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 based on the amplification of small-subunit ribosomal DNA (16S rRNA gene sequences) from biological samples 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:

Microbial diversity in extreme environments

Our lab has an on-going collaboration with Dr. Rick Bizzoco (SDSU) to study the phylogenetic diversity of microbial communities living in acidic thermal springs and steam fumaroles around the world. Using phylogenetic methods and carefully controlled studies, we have explored the relationship between sediment chemistry and bacterial diversity. More recently, we have developed sampling methods to collect and examine microbial diversity of geothermal spring waters as they are pumped out of the ground. This has allowed us to determine the contribution of the subsurface to surface sediment communities, assess the degree of geographic isolation of geothermal communities, and discover bacterial divisions with no cultured representatives. We are also the first group to develop efficient sterile sampling methods for high temperature (120 C) steam vents (fumaroles). Our study environments so far have included Yellowstone National Park, Lassen National Park, New Mexico, Hawaii, Kamchatka (Russia), and Italy.

Culture-independent analysis of bacterial contamination in human environments

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 vascular dysfunction

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.

Gut Microbiome of Herbivorous Insects

The goal of this research will be to establish the role microorganisms play in the adaptation of herbivorous insects to highly toxic hostplants. Working with Susanne Dobler at the University of Hamburg, we are using a combination of culture-independent molecular approaches, Bioinformatics (phylogenetic and statistical) analyses, and experimental manipulation to determine how microbes in the insect digestive tract affect, and are affected by, secondary plant compounds ingested and sequestered by these beetles. Specifically, we will test whether evolutionary shifts in host-plant utilization lead to concomitant shifts in gut-flora diversity, and we will determine what microbes are most strongly associated with host-shifts. Having established these correlations, we will then pursue a combination of experimental manipulation (rearing insects on plants and media with and without specific compounds) and culture-independent molecular approaches to determine how microbes affect beetle survival and ability to sequester secondary compounds. The long term goal of this research will be to establish a well-funded collaborative international research program for the study of insect-microbe interactions at SDSU.

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.