Computational protocol: Microbial community compositions in the gastrointestinal tract of Chinese Mongolian sheep using Illumina MiSeq sequencing revealed high microbial diversity

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[…] Bioinformatics analysis was performed on the website (http://www.mothur.org/wiki/MiSeq_SOP). The bacterial sequence reads were assembled using mothur v 1.32 (Schloss et al. ). To increase the analysis quality, the USEARCH software was used to remove chimeric sequences (Edgar et al. ). Operational Taxonomic Units (OTUs) were selected by using sequences with a 3% dissimilarity level. The microbial diversity structures (alpha and beta diversity) in different samples were analyzed using the QIIME software (Caporaso et al. ) with Python scripts. Alpha diversity was performed using the Shannon index, Chao 1, Observed species index and Simpson index. The taxonomy assignment of OTUs was investigated by comparing sequences to the Green-gene (http://rdp.cme.msu.edu/). Gene prediction was performed using PICRUSt 1.0.0 and Greengenes database v13.5 (Langille et al. ). The Venn diagrams were constructed on the basis of the relative abundance of bacteria on the level of genus. The R packages “Biom”, “Phyloseq”, and “Pheatmap” were used for data analysis and plotting (Mcdonald et al. ; Mcmurdie and Holmes ). The original sequencing data of raw reads were deposited in the sequence read archive of the National Center for Biotechnology (Aaccession Nos. PRJNA294127, SRR2242800, and SRS1048835). […]

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