Long-term daily high-protein, drained yoghurt consumption alters abundance of selected functional groups of the human gut microbiota and fecal short-chain fatty acid profiles in a cohort of overweight and obese women

•A cohort of overweight and obese women consumed Skyr daily for 4 months.•This study combines longitudinal analysis, quantitative microbiota profiling, and in-depth fecal metabolite analysis.•Skyr consumption successfully transmitted both starter cultures to the gastrointestinal tract.•Intervention-dependent changes in fecal microbiota composition and short chain fatty acid profiles were linked to metabolites of dairy fermentations.•Skyr consumption had major impact on intestinal microbial cross-feeding.