Unraveling the Role of Microbiomes in the Environment, Human Health, and Disease
We are a diverse and interdisciplinary group studying microbial ecology, viruses, metabolic interactions, and biogeochemistry with a focus on sulfur metabolism in environmental and human microbiomes.
Microbial metabolism has the potential to impact the evolutionary ecology of a system across various spatial and temporal scales ranging from the scope of a single cell, ecosystem, to the earth as a whole. We utilize a combination of fieldwork, laboratory experiments, and multi-omics based approaches to investigate the microbial and viral ecology of human and environmental systems such as deep-sea hydrothermal vents, oxygen minimum zones, the pelagic ocean water column, freshwater ecosystems, and the human gut.
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Microbial sulfur metabolism
Microorganisms control and modulate transformations associated with the element sulfur in natural and engineered systems. Sulfur plays a central role in biochemistry, impacts carbon and nitrogen turnover in various environments, and is critical to maintaining the health of oceans in the future. We use biotic sulfur transformations as a model to study the evolution and ecology of microbial energy metabolism and viral auxiliary metabolism.
Microbial and viral community interactions
Recent advances in DNA sequencing and bioinformatics approaches have enabled the recovery of thousands of strain-resolved microbial genomes from a single ecosystem thereby providing a window into fine scale microbial interactions and metabolic networks in complex communities. Broadly, we are interested in studying three types of interactions in microbial communities using sulfur transformations as a model – virus-microbe, microbe-microbe, and microbial “metabolic handoffs”. We focus on virus-microbe interactions involving “auxiliary metabolic genes”, which are host-derived genes utilized by viruses in selfishly altering microbial metabolism. We also study microbe-microbe interactions, and “metabolic handoffs” primarily focused on sulfur metabolism. We seek to quantify and predict the impact of such interactions on biogeochemical cycling at cellular, ecosystem, and global scales.
Developing omics-based approaches to advance microbial and viral ecology
We are developing new bioinformatic approaches to identify and characterize viruses, microbes, and their interactions and connections in microbiomes based on different types of omics data. Tools developed by our laboratory include VIBRANT (to study and characterize viruses), METABOLIC (to identify microbial metabolism and quantify community interactions based on metabolism), PROPAGATE (to identify the activity of proviruses), and vRHYME (to enable binning of viral genomes from metagenomes).
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