Karthik Anantharaman

The fundamental focus of our interdisciplinary research program is to integrate microbial and viral ecology with data science to study human health, ecosystem change, and biogeochemistry. Towards this, we study the basic biology and ecology of phage and microbial metabolic interactions in human and environmental microbiomes, and integrate omics approaches with ecological data to enhance our ability to predict microbiome, ecosystem, and host health states.

There are three distinct facets of our research program:

1. Computational Biology (Microbial and Viral bioinformatics)

Our research program in computational biology is focused on microbial and viral bioinformatics with a concentration on developing algorithms, software, and databases to advance ecological interpretations from microbiome and genomic data. We have developed widely used scalable approaches and software to use metagenomic data and characterize viruses (VIBRANT, vRhyme, PropagAtE, ViWrap) and microbial metabolism and interactions from microbiomes (METABOLIC).

2. Viral and Microbial Ecology

Our research program in viral and microbial ecology spans both human and environmental systems with a focus on studying the ecological roles and contributions of individual organisms and viruses. Our research involves collaborations with clinicians to study human microbiomes, as well as fieldwork in freshwater and deep-sea systems to study environmental microbiomes.

3. Sulfur Metabolism and Biogeochemistry

Our research program in sulfur metabolism and biogeochemistry focuses on (i) unraveling the role of viruses in modulating sulfur metabolism and biogeochemistry, and (ii) characterizing the ecology and physiology of microorganisms and metabolic pathways in sulfur transformations.