Reproducibility of saliva microbiota profiling in six protocols of Illumina 16S rDNA sequencing

Culture-independent molecular techniques and advances in next generation sequencing (NGS) technologies makes large scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain the sufficient sequence depth and accuracy to ensure high reproducibility and repeatability. High-quality library protocols are essential for obtaining high-quality data needed. We aimed to assess the reproducibility of saliva microbiota profiles using two library preparation kits (Truseq and Nextera) with dual index and dual index plus 6 bp molecular barcodes/internal index by comparing triplicate samples.