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

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 (Roseb...

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Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237439/
https://www.ncbi.nlm.nih.gov/pubmed/30322445
http://dx.doi.org/10.7554/eLife.37090
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author 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
author_facet 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
author_sort D'hoe, Kevin
collection PubMed
description 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.
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spelling pubmed-62374392018-11-19 Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community 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 eLife Computational and Systems Biology 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. eLife Sciences Publications, Ltd 2018-10-16 /pmc/articles/PMC6237439/ /pubmed/30322445 http://dx.doi.org/10.7554/eLife.37090 Text en © 2018, D'hoe et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Computational and Systems Biology
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
Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
title Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
title_full Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
title_fullStr Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
title_full_unstemmed Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
title_short Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
title_sort integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community
topic Computational and Systems Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237439/
https://www.ncbi.nlm.nih.gov/pubmed/30322445
http://dx.doi.org/10.7554/eLife.37090
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