Objective: to characterize the plaque bacteria in subjects enrolled in five biofilm-gingival interface (BGI) groups, and to determine whether re-institution of oral hygiene regimen would lead to a change in the biofilm composition. Methods: participants from each of the five BGI groups abstained from brushing and flossing teeth in two posterior sextants during a three week period. Participants reinstated normal oral hygiene (Day 21), and were followed for four weeks. Clinical parameters were recorded, and subgingival plaque samples were analyzed by the Human Oral Microbe Identification Microarray (HOMIM). Results: at baseline Synergystetes were more abundant in BGI-P2 and BGI-P3 than BGI-P1 and -G (p[less than or equal to]0.05). Overall, at the peak of induction there was an increase in levels of Firmicutes (p[less than or equal to]0.001), Fusobacteria (p=0.003), Proteobacteria (p ≤ 0.001), Synergistetes (p=0.04), and Bacteroidetes (p ≤ 0.001). At the resolution phase, the Synergistetes did not rebound. When analyzing each BGI group, plaque induced inflammation prompted distinguished changes in subgingival biofilm composition in most of the BGI groups except BGI-P3. Removal of plaque significantly reduced to baseline levels most bacteria in all BGI groups except a few bacterial phylum, such as Sinergistetes in BGI-P1, which were also detected in increased levels in the high pocket depth responders. Conclusions: it is indicated that the Synergistetes phylum may be highly involved in the progression of periodontal disease.