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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Egg and Poultry Production Safety Research Unit » Research » Publications at this Location » Publication #410256
Research Project: Reduction of Foodborne Pathogens and Antimicrobial Resistance in Poultry Production Environments

Location: Egg and Poultry Production Safety Research Unit

Title: Comparison of metagenomic sequencing methods using Salmonella Heidelberg infected broilers

Author
item Li, Xiang
item Oladeinde, Adelumola - Ade
item Rothrock, Michael

Submitted to: International Poultry Scientific Forum
Publication Type: Abstract Only
Publication Acceptance Date: 11/29/2023
Publication Date: 1/29/2023
Citation: Li, X., Oladeinde, A.A., Rothrock Jr, M.J. 2023. Comparison of metagenomic sequencing methods using Salmonella Heidelberg infected broilers. International Poultry Scientific Forum. IPSF:2024.

Interpretive Summary:

Technical Abstract: Shotgun metagenomics sequencing is frequently employed to determine the microbial populations in complex samples. As one of the newer molecular techniques, it exhibits the theoretical capability to capture all genes, making it more advanced when compared to other techniques like 16S rRNA gene sequencing, Polymerase Chain Reactions, cloning, blotting, microarrays, and so on, that are widely used in poultry-related research. However, one of the limitations of shotgun metagenomics sequencing is that it cannot accurately answer the question of “what bacterial genome harbors a mobile DNA/gene of interest”? The introduction of chromosome conformation capture (Hi-C), a novel method that reveals physical associations between two DNA fragments has the potential to link functional genes with their bacterial host/genome. Therefore, in this study, we applied both techniques (Shotgun and Hi-C metagenomics sequencing) to sequence two cecal samples collected from broiler chickens infected with Salmonella enterica serovar Heidelberg. Our goal was to determine which method was more suitable for reconstructing bacterial genomes, and the antibiotic resistance and virulence genes present in the ceca of broiler chickens. The results demonstrated that shotgun and Hi-C metagenomics sequencing can efficiently assemble bacterial genomes that are present in high abundance in ceca, however, the shotgun method performed better when dealing with small bacterial genomes (approximately ~2.4 Mbp in size). Furthermore, both methods exhibited equal performance for the identification of antimicrobial resistance and virulence genes. In conclusion, our results support the notion that shotgun and Hi-C metagenomics are valuable tools for profiling bacterial communities and for surveying genes present in the gut microbiome of chickens.