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

Whereas the composition of the human gut microbiome is well resolved,
predictive understanding 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 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
depended on initial conditions. Our work has important implications for
gut microbial community modeling as well as ecological interaction
detection from batch cultures.