My lab combines phylogenetic (Bioinformatics) methods and culture-independent molecular tools to study environmental microbiology. The discipline of molecular phylogenetics uses information from DNA or proteins to reconstruct the evolutionary history of life. One of the most powerful applications of molecular phylogenetics has been in the field of environmental microbiology. Less than 1% of the existing microbial diversity on the planet has been cultured, and it is well-established that standard culturing methods significantly underestimate the microbial diversity of environmental communities. The development of culture-independent techniques DNA-based methods has revolutionized our understanding of microbial diversity. Scientists have uncovered astounding microbial diversity in everything from hot springs to soils to animal intestines. In our lab, we apply molecular phylogenetics and culture-independent approaches in areas:

Culture-independent analysis of THE BUILT ENVIRONMENT

Human environments provide fascinating and complex habitats for microbial diversity. Despite the fact that Westerners spend approximately 90% of their time indoors, we know little about the diversity of microbes in these environments. Our studies of hospitals, daycare centers, therapeutic pools, shower curtains and airplanes have shown human environments to contain a rich mixture of environmental (soil, water) and human-associated microbes. Moreover, each of the artificial environments appears to select and enrich for particular groups of microbes depending on physical and chemical conditions. For example, warm hospital pools enrich for Mycobacteria, shower curtains contain Sphingomonads and Methylobacteria, and daycare surfaces are covered with slime-producing Pseudomonads. With member of the Knight lab (UC Boulder) we have developed software to track sources of contamination. Recently, we have also been funded by the Sloan Foundation to study viruses in artificial environments using metagenomic methods.

Periodontal Disease and ORAL HEALTH

The “single agent, single disease” model has proven to be a powerful tool for detecting and treating many infectious diseases. However, there is a growing recognition that many conditions, including autoimmune diseases and complex medical syndromes, are polymicrobial in origin, involving multiple pathogens or complex interactions between the human host and associated microbial communities. Recently, researchers have identified a correlation between periodontal disease (PD), a polymicrobial condition, and atherosclerosis. Chronic inflammation arising from PD has systemic effects that may be related to aspects of polymicrobial disease. We have an ongoing project, funded by the NIH, to examine patients with or without PD for vascular dysfunction and systemic inflammation, both of which are predictive of atherosclerosis, and to determine whether these conditions correlate with the polymicrobial oral flora. Our metagenomics and bioinformatics approaches will provide the most comprehensive assessment of polymicrobial diversity (both bacterial and viral) so far assembled and will allow rigorous examination of the correlation between polymicrobial diversity and atherosclerosis.

Human Microbiome Project

In collaboration with the Human Microbiome Project, my lab is developing methods to analyze 16S and Whole Genome Shotgun datasets of the microbes associated with healthy humans.