Computational protocol: Effects of molecular hydrogen-dissolved alkaline electrolyzed water on intestinal environment in mice

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Protocol publication

[…] Post-processing sequencing data were analyzed using software (Quantitative insights into Microbial Ecology (QIIME) pipeline ver. 1.8.0). Paired-end reads were assembled using the default parameters. Sequence reads with average quality < Q20 were removed. Chimeric sequences were removed using Usearch V6.1.544, based on the Uchime algorithm implemented in QIIME. Clean Fastq data were aligned into operational taxonomic units (OTUs) at 97% similarity, using open reference OTU picking against the 16S database (Greengenes database ver. 13.8). Taxonomic identification was performed at the phylum and genus levels. The representative (most abundant) sequence of each genus was investigated using basic local alignment search tool (BLAST) searches (http://blast. ncbi.nlm.nih.gov/Blast.cgi) to confirm the closest species. Alpha and beta diversity indices were computed at a sequence depth of 9,379 sequences for the sample of lowest sequence. Principal coordinate analysis (PCoA) was applied to plot the variation in the unweighted UniFrac distance between samples. In addition, unweighted-pair group method using arithmetic means (UPGMA) clustering was applied to unweighted UniFrac distance matrices to build an UPGMA tree. […]

Pipeline specifications

Software tools QIIME, USEARCH, UCHIME, BLASTN, UniFrac
Application 16S rRNA-seq analysis
Organisms Mus musculus
Chemicals Alanine, Cholesterol, Hydrogen