Project Summary/Abstract In this Phase 2 of the Functional Microbiomics, Inflammation and Pathogenicity COBRE, the primary goal of the Functional Microbiomics Core (FMC) is unchanged. We will sustain and enhance the well-established integrated service center that functions as a critical resource for the Research Project Leaders (RPLs) as a priority, and secondarily for all investigators of the Center. Since all new COBRE projects also utilize mouse models to explore the inter-relationships between inflammation and pathogenesis, and the contribution of microbiota to this process, our well-established germ-free and gnotobiotic mice facility (GMF) will continue to play a central role in services provided by the FMC. We will continue to provide anaerobic culturing of mixed and/or mono bacterial strains to facilitate the specific colonization of the germ-free mice. 16S ribosomal DNA will be profiled with the in-house developed Oxford nanopore sequencing as well as PacBio-long read sequencing tools, and bioinformatic support provided. Our most extensively used resource; multiplex-based analysis of inflammatory mediators in biological samples, will continue to function using the Bio-Plex 200 (Bio-Rad) multiplex system. In addition, several recent advances allow us to augment the services provided by the FMC. First, the recently developed, highly successful rederivation service of transgenic and KO mouse models as germ-free, will greatly expand the scope and utility of the GMF. Related to this service is the development of a new area of research on the role of microbiota in Alzheimer’s Disease (AD) supported by an administrative supplement to the FMC from NIA/NIGMS. The GMF has already rederived several AD mouse models. For this project, the FMC also developed a suite of mouse behavior analysis models including the Morris Water Maze and Novel Object Recognition tests. These services will support all future ageing related research at the center including a new project on the role of edible-plant derived exosomes in restoring the integrity of the Blood Brain Barrier. We also now include imaging support, in particular Multiphoton Intravital Microscopy for imaging of live tissue and an In Vivo Imaging System (IVIS) for live mouse imaging. Besides functioning as a service center, another major goal of the FMC is to promote the education and training of researchers, primarily the RPLs. The FMC will also interact with other Core facilities at the University of Louisville, such as the Genomics, Metabolomics and Bioinformatics core facilities established with the support of other highly successful COBRE/INBRE programs. In particular, the newly funded Cancer Immunology and Immunotherapy COBRE-operated Functional Immunomics Core (FIC) facility also directed by Dr. Bodduluri has several joint initiatives with the FMC including the establishment of a histopathology service center. The FMC will work with these and other UofL resources in order to avoid duplication of equipment, and to train individual investigators in specific protocols, foster innovative protocol development and integrate analysis of data.