Greater relative and absolute abundance of Streptococcus species in stool microbiota samples (a proxy for the gastrointestinal microbiome composition) was associated with more severe knee osteoarthritis (OA) and increased OA-related knee pain in a study of 1,427 patients from the population-based Rotterdam Study (RSIII) cohort. The association was independent of smoking, alcohol intake and BMI. The association between Streptococcus spp. abundance and OA pain was replicated in an independent Dutch cohort (n = 867). Streptococcus spp. abundance was associated with MRI-detected inflammation in the knee joints, suggesting a possible explanation for its link with knee pain.