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.




Welcome to the Anantharaman Microbiome Laboratory!


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. Understanding how microbial communities function is critical to unraveling how they underpin human health, and predicting global ecosystem dynamics, especially in the context of environmental perturbations like anthropogenic global change.

Evolutionary ecology of 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. These processes are abundant across both aerobic (sulfur oxidation) and anaerobic environments (sulfate reduction). We utilize a combination of fieldwork, laboratory experiments, and multi-omics based approaches to investigate the microbiology of sulfureous environments such as deep-sea hydrothermal vents, oxygen minimum zones and the pelagic ocean water column, freshwater ecosystems, and the human gut.

Microbial 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 dissimilatory sulfur metabolism. We seek to quantify and predict the impact of such interactions on biogeochemical cycling at cellular, ecosystem, and global scales.

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