16SrRNA_Gut_Broiler
16S rRNA gene amplicon sequencing was performed at Life & Brain as described recently in detail (Beller et al., 2024). QIIME 2 version 2022.8 was used to process the 16S sequencing data (Bolyen et al., 2019). Raw sequencing data were deposited as FASTQ files at the NCBIs Sequence Read Archive (SRA) repository. DADA2 was deployed for sequencing quality control, including filtering for PhiX reads and chimeric sequences, and denoising (Callahan et al., 2016). To identify amplicon sequencing variants (ASV) with >99% similarity, a pretrained SILVA classifier (silva-138-nr99-16S-V3-V4-classifier) was used. The -diversity, -diversity, and relative abundance were analyzed with the MicrobiomeAnalyst platform using the default settings (Chong et al., 2020; Dhariwal et al., 2017).