Performing Department
Animal Science
Non Technical Summary
Within the past decade, we have started to realize that bacteria are not only responsible for causing disease but can actually be used in favor of increasing animal health and productivity. For example, several probiotic products are currently marketed for improved performance in various animal species.The work proposed here aims to understand how changes in the collection of bacteria living in our animals (microbiome) are associated to improved productive performance, and with that knowledge, create targeted approaches that can be applied in specific food production systems.It is not surprising that the gut of food-producing animals harbors several potentially disease-causing organisms. Another goal of the research proposed here is to investigate the composition and presence of antimicrobial resistance genes across various production systems and identify management practices that can be adopted to decrease the prevalence of pathogenic bacteria and the spread of antimicrobial resistance genes across the food supply.
Animal Health Component
100%
Research Effort Categories
Basic
40%
Applied
40%
Developmental
20%
Goals / Objectives
1. Development of a sequencing-based antimicrobial resistance surveillance tool that is cost-effective and accurate for tracking AMR genes from farm-to-fork2. Investigate the effect of alternatives to antimicrobials in the microbiome and the production of broilers (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. Development of drug-free microbiome modulating approaches that mimic sub-therapeutic doses of antimicrobials administered to production animals for increased production efficiency
Project Methods
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.