Correction: 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, Lendert Gelens, Jan Danckaert, Luc De Vuyst, Jeroen Raes

Research output: Contribution to journalArticle

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 number53217
Number of pages29
JournaleLife
Volume2019
Issue number8
Publication statusPublished - 4 Nov 2019

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