Abstract
BackgroundLaying hens with access to outdoor ranges are exposed to additional environmental factors and microorganisms, including potential pathogens. Differences in composition of the cloacal microbial community between indoor- and outdoor-housed layers may serve as an indicator for exposure to the outdoor environment, including its pathogens, and may yield insights into factors affecting the chickens’ microbiota community dynamics. However, little is known about the influence of outdoor housing on microbiota community composition in commercial layer flocks. We performed a cross-sectional field study to evaluate differences in the cloacal microbiota of indoor- vs outdoor-layers across farms.Eight layer flocks (four indoor, four outdoor) from five commercial poultry farms were sampled. Indoor and outdoor flocks with the same rearing flock of origin, age, and breed were selected. In each flock, cloacal swabs were taken from ten layers, and microbiota were analysed with 16S rRNA gene amplicon sequencing.ResultsHousing type (indoor vs outdoor), rearing farm, farm and poultry house within the farm all significantly contributed to bacterial community composition. Poultry house explained most of the variation (20.9%), while housing type only explained 0.2% of the variation in community composition. Bacterial diversity was higher in indoor-layers than in outdoor-layers, and indoor-layers also had more variation in their bacterial community composition. No phyla or genera were found to be differentially abundant between indoor and outdoor poultry houses. One amplicon sequence variant was exclusively present in outdoor-layers across all outdoor poultry houses, and was identified as Dietzia maris.ConclusionsThis study shows that exposure to an outdoor environment is responsible for a relatively small proportion of the community variation in the microbiota of layers. The poultry house, farm, and rearing flock play a much greater role in determining the cloacal microbiota composition of adult laying hens. Overall, measuring differences in cloacal microbiota of layers as an indicator for the level of exposure to potential pathogens and biosecurity seems of limited practical use. To gain more insight into environmental drivers of the gut microbiota, future research should aim at investigating community composition of commercial layer flocks over time.
Highlights
Laying hens with access to outdoor ranges are exposed to additional environmental factors and microorganisms, including potential pathogens
The evaluation of differences between the cloacal microbiota of indoor- and outdoor-layers in commercial flocks may contribute to an increased understanding of interactions between gut microbiota, housing conditions, and other environmental factors, and help to determine whether the microbiota composition might be used as an indicator of the risk of potential pathogen exposure from the farms’ outdoor environments
Future research should aim at better understanding the interactions between the gut microbiota in layers and environmental factors at the level of the poultry house over time. This may shed light on important drivers of microbiota community composition in commercial layers and could contribute to better understanding of ways to modulate the microbiota in favour of chicken health and production. This cross-sectional field study shows that exposure to an outdoor environment is responsible for a relatively small proportion of the community variation in the microbiota of layers
Summary
Laying hens with access to outdoor ranges are exposed to additional environmental factors and microorganisms, including potential pathogens. Layers with access to an outdoor range have an increased risk of low pathogenic AIV introduction [5] via oral ingestion of infected wild bird feces directly or indirectly via an environmental virus reservoir [6, 7]. These environmental factors may affect the gut microbiota of the layers, and altered cloacal bacterial communities may indicate exposure to the outdoor environment, which may potentially serve as an indicator for the level of biosecurity and exposure to pathogens. This could contribute to better understanding of ways to modulate the microbiota in favour of chicken health and production
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