Computational protocol: Comprehensive analysis of the fecal microbiota of healthy Japanese adults reveals a new bacterial lineage associated with a phenotype characterized by a high frequency of bowel movements and a lean body type

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Protocol publication

[…] The detailed procedures for the Illumina sequencing and microbiological analyses are described in the Additional file . Briefly, the V1–V2 hypervariable region of the bacterial 16S rRNA gene sequence was determined by using an Illumina Miseq gene and small genome sequencer (Illumina, CA, USA). By using the Quantitative Insights Into Microbial Ecology (QIIME) bioinformatics pipeline [], 5,290,023 high-quality reads (10,252 ± 2406 reads/sample) were generated (Additional file : Table S2) and assigned to operational taxonomic units (OTUs). Representative sequences for each OTU were then aligned by using the MUSCLE multiple sequence alignment algorithm [], taxonomically classified by using RDP Classifier v2.2 [], and then used to construct an OTU table. […]

Pipeline specifications

Software tools QIIME, MUSCLE, RDP Classifier
Applications 16S rRNA-seq analysis, Nucleotide sequence alignment
Organisms Homo sapiens