16S rRNA evaluation of common broiler chicken sampling methods: evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations

16S rRNA sequencing for characterization of poultry associated microbiomes has been increased in use in poultry research as sequencing costs fall and computational resources become more accessible. As these tools are put into wider use, they can not only be used to answer specific research questions but also help determine the most appropriate sampling techniques. The objective of this study was to use 16S rRNA sequencing to examine common sampling practices in broiler chicken studies such as: the number of birds selected from a flock to capture microbiome diversity, the differences between cecal pairs within the same bird, and using cloacal swabs as a representation of other alimentary tract (AT) locations.