Harnessing the power of microbes for human and environmental health
~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 "microbial dark matter" or the "uncultivated majority" to disentangle complex microbial community level interactions and structuring. The lab's research interests lie at the interface of microbiology, 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.
Reimagining the microbiome landscape: The microbiome field has seen a massive surge in the recent decades with significant advances made in linking the human gut microbiome to a wide range of diseases. However, most microbiome-based studies interrogate microbial community compositional differences (primarily via high-throughput 16S sequencing) across space and time, which is primarily correlative and has its limitations in uncovering the mechanistic understanding of microbial interactions in complex communities. Additionally, studies commonly use stool samples to study gut microbiota; however, stool is not representative of the entire gastrointestinal tract microbiota, especially tissue-associated microbes, which interact more directly with the host. Bulk sample processing is also insufficient, as microbial cells exhibit heterogenous gene expression that can only be analyzed via single cell resolution analyses. New techniques and investigations are necessary to determine the functional roles of specific microbes in complex natural assemblages such as the gut microbiome as well as deciphering the mechanisms underlying specific interactions post disturbances or environmental changes. To this end we develop techniques to link identity to function at the cellular level in microbial communities as well as locate and map metabolically active cells on a spatial scale which is currently one of the biggest bottlenecks in inferring the specific role of microbes i.e. who is doing what?Active Research Areas:
- Unraveling microbial community dynamics and implications for soil C fluxes under drought stress
- Integrated meta-omic and isotopically labeled microspectroscopy approaches for discerning metabolic determinants of antibiotic efficacy in the gut microbiome
- Identifying and quantifying pathways and drivers of environmental evolution and transmission of antibiotic resistance
- Rhizosphere microbiome interactions