Computational protocol: Loss of Vancomycin-Resistant Enterococcus Fecal Dominance in an Organ Transplant Patient With Clostridium difficile Colitis After Fecal Microbiota Transplant

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Protocol publication

[…] The 16S rDNA V4 region analysis of fecal microbiota was performed as previously described []. Illumina sequencing of the 6 samples resulted in average 142 350 (range 94 170–168 596) paired end reads. After merging the paired reads and performing quality control steps, the samples were normalized at 70 409 single end reads (250 bases). The remainder of the analysis was performed with the Quantitative Insight into Microbial Ecology (QIIME), version 1.7 (Supplementary Methods). The alpha (Shannon and Simpson) and beta diversity (weighted UniFrac) were calculated using QIIME scripts. […]

Pipeline specifications

Software tools QIIME, UniFrac
Application 16S rRNA-seq analysis
Organisms Homo sapiens, Clostridioides difficile
Diseases Colitis, Infection
Chemicals Vancomycin