scholarly journals Seasonal and ontogenetic variation of skin microbial communities and relationships to natural disease dynamics in declining amphibians

2015 ◽  
Vol 2 (7) ◽  
pp. 140377 ◽  
Author(s):  
Ana V. Longo ◽  
Anna E. Savage ◽  
Ian Hewson ◽  
Kelly R. Zamudio
Keyword(s):  
Bacterial Diversity ◽  
Batrachochytrium Dendrobatidis ◽  
Developmental Stages ◽  
Pathogenic Fungus ◽  
Natural Populations ◽  
Amplicon Sequencing ◽  
Protective Role ◽  
Skin Microbiome ◽  
Skin Bacteria

Recently, microbiologists have focused on characterizing the probiotic role of skin bacteria for amphibians threatened by the fungal disease chytridiomycosis. However, the specific characteristics of microbial diversity required to maintain health or trigger disease are still not well understood in natural populations. We hypothesized that seasonal and developmental transitions affecting susceptibility to chytridiomycosis could also alter the stability of microbial assemblages. To test our hypothesis, we examined patterns of skin bacterial diversity in two species of declining amphibians ( Lithobates yavapaiensis and Eleutherodactylus coqui ) affected by the pathogenic fungus Batrachochytrium dendrobatidis ( Bd ). We focused on two important transitions that affect Bd susceptibility: ontogenetic (from juvenile to adult) shifts in E. coqui and seasonal (from summer to winter) shifts in  L. yavapaiensis . We used a combination of community-fingerprinting analyses and 16S rRNA amplicon sequencing to quantify changes in bacterial diversity and assemblage composition between seasons and developmental stages, and to investigate the relationship between bacterial diversity and pathogen load. We found that winter-sampled frogs and juveniles, two states associated with increased Bd susceptibility, exhibited higher diversity compared with summer-sampled frogs and adult individuals. Our findings also revealed that hosts harbouring higher bacterial diversity carried lower Bd infections, providing support for the protective role of bacterial communities. Ongoing work to understand skin microbiome resilience after pathogen disturbance has the potential to identify key taxa involved in disease resistance.

scholarly journals Skin bacteria of rainbow trout antagonistic to the fish pathogen Flavobacterium psychrophilum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mio Takeuchi ◽  
Erina Fujiwara-Nagata ◽  
Taiki Katayama ◽  
Hiroaki Suetake
Keyword(s):  
Rainbow Trout ◽  
Culture Media ◽  
Amplicon Sequencing ◽  
Effective Vaccine ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Fish Disease ◽  
Flavobacterium Psychrophilum ◽  
Skin Bacteria ◽  
Coldwater Disease

AbstractRainbow trout fry syndrome (RTFS) and bacterial coldwater disease (BCWD) is a globally distributed freshwater fish disease caused by Flavobacterium psychrophilum. In spite of its importance, an effective vaccine is not still available. Manipulation of the microbiome of skin, which is a primary infection gate for pathogens, could be a novel countermeasure. For example, increasing the abundance of specific antagonistic bacteria against pathogens in fish skin might be effective to prevent fish disease. Here, we combined cultivation with 16S rRNA gene amplicon sequencing to obtain insight into the skin microbiome of the rainbow trout (Oncorhynchus mykiss) and searched for skin bacteria antagonistic to F. psychrophilum. By using multiple culture media, we obtained 174 isolates spanning 18 genera. Among them, Bosea sp. OX14 and Flavobacterium sp. GL7 respectively inhibited the growth of F. psychrophilum KU190628-78 and NCIMB 1947T, and produced antagonistic compounds of < 3 kDa in size. Sequences related to our isolates comprised 4.95% of skin microbial communities, and those related to strains OX14 and GL7 respectively comprised 1.60% and 0.17% of the skin microbiome. Comparisons with previously published microbiome data detected sequences related to strains OX14 and GL7 in skin of other rainbow trout and Atlantic salmon.

scholarly journals Assessment of the Microbiome Role in Skin Protection Against UV Irradiation Via Network Analysis

2020 ◽  
Vol 11 (3) ◽  
pp. 238-242
Author(s):  
Mohammad Hossein Heidari ◽  
Mohammadreza Razzaghi ◽  
Alireza Akbarzadeh Baghban ◽  
Mohammad Rostami-Nejad ◽  
Mostafa Rezaei-Tavirani ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Uv Irradiation ◽  
Microarray Dataset ◽  
Protective Role ◽  
Skin Microbiome ◽  
Specific Pathogen ◽  
Proteinprotein Interaction ◽  
Centrality Analysis

Introduction: Diverse microbiotas which have some contributions to gene expression reside in human skin. To identify the protective role of the skin microbiome against UV exposure, proteinprotein interaction (PPI) network analysis is used to assessment gene expression alteration. Methods: A microarray dataset, GEO accession number GSE117359, was considered in this respect. Differential expressed genes (DEGs) in the germ-free (GF) and specific pathogen-free (SPF) groups are analyzed by GEO2R. The top significant DEGs were assigned for network analysis via Cytoscape 3.7.2 and its applications. Results: A total of 28 genes were identified as significant DEGs and the centrality analysis of the network indicated that only one of the seven hub-bottlenecks was from queried genes. The gene ontology analysis of Il6, Cxcl2, Cxcl1, TNF, Il10, Cxcl10, and Mmp9 showed that the crucial genes were highly enriched in the immune system. Conclusion: The skin microbiome plays a significant role in the protection of skin against UV irradiation and the role of TNF and IL6 is prominent in this regard.

scholarly journals The Fungicide Chlorothalonil Changes the Amphibian Skin Microbiome: A Potential Factor Disrupting a Host Disease-Protective Trait

2021 ◽  
Vol 1 (1) ◽  
pp. 26-37
Author(s):  
Randall R. Jiménez ◽  
Gilbert Alvarado ◽  
Clemens Ruepert ◽  
Erick Ballestero ◽  
Simone Sommer
Keyword(s):  
Batrachochytrium Dendrobatidis ◽  
Bacterial Community Composition ◽  
Model Organism ◽  
Amplicon Sequencing ◽  
Anthropogenic Factors ◽  
Skin Microbiome ◽  
Amphibian Skin ◽  
16S Rrna Amplicon Sequencing ◽  
Potential Factor ◽  
Inhibitory Bacteria

The skin microbiome is an important part of amphibian immune defenses and protects against pathogens such as the chytrid fungus Batrachochytrium dendrobatidis (Bd), which causes the skin disease chytridiomycosis. Alteration of the microbiome by anthropogenic factors, like pesticides, can impact this protective trait, disrupting its functionality. Chlorothalonil is a widely used fungicide that has been recognized as having an impact on amphibians, but so far, no studies have investigated its effects on amphibian microbial communities. In the present study, we used the amphibian Lithobates vibicarius from the montane forest of Costa Rica, which now appears to persist despite ongoing Bd-exposure, as an experimental model organism. We used 16S rRNA amplicon sequencing to investigate the effect of chlorothalonil on tadpoles’ skin microbiome. We found that exposure to chlorothalonil changes bacterial community composition, with more significant changes at a higher concentration. We also found that a larger number of bacteria were reduced on tadpoles’ skin when exposed to the higher concentration of chlorothalonil. We detected four presumed Bd-inhibitory bacteria being suppressed on tadpoles exposed to the fungicide. Our results suggest that exposure to a widely used fungicide could be impacting host-associated bacterial communities, potentially disrupting an amphibian protective trait against pathogens.

scholarly journals Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

2018 ◽  
Author(s):  
Pablo de Jesús Suárez-Moo ◽  
Andrew P. Vovides ◽  
M. Patrick Griffith ◽  
Francisco Barona-Gómez ◽  
Angélica Cibrián-Jaramillo
Keyword(s):  
Bacterial Diversity ◽  
Natural Populations ◽  
Amplicon Sequencing ◽  
Botanical Garden ◽  
Taxonomic Composition ◽  
Rrna Gene ◽  
Biological Interactions ◽  
Plant Growth Promoting ◽  
Coralloid Roots ◽  
Root Microbiome

AbstractCycads are among the few plants that have developed specialized roots to host nitrogen-fixing bacteria. We describe the bacterial diversity of the coralloid roots from sevenDioonspecies and their surrounding rhizosphere and soil. Using 16S rRNA gene amplicon sequencing, we found that all coralloid roots are inhabited by a broad diversity of bacterial groups, including cyanobacteria and Rhizobiales among the most abundant groups. The diversity and composition of the endophytes are similar in the six Mexican species ofDioonthat we evaluated, suggesting a recent divergence ofDioonpopulations and/or similar plant-driven restrictions in maintaining the coralloid root microbiome. Botanical garden samples and natural populations have a similar taxonomic composition, although the beta diversity differed between these populations. The rhizosphere surrounding the coralloid root serves as a reservoir and source of mostly diazotroph and plant growth-promoting groups that colonize the coralloid endosphere. In the case of cyanobacteria, the endosphere is enriched withNostocspp andCalothrixspp that are closely related to previously reported symbiont genera in cycads and other early divergent plants. The data reported here provide an in-depth taxonomic characterization of the bacterial community associated with coralloid root microbiome. The functional aspects of the endophytes, their biological interactions, and their evolutionary history are the next research step in this recently discovered diversity within the cycad coralloid root microbiome.

scholarly journals Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity

2016 ◽  
Vol 283 (1839) ◽  
pp. 20161553 ◽  
Author(s):  
Jordan G. Kueneman ◽  
Douglas C. Woodhams ◽  
Reid Harris ◽  
Holly M. Archer ◽  
Rob Knight ◽  
...  
Keyword(s):  
Batrachochytrium Dendrobatidis ◽  
Life Stage ◽  
Skin Microbiome ◽  
Janthinobacterium Lividum ◽  
Probiotic Treatment ◽  
In Captivity ◽  
Boreal Toads ◽  
Inhibitory Bacteria

Host-associated microbiomes perform many beneficial functions including resisting pathogens and training the immune system. Here, we show that amphibians developing in captivity lose substantial skin bacterial diversity, primarily due to reduced ongoing input from environmental sources. We combined studies of wild and captive amphibians with a database of over 1 000 strains that allows us to examine antifungal function of the skin microbiome. We tracked skin bacterial communities of 62 endangered boreal toads, Anaxyrus boreas , across 18 time points, four probiotic treatments, and two exposures to the lethal fungal pathogen Batrachochytrium dendrobatidis ( Bd ) in captivity, and compared these to 33 samples collected from wild populations at the same life stage. As the amphibians in captivity lost the Bd -inhibitory bacteria through time, the proportion of individuals exposed to Bd that became infected rose from 33% to 100% in subsequent exposures. Inoculations of the Bd -inhibitory probiotic Janthinobacterium lividum resulted in a 40% increase in survival during the second Bd challenge, indicating that the effect of microbiome depletion was reversible by restoring Bd -inhibitory bacteria. Taken together, this study highlights the functional role of ongoing environmental inputs of skin-associated bacteria in mitigating a devastating amphibian pathogen, and that long-term captivity decreases this defensive function.

scholarly journals Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection

2021 ◽  
Author(s):  
Milind C. Mutnale ◽  
Gundlapally S. Reddy ◽  
Karthikeyan Vasudevan
Keyword(s):  
Bacterial Community ◽  
Relative Abundance ◽  
Frog Skin ◽  
Batrachochytrium Dendrobatidis ◽  
Bacterial Community Composition ◽  
Skin Microbiome ◽  
Bacterial Phyla ◽  
Frog Species ◽  
Generation Sequencing

AbstractChytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.

The Skin Microbiome in Atopic Dermatitis and Its Relationship to Emollients

2015 ◽  
Vol 20 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Charles W. Lynde ◽  
Anneke Andriessen ◽  
Vince Bertucci ◽  
Catherine McCuaig ◽  
Sandy Skotnicki ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Expert Panel ◽  
Treatment Strategies ◽  
Skin Microbiome ◽  
Microbiome Diversity ◽  
Atopic Skin ◽  
Clinical Dermatology

Background: Human-associated bacterial communities on the skin, skin microbiome, likely play a central role in development of immunity and protection from pathogens. In atopic patients, the skin bacterial diversity is smaller than in healthy subjects. Objective: To review treatment strategies for atopic dermatitis in Canada, taking the skin microbiome concept into account. Methods: An expert panel of 8 Canadian dermatologists explored the role of skin microbiome in clinical dermatology, specifically looking at atopic dermatitis. Results: The panel reached consensus on the following: (1) In atopic patients, the skin microbiome of lesional atopic skin is different from nonlesional skin in adjacent areas. (2) Worsening atopic dermatitis and smaller bacterial diversity are strongly associated. (3) Application of emollients containing antioxidant and antibacterial components may increase microbiome diversity in atopic skin. Conclusion: The skin microbiome may be the next frontier in preventive health and may impact the approach to atopic dermatitis treatment.

scholarly journals Adaptive tolerance to a pathogenic fungus drives major histocompatibility complex evolution in natural amphibian populations

2016 ◽  
Vol 283 (1827) ◽  
pp. 20153115 ◽  
Author(s):  
Anna E. Savage ◽  
Kelly R. Zamudio
Keyword(s):  
Major Histocompatibility Complex ◽  
Mhc Class Ii ◽  
Batrachochytrium Dendrobatidis ◽  
Pathogenic Fungus ◽  
Natural Populations ◽  
Major Histocompatibility ◽  
Evolutionary Potential ◽  
Histocompatibility Complex ◽  
Molecular Signal ◽  
Major Histocompatibility Complex Evolution

Amphibians have been affected globally by the disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis ( Bd ), and we are just now beginning to understand how immunogenetic variability contributes to disease susceptibility. Lineages of an expressed major histocompatibility complex (MHC) class II locus involved in acquired immunity are associated with chytridiomycosis susceptibility in controlled laboratory challenge assays. Here, we extend these findings to natural populations that vary both in exposure and response to Bd . We find that MHC alleles and supertypes associated with Bd survival in the field show a molecular signal of positive selection, while those associated with susceptibility do not, supporting the hypothesis that heritable Bd tolerance is rapidly evolving. We compare MHC supertypes to neutral loci to demonstrate where selection versus demography is shaping MHC variability. One population with Bd tolerance in nature shows a significant signal of directional selection for the same allele (allele Q) that was significantly associated with survival in an earlier laboratory study. Our findings indicate that selective pressure for Bd survival drives rapid immunogenetic adaptation in some natural populations, despite differences in environment and demography. Our field-based analysis of immunogenetic variation confirms that natural amphibian populations have the evolutionary potential to adapt to chytridiomycosis.

The dense indumentum with its polyphenol content may replace the protective role of the epidermis in some young xeromorphic leaves

1996 ◽  
Vol 74 (3) ◽  
pp. 347-351 ◽  
Author(s):  
George Karabourniotis ◽  
Costas Fasseas
Keyword(s):  
Radiation Damage ◽  
Leaf Development ◽  
Olea Europaea ◽  
Quercus Ilex ◽  
Developmental Stages ◽  
Protective Role ◽  
Ultraviolet B ◽  
Young Leaves ◽  
Olea Europaéa

The bright, yellow-green, ammonia-induced fluorescence of polyphenol compounds contained in the nonglandular hairs and within the epidermis of Olea europaea and Quercus ilex leaves was age dependent. Epifluorescence microscopic examination of transverse sections of leaves from both species showed that abaxial and adaxial epidermal layers emitted the characteristic green-yellow bright fluorescence only in late developmental stages, when a considerable decrease of the trichome density had already occurred. At earlier developmental stages, only the dense and thick trichome layer emitted the bright green-yellow fluorescence. In addition, the trichomes of young leaves of Olea and Quercus resembled the glandular ones of other species morphologically and possibly functionally. These findings suggest that the protective role of the trichome against ultraviolet-B radiation damage and (or) other environmental factors is particularly significant during the early stages of leaf development and may be less important at later stages, when the protective role is taken over by the epidermis. Keywords: leaf hairs, phenolics, UV-B radiation damage, leaf development, Olea europaea L., Quercus ilex L.

scholarly journals Bacterial but not protist gut microbiota align with ecological specialization in a set of lower termite species

2016 ◽  
Author(s):  
Lena Waidele ◽  
Judith Korb ◽  
Sven Küenzel ◽  
Franck Dedeine ◽  
Fabian Staubach
Keyword(s):  
Gut Microbiota ◽  
Bacterial Diversity ◽  
Amplicon Sequencing ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ecological Specialization ◽  
Termite Species ◽  
Lower Termite ◽  
Termite Gut

AbstractThe role of microbes in adaptation of higher organisms to the environment is becoming increasingly evident, but remains poorly understood. Protist and bacterial microbes facilitate that lower termites thrive on wood and are directly involved in substrate break down. During the course of evolution lower termites adapted to different diets and lifestyles. In order to test whether there are changes of the termite gut microbiota that co-occur and hence could be related to diet and lifestyle adaptation, we assessed the bacterial and protist communities in a multispecies framework profiling three wood-dwelling and two foraging lower termite species using 16S and 18S rRNA gene amplicon sequencing. Termites were kept under controlled conditions on the same diet to minimize environmental effects on their gut microbiota. We found that protist communities group according to host phylogeny while bacterial communities group according to lifestyle. The change from the ancestral wood-dwelling to a foraging lifestyle coincides with exposure to more diverse and higher concentrations of pathogens as well as a more diverse diet. Accordingly, we identified bacteria that are associated with foraging termites of the genus Reticulitermes and could function as probiotics or be metabolically important on a more diverse diet. Furthermore, protist and bacterial diversity are correlated, suggesting not only that many termite gut bacteria are associated with protists, but also suggesting a role of protist diversity in the evolution of bacterial diversity in the termite gut or vice versa.

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