16S Targeted Sequencing data of mus musculus: adult male oral microbiota during the course of periodontitis
Bacteria were obtained by oral swabbing of the teeth and gingival surface with Ultra-Fine polystyrene swab (Puritan Medical Products) and placed in DNA/RNA Shield (Zymo Research, Irvine, CA). Samples were set to ZymoBIOMICS for Targeted Metagenomic Sequencing. DNA Extraction was performed using ZymoBIOMICS-96 MagBeadDNA Kit (Zymo Research, Irvine, CA). The DNA samples were prepared for targeted sequencing with the Quick-16S NGS Library Prep Kit (Zymo Research, Irvine, CA). The primer sets used were Quick-16S Primer Set V3-V4 (Zymo Research, Irvine, CA). These primers were custom-designed by Zymo Research to provide the best coverage of the 16S gene while maintaining high sensitivity. The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator (Zymo Research, Irvine, CA) then quantified with TapeStation (Agilent Technologies, Santa Clara, CA) and Qubit (Thermo Fisher Scientific, Waltham, WA). The ZymoBiomics Microbial Community Standard (Zymo Research, Irvine, CA) was used as a positive control for each DNA extraction and each targeted library preparation. Negative controls (blank extraction control, blank library preparation control) were included to assess the level of bioburden carried by the wet-lab process