Microbiota plays an increasingly important role for the wellbeing of the host. It has been correlated with a plethora of conditions ranging from gastrointestinal to immunological and metabolic diseases. It is believed microbiota plays an important role in the onset, development and treatment of obesity with exact mechanisms still unclear. Diet is one of the major factors affecting microbiota - especially intake of dietary fibers (prebiotics) which are believed to positively affect microbiota composition. We had tested the concept of modulating microbiota composition using prebiotics in a moderately physically active obese male. Dietary intake and fiber intake were assessed at the beginning using a food frequency questionnaire (FFQ, 24-hour dietary recall and 3-day food record. Intervention consisted of daily supplementation with commercial prebiotic NUTRIOSE® FB06 till recommended daily intake of fiber was achieved. No major change of dietary style and calorie intake was recommended. Intervention was carried out for 30 days and body height, weight and composition were measured and stool samples were taken at the beginning, after 15 days and after 30 days of intervention. Anthropometric parameters showed 4.8% decrease in body weight with a significant reduction of body fat (12.2%) and a decrease in visceral fat rating from 15 to 13. Microbiota composition showed a significant increase in the beneficial bacterial genus Bifidobacterium which increased tenfold during intervention.