Microbiology Research
My research spans several sub-disciplines of microbiology.
Broadly, I use ‘omics techniques to study microbial ecology and environmental microbiology.
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Microbial ecology of wastewater:
Wastewater represents a unique habitat that is both representative of the overall sewershed ecology and contains microbes that are specific to wastewater itself. Our research aims to investigate the metatranscriptomic diversity of wastewater and the putative functions that transcriptionally-active microorganisms have. We are developing eDNA/eRNA methods to passively sample organisms from all domains of life throughout Southern California.
Wastewater-based epidemiology:
We use metagenomic, metatranscriptomic, and amplicon-based sequencing techniques to study pathogens and antimicrobial resistance found in Southern California’s wastewater. We are specifically interested in the spread of bacterial and viral variants that represent “unseen evolution” and viral dark matter. Our main focuses are on human pathogens (i.e. SARS-CoV-2, Noroviruses) and agricultural pathogens (i.e. Tobamoviruses).
Adopt-A-Genome:
In collaboration with the Joint Genome Institute (JGI) of the US Dept. of Energy, we are analyzing genomes that have been sequenced, but not formally described and reported yet. Students have the opportunity to learn computational genomics, bioinformatics, publishing and writing skills, and scientific literacy.
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