The amphibian microbiome: natural range of variation, pathogenic dysbiosis, and role in conservation

Jiménez, Randall R.; Sommer, Simone

doi:10.1007/s10531-016-1272-x

Cited by 144 publications

(178 citation statements)

References 98 publications

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“…Many diseases (e.g., obesity, diabetes, and autistic disorder) are caused by specific gut microorganisms (Forslund et al, ; Kostic et al, ; Ley et al, ; Mulle, Sharp, & Cubells, ; Turnbaugh et al, ); therefore, a better understanding of the relationship between humans and the gut microbiome would be beneficial for human health and disease treatment. Beyond the application in the treatment of human disease, in recent years, some scientists have considered the application of the gut microbiome in the conservation of endangered animals (Bahrndorff, Alemu, Alemneh, & Lund Nielsen, ; Jiménez & Sommer, ; Redford, Segre, Salafsky, del Rio, & McAloose, ; Stumpf et al, ; Trevelline, Fontaine, Hartup, & Kohl, ; Wei et al, ; Yao, Xu, Lu, & Zhu, ). The scientists first propose the concept of conservation metagenomics, which is along with current methods, major scientific issues and significant implications in the study of host evolution, nutrition, physiology, and ecology and conservation (Wei et al, ).…”

Section: Introductionmentioning

confidence: 99%

Lessons from bamboo‐eating pandas and their gut microbiome: Gut microbiome flow and applications

Zhang

et al. 2020

Evolutionary Applications

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The giant panda is one of the most endangered mammals in the world, and many studies have revealed their evolutionary adaptation to the local environment (e.g., dietary cellulose and cyanide) on the evidences from population genetics and their gut microbiome. Here, based on the results of our analysis of the giant panda gut microbiome, we concluded that instability and resilience are the two primary characteristics of the giant panda gut microbiome. This basic information may have an impact on giant panda conservation, as well the management of other animal species.

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Section: Introductionmentioning

confidence: 99%

Lessons from bamboo‐eating pandas and their gut microbiome: Gut microbiome flow and applications

Zhang

et al. 2020

Evolutionary Applications

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“…Amphibians represent a unique group and are currently experiencing severe population declines and extinctions primarily due to habitat destruction, environmental pollution, overexploitation, and emerging disease spread (Jiang et al, ). Previous research has focused on mitigating a devastating amphibian fungal pathogen, Batrachochytrium dendrobatidis , by focusing on cutaneous bacteria or antimicrobial peptides (Bai, Liu, Fisher, Garner, & Li, ; Briggs, Knapp, & Vredenburg, ; Colston & Jackson, ; Jiménez & Sommer, ; Ley, Hamady, et al, ).…”

Section: Introductionmentioning

confidence: 99%

Age‐related changes in the gut microbiota of the Chinese giant salamander (Andrias davidianus)

et al. 2018

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The composition of the intestinal microbial community may vary across developmental stages. In this study, we explored how this microbial community shifted along the intestinal tract of the Chinese giant salamander ( Andrias davidianus ) at various ages. Next‐generation sequencing was used to sequence the bacterial 16S rRNA gene from different kind of samples, including the stomach, duodenum, ileum, and rectum. The highest mean relative abundance of the bacterial community in the gastrointestinal tract shifted in relation to age: within the first year, Bacteroidetes (47.76%) dominated the gut microbiome, whereas Proteobacteria was the most dominant at age 2 (32.88%) and age 3 (30.78%), and finally, Firmicutes was the most dominant at age 4 (34.70%). The overall richness of the gut bacterial community also generally increased from age 2 to 4. Hierarchical cluster analysis revealed that the gut microbiome at age 2 had greater variability than that at either age 3 or 4, likely representing a shift in diet from yolk or redworms as a juvenile to shrimp or crab as an adult. As these salamanders develop, their gastrointestinal tracts increase in complexity, and this compartmentalization may also facilitate an increase in microbial gut diversity.

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“…These taxa are described as common environmental microbes; however, all three also contain numerous opportunistic pathogenic species that affect humans, animals and plants (Teixeira & Merquior, ; Willems, ). Within amphibians, members of these families are commonly described as part of the skin microbiota (Jiménez & Sommer, ). However, Batrachochytrium dendrobatidis infection can induce a positive response in the abundance of Comamonadaceae , Flavobacteriaceae and Moraxellaceae (Federici et al., ; Jani & Briggs, ; Walke et al., ), and studies recording the effects of captivity on the skin of amphibians have recorded positive responses in members of these families as well (Becker et al.…”

Section: Discussionmentioning

confidence: 99%

“…Our investigation of Missouri hellbender immunogenetics and cutaneous microbiota provided several insights related to the possible link between host traits and the cutaneous microbiome within amphibians. Disentangling the complex association between hosts, parasites and the microbiome is important to understanding the role of skin symbionts on pathogen defence among this class (Jiménez & Sommer, ). Our results support the role of individual host characteristics on the assembly processes of the cutaneous microbiome of amphibians.…”

Section: Discussionmentioning

confidence: 99%

Influence of immunogenetics, sex and body condition on the cutaneous microbial communities of two giant salamanders

2018

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The complex association between hosts and microbial symbionts requires the implementation of multiple approaches to evaluate variation in host physiology. Within amphibians, heterogeneity in immunogenetic traits and cutaneous microbiota is associated with variation in disease resistance. Ozark (Cryptobranchus alleganiensis bishopi) and eastern hellbenders (C. a. alleganiensis) provide a model system to assess variation in host traits and microbial communities. Ozark hellbenders have experienced declines throughout their range, are federally endangered and experience wound retardation that is absent in the eastern subspecies. Previous microbial investigations indicate differentiation in the composition of the skin microbiota of both hellbender subspecies, but it is not clear whether these patterns are concurrent with diversity in the major histocompatibility complex (MHC) genes. We characterized the MHC IIB and the skin microbiota of hellbenders in Missouri, where both subspecies co-occur though not sympatric. We compared the microbiota composition and MHC diversity between both subspecies and investigated whether individual-level MHC diversity, sex and body condition were associated with microbiota composition. Overall, MHC IIB diversity was lower in Ozark hellbenders compared to the eastern subspecies. Multivariate statistical comparisons identified microbiota differentiation between Ozark and eastern hellbenders. MHC IIB allele presence/absence, allele divergence, body composition and sex defined grouping of hellbender microbiotas within populations. Differentiation of the cutaneous microbiotas and MHC IIB genes between eastern and Ozark hellbenders suggests that differences exist in immunity between the two subspecies. This study demonstrates how simultaneous assessments of host genetic traits and microbiotas can inform patterns of microbial community structure in natural systems.

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The amphibian microbiome: natural range of variation, pathogenic dysbiosis, and role in conservation

Cited by 144 publications

References 98 publications

Lessons from bamboo‐eating pandas and their gut microbiome: Gut microbiome flow and applications

Lessons from bamboo‐eating pandas and their gut microbiome: Gut microbiome flow and applications

Age‐related changes in the gut microbiota of the Chinese giant salamander (Andrias davidianus)

Influence of immunogenetics, sex and body condition on the cutaneous microbial communities of two giant salamanders

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