Microscopy image showing microbial oil degradation at the oil-water interface

Image: Smruthi Karthikeyan

Research Areas

~99% of the observed microbial diversity in the environment remain uncultured. Hence, it’s crucial to look at microbial systems as a whole to understand the underlying interactions between microbes and their physicochemical environments to be able to successfully tailor responses to environmental perturbations. Our lab develops integrated, culture-independent, laboratory and computational tools that mine this “uncultivated majority” to disentangle complex microbial community level interactions and structuring.

The lab’s research interests lie at the interface of engineering, computational biology and microbial ecology. We use a combination of isotopic tracer based mass spectrometry and imaging along with ‘meta-omic’ techniques to probe ecophysiology of microbial community assemblages in their natural environment.

The overarching goals of the lab’s research is to broaden understanding of the genetic and metabolic diversity of the microorganisms to better manage ecosystem function, the value of this biodiversity for adaptation to anthropogenic perturbations and causing or preventing disease in humans.

  • Linking meta-omics data with isotopic tracer-based mass spectrometry and imaging (SIP metabolomics)

    Integrated meta-omic and isotopically labeled microspectroscopy approaches for discerning metabolic determinants of antibiotic efficacy in the gut microbiome 

  • Exploring metabolic plasticity in soil microbiomes and their ability to enable acclimation to periodic drought conditions.

  • Developing proximity ligation (Hi-C) and imaging (HCR-FISH) based techniques for tracking gene mobility in the environment

  • Re-optimizing agricultural microbiomes via root exudate engineering: Determine which plant metabolites recruit and enrich plant growth-promoting traits (PGPT), and whether and how these compounds stimulate the desirable microbial metabolic functions (nutrient cycling, drought alleviation, pathogen suppression)

    Synthetic (liposome) Cell-Based Biosensors for Monitoring Plant-Microbiome Communication in Soil