Background: This study evaluated the microbiological effects of full-mouth (FM) and partial-mouth (PM) scaling and root planing (SRP) in type 2 diabetic subjects with chronic periodontitis (ChP), up to 12 months. Methods: Thirty-four type 2 diabetic subjects with ChP received either FMSRP (n = 17), in two sessions within two consecutive days, or PMSRP (n = 17) in four sessions within 21 days. Six subgingival biofilm samples per subject were analysed by checkerboard DNA-DNA hybridization for 40 bacterial species at baseline, 3 and 12 months. Results: Both therapies significantly reduced the levels of the red complex species up to 12 months (p < 0.05). The levels of three putative pathogens from the orange complex were significantly reduced in the FMSRP group, whereas a single orange complex species was significantly decreased in the PMSRP group (p < 0.05). Furthermore, the proportions of the host-compatible Actinomyces species were significantly increased in both groups at 3 and 12 months. No significant differences were observed between groups for the counts and proportions of the individual species and the proportions of microbial complexes at any time point (p > 0.05). Conclusions: There were no differences in the bacterial species evaluated after FMSRP and PMSRP in the treatment of type 2 diabetic subjects with ChP, up to 12 months.

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