Research

Metabolic strategies of human gut bacteria

Differentially abundant metabolite features in E. lenta supernatant

Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its nutrient niche remains unclear. We combined traditional culture experiments with metabolomics and genome-scale metabolic modeling to identify key growth pathways for this species, with implications for host immunity and pharmacology.

Check out our preprint! “Systems biology illuminates alternative metabolic niches in the human gut microbiome”

Strain variation and genome evolution in low-abundance gut microbes

E. lenta colonies isolated from a healthy subject

Using metagenomics, microbiome researchers have uncovered extensive strain variation among the diverse microbial species that colonize humans. However, the genome diversity of many low-abundance microbes is still relatively unknown, even though they may associate closely with their hosts and play outsize roles in host physiology and disease. We are applying a novel selective isolation workflow to analyze Eggerthella genomes across healthy humans and to link genome variation with host immune traits.

Computational tools for modeling microbiomes and metabolomes

MIMOSA2 analysis of gut microbiota and metabolites in inflammatory bowel disease

In my PhD research, I developed and applied conceptual frameworks and software for interpreting microbiome and metabolomics data in the context of existing genomic and biochemical reference knowledge. You can find a talk I gave on this work for the 2020 Intelligent Systems for Molecular Biology meeting here.

Data processing, statistical analysis, and visualization for microbiome studies

I enjoy contributing to microbiome studies as a computational collaborator in the areas of experimental design, data processing, statistical analysis and/or visualization of microbiome -omics data. Past projects have addressed varied questions about microbial communities including, among others:

  • what novel microbial (metagenomic) diversity exists in wild Peromyscus mice that habitually eat toxic monarch butterflies (in preparation)

  • what microbial strains are linked to host genetics and behavior in lab mice (Buffington, Dooling et al 2021)

  • whether and which microbes are shared between humans, livestock and the built environment in Kenyan villages (Mosites et al 2017)