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ARS Home » Southeast Area » Fayetteville, Arkansas » Poultry Production and Product Safety Research » Research » Publications at this Location » Publication #418399
Research Project: Multi-hurdle Approaches for Controlling Foodborne Pathogens in Poultry

Location: Poultry Production and Product Safety Research

Title: Standardization of methodologies in poultry microbiome research: One year of progress

Author
item Lyte, Joshua - Josh
item AYALA, DIANA - Cargill Corporation
item DE OLIVEIRA, JEAN - Cargill Corporation
item DRIDI, SAMI - University Of Arkansas
item GRUM, DANIEL - Land O' Lakes Purina Feed, Llc
item JOHNSON, TIMOTHY - University Of Minnesota
item KERS, JANNIGJE - Wageningen University
item Kogut, Michael - Mike
item REHBERGER, JOSHUA - Arm & Hammer Animal And Food Production
item SEYOUM, MITIKU - University Of Arkansas
item SMITH, ALEXANDRA - Arm & Hammer Animal And Food Production
item ZHANG, GUOLONG - Oklahoma State University
item Proszkowiec-Weglarz, Monika

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 10/4/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The gastrointestinal microbiome has been implicated in virtually every aspect of poultry physiology and performance. While 16S rRNA sequencing continues to be the most popular method to characterize the avian microbiota, methodological variation often complicates data interpretation, negatively affects reproducibility, and prevents meaningful inter-laboratory comparison of 16S rRNA results. As such, there exists a need for a set of guidelines that establish a standardized framework in poultry microbiota experimental design. At the 2023 Symposium on Gut Health in Production of Food Animals a committee was created comprised of experts from academia, industry, and government and tasked with the generation of an evidence-based, best-practices approach that would help eliminate errors or biases that arise from methodological inconsistencies at each stage of a poultry microbiota study. This abstract marks the one-year anniversary since the formation of the committee, and presents the research community an update on committee activities. A 16S rRNA study involves multiple stages that may be broadly generalized into sample collection, DNA extraction, library preparation, sequencing, bioinformatic analysis, and data deposition. Poultry researchers must consider unique species considerations and challenges that are not present in mammals, such as bifurcated ceca. Committee discussions have yielded a draft poultry-focused methodological framework that engages each of these experimental stages that will be submitted to Poultry Science for publication in 2025. In addition, data that support this manuscript include that generated by committee members which demonstrated the choice of 16S primers as well as taxonomic database selection has significant (P<0.05) effects on poultry microbiota composition and classification. Committee members are actively engaged in the planning stage of implementing a robust and comprehensive testing pipeline to empirically evaluate a standardized poultry microbiota study protocol, as well as develop specific reagents for poultry microbiota research.