Ultrasmall episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss through host bacterial modulation

Briefly, 150 uL of PBS bacteria was mixed with 150 uL of Tris-EDTA (TE) buffer and transferred to a stock tube containing glass beads (Sigma G8772). The final concentration of lysozyme was added to the final concentration of 2 mg/mL, and incubated for 1 hour at 37C. Subsequently, the cells were disrupted by bead beater for 3 x 30 s each at 6 m/s speed with 1 minute short pauses at 4C. g DNA was isolated using the manufacturer’s protocol here on.

Isolated gDNA was sent to Zymo sequencing core for sequencing of the V1-V3 region of the 16S rRNA gene using 250bp pair-end sequencing chemistry. Ligature_microbiome: Ligature from the mouse 2nd molar was removed and placed in 150 µL of sterile PBS buffer. Cells from the ligature was resuspended by vortexing the sample. 140 µL cells were mixed with 150 µL of TE buffer and the gDNA was isolated using MasterPure DNA isolation kit supplemented with bead beating.

Isolated DNA was sent for 16S rRNA sequencing to Forsyth Institute or Zymo sequencing core. A static version of the code used for the microbiome analyses is included here as 'narrative_methods.html'