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Geography, Host Genetics, and Cross-Domain Microbial Networks Structure the Skin Microbiome of Fragmented Brazilian Atlantic Forest Frog Populations
  • +2
  • Anat Belasen,
  • Maria Riolo,
  • Mariana Lúcio Lyra,
  • Felipe Toledo,
  • Tim James
Anat Belasen
University of Michigan
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Maria Riolo
University of Michigan
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Mariana Lúcio Lyra
Universidade Estadual Paulista Julio de Mesquita Filho - Campus de Rio Claro
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Felipe Toledo
University of Campinas Institute of Biology
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Tim James
University of Michigan
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Abstract

The host-associated microbiome plays a significant role in health. However, the roles of factors such as host genetics and microbial interactions in determining microbiome diversity remain unclear. We examined these factors using amplicon-based sequencing of 175 Thoropa taophora frog skin swabs collected from a naturally fragmented landscape in southeastern Brazil. Specifically, we examined (1) the effects of geography and host genetics on microbiome diversity and structure; (2) the structure of microbial eukaryotic and bacterial co-occurrence networks; and (3) co-occurrence between microeukaryotes with bacterial OTUs known to affect growth of the fungal frog pathogen Batrachochytrium dendrobatidis (including anti-Bd bacteria commonly referred to as “antifungal”). Microbiome structure correlated with geographic distance, and microbiome diversity varied with both overall host genetic diversity and diversity at the frog MHC IIB immunity locus. Our network analysis showed the highest connectivity when both eukaryotes and bacteria were included, implying that ecological interactions occur among Domains. Lastly, anti-Bd bacteria did not demonstrate broad negative co-occurrence with fungal OTUs in the microbiome, indicating that these bacteria are unlikely to be broadly antifungal. Our findings emphasize the importance of considering both Domains in microbiome research, and suggest that probiotic strategies for amphibian disease management should be considered with caution.

Peer review status:UNDER REVIEW

03 May 2020Submitted to Ecology and Evolution
04 May 2020Submission Checks Completed
04 May 2020Assigned to Editor
05 May 2020Reviewer(s) Assigned
26 May 2020Review(s) Completed, Editorial Evaluation Pending
29 May 2020Editorial Decision: Revise Minor
31 Aug 20201st Revision Received
01 Sep 2020Submission Checks Completed
01 Sep 2020Assigned to Editor
01 Sep 2020Review(s) Completed, Editorial Evaluation Pending
09 Sep 2020Reviewer(s) Assigned