ANIMAL MICROBIOMES IN A ONE-HEALTH PERSPECTIVE: LEVERAGING TECHNOLOGY TO WORK TOWARDS SUSTAINABLE AND SAFE PRODUCTION OF ANIMAL-BASED FOODS.

<b>Project Methods</b><br> 1. The goal of this project is to develop straightforward and scalable approaches to track ARGs from farm-to-fork. To do so, we will apply a recently developed highly multiplexed amplicon sequencing platform. A primer panel targeting key organisms will be developed and subsequently be used to amplify genomic DNA extracted from samples collected from broiler samples. A library of amplicons will be sequenced, and the ability of such targeted screening to reliably and cost-effectively track ARGs will be evaluated comparing to standard culture-based methods, as well as deep untargeted sequencing to provide ground-truth.2. Compare the use of antibiotics, probiotics, prebiotics, and placebo in broilers in a randomized, controlled trial at the Poultry Research and Education Center. The microbiome will be determined longitudinally and associations between production outcomes, treatment group, and specific bacterial taxa will be investigated.(NOTE: Vertebrate animals will only be used in this objective; and at that time a project amendment will be submitted to include theIACUC protocol number.)3. Identify putative beneficial microbes, consortia of microbes, or metabolites associated with increased productivity. Beneficial microbes or consortia of microbes will be isolated from samples of selected high-performance animals. Isolated bacteria will then be characterized phenotypically for their ability to produce metabolites such as short-chain fatty acids and identified through sequencing of the 16S rRNA gene. Bacteria and/or metabolites identified as possible microbiome modulating approaches will be produced in the laboratory and administered to broilers held in a research facility. Animals will be evaluated daily for one week after the administration of treatment for possible adverse effects. Given that no adverse effects are identified, animals will be raised and slaughtered, and production outcomes will be compared, as well as different portions of their gastrointestinal tract will be analyzed through shotgun metagenomics.