My interests span a wide array of research questions, but the majority of my research is focused on interactions with fungi and bacteria with host-organisms. In the context of my research these hosts may be plants or animals, or interactions with other microorganisms.
My PhD work consisted of characterizing the role of mycorrhizal fungi in eliciting plant genetic responses with a specific role of the Jasmonic Acid pathway. I measured JA pathway products and devised experiments and optimized primers to elucidate the oxylipin pathway gene expression.
During my PhD work, new technologies became available so that I was able to start to address questions previously untenable – it was here that I began to use metagenomic techniques.
A major aspect of my current research is focused on the study of metagenomics of environmental samples - mainly soil from forests - to investigate microbial species distribution and functional diversity. Because of the dominance of bacterial nucleotides in metagenomic samples I have had to develop new analysis algorithms and take advantage of marker-based amplicon sequencing as well as metatranscriptomics to understand gene expression in situ.
During my PhD work I focused on the microbial diversity associated with trees grown for bioenergy purposes with the hypothesis that plants will harbor specific microbes tailored for the breakdown of their specific biochemical components (See Figure 1). Also, I began surveying the presence of Septoria canker, a serious pathogen in the environment, in our Poplar plantations using metagenomic sequencing.
I am currently involved with numerous genome sequencing projects of mycorrhizal fungi for comparative purposes. Most of these projects are challenging because many of these fungi cannot be cultured from the environment and they harbor bacterial intercellularly, so I analyze them as “simple” metagenomes.
In addition to this project specifically focusing on mycorrhizal fungi, I have contributed to studying fungal metatranscriptomes.
I am currently focusing my efforts on a large comparative genome sequencing project with numerous collaborators to sequence a phylogenetically diverse array of Amanita genomes across the genus to characterize the loss of saprophytism, the gain of toxicity and mycorrhization, the diversity of symbiotic bacteria, and the evolution of toxicity.
More recently I have moved toward investigating the role of fungal-bacterial interactions in gut samples (ranging from beetle to human) with a focus on mining metagenomic sequence data to understand microbial metabolic processes. Numerous studies have concerned the sequencing of the Asian Longhorned Beetle microbiome – at the level of metagenome and also selective sequencing of a novel Fusarium isolate and yeasts.
We sequenced beetle gut metagenomes after assays showed the beetle is able to break down cellulose. Our research question here is to understand how we can harness the genomic diversity of Fusarium species (main microbial component to the insect gut) to characterize novel genes responsible for the breakdown of cellulosic biomass. We have sequenced the genome of a new species of Fusarium and are currently studying its transcriptome when interacting with different host plants and insects.
I recently have been investigating, with the help of an NIH fellowship grant, the metagenomics of fungi and bacteria interactions in regulating species composition in the human gut. Like insect guts, the human gut has a large portion of both ascomycete and basidiomycete yeasts that interact with bacteria and harbor antibiotic compounds that may be harnessed to regulate human gut health.