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Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing.

ABSTRACT: Elucidating the complex microbial interactions in biological environments requires the identification and characterization of not only the bacterial component but also the eukaryotic viruses, bacteriophage, and fungi. In a proof of concept experiment, next generation sequencing approaches, accompanied by the development of novel computational and bioinformatics tools, were utilized to examine the evolution of the microbial ecology of the avian trachea during the growth of a healthy commercial broiler flock. The flock was sampled weekly, beginning at placement and concluding at 49 days, the day before processing. Metagenomic sequencing of DNA and RNA was utilized to examine the bacteria, virus, bacteriophage, and fungal components during flock growth. The utility of using a metagenomic approach to study the avian respiratory virome was confirmed by detecting the dysbiosis in the avian respiratory virome of broiler chickens diagnosed with infection with infectious laryngotracheitis virus. This study provides the first comprehensive analysis of the ecology of the avian respiratory microbiome and demonstrates the feasibility for the use of this approach in future investigations of avian respiratory diseases.

SUBMITTER: Mulholland KA

PROVIDER: S-EPMC8065701 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Alternative hatching systems have been developed for broiler chickens to provide immediately feed and water after hatch and reduce the number or severity of early life stressors. Besides beneficial effects of these alternative hatching systems on chick quality and performance, broiler health and welfare may be positively affected as well. Especially offspring from young broiler breeder flocks may benefit, as they have been shown to be more sensitive to preturbations than offspring from older breeder flocks. This study evaluated effects of hatching systems on chick quality, health and welfare of young breeder flock offspring, using 3 different hatching systems: conventional hatchery-hatched (HH), hatchery-fed (HF), and on-farm hatching (OH). A total of 24 pens were used in a completely randomized block design, with 8 pens per hatching system and 30 chickens per pen. Chick quality at hatch and performance until 35 d of age was improved in the HF and OH compared to HH treatment, but only minor effects were found on the welfare indicators: footpad dermatitis, hock burn, cleanliness, skin lesion and gait score. No effect was observed on the dynamics of a humoral immune response after NCD vaccination, given at d 0 and 14 of age, as no differences between NCD titers were found at d 18. Animals were vaccinated with a live attenuated infectious bronchitis vaccine virus (IBV) at d 28 to address treatment related differences to disease resilience. The expressions of inflammation and epithelial integrity related genes in the trachea and histo-pathological changes in the trachea were examined at 3 d after vaccine administration. No differences between treatment groups were observed. Although beneficial effects of HF and OH systems were found for young breeder flock offspring on chick quality at hatch and body weight posthatch, only one effect of alternative hatching systems on welfare and health indicators were found. No effect of hatching system on humoral immune response or disease resilience was found.

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Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing.

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