Computational protocol: Oral administration of Bifidobacterium bifidum G9-1 alleviates rotavirus gastroenteritis through regulation of intestinal homeostasis by inducing mucosal protective factors

Similar protocols

Protocol publication

[…] Demultiplexing and removal of indices were performed using the MiSeq Reporter software (Illumina). Subsequently, sequence files were exported from the MiSeq Reporter software for further steps. Quality filtering (QV ≥ 30) and merging of paired reads to be joined together were conducted using CLC Genomics Workbench (CLC Bio, Qiagen, Aarhus, Denmark). The determined 16S rDNA sequences were subjected to homology searching using local_RDP_classifier (World fusion, Tokyo, Japan). Obtained sequences were assigned to genus levels with 50% confidence threshold using Metagenome@KIN software (World fusion). […]

Pipeline specifications

Software tools CLC Genomics Workbench, RDP Classifier
Application 16S rRNA-seq analysis
Organisms Mus musculus, Bifidobacterium bifidum, Homo sapiens
Diseases Gastroenteritis, Rotavirus Infections