Computational protocol: Combined analysis of the salivary microbiome and host defence peptides predicts dental disease

Similar protocols

Protocol publication

[…] Reads with an average quality value lower than 20 and/or with more than 4 ambiguities in homopolymeric regions in the first 360 flows were excluded from the analysis. Read ends were trimmed in 10-bp windows if they had a quality value lower than 20. Only reads longer than 200 bp and without mismatches in the primer region were considered. Chimeric sequences were filtered using Uchime and 5.4% of the reads were filtered out as potential chimeras. Singletons were not excluded from the analysis. Sequences were assigned to each sample by the 8-bp barcode and analyzed with the Ribosomal Database Project classifier. Each read was taxonomically assigned down to the genus level with an 80% confidence threshold, and reads giving no bacterial hits were excluded from the analysis. To estimate total diversity, sequences were clustered at 97% nucleotide identity over 90% sequence alignment length UCLUST, and rarefaction curves obtained using the RDP pyrosequencing pipeline. Principal coordinates analysis (PCoA) was performed with FastUnifrac, which compares the shared and unique branches in bacterial communities based on 16S rRNA gene analysis with a phylogenetic approach that takes into account both taxonomically assigned and unassigned reads. […]

Pipeline specifications

Software tools UCHIME, RDP Classifier, UCLUST
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Homo sapiens
Diseases Stomatognathic Diseases