1) Microbially-Mediated Ethanol Sensitivity in Drosophila
In summer of 2015, I joined the labs of Will Ludington and Mike Eisen at UC Berkeley. I am investigating how the microbiome mediates the interaction between animals and ingested toxins, using D. melanogaster and dietary ethanol as a model system. This work has implications for evolutionary biology, as the microbiome may be a factor allowing D. melanogaster to expand its niche to high-ethanol diets (that is, rotting fruit), as well as informing human health since there is a known role of microbes and microbial byproducts in alcoholic liver disease. This work has shown that microbes ameliorate the negative effects of ethanol consumption in D. melanogaster (Chandler et al., preprint). The reproductive output of bacterially-colonized flies remains high with dietary ethanol, while that of bacteria-free flies decreases dramatically. Likewise, I find a significant microbiome-by-ethanol interaction on fly lifespan – it remains constant after ethanol ingestion in bacterially-colonized flies, but decreases in a dose-dependent manner in bacteria-free flies. This suggests that bacteria are masking the negative effect of dietary ethanol. Ongoing research is investigating the mechanisms responsible for these fitness effects, including the role of systemic inflammation, stem cell regeneration, and intestinal barrier failure.
2) Virus Discovery in Mosquitoes
From June 2013 to June 2015, I was a postdoctoral researcher in Shannon Bennett’s lab in the Department of Microbiology at the California Academy of Sciences (a research institution and public museum in Golden Gate Park, San Francisco), I used shotgun metagenomic sequencing, genomic reconstruction, and phylogenetics to discover novel viral lineages in mosquitoes, thus providing insight into how human viral pathogens evolve from animal reservoirs. I uncovered the nearly complete genome of a Bunyavirus from a Thai population of Aedes aegypti (Chandler et al.,_2014). This novel virus is basal to the Phleboviruses (which contains numerous human pathogens) and is missing a gene necessary for virulence in humans. Together, this informs the evolution of pathogenicity within this clade. A subsequent study investigated three species of mosquitoes collected in Northern California and showed that most individual mosquitoes harbored viruses that were closely related to known human pathogens (Chandler et al., 2015). An additional component of this research was to understand how urbanization affects microbial diversity in mosquitoes. We determined that bacterial and eukaryotic microbial communities are less diverse in urban versus rural settings (Thongsripong, Chandler et al., accepted at Ecology and Evolution), whereas viral communities have species-specific host shifts in response to habitat changes (Chandler and Bennett, in prep).
3) Composition and Assembly of the Drosophila microbiome
In June of 2013, I completed my dissertation in the Population Biology Graduate Group at the University of California, Davis. I was advised by Artyom Kopp and my research focused on the microbial communities that are associated with natural Drosophila populations. By investigating Drosophila species that feed upon a variety of natural substrates, I found that diet is the most important factor shaping the Drosophila microbiome and that fruit-, flower-, mushroom-, and cacti-feeding flies harbor different microbial communities (Chandler et al., 2011 and 2012). I showed that bacteria and yeasts have different community structures among fly hosts, suggesting different mechanisms underlying the assembly of these two types of microbial communities (Chandler et al., 2012). I also found that the most common microbes associated with wild Drosophila are only sometimes used in laboratory experiments, suggesting that these experiments may not fully capture natural Drosophila-microbe interactions. I have confirmed the importance of this result by showing that flies respond differently to wild yeasts than domesticated ones (Hoang, Kopp, and Chandler, 2015). Finally, I focused on Drosophila suzukii, an emerging agriculture pest that, in contrast to nearly every other species of fly, feeds on fresh undamaged fruit. I found that this unique diet leads to a microbiome that is distinct among flies (Chandler et al., 2014).