Computational protocol: Gut Microbiota-Mediated Personalized Treatment of Hyperlipidemia Using Berberine

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Protocol publication

[…] Gut bacterial composition in the ND- or HFD-fed hamsters was analyzed via 16S rRNA genes analysis. The 16S rRNA genes were amplified using the specific primer for 16S V3-V4: 340F-805R to target the V3-V4 regions of 16S rRNA. PCR products were mixed in equimolar ratios. Subsequently, mixture of PCR products was purified with the GeneJET Gel Extraction Kit (QIAGEN, Germany). Sequencing libraries were generated using the NEXTflex Rapid DNA-seq kit for Illumina (New England Biolabs, USA) following manufacturer's recommendations and index codes were added. The library quality was assessed on the Qubit 2.0 Fluorometer (Thermo Scientific, USA) and Agilent Bioanalyzer 2100 system (Agilent Technologies, USA). Finally, the library was sequenced on the HiSeq2500 (Illumina, USA) platform and 250 bp paired-end reads were generated. Sequences were analyzed using the QIIME software package (Quantitative Insights Into Microbial Ecology). First, the reads were filtered by the QIIME quality filters. Next, we picked representative sequences for each OTU (operational taxonomic units) and used the RDP (ribosomal database project) classifier to annotate taxonomic information for each representative sequence. Sequences with a similarity over 97% were assigned to the same OTUs . […]

Pipeline specifications

Software tools QIIME, RDP Classifier
Application 16S rRNA-seq analysis
Organisms Bacteria, Escherichia coli, Homo sapiens
Diseases Hyperlipidemias, Hypertension
Chemicals Berberine