Cecal microbiota composition of laying hens fed with Fermented Aronia melanocarpa pomace

Briefly, the total microbial DNA of cecal contents was extracted and amplified with specific primers (forward primer: 5′-ACTCCTACGGGAGGCAGCA-3′ and reverse primer: 5′-GGACTACHVGGGTWTCTAAT-3′) to obtain bacterial V3-V4 sequences. After purification and amplification, the PCR products were paired-end sequenced on an Illumina NovaSeq platform (Illumina, San Diego, CA, USA).

After quality control and chimera removal, amplified sequence variants (ASVs) were taxonomically aligned with species annotation using the Greengenes database. Alpha- and beta-diversity indices were analyzed to detect the diversity, richness, and dissimilarity of the microbiota. The Kruskal-Wallis test was performed to determine the differential phyla and genera.