Computational protocol: Sasa quelpaertensis leaf extract regulates microbial dysbiosis by modulating the composition and diversity of the microbiota in dextran sulfate sodium-induced colitis mice

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Protocol publication

[…] The 16S rRNA gene (targeted V1-V3 regions) was amplified from the extracted DNA using barcoded primers (27 F and 518R). The resulting PCR products were confirmed by gel electrophoresis and purified. Sequencing of the amplicons was conducted using a Roche/454 GS Junior system (ChunLab, Inc., Seoul, Korea). Data analysis was performed according to previously described method []. Each sample was sorted according to a unique barcode. Low quality reads (average quality score < 25 or read length < 300 bp) did not undergo further analysis. The primer sequences were trimmed and clustered for correcting sequencing errors. The taxonomic positions of the representative sequences for each cluster were identified using the EzTaxon-e database []. Chimeric sequences were removed using the UCHIME program [] and the diversity indices were calculated with the Mothur program []. The pyrosequences presented in this study are available in the EMBL SRA database under the study PRJEB13815 (http://www.ebi.ac.uk/ena/data/view/PRJEB13815). The operational taxonomic unit (OTUs) were mathematically defined as having a 3% sequence distance (e.g. 97% similarity). Diversity and richness were calculated using the Cluster Database at High Identity with Tolerance (CD-HIT). Alpha diversity indices such as Chao1 and Shannon diversity were used to estimate species richness using the Mothur program and the matrix of Fast UniFrac. Principal coordinate analysis (PCoA) was used to represent the relationships between samples based on calculations of Jaccard abundance similarity and Bray-Curtis similarity [, ]. […]

Pipeline specifications

Software tools UCHIME, mothur, CD-HIT, Fast Unifrac
Databases EzBioCloud
Application 16S rRNA-seq analysis
Organisms Mus musculus
Diseases Colitis, Inflammatory Bowel Diseases
Chemicals Sodium