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.
RNA-seq results have been deposited to the Short Read Archive under the study identifier SRP136465 (https://www.ncbi.nlm.nih.gov/sra/SRP136465). Fermentation data have been submitted to Dryad (doi:10.5061/dryad.g83f29f). Source data has been provided for Figures 3 to 6.
Data from: Integrated culturing, modeling and transcriptomics uncovers emergent behavior in a synthetic gut communityAvailable at Dryad Digital Repository under a CC0 Public Domain Dedication.
Article and author information
Vrije Universiteit Brussel
- Kevin D'hoe
Fonds Wetenschappelijk Onderzoek
- Kevin D'hoe
- Karoline Faust
- Frédéric Moens
- Verónica Lloréns-Rico
Interuniversity Institute of Bioinformatics in Brussels
- Stefan Vet
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Xochitl Morgan, University of Otago, New Zealand
- Received: March 29, 2018
- Accepted: October 4, 2018
- Accepted Manuscript published: October 16, 2018 (version 1)
- Version of Record published: November 15, 2018 (version 2)
- Version of Record updated: November 4, 2019 (version 3)
© 2018, D'hoe et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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