Model-guided Engineering of Complex Microbial Communities

Project Information

ModEM

Grant agreement ID: 866028

DOI

10.3030/866028

EC signature date 22 September 2020

Start date 1 October 2020

End date 31 March 2027

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 995 818,00

EU contribution

€ 1 995 818,00

Coordinated by

THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
United Kingdom

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 .

Publications

Other (6)

<i>Bacteroides</i> -driven metabolic remodelling suppresses <i>Clostridioides difficile</i> toxin expression in mixed biofilm communities

Author(s): Kavana Kalea Bywater-Brenna, Simran Kaur Aulakh, Kiran Raosaheb Patil, Niranjan Nagarajan, Meera Unnikrishnan
Published in: 2026
Publisher: openRxiv
DOI: 10.1101/2025.09.03.674004

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes

Author(s): Francisco Zorrilla, Kiran R. Patil, Aleksej Zelezniak
Published in: 2026
Publisher: openRxiv
DOI: 10.1101/2020.12.31.424982

Fluctuating Environment Can Negate Cheater Success Due to Speed-Agility Trade-Off

Author(s): Naomi Iris van den Berg, Lajos Kalmar, Kiran R. Patil
Published in: 2026
Publisher: openRxiv
DOI: 10.1101/2021.06.03.446957

Impact of low-calorie sweeteners on gut bacteria is modulated by common xenobiotics

Author(s): Sonja Blasche, Vinita Periwal, Nonantzin Beristain Covarrubias, Anna Lindell, Indra Roux, Stephan Kamrad, Rob Bradley, Rui Guan, Hilal Ozgur, Bini Ramachandran, Vladimir Benes, Kiran Raosaheb Patil
Published in: 2026
Publisher: openRxiv
DOI: 10.1101/2025.03.28.645995

Interspecies interactions drive bacterial proteome reorganisation and emergent metabolism

Author(s): Stephan Kamrad, Simone Mozzachiodi, Sonja Blasche, Simran K. Aulakh, David Scheidweiler, Arianna Basile, Rui Guan, Rob Bradley, Naomi Iris van den Berg, Michael Mülleder, Markus Ralser, Kiran R. Patil
Published in: 2026
Publisher: openRxiv
DOI: 10.1101/2025.05.14.653412

Predictive evolution of metabolic phenotypes using model-designed selection niches

Author(s): Paula Jouhten, Dimitrios Konstantinidis, Filipa Pereira, Sergej Andrejev, Kristina Grkovska, Payam Ghiachi, Gemma Beltran, Eivind Almaas, Albert Mas, Jonas Warringer, Ramon Gonzalez, Pilar Morales, Kiran R. Patil
Published in: 2026
Publisher: openRxiv
DOI: 10.1101/2021.05.14.443989

Peer reviewed articles (9)

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes

Author(s): Francisco Zorrilla, Filip Buric, Kiran R Patil, Aleksej Zelezniak
Published in: Nucleic Acids Research, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab815

Unravelling metabolic cross‐feeding in a yeast–bacteria community using <scp> ¹³ C </scp> ‐based proteomics

Author(s): Natalia Gabrielli; Christoniki Maga‐Nteve; Eleni Kafkia; Mandy Rettel; Jakob Loeffler; Stephan Kamrad; Athanasios Typas; Kiran Raosaheb Patil
Published in: Molecular Systems Biology, Issue 1, 2023, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202211501

Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion

Author(s): Dimitrios Konstantinidis; Filipa Pereira; Eva‐Maria Geissen; Kristina Grkovska; Eleni Kafkia; Paula Jouhten; Yongkyu Kim; Saravanan Devendran; Michael Zimmermann; Kiran Raosaheb Patil
Published in: Molecular Systems Biology, Issue 17:e10189, 2021, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202010189

Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes

Author(s): Payam Ghiaci, Paula Jouhten, Nikolay Martyushenko, Helena Roca-Mesa, Jennifer Vázquez, Dimitrios Konstantinidis, Simon Stenberg, Sergej Andrejev, Kristina Grkovska, Albert Mas, Gemma Beltran, Eivind Almaas, Kiran R Patil, Jonas Warringer
Published in: Molecular Systems Biology, Issue 20, 2025, Page(s) 1109-1133, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.1038/s44320-024-00059-0

Impact of drugs and environmental contaminants on amine production by gut bacteria

Author(s): Stephan Kamrad, Tara F Davis, Kiran R Patil
Published in: Molecular Systems Biology, Issue 21, 2025, Page(s) 1351-1370, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.1038/s44320-025-00130-4

Predictive evolution of metabolic phenotypes using model-designed environments

Author(s): Jouhten, Paula; Konstantinidis, Dimitrios; Pereira, Filipa; Andrejev, Sergej; Grkovska, Kristina; Castillo, Sandra; Ghiachi, Payam; Beltran, Gemma; Almaas, Eivind; Mas, Albert; Warringer, Jonas; Gonzalez, Ramon; Morales, Pilar; Patil, Kiran R.; 0000-0003-1075-7448; 0000-0002-9125-326X; 0000-0002-0763-1679; 0000-0001-6144-2740; 0000-0002-0130-6111; 0000-0002-6166-8640
Published in: Molecular Systems Biology, Issue 2, 2022, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202210980

Conformable Device for Independent Measurements of Mucosal and Vascular Barriers in a Complex In Vitro Intestinal Model

Author(s): Alexandra Elisabeth Wheeler, Sonja Blasche, Rob Bradley, Rachana Acharya, Sophie Oldroyd, David Bulmer, Kiran R. Patil, Róisín Meabh Owens
Published in: Advanced Science, Issue 13, 2026, ISSN 2198-3844
Publisher: Wiley
DOI: 10.1002/advs.202511686

Ecological modelling approaches for predicting emergent properties in microbial communities

Author(s): Naomi Iris van den Berg, Daniel Machado, Sophia Santos, Isabel Rocha, Jeremy Chacón, William Harcombe, Sara Mitri & Kiran R. Patil
Published in: Nature Ecology and Evolution, 2022, ISSN 2397-334X
Publisher: Springer Nature
DOI: 10.1038/s41559-022-01746-7

Microbial interactions shape cheese flavour formation

Author(s): Chrats Melkonian, Francisco Zorrilla, Inge Kjærbølling, Sonja Blasche, Daniel Machado, Mette Junge, Kim Ib Sørensen, Lene Tranberg Andersen, Kiran R. Patil, Ahmad A. Zeidan
Published in: Nature Communications, Issue 14, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-41059-2

Thesis and dissertations (1)

Mathematical Modelling of Emergent Survival in Microbial Communities

Author(s): van den Berg, Naomi
Published in: 2025
Publisher: University of Cambridge
DOI: 10.17863/cam.119712