This ready to load phyloseq R S4 object contains the ASV table, taxonomy table and sample metadata. This data was build using the DaDa2 (version 1.6.0) and phyloseq (version 1.223) R packages using our raw MiSeq PE300 sequencing data deposited at NCBI-SRA under BioProject: PRJNA673103. The accompanying (peer-reviewed) scientific article can be found here: https://www.frontiersin.org/articles/10.3389/fmicb.2020.626713/abstract DOI: 10.3389/fmicb.2020.626713 Study/paper J. Schreuder, F.C. Velkers, A. Bossers, R.J. Bouwstra, W.F. de Boer, P. van Hooft, J.A. Stegeman, S.D. Jurburg. Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 % and 4.4 % of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.

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