Integrating Microbial and Viral Ecology with Data Science to Study
Human Health, Ecosystem Change, and Biogeochemistry
OUR RESEARCH
The fundamental focus of our laboratory is to understand the basic biology of phage and metabolic interactions in environmental and host-associated microbiomes, and their overall impacts on microbiome fluctuation, ecosystem change, and biogeochemistry. Our research occurs at the interface of three diverse fields, namely, Computational Biology, Microbial and Viral Systems Ecology, and Biogeochemistry.
- We are developing bioinformatics approaches and tools to study uncultivated viruses, with a specific focus on bacteriophages (phages). Through our open access software and tools, we hope to enable and drive microbial and viral ecology studies in the future.
- We are integrating omics approaches with ecological data to enhance our ability to predict microbiome, ecosystem, and host health states.
- We utilize a combination of fieldwork, laboratory experiments, and multi-omics based approaches to investigate the microbial and viral ecology of environmental systems such as deep-sea hydrothermal vents, oxygen minimum zones, the pelagic ocean water column, freshwater ecosystems, and peatland soils.
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Developing omics-based computational biology and bioinformatics 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 and viral auxiliary metabolic genes), METABOLIC (to identify microbial metabolism and quantify community interactions based on metabolism), PROPAGATE (to identify the activity of proviruses), vRHYME (to enable binning of viral genomes from metagenomes), ViWrap (to enable comprehensive characterization of viruses from metagenomes). More recent developments include Protein Set Transformer (to relate viral genomes based on shared protein content), CheckAMG (to identify and curate auxiliary genes in viral genomes), and Prophage-DB (a comprehensive database of prophage genomes, proteins, and associated metadata).
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 – 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’re also investigating virus-microbe interactions through the lens of virus life cycles and life-history switches. We 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.
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.
OUR RESEARCH IS FUNDED BY
