Computational protocol: The effect of Clostridium butyricum on symptoms and fecal microbiota in diarrhea-dominant irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial

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Protocol publication

[…] 16 s rRNA pyrosequencing was processed at Majorbio (Shanghai, China) by using Illumina Miseq system. Similar sequences were clustered into the same operational taxonomy unit (OTU) with a 97% sequence identity. The Chao index, Sobs index and Shannon index were calculated to assess the alpha-diversity in each sample. The cluster analysis based on the Euclidean distance was conducted based on the relative abundances of all OTUs. The principal co-ordinates analysis (PCoA) based on the Braycurtis distance was performed to assess the beta-diversity.The metagenome sequencing was performed and analyzed at Majorbio (Shanghai, China) by using Illumina Hiseq system. The raw sequences were decoded, denoised, trimmed and then assembled for gene prediction by MetaGene (http://metagene.cb.k.u-tokyo.ac.jp/). The predicted genes were clustered (95% identity, 90% coverage) by CD-HIT (http://www.bioinformatics.org/cd-hit/) into a non-redundant gene catalog. EggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups, http://eggnog.embl.de/) and KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) databases were used to predict gene function. The LEfSe (Linear discriminant analysis Effect Size) was conducted to indicate the significant factors between the groups. The STAMP analysis was used to assess function richness between groups. The whole metabolic pathways were mapped by iPath2.0 (http://pathways.embl.de). […]

Pipeline specifications

Software tools CD-HIT, LEfSe, iPath
Databases KEGG
Application Metagenomic sequencing analysis
Organisms Clostridium butyricum, Homo sapiens
Diseases Gastrointestinal Diseases, Irritable Bowel Syndrome, Ichthyosis Bullosa of Siemens