16S amplicon-based microbiome biomapping of a commercial broiler hatchery

Authors: Rothrock, Michael; ZWIRZITZ, BENJAMIN - Vienna University; AL HAKEEM, WALID G - Department Of Energy; Oladeinde, Adelumola - Ade; GUARD, JEAN - Former ARS Employee; Li, Xiang

Submitted to: Animal Microbiome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/5/2024
Publication Date: 8/9/2024
Citation: Rothrock Jr, M.J., Zwirzitz, B., Al Hakeem, W., Oladeinde, A.A., Guard, J.Y., Li, X. 2024. 16S amplicon-based microbiome biomapping of a commercial broiler hatchery. Animal Microbiome. https://doi.org/10.1186/s42523-024-00334-3.
DOI: https://doi.org/10.1186/s42523-024-00334-3

Interpretive Summary: Hatcheries, where eggs from multiple breeder farms are incubated and hatched before being sent to numerous farms, represent a nexus point in the commercial production of broilers in the United States. Considering all downstream microbial quality and safety aspects of broiler production (live production, processing, consumer use) can be potentially affected by the hatchery, a better understanding of microbial ecology within commercial hatcheries is essential. Therefore, a commercial broiler hatchery was biomapped using 16S rRNA amplicon-based microbiome analyses of four sample type categories (Air, Egg, Water, Facility) across five different places in the pre-hatch, hatch, and post-hatch areas. While distinct microbiomes were found for each sample type category and hatchery area, microbial community analyses revealed that Egg microbiomes trended towards clustering with the facility-related samples when moving from the prehatch to post-hatch areas, highlighting the potential effect of the hatchery environment in shaping the pre-harvest broiler-related microbiome. Prevalence analyses revealed 20 ASVs (Core20) present in the core microbiomes of all sample types and areas, with each ASV possessing a unique distribution throughout the hatchery. Interestingly, three Enterobacteriaceae ASVs were in the Core20, including Salmonella. Subsequent analyses showed that Salmonella, while a minor prehatch and hatch Core20ASV, dominated the Enterobacteriaceae niche and total microbiome in the chick pad feces in the post-hatch area of the hatchery, and the presence of this Salmonella ASV in the post-hatch feces was associated with swabs of breakroom tables. These findings highlight the complexity of commercial hatchery microbiomes, including identifying chick pad feces and breakroom tables as potentially important sampling or disinfection targets for hatchery managers to focus their Salmonella mitigation efforts to reduce loads entering live production farms.

Technical Abstract: Hatcheries, where eggs from multiple breeder farms are incubated and hatched before being sent to numerous farms, represent a nexus point in the commercial production of broilers in the United States. Considering all downstream microbial quality and safety aspects of broiler production (live production, processing, consumer use) can be potentially affected by the hatchery, a better understanding of microbial ecology within commercial hatcheries is essential. Therefore, a commercial broiler hatchery was biomapped using 16S rRNA amplicon-based microbiome analyses of four sample type categories (Air, Egg, Water, Facility) across five different places in the pre-hatch, hatch, and post-hatch areas. While distinct microbiomes were found for each sample type category and hatchery area, microbial community analyses revealed that Egg microbiomes trended towards clustering with the facility-related samples when moving from the prehatch to post-hatch areas, highlighting the potential effect of the hatchery environment in shaping the pre-harvest broiler-related microbiome. Prevalence analyses revealed 20 ASVs (Core20) present in the core microbiomes of all sample types and areas, with each ASV possessing a unique distribution throughout the hatchery. Interestingly, three Enterobacteriaceae ASVs were in the Core20, including Salmonella. Subsequent analyses showed that Salmonella, while a minor prehatch and hatch Core20ASV, dominated the Enterobacteriaceae niche and total microbiome in the chick pad feces in the post-hatch area of the hatchery, and the presence of this Salmonella ASV in the post-hatch feces was associated with swabs of breakroom tables. These findings highlight the complexity of commercial hatchery microbiomes, including identifying chick pad feces and breakroom tables as potentially important sampling or disinfection targets for hatchery managers to focus their Salmonella mitigation efforts to reduce loads entering live production farms.