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Antibioticinhibition mechanisms against bacteria are well known; however, metabolicinteractions and cross talk with host and pathogen is mostly uncharacterized(He et al.,2013). While there iswidespread use of subtherapeutic doses of antibiotics in animals for growthpromotion, the exact metabolite shifts are unknown (Lowell et al., 2018). A precise elucidation of antibiotic host-pathogen metabolicinteraction can lead to well targeted approach in combating pathogens andpromoting animal growth. The current existing method for testing antibioticefficacy is in vitro, which does not provide the host-pathogen context, thisstudy uses a novel approach by employing intestinal organoid as an ex vivomodel for antibiotic efficacy.

 A tripartite effect between the host tissue, theinfecting microbe and the antibiotic will change the immune response, themetabolome and the associated microbiome. Salmonella alters themetabolic profile during infection and was shown to alter the effectiveness ofantibiotics in vivo mouse models. We seek to untangle the interaction betweenthe host, the microbiome, and antibiotics using multi-omics in an avian intestinalorganoid. This is a novel platform to understand the impact of the metabolomeand has the advantage of providing an ex vivo model.

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  We hypothesize that antibiotic use will shiftthe metabolome within an organoid independent of Salmonella infection. Host-pathogeninteraction has been recently demonstrated in ex vivo three-dimensional (3D)primary enteroid and intestinal organoid models. While optimization of theorganoid growth is needed this aspect is not high risk. Tissues from theintestine will be harvested and crypts will be extracted and  cultured using appropriate media and growthfactors for the system. Intestinal stem cells will differentiate into large 3Dorganoids possessing the entire range of cell types. This featuresupercedes  prior cancer cell derivedcultures that are of a single cell type.

Successfully isolated intestinal stemcells can be passaged to retain the stem cell characteristics. Previous studiesin human enteroids have tested the effect of cholera toxin, rotavirus, enterohemorrhagicE. coli serine protease, and Clostridium difficile. Prior studies have only employed an invivo mouse or cancer derived model.

Cell culture models do not have the varietyof cells the intestinal organoid offer. This is the first use of this model touncover metabolites that will mitigate infection with antibiotics.

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