Experimental and Computational Determination of Microbial Genotypes and Phenotypes

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Bacteria are all around us and affect our environment, producing, for example, 50% of the oxygen we breathe. Despite our advances in biotechnology, we still don't understand all of the functions that bacteria perform. Scientists are good at understanding the genetics of different bacteria, but more data is required to place the genetic data in a broader context. This project uses high-throughput techniques to understand all the different things that bacteria do in order to survive and grow. First, the growth of hundreds of different bacteria will be measured in hundreds of different growth conditions. This provides a database for all scientists to use so that they can compare the metabolic capacity of different types of bacteria. Second, new sequencing technology will be used to understand the bacteria at the genetic level. This includes identifying the genes that are being used by the bacteria during growth under different conditions. Third, new computational tools will be developed to allow scientists to analyze these complex data sets. The tools and data being generated will be available to the broader scientific community so that they can compare genotypes to phenotypes. Even though this work focuses on bacteria because they are easy to grow and manipulate, much of the data that will be generated applies to more complex organisms, including humans.Broader Impacts: San Diego State University (SDSU) is a Hispanic serving institute that has had the largest improvement in graduation rates in the nation. PI Edwards and Co-PI Dinsdale teach dynamic classes to students that introduce them to the newest sequencing technologies and data sets. Over 130 students have taken the DNA sequencing and analysis classes which introduce the students to practical aspects of DNA sequencing and data analysis using the newest technologies available. The students write scientific publications based on the work they do in classes. High school students are trained over the summer, and participate in the BRIDGES program that teaches community college students how to adapt to studying at SDSU. This project supports SDSU's work with K-12 education in San Diego, the Republic of Kiribati, Brazil, and Australia, as well as open days at San Diego State University and its Coastal and Marine Institute Laboratory.