The contribution of Gordonibacter to the different abilities, both qualitative and quantitative, of individuals to transform dietary ellagic acid into anti-inflammatory urolithins was investigated. A specific and suitable q-PCR system was developed for the detection and quantification of Gordonibacter. Ellagic acid metabolism in the gut and faecal microbiota of healthy individuals, who consumed walnuts (n = 20) or a pomegranate extract (n = 49), were studied. Urolithin-A was positively correlated to Gordonibacter in faeces, whereas excretion of isourolithin-A and/or urolithin-B was inversely correlated to both. The relationship between Gordonibacter and urolithin-A found in vivo was also confirmed in vitro. This suggests that the beneficial effects attributed to the consumption of foods containing ellagic acid could be mediated by the individuals' Gordonibacter levels. The development of prebiotics, probiotics or synbiotic aimed at increasing Gordonibacter and related species could improve the individual's ability to produce the anti-inflammatory, cardioprotective and anticancer metabolite urolithin-A.