par D’hoe, Kevin;Vet, Stefan ;Faust, Karoline ;Moens, Frédéric;Falony, Gwen;Gonze, Didier ;Lloréns-Rico, Verónica;Gelens, Lendert;Danckaert, Jan;De Vuyst, Luc;Raes, Jeroen JR
Référence eLife, 7, e37090
Publication Publié, 2018-10-01
Référence eLife, 7, e37090
Publication Publié, 2018-10-01
Article révisé par les pairs
Résumé : | The composition of the human gut microbiome is well resolved, but predictive understanding of its dynamics is still lacking. Here, we followed a bottom-up strategy to explore human gut community dynamics: we established a synthetic community composed of three representative human gut isolates (Roseburia intestinalis L1-82, Faecalibacterium prausnitzii A2-165 and Blautia hydrogenotrophica S5a33) and explored their interactions under well-controlled conditions in vitro. Systematic mono-and pair-wise fermentation experiments confirmed competition for fructose and cross-feeding of formate. We quantified with a mechanistic model how well tri-culture dynamics was predicted from mono-culture data. With the model as reference, we demonstrated that strains grown in co-culture behaved differently than those in mono-culture and confirmed their altered behavior at the transcriptional level. In addition, we showed with replicate tri-cultures and simulations that dominance in tri-culture sensitively depends on the initial conditions. Our work has important implications for gut microbial community modeling as well as for ecological interaction detection from batch cultures. |