Computational protocol: Flos Lonicera Combined with Metformin Ameliorates Hepatosteatosis and Glucose Intolerance in Association with Gut Microbiota Modulation

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Protocol publication

[…] Obtained sequence data were sorted by a unique barcode in the demultiplexing step, and low quality reads (average quality score <25 or read length <300 bp) were not considered for analysis. Sequences were assigned to the operational taxonomic units (OTUs; 97% identity; Greengenes database: http://greengenes.lbl.gov) followed by the selection of representative sequence using the Quantitative Insights into Microbial Ecology (QIIME) software package (Caporaso et al., ). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PiCRUSt) was performed to identify functional genes in the sampled microbial community on the basis of the data in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database (Langille et al., ). To identify taxa with differentiating relative abundance in the groups, the LEfSe analyses were performed using the web-based program (http://huttenhower.sph.harvard.edu/galaxy; Segata et al., ) for which the following conditions were applied: the alpha value of the factorial Kruskal-Wallis test among classes was set to <0.05 and the threshold on the logarithmic LDA score for discriminative feature was set to >2.0. […]

Pipeline specifications

Software tools QIIME, PICRUSt, LEfSe
Databases KEGG PATHWAY
Applications Phylogenetics, Metagenomic sequencing analysis, 16S rRNA-seq analysis
Chemicals Cholesterol, Glucose, Malondialdehyde, Metformin