Statistical differences in metagenome composition. Metagenome hit counts were first normalized using GASIC. Normalized counts were then analyzed using LEfSe with default parameters, to identify significant differences at species level between the microbial communities compared. (A) Comparison baseline samples from active sites vs. progressing samples from active sites (that is, samples collect at the visit when an increase in CAL ≥2 mm was detected). (B) Comparison baseline samples from stable sites vs. follow-up samples from stable sites (that is, collected 2 months after baseline). (C) Comparison baseline samples from active sites vs. baseline samples from stable sites.