
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Zürich, Switzerland
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Ienes-Lima J, Prichula J, Abadie M, Borges-Martins M, Frazzon APG. First Report of Culturable Skin Bacteria in Melanophryniscus admirabilis (Admirable Redbelly Toad). MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02069-7. [PMID: 35859070 DOI: 10.1007/s00248-022-02069-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Melanophryniscus admirabilis is a small toad, critically endangered with a microendemic distribution in the Atlantic Forest in southern Brazil. The amphibian skin microbiome is considered one of the first lines of defense against pathogenic infections, such as Batrachochytrium dendrobatidis (Bd). The knowledge of skin amphibian microbiomes is important to numerous fields, including species conservation, detection, and quantification of environmental changes and stressors. In the present study, we investigated, for the first time, cultivable bacteria in the skin of wild M. admirabilis, and detected Bd fungus by nested polymerase chain reaction (PCR) technique. Skin swab samples were collected from 15 wild M. admirabilis, and the isolation of bacteria was performed by means of different culture strategies. A total of 62 bacterial isolates being Bacillus (n = 22; 34.48%), Citrobacter (n = 10; 16.13%), and Serratia (n = 12; 19.35%) were more frequently isolated genera. Interestingly, all skin samples tested were Bd negative. Some bacterial genera identified in our study might be acting in a synergic relationship and protecting them against the Bd fungus. In addition, these bacteria may play an essential role in maintaining this species in an environment modulated by anthropic actions. This first report of skin cultivable bacteria from M. admirabilis natural population improves our knowledge of skin amphibian microbiomes, contributing to a better understanding of their ecology and how this species has survived in an environment modulated by anthropic action.
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Affiliation(s)
- Julia Ienes-Lima
- Post-Graduation Program in Agricultural and Environmental Microbiology, Department of Microbiology, Immunology, and Parasitology, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Janira Prichula
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Michelle Abadie
- Post-Graduation Program in Animal Biology, Department of Zoology, Biosciences Institute, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Márcio Borges-Martins
- Post-Graduation Program in Animal Biology, Department of Zoology, Biosciences Institute, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Ana Paula Guedes Frazzon
- Post-Graduation Program in Agricultural and Environmental Microbiology, Department of Microbiology, Immunology, and Parasitology, Federal University of Rio Grande Do Sul, Porto Alegre, Brazil.
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McKnight DT, Huerlimann R, Bower DS, Schwarzkopf L, Alford RA, Zenger KR. The interplay of fungal and bacterial microbiomes on rainforest frogs following a disease outbreak. Ecosphere 2022. [DOI: 10.1002/ecs2.4037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Donald T. McKnight
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Roger Huerlimann
- College of Science and Engineering James Cook University Townsville Queensland Australia
- Marine Climate Change Unit Okinawa Institute of Science and Technology Onnason Okinawa Japan
| | - Deborah S. Bower
- College of Science and Engineering James Cook University Townsville Queensland Australia
- School of Environmental and Rural Science University of New England Armidale New South Wales Australia
| | - Lin Schwarzkopf
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Ross A. Alford
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Kyall R. Zenger
- College of Science and Engineering James Cook University Townsville Queensland Australia
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García-Sánchez JC, Arredondo-Centeno J, Segovia-Ramírez MG, Tenorio Olvera AM, Parra-Olea G, Vredenburg VT, Rovito SM. Factors Influencing Bacterial and Fungal Skin Communities of Montane Salamanders of Central Mexico. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02049-x. [PMID: 35705744 DOI: 10.1007/s00248-022-02049-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Host microbial communities are increasingly seen as an important component of host health. In amphibians, the first land vertebrates that are threatened by a fungal skin disease globally, our understanding of the factors influencing the microbiome of amphibian skin remains incomplete because recent studies have focused almost exclusively on bacteria, and little information exists on fungal communities associated with wild amphibian species. In this study, we describe the effects of host phylogeny, climate, geographic distance, and infection with a fungal pathogen on the composition and structure of bacterial and fungal communities in seven tropical salamander species that occur in the Trans-Mexican Volcanic Belt of Central Mexico. We find that host phylogenetic relatedness is correlated with bacterial community composition while a composite climatic variable of temperature seasonality and precipitation is significantly associated with fungal community composition. We also estimated co-occurrence networks for bacterial and fungal taxa and found differences in the degree of connectivity and the distribution of negative associations between the two networks. Our results suggest that different factors may be responsible for structuring the bacterial and fungal communities of amphibian skin and that the inclusion of fungi in future studies could shed light on important functional interactions within the microbiome.
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Affiliation(s)
- Julio César García-Sánchez
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - José Arredondo-Centeno
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
- Instituto Tecnológico Superior de Irapuato, Irapuato, Guanajuato, México
| | - María Guadalupe Segovia-Ramírez
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Ariadna Marcela Tenorio Olvera
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
- Instituto Tecnológico Superior de Irapuato, Irapuato, Guanajuato, México
| | - Gabriela Parra-Olea
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Vance T Vredenburg
- Department of Biology, San Francisco State University, San Francisco, CA, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Sean M Rovito
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México.
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50
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Forsythe A, Fontaine N, Bissonnette J, Hayashi B, Insuk C, Ghosh S, Kam G, Wong A, Lausen C, Xu J, Cheeptham N. Microbial isolates with Anti-Pseudogymnoascus destructans activities from Western Canadian bat wings. Sci Rep 2022; 12:9895. [PMID: 35701553 PMCID: PMC9198084 DOI: 10.1038/s41598-022-14223-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/02/2022] [Indexed: 11/29/2022] Open
Abstract
Pseudogymnoascus destructans (Pd) is the causative agent of white-nose syndrome, which has resulted in the death of millions of bats in North America (NA) since 2006. Based on mortalities in eastern NA, the westward spread of infections likely poses a significant threat to western NA bats. To help prevent/reduce Pd infections in bats in western NA, we isolated bacteria from the wings of wild bats and screened for inhibitory activity against Pd. In total, we obtained 1,362 bacterial isolates from 265 wild bats of 13 species in western Canada. Among the 1,362 isolates, 96 showed inhibitory activity against Pd based on a coculture assay. The inhibitory activities varied widely among these isolates, ranging from slowing fungal growth to complete inhibition. Interestingly, host bats containing isolates with anti-Pd activities were widely distributed, with no apparent geographic or species-specific pattern. However, characteristics of roosting sites and host demography showed significant associations with the isolation of anti-Pd bacteria. Specifically, anthropogenic roosts and swabs from young males had higher frequencies of anti-Pd bacteria than those from natural roosts and those from other sex and age-groups, respectively. These anti-Pd bacteria could be potentially used to help mitigate the impact of WNS. Field trials using these as well as additional microbes from future screenings are needed in order to determine their effectiveness for the prevention and treatment against WNS.
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Affiliation(s)
- Adrian Forsythe
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Nick Fontaine
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Julianna Bissonnette
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Brandon Hayashi
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Chadabhorn Insuk
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada.,Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Soumya Ghosh
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada.,Department of Genetics, Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Gabrielle Kam
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Aaron Wong
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Cori Lausen
- Wildlife Conservation Society Canada, P.O. Box 606, Kaslo, BC, V0G 1M0, Canada.
| | - Jianping Xu
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada.
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