Current Projects

Marine Metazoan Microbiomes

​Marine microorganisms are major contributors to biogeochemical cycling and the maintenance of global homeostasis, yet relatively little is known about the diversity and function of microbes found in intimate association with marine metazoan species. Our current understanding is largely based on cultivation-based techniques and a few cultivation-independent studies measuring phylogenetic diversity via 16S rRNA gene markers. We use both vertebrate (fish gut) and invertebrate (sponge) microbiomes as model systems to investigate the host-associated microbial biology of our oceans, employing metabolic functional gene markers as well as metagenomic sequencing and assembly to complement more traditional phylogenetic techniques such as 16S rRNA gene amplification.

Marine Microbial HOC Genomics

Halogenated organic compounds (HOCs)are widely distributed among organisms occupying higher trophic levels of the marine food web. Chemical analysis of environmental and biological samples have shown that these HOCs originate from both natural and anthropogenic sources, but in most cases their precise species of origin and food web entry points are unknown.  As members of the Scripps Center for Oceans and Human Health, we seek a molecular-level understanding of the genes and enzymatic processes responsible for the biosynthesis of HOCs produced by marine microorganisms, with the ultimate goal of enabling genetic source tracking through DNA sequence-based  biosynthetic signatures, across all trophic levels of the marine food web. 


We develop and apply bioinformatic tools and pipelines for the annotation and analysis of microbial genomes and metagenomes, collaborating with colleagues in many diverse areas of experimental biology and microbial ecology, as well as natural product chemistry and marine geochemistry. Our special interests include metagenomic sequence assembly of environmental and host-associated DNA samples, determining the role of specific environmental habitats in cross-species transmission of microbial genes (a process known as horizontal gene transfer, or HGT), and developing in silico tools for the discovery and novelty assessment of secondary metabolite genes within microbial genomes and metagenomes.

Omega-3 PUFAs

Microbial synthesis of fatty-acid-derived hydrocarbon molecules (alkanes and alkenes) has garnered intense interest in recent years as potential sources of renewable fuels and chemicals. Realization of this potential necessitates a molecular-level understanding of the genes and gene functions involved in microbial hydrocarbon biosynthesis and their relationship with the fatty acid biosynthetic processes that provide the chemical backbone for these hydrocarbon products. Current projects focus on several newly discovered microbial biosynthetic pathways catalyzing the formation of secondary lipids, accessory lipid molecules that are chemically distinct from core (primary) fatty acid products and synthesized via a novel biosynthetic mechanism in diverse microbial lineages.