Geography, Host Genetics, and Cross-Domain Microbial Networks Structure
the Skin Microbiome of Fragmented Brazilian Atlantic Forest Frog
Populations
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.