Microbiome Profiling by 16S Amplicon Sequencing

Total DNA was extracted from swab samples by Plant Genome DNA Extraction Kit (Tiangen Biotech Co., Ltd., Beijing.,China). 16S rDNA amplicon sequencing was performed on the Illumina HiSeq2500 sequencer (Illumina, Inc., San Diego, CA, US). Sequencing libraries were generated using TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina, Inc., San Diego, CA, United States). Using FLASH v1.2.7 and QIIME v1.7.0, the high-quality clean tags from the raw sequence data were obtained (Caporaso et al., 2010 (link)). Chimeras were removed using UCHIME algorithm (Edgar et al., 2011 (link)). Using Uparse v7.0.1001 (with default sequence similarity of 97%), Operational Taxonomic Units (OTU) classification was determined (Edgar, 2013 (link)). The raw sequencing datasets are available at NCBI SRA repository (accession PRJNA942587).