Microbial ecology and predicted metabolic pathways in different oral environments from patients with acute endodontic infections

This clinical study assessed the effect of antibiotics on the diversity, structure and metabolic pathways of bacterial communities in different oral environments in patients with acute primary infections. Samples of saliva (SA), supragingival biofilm (SB), and pulp cavity (PC) were collected from teeth with acute primary infections and were grouped according to previous antibiotics use (NoAtb = no antibiotics [n=6]; Atb = antibiotics [n=6]). DNA sequencing was conducted using MiSeq (Illumina). The V1-V3 hyper-variable region of the 16S rRNA gene was amplified. A custom Mothur pipeline was used for 16S rRNA processing. Subsequent analyses of the sequence dataset were performed in R (using vegan, phyloseq, and ggplot2 packages) or QIIME.