Genetic similarity enhances the strength of the relationship between gut bacteria and host DNA methylation

Abstract

Factors such as host age, sex, diet, health status and genotype constitute the environmental envelope shaping microbial communities in the host’s gut. It has also been proposed that gut microbiota may be influenced by host epigenetics. Although the relationship between the host’s genotype/epigenotype and its associated microbiota has been the focus of a number of recent studies, the relative importance of these interactions and their biological relevance are still poorly understood. We used methylation-sensitive genotyping by sequencing to genotype and epigenotype invasive cane toads (Rhinella marina) from the species’ Australian range-core (three sites) and the invasion-front (three sites), and 16S rRNA gene sequencing to characterize their gut bacterial communities. We tested the effect of host genotype and epigenotype (i.e., methylome) on gut bacterial communities. Our results indicate that the genotypes, epigenotypes and gut communities of the range-core and invasion-front are significantly different from one another. We found a positive association between host pairwise genetic and epigenetic distances. More importantly, a positive relationship was found between the host’s epigenetic and gut bacterial pairwise distances. Interestingly, this association was stronger in individuals with low genetic differentiation. Our findings suggest that in range-expanding populations, where individuals are often genetically similar, the interaction between gut bacterial communities and host methylome may provide a mechanism through which invaders increase the plasticity of their response to novel environments, potentially increasing their invasion success.

Maternal body condition affects the response of larval spined toads’ faecal microbiome to a widespread contaminant

“…forest sites, see Tartu et al (2022)), and that their gut bacterial composition would be more sensitive to AMPA-exposure, however maternal body-condition was not related to habitat (agricultural vs. forested, LME estimate: -2.31 ± 3.69, p = 0.538). The observed relationships underline the dependence of the gut microbiome on interactions among other deterministic factors that were not accounted for in this study, such as host genetic and epigenetic background, age, diet or other environmental stressors (Chen et al, 2022; Shu et al, 2019; Song et al, 2021; Zhou et al, 2021). Nevertheless, we were able to identify a modification of the abundance of two major phyla in tadpoles gut microbiota, Bacteroidota and Actinobacteriota, which varied according to both maternal body conditionand AMPA exposure.…”

The gut bacteria of an invasive amphibian respond to the dual challenges of range-expansion and parasite attack

“…Predicted bacterial functions better explained cane toad righting behaviour than did gut bacterial community composition. Intriguingly, similarity between gut bacterial communities between individuals within regions in Australia is related to the similarity of their host’s epigenome, and this relationship is strengthened in populations where genetic diversity is lowest, such as on the invasion front [44]. Relationships between gut bacterial communities and their hosts are complex, and that a clear understanding of these relationships requires careful consideration of numerous environmental, host and gut bacterial factors.…”