Do different probing depths exhibit striking differences in microbial profiles?

Aim To perform a thorough characterization of the subgingival microbiota of shallow, moderate and deep sites in subjects with chronic periodontitis (ChP). Material and methods Subgingival samples were collected from subjects with ChP (n = 3/category of probing depth: ≤3, 4–6 and ≥7 mm) and periodontal health (PH). Individual samples were submitted to 16S rDNA high‐ throughput sequencing and the analysis was made using mothur and R packages. Results Nine subjects with ChP and seven with PH were included and 101 samples were evaluated. Thirteen phyla, 118 genera and 211 OTUs were detected. Taxa from Chloroflexi and Spirochaetes phyla were associated with initial stages of disease. Fretibacterium, Eubacterium[XI][G‐6], Desulfobulbus, Peptostreptococcaceae[XI][G‐1] and [G‐3], Bacteroidetes[G‐3], Bacteroidaceae[G‐1] genera and Filifactor alocis, Fretibacterium fastidiosum, Johnsonella spHOT166, Peptostreptococcaceae[XIII][G‐1]HOT113, Porphyromonas endodontalis and Treponema sp. HOT258, which are not conventionally associated with disease, increased with the deepening of the pockets and/or were elevated in ChP; while Streptococcus, Corynebacterium and Bergeyella genera were associated with PH (p