Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

Kevin D'hoe, Stefan Vet, Karoline Faust, Frédéric Moens, Gwen Falony, Didier Gonze, Veronica Llorens-Rico, Lendert Gelens, Jan Danckaert, Luc De Vuyst, Jeroen Raes

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

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.
Original languageEnglish
Article numbere37090
Number of pages30
JournaleLife
Volume7
Issue number7
DOIs
Publication statusPublished - 2018

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