Microbial Ecology

, Volume 78, Issue 1, pp 257–267 | Cite as

The Influence of Habitat and Phylogeny on the Skin Microbiome of Amphibians in Guatemala and Mexico

  • Silas Ellison
  • Sean RovitoEmail author
  • Gabriela Parra-Olea
  • Carlos Vásquez-Almazán
  • Sandra V. Flechas
  • Ke Bi
  • Vance T. Vredenburg
Host Microbe Interactions


Microbial symbionts are increasingly recognized as playing a critical role in organismal health across a wide range of hosts. Amphibians are unique hosts in that their skin helps to regulate the exchange of water, ions, and gases, and it plays an active role in defense against pathogens through the synthesis of anti-microbial peptides. The microbiome of amphibian skin includes a diverse community of bacteria known to defend against pathogens, including the global pandemic lineage of Batrachochytrium dendrobatidis associated with mass amphibian die-offs. The relative influence of host phylogeny and environment in determining the composition of the amphibian skin microbiome remains poorly understood. We collected skin swabs from montane amphibians in Mexico and Guatemala, focusing on two genera of plethodontid salamanders and one genus of frogs. We used high throughput sequencing to characterize the skin bacterial microbiome and tested the impact of phylogeny and habitat on bacterial diversity. Our results show that phylogenetic history strongly influences the diversity and community structure of the total bacterial microbiome at higher taxonomic levels (between orders), but on lower scales (within genera and species), the effect of habitat predominates. These results add to a growing consensus that habitat exerts a strong effect on microbiome structure and composition, particularly at shallow phylogenetic scales.


Microbiome Amphibian Salamander Habitat Phylogeny Central America 



Funding was provided by UC MEXUS Collaborative Grant #CN-13-614 to G. Parra-Olea and D.B. Wake; NSF #IOS-1258133, and the Belmont Forum project People, Pollution, and Pathogens (P3), NSF 1633948 to V.T. Vredenburg; NSF #DEB-1026396 to R. Bowie and D.B. Wake; and by a Fulbright Colombia “Estudiante Doctoral Colombiano” Scholarship to S.V. Flechas. This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation or the National Institute of Health.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Ethics Statement

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted. The article does not contain any studies with human participants performed by any of the authors.

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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of BiologySan Francisco State UniversitySan FranciscoUSA
  2. 2.Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyUSA
  3. 3.Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuatoMexico
  4. 4.Departamento de Zoología, Insituto de BiologíaUniversidad Nacional Autónoma de MéxicoMéxicoMexico
  5. 5.Museo de Historia Natural y Escuela de BiologíaUniversidad de San CarlosGuatemalaGuatemala
  6. 6.Department of Biological SciencesUniversidad de los AndesBogotáColombia
  7. 7.Instituto de Investigación de Recursos Biológicos Alexander von HumboldtBogotáColombia
  8. 8.Computational Genomics Resource LaboratoryCalifornia Institute for Quantitative Biosciences University of CaliforniaBerkeleyUSA

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