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.

随着测序成本持续下降、计算资源愈发易得，用于表征家禽相关微生物组的16S rRNA测序（16S rRNA sequencing）技术在家禽研究中的应用日益广泛。随着这类技术的推广普及，其不仅可用于解答特定的科研问题，还能助力确定最适配的采样策略。本研究旨在通过16S rRNA测序，探究肉鸡研究中的常见采样实践，具体包括：从禽群中选取以获取微生物组多样性的肉鸡个体数量、同一只肉鸡的双侧盲肠样本间的差异，以及使用泄殖腔拭子作为消化道（alimentary tract, AT）其他部位样本的替代表征。