Computational protocol: Airborne Bacterial Communities in Three East Asian Cities of China, South Korea, and Japan

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Protocol publication

[…] After preprocessing of quality filter (Q > 20) and trimming (removing adaptor and primers) steps using a FastX-toolkit, the sequences were assigned to operational taxonomic units (OTUs; 97% identity) using the Greengenes database (gg_13_5), followed by selection of representative sequences using Quantitative Insights Into Microbial Ecology (QIIME 1.8.0). A chimeric check was performed and 15% of reads were dropped during this process. The final 16S rRNA genes of the air samples yielded 906,573 reads.Microbial classification based on 16S rRNA gene sequences was performed using the ribosomal database project (RDP) classifier naïve Bayesian algorithm. Taxonomic identities of the phylotypes were assigned using RDP taxonomic annotations. Complete sequences were aligned by nearest-alignment space termination (NAST) with greater than 75% identity based on a nonchimeric core set of at least 1,250 nt in length and filtered by lanemask to remove columns comprising only gaps before building the tree. Phylogenetic trees were produced using the FastTree method. […]

Pipeline specifications

Software tools FASTX-Toolkit, QIIME, RDP Classifier, PyNAST, FastTree
Databases Greengenes
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Bacteria, Homo sapiens