Residual bacteriome after chemomechanical preparation of root canals in primary and secondary infections

Secondary infections may be linked to the presence of residual microorganisms within dental root canals. The purpose of this study was to investigate the bacterial composition of primary and secondary root canal infections, before and after chemomechanical treatment. Samples were collected before chemomechanical preparation (S1) and prior obturation (S2) from 19 subjects (10 primary and 9 secondary infections). DNA was extracted and the V3/V4 region of the 16SrRNA gene was amplified using the 347F/803R primers and paired-end sequenced using the Illumina MiSeq instrument. Sequencing analysis yielded partial 16S rRNA gene sequences that were taxonomically classified into 10 phyla and 143 genera. The most prevalent phyla in S1 and S2 samples were found to be Firmicutes and Bacteroides, however, when comparing between sample groups, Proteobacteria seem to have been enriched in secondary infections. The dominant genera in the primary S1 samples were Bacillus, Streptococcus and Prevotella while Bacillus, Streptococcus and Selenomonas dominated the secondary infection S1 samples. Bacillus and Marinilactibacillus were the most dominant genera in primary and secondary S2. The mean number of OTUs per sample was 32,656 (±12,124 SD) and 37,113 (± 16,994 SD) in S1 and S2 samples, respectively. Alpha and Beta diversities presented the same pattern within samples from both groups. Great inter-individual variations in the bacterial composition of the root canal biofilms were observed. There was no difference in the bacterial composition before and after treatment, although some genera survived and seems to be part of a residual microbiome. Our findings revealed a high diversity of the bacterial communities present in root canal infections after chemomechanical treatment, although the majority of the taxa detected were in low abundance.