Molecular Microbial Ecology (MME)

Our research group uses molecular approaches for the study of a variety of natural microbial communities. This includes the development of new techniques to dissect the microbial diversity of complex ecosystems. The long-term goal of this research is to integrate different fields of biology (i.e., genomics, ecology, molecular biology, proteomics, bioinformatics and metagenomics) to provide insight into the survival of environmental microorganisms under stressful conditions. Current research in the lab focuses on the microbial ecology of a number of environments including the air, water, soil, and deep subsurface with an emphasis on the natural distribution of pathogens in the environment. By understanding processes that allow specific bacteria to exploit unique environments we hope to better understand critical mechanisms for survival.

Our laboratory is a center for microarray research at LBNL. We are working on advanced technologies to measure microbial species composition, whole-genome transcriptional analysis, and SNP discovery for epidemiology studies. We use Affymetrix high-density microarrays for much of our work. The combinatorial power of at least 500,000 oligonucleotide probes has greatly increased precision and reproducibility in our measurements. We have designed arrays for the broad characterization of species in a microbial community using the 16S rRNA gene, pathogen specific diagnostics using unique signatures, bacterial gene expression using whole genome sequence, and SNP discovery for genotyping of bacterial strains.

Current projects in our lab include understanding mechanisms of bacterial diversity using 16S rRNA gene sequence to measure relative abundance of individual members of microbial communities. We have developed novel microarray systems to measure dynamic changes and we are working with the Joint Genome Institute in Walnut Creek, CA to develop a rapid system for classifying the thousands of individual sequences from clone libraries that we a constructing. We are also measuring whole genome transcriptional expression of bacteria subjected to different environmental stresses. With collaborators at Stanford University and the University of California at Berkeley, we are developing systems for Caulobacter crescentus, Dehalococcoides ethenogenes, and Thiobacillus ferrooxidans.

We are also interested in the survival and spread of pathogens in the environment. We are studying two related pathogens with very distinctive disease lifecycles, Salmonella enterica serovar Enteritidis and Yersinia pestis. We have completed a 10X draft genome sequence of a phage type 4 strain of Salmonella enteritidis and have recently finished two strains of Yersinia pestis, Nepal516, and Antiqua. To better understand the epidemiology of these pathogens, we are identifying novel SNPs for high accuracy genotyping in a partnership with Perlegen Sciences from Mountain View, CA. We are also assisting Callida Genomics in a project to develop a diagnostic system for the identification of plague (Yersinia pestis) and anthrax (Bacillus anthracis) using a revolutionary SBH system. Details of individual projects may be seen by selecting the Research Projects link on the left.