Computational protocol: Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial

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Protocol publication

[…] DNA was extracted from frozen stool samples and amplified by PCR targeting 16S gene regions using primers described elsewhere []. We performed library preparation followed by Illumina sequencing according to standard protocols described previously []. The taxonomic composition of the intestinal microbiota was characterized by grouping sequences into OTUs (Organizational Taxonomic Units). We used the QIIME open source algorithm for handling and interpretation of the data from the raw sequences; following quality assessment of sequence data, we assigned taxonomic affiliations using the RDP_classifier from the Ribosomal Database Project []. […]

Pipeline specifications

Software tools QIIME, RDP Classifier
Application 16S rRNA-seq analysis
Organisms Saccharomyces cerevisiae, Human immunodeficiency virus 2, Homo sapiens, Bacteria, Lachnospiraceae