Laboratory Tool Development

Exploration of environmental and host-associated microbiota relies on robust, high-throughput molecular and microbiological techniques to produce high-quality reproducible data. To support our projects, there are on-going development efforts to establish and augment existing pipelines. We are always interested to share expertise and protocols as well as participate in the development of new methods, in order to facilitate the establishment of standardized protocols and rigorous data standards (Yilmaz et al., 2011;Knight et al., 2012). We have implemented a highly efficient, semi-automated pipeline for DNA extraction, PCR amplification, and high throughput sequencing of microbial samples using the Illumina platform (contact: Greg Humphrey) (Caporaso et al., 2012). One of the largest gaps in microbiome research currently is our ability to determine the function of individual microbes and of the microbial communities as a whole. In an effort to improve our knowledge in this area, we are establishing a microculture project and genome sequencing pipeline (contact: Dorota Porazinska) that will allow us to isolate microbes of interest and learn more about their function both through the use of traditional culturing techniques and genomic analysis.