Research Projects

Cystic Fibrosis

Together with members of the Rohwer Lab, we are studying how microbes and viruses persist in long term infections in the lungs of people with Cystic Fibrosis. The airways of CF patients are characterized by complex polymicrobial infections that are not fully characterized by standard microbial assessments. CF patients experience intermittent pulmonary exacerbations that correlate with accelerated loss of lung function. A primary goal of therapy is to reduce the frequency and severity of these exacerbations, yet clinicians lack biomarkers to detect oncoming disease flares before the symptoms and irreversible lung damage occur. Antibiotic treatment is not typically administered until irreversible damage from inflammation has occurred. We are using a combination of microbial and viral DNA sequencing (metagenomics), community RNA sequencing (metatranscriptomics) and breath gas analysis (metabolomics) in collaboration with Don Blake and Simone Meinardi at UC Irvine to characterize CF lung infections over time. Our long term goal is to find molecules in breath gas samples that are specific to an individual CF patient or disease state (i.e. stable vs exacerbated) that could be used as biomarkers to monitor infection and direct antibiotic treatment. Most of the ~100 biomarkers used in medical diagnostics and disease monitoring are metabolites, or small molecules (<1500 Da) that are produced in the course of metabolism. Metabolites that are specific to particular strains of bacteria (15, 16), or even interactions between bacteria (17, 18), are observable with chromatography and mass spectrometry. These molecules may enable detection of specific microbial metabolisms in a particular microbial community and disease state. Linking metabolite data with microbial sequence data will enable us to understand the identity and physiology of the most active microbes. Ultimately, we may unveil mechanisms that explain how bacteria persist in the CF lung. This information could allow doctors to diagnose and treat infections specifically.

Fecal Dark Matter (i.e. characterizing phage genes of unknown function in lean and obese twins)

Most predicted genes in viral metagenomes have diverged so extensively that they cannot be characterized with current bioinformatics. However, they are actually homologs (or functional analogs) of previously characterized proteins, and we can use existing methods to elucidate their function. The goal of this project is to characterize the structure and function of abundant unknown phage genes that are likely to have metabolic functions that are important for viral-host interactions using a combination of computational, structural and physiological approaches.

Structure of Human Oral Microbial Communities

Healthy human oral microbial communities are unique to each person and stable over time; we are using high throughput sequencing and ecological statistics to understand the distribution and composition of bacterial communities across people, families and disease states, such as the facial-gangrene inducing condition that occurs in malnourished humans, called NOMA.

Analysis of a novel bacterial genus and species using high throughput sequencing

A novel bacteria discovered in the lungs of a petshop parakeet in Basel, Switzerland was sequenced and assembled, leading to the designation of a novel bacterial genus and species, Basilia psittacopulmonis DSM24701. Annotation and analysis of this genome, containing a large number of unknown sequences and lacking close neighbors that have been sequenced, led to the exploration of several themes related to how bacterial genomes evolve.

Molecular Basis of Human Disease Book

Conducting interviews with people affected by human diseases, and incorporating them into a book that will be published by Garland Science. The book roughly follows the structure of the course I developed in UC Irvine's Molecular Biology and Biochemistry department. Syllabus

I currently work in Forest Rohwer's lab at SDSU

More about our work on Cystic Fibrosis and other human systems here.

I have a desk in Jennifer Martiny's lab at UC Irvine

I also worked at the Genomic Research Lab of the public hospital at University of Geneva Hospitals

I am working with Steve Giles to develop lab databases and websites

Last modified: Wed Jun 26 12:11:36 PDT 2013