Computational protocol: Food Starch Structure Impacts Gut Microbiome Composition

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Protocol publication

[…] The raw 16S rRNA gene sequence data were analyzed by Quantitative Insight Into Microbial Ecology (QIIME) version 1.9.1 (). Sequences with a Phred score of lower than 20 were removed. Chimeric sequences were checked and removed using USEARCH version 6.1.544 (). The remaining high-quality reads were clustered into operational taxonomic units (OTUs) by PyNAST () with a 97% sequence identity threshold against the Greengenes core set database version 13.8 (). The generated biome table was normalized using an equal subsampling size of 2,938 sequences. Distances between bacterial communities in different samples were calculated by the weighted UniFrac distance metric () in QIIME. Calypso () version 5.2 was used to generate hierarchical clustering, principal-coordinate analysis (PCoA) plots, and microbial network maps. Metagenomic function was predicted using PICRUSt () online Galaxy version by the method of Umu et al. (). Heat maps were generated using Calypso and gplots package in R.The White’s nonparametric t test and Kruskal-Wallis H test were performed to compare the relative abundance of genera for two groups and more than three groups, respectively. Statistical significance was analyzed by Prism version 6.0g (GraphPad Software, La Jolla, CA). A P value of less than 0.05 was regarded as statistically significant. […]

Pipeline specifications

Software tools QIIME, USEARCH, PyNAST, UniFrac, Calypso, PICRUSt, gplots
Databases Greengenes
Applications Metagenomic sequencing analysis, 16S rRNA-seq analysis
Organisms Homo sapiens