SEP 08, 2016 10:30 AM PDT

The Serious Science of Schmutz: Deep-sequencing the built environment

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  • Professor of Biology, San Diego State University
      Dr. Kelley received training in microbial diversity and metagenomics from one of the founders of this research field, Dr. Norman Pace, as a postdoctoral fellow at the University of Colorado. He was also trained in Bioinformatics by one of the earliest and most influential Bioinformaticians, Dr. Gary Stormo. Since that time, he have published 53 papers (76 total) related to microbial metagenomics and bioinformatics in many influential journals (e.g., Nature, Nature Methods, Nature Biotechnology, PNAS, ISME J, PLoS Computational Biology). His studies include both DNA sequence-based analysis of microbial diversity of numerous different environments, including the Built Environment, human gut microbiome habitats and numerous papers on Bioinformatics software tools and novel analytical approaches to data analysis. Dr. Kelley is a pioneer in the application of molecular and NGS analysis of microbial diversity in the Built Environment. Humans in industrialized societies spend greater than 90% of their time indoors and we know precious little about indoor microbial communities. Along with Dr. Norman Pace, he published the first paper that used culture-independent methods to study an indoor environment, namely shower curtain biofilms. Since then, he has studied a broad range of indoor environments including Mycobacterium-contaminated hospital pool air and surfaces in neonatal intensive care units, offices, airplanes, daycare facilities, and restrooms. These papers are well cited and helped inspire the Alfred P. Sloan Foundation's Microbes in the Built Environment program.


    The global trend towards industrialization and urbanization has led to ever more people living and working indoors. Some studies estimate that humans in industrialized countries spend as much as 90% of their lives inside. Thus, for billions of humans the built environment (BE) now represents the modern ecological habitat of Homo sapiens sapiens. In this talk, I will review our groundbreaking studies using molecular tools and bioinformatics to explore BEs such as therapy pools, offices, hospitals and airplanes. I will then discuss our experimental time-series 16S and metagnomic analysis of bacterial and viral community that demonstrated rapid ecological succession and stabilization of communities on restroom surface. Finally, I will describe the SourceTracker program, inspired by our BE studies, which determines how many different communities have contributed to contaminated environment.

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