Ecosystem in a box: Dissecting the dynamics of a defined microbial community in vitro

Project Information

EcoBox

Grant agreement ID: 801747

DOI

10.3030/801747

Project closed

EC signature date 17 October 2018

Start date 1 January 2019

End date 31 December 2023

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 493 899,00

EU contribution

€ 1 493 899,00

Coordinated by

KATHOLIEKE UNIVERSITEIT LEUVEN
Belgium

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Open Research Data Pilot (1)

Data Management Plan

Compilation of the Open Research Data Management Plan

Publications

Thesis and dissertations (2)

Single-Cell Analysis and Metabolic Modelling of Pairwise Interactions in the Gut Microbiome

Author(s): Clémence Joseph
Published in: 2023
Publisher: KU Leuven

Towards a microbial network inference and analysis platform

Author(s): Lisa Röttjers
Published in: 2021
Publisher: KU Leuven

Peer reviewed articles (12)

Predicting microbial interactions with approaches based on flux balance analysis: an evaluation

Author(s): Clémence Joseph, Haris Zafeiropoulos, Kristel Bernaerts and Karoline Faust
Published in: BMC Bioinformatics, 2024, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-024-05651-7

Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification

Author(s): Charlotte C. van de Velde, Clémence Joseph, Anaïs Biclot, Geert R. B. Huys, Vitor B. Pinheiro, Kristel Bernaerts, Jeroen Raes and Karoline Faust
Published in: ISME Communications, 2022, ISSN 2730-6151
Publisher: Springer
DOI: 10.1038/s43705-022-00123-6

Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis

Author(s): Bin Liu, Daniel Rios Garza, Didier Gonze, Anna Krzynowek, Kenneth Simoens, Kristel Bernaerts, Annelies Geirnaert, Karoline Faust
Published in: The ISME Journal, 2023, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1038/s41396-023-01501-1

Metabolic models of human gut microbiota: Advances and challenges

Author(s): Daniel Rios Garza, Didier Gonze, Haris Zafeiropoulos, Bin Liu, Karoline Faust
Published in: Cell Systems, 2023, ISSN 2405-4712
Publisher: Elsevier
DOI: 10.1016/j.cels.2022.11.002

Fast and flexible analysis of linked microbiome data with mako

Author(s): Lisa Röttjers, Karoline Faust
Published in: Nature Methods, 2022, Page(s) 51-54, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01335-9

Null-model-based network comparison reveals core associations

Author(s): Lisa Röttjers, Doris Vandeputte, Jeroen Raes, Karoline Faust
Published in: ISME Communications, Issue 1/1, 2021, ISSN 2730-6151
Publisher: Springer Nature
DOI: 10.1038/s43705-021-00036-w

manta: a Clustering Algorithm for Weighted Ecological Networks

Author(s): Lisa Röttjers, Karoline Faust
Published in: mSystems, Issue 5/1, 2020, ISSN 2379-5077
Publisher: Scientific Society Publisher Alliance
DOI: 10.1128/msystems.00903-19

Synthetic ecology of the human gut microbiota

Author(s): Gino Vrancken, Ann C. Gregory, Geert R. B. Huys, Karoline Faust, Jeroen Raes
Published in: Nature Reviews Microbiology, Issue 17/12, 2019, Page(s) 754-763, ISSN 1740-1526
Publisher: Nature Publishing Group
DOI: 10.1038/s41579-019-0264-8

Towards a Better Understanding of Microbial Community Dynamics through High-Throughput Cultivation and Data Integration

Author(s): Karoline Faust
Published in: mSystems, Issue 4/3, 2019, ISSN 2379-5077
Publisher: mSystems
DOI: 10.1128/msystems.00101-19

miaSim: an R/Bioconductor package to easily simulate microbial community dynamics

Author(s): Yu Gao, Yağmur Şimşek, Emma Gheysen, Tuomas Borman, Yi Li, Leo Lahti, Karoline Faust, Daniel Rios Garza
Published in: Methods in Ecology and Evolution, 2023, ISSN 2041-210X
Publisher: John Wiley and Sons Inc.
DOI: 10.1111/2041-210x.14129

Open challenges for microbial network construction and analysis

Author(s): Karoline Faust
Published in: The ISME Journal, 2021, ISSN 1751-7362
Publisher: Nature Publishing Group
DOI: 10.1038/s41396-021-01027-4

Technical versus biological variability in a synthetic human gut community

Author(s): van de Velde C, Joseph C, Simoens K, Raes J, Bernaerts K and Faust K
Published in: Gut Microbes, 2023, ISSN 1949-0976
Publisher: Landes Bioscience
DOI: 10.1080/19490976.2022.2155019