Computational protocol: 16S rDNA analysis of periodontal plaque in chronic obstructive pulmonary disease and periodontitis patients

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Protocol publication

[…] The Illumina-generated FASTQ files (.fastq) and quality files were acquired as raw and mapped sequence data. Each operational taxonomic unit (OTU) was generated using the default settings in the QIIME software (v1.9.1) []. Classifications were based on the Greengenes database (http://greengenes.lbl.gov/) []. The output classified the reads at several taxonomic levels. Alpha- and beta-diversity analyses were computed from the previously constructed OTU table using Mothur software (v1.21.1) and weighted UniFrac analysis. Abundance analysis was determined from rarefaction files using the Kruskal–Wallis test among four groups and the Mann–Whitney test between each of two groups (IBM SPSS Statistics for Windows v20 and GraphPad Prism software, v6.01). Additionally, weighted Student’s t-tests were performed between the COPD (C+P+ and C+P− groups) and non-COPD (C−P+ and C−P− groups) patients. The minimum abundance cut-off was set at 0.1% abundance. […]

Pipeline specifications

Software tools QIIME, mothur, SPSS
Application Miscellaneous
Organisms Homo sapiens, Prevotella intermedia
Diseases Periodontitis, Pulmonary Fibrosis, Pulmonary Disease, Chronic Obstructive