Cecum Microbiome Profiling via 16S Sequencing

Each group had cecum fecal DNA samples collected for the 16S rRNA gene sequencing and analysis. Utilizing the Qiagen Stool DNA Extraction Kit, DNA was extracted and utilized at Novogene (Tianjin, China) for sequencing on an Illumina MiSeq instrument. Using Vsearch, the sequences that shared a similarity level of greater than 97% were clustered into operational taxonomic units (OTU). A USEARCH and VSEARCH-based pipeline was used to evaluate raw sequence data. Using QIIME, a PCoA plot was generated using the Bray-Curtis and UniFrac distances (Ramette, 2007 (link)). For the purpose of identifying differentiated taxa, the linear discriminant analysis (LDA) effect size (LEfSe) was then determined (Segata et al., 2011 (link)). The significance of the LEfSe differences between biological groups was assessed using the non-parametric factorial Kruskal-Wallis test and the Wilcoxon rank-sum test. 16S rRNA sequencing data have been deposited in the NCBI Sequence Read Archive (SRA) repository under accession number: PRJNA1038794.