A reasonable correlation between cloacal and cecal microbiomes in broiler chickens

Area of Science:

• Animal Science
• Microbiology
• Genomics

Background:

• Gut microbiota are crucial for livestock health, influencing productivity, welfare, and food safety.
• Investigating poultry mid-gut and hind-gut microbiota typically requires postmortem analysis.
• Cloacal sampling offers a potential method for assessing gut microbiota in live animals.

Purpose of the Study:

• To determine if cloacal microbiota composition accurately reflects cecal microbiota composition in European broiler poultry.
• To assess the feasibility of using cloacal sampling as a non-invasive method for studying broiler gut microbiomes.
• To evaluate the impact of animal age and location on both cecal and cloacal microbiomes.

Main Methods:

• Analysis of paired cecal and cloacal microbiome samples from 47 European broiler poultry.
• 16S rRNA gene amplicon sequencing using MiSeq 250 bp paired-end reads.
• Statistical analysis of microbiome composition, including abundance, taxa types, and correlations.

Main Results:

• Cloacal and cecal microbiomes showed high overlap in abundant taxa (99.5% abundance, 59% types).
• Significant positive correlation (Rho = 0.66) found between specific taxa abundances in cloacal and cecal samples.
• Paired analysis confirmed cloacal communities are more related to cecal communities within the same bird than by chance.

Conclusions:

• Cloacal microbiota sampling is a promising, cost-effective, and welfare-friendly method to estimate cecal microbiota in live broiler poultry.
• Abundant bacterial taxa in the cecum can be reasonably inferred by analyzing cloacal samples.
• Findings support non-invasive monitoring of gut health in broiler chickens for research and husbandry purposes.