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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Food Safety and Enteric Pathogens Research » Research » Publications at this Location » Publication #417362
Research Project: Analysis of Genetic Factors that Increase Foodborne Pathogen Fitness, Virulence, and Antimicrobial Resistance Transfer, to Identify Interventions against Salmonella and Campylobacter in Food Animals

Location: Food Safety and Enteric Pathogens Research

Title: A meta-analysis of 16S rRNA amplicon studies to determine a core microbiome in chicken cecal contents

Author
item WICKWARE, CARMEN - Oak Ridge Institute For Science And Education (ORISE)
item HARRIS, DYLAN - Oak Ridge Institute For Science And Education (ORISE)
item Oladeinde, Adelumola - Ade
item Looft, Torey

Submitted to: Beneficial Microbes
Publication Type: Abstract Only
Publication Acceptance Date: 7/21/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Studies of the chicken gastrointestinal tract have shown age and breed to be major contributors of microbiota differences in birds. However, composition of the chicken gut is impacted by other factors (e.g., geographical regions, breed, and production constraints). A meta-analysis of microbiota sequencing studies of 16S rRNA gene V4 region within chicken cecal contents was conducted to determine key taxa across various factors. Data from studies were included if they met the following criteria: 1) contained key words (e.g., “cecal”, “chicken”, “amplicon”); 2) had publicly available sequences and metadata; 3) the majority of samples within a study met read quality threshold. Each study was individually analyzed for sequence variants and subsequently combined for taxonomic classification. Alpha- and beta-diversity statistical analyses were performed using non-parametric significance tests with multiple test correction adjusted p (adj.p) < 0.05. 39 studies were included, and their metadata was used to create broad categories for comparisons of similar studies (e.g., breed, age, study country). There were overall differences in alpha and beta diversity for breed, country, host age, and study objective; however, post-hoc testing did not show pairwise differences within factor levels. Whether an animal was challenged with a pathogen and the type of treatment used (e.g., antibiotics, prebiotics, probiotics, bacteriophage) had significant differences between factor levels. These data support the notion that chicken gut microbial communities are influenced by multiple factors and more modeling is needed to determine which taxa are resilient to study factors and form a core microbiome.