A cross-sectional observational study of the fecal microbiota in adult laying hens with and without an outdoor range



Background: Laying hens with access to outdoor ranges are exposed to additional environmental micro-organisms, including potential pathogens from wild birds. Alterations in the fecal microbiota or the relative abundance of individual genera of outdoor-housed layers may serve as an indicator for risks of exposure to potential pathogens. We therefore performed a cross-sectional field study to evaluate differences in the fecal microbiota of outdoor- vs indoor-layers across farms. Eight layer flocks (four indoor and four outdoor), from five poultry farms were sampled. Indoor and outdoor flocks were selected that had the same rearing flock of origin, and breed. In each flock, cloacal swabs were taken from ten layers, and microbiota compositions were analysed with 16S rRNA gene amplicon sequencing (region V3-V4). Conclusions: Our study shows that the cloacal microbial composition of adult laying hens in field conditions is to a limited extent, affected by the access to an outdoor range (i.e. housing type), but that the poultry house, farm, and rearing flock play a greater role in determining microbial composition. Overall, our study indicates that measuring differences in the cloacal fecal microbiota of layers as an indicator for the level of exposure to potential pathogens and the level of biosecurity seems of limited practical use.
Date made available18 Mar 2020
PublisherWageningen University & Research


  • Raw sequence reads

Accession numbers

  • PRJNA613267

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