Summary The overall objective of the Microbiomics and Functional Genomics Core is to facilitate digestive diseases research by providing advanced microbiomics and functional genomics services to members of the San Diego Digestive Diseases Research Center (SDDRC). Central to the Core services are next-generation sequencing technologies, which have revolutionized basic and translational medical research over the last several years and are in increasing demand in digestive diseases research. The Core enables Center investigators to conduct and interpret studies based on large-scale sequencing by removing technical and cost barriers that can limit successful application of these powerful tools. In addition, the Core provides a comprehensive set of services beyond sequencing that empower Center members to use microbiomics and functional genomics technologies without extensive preexisting expertise on their side for sample preparation and data analysis. The Core is directed by internationally recognized experts in microbiomics (Dr. David Pride) and functional genomics (Dr. Sven Heinz). Together with a team of experts in microbiome science, molecular genetics, bioinformatics and computational biology, the Core leadership has a wealth of experience in guiding SDDRC members in the use and analysis of cutting-edge and cost-effective technologies for microbiomics and functional genomics. The Core has had excellent success in serving its membership as evidenced by usage by 70% of SDDRC members; processing and sequencing of ~10,000 microbiome and ~4,000 genomic samples; over 6,000 hours of bioinformatic analysis; and acknowledgement of Center support on 72 publications based upon primary usage of services by this Core. Building on these achievements, the Core will continue to leverage three established institutional shared resources for providing services: the Microbiome Core at the University of California, San Diego (UCSD), the Genomics Center of the Institute for Genomic Medicine (IGM) at UCSD, and the UCSD Center for Computational Biology and Bioinformatics. Service entails sample preparation, sequencing and data analysis in an integrated workflow whereby samples are processed either at the Microbiome Core or IGM Genomics Center, sequencing is performed at the IGM Genomics Center, and data are seamlessly transferred and analyzed in the Center for Computational Biology and Bioinformatics. The Core also offers consultation and training in genomics technologies to enhance the ability of members to implement these technologies in their research. The Core has established rigorous procedures for quality control and data validation, and interacts with and complements the other SDDRC Cores. Together, the unique combination and integration of outstanding existing infrastructure and expertise enables the Core to provide a range of high quality and cost-effective microbiomics and functional genomics services that greatly enhance the ability of Center members to adv...