Cecal microbiota composition of laying hens fed with Fermented Aronia melanocarpa pomace|动物微生物组数据集|功能基因组学数据集

The cecal microbiota composition analysis was performed by the Shanghai Personal Biotechnology Co., Ltd., Shanghai, China. 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. The linear discriminant analysis (LDA) effect size (LEfSe; LDA ≥ 2, P < 0.05) and random forest analysis were applied to detect and distinguish the microbiota of the four groups. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the microbiota was conducted with the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) method. The correlation between cecal microbiota abundance (top 50 genera) and phenotypes was performed using Spearman correlation with the R package (|R| > 0.50, P < 0.05).