Microbial communities: current approaches and open challenges

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Workshop theme

Microbial communities are ubiquitous and are crucially relevant to biogeochemical cycles as well as to plant and animal health. Given these central roles, research into microbial communities has been expanding over the last decade and is bound to continue to do so for decades to come. Since microbial communities are physically organised, dynamical, complex systems, this research necessitates combination of biological, physical, and mathematical approaches. The healthy development of this interdisciplinary field thus requires continued facilitation of crossing of disciplinary boundaries, both by established scientists and by emerging generation of new scientists. This follow-on workshop, following from its parent programme that was run in 2014, will enable a continued dialog among different researchers working on microbial communities and will draw in new talent. The main aim of this follow-on workshop is to further facilitate the interdisciplinary exchanges in microbial communities’ research and identify the emerging challenge areas in light of latest technological and conceptual developments in the field.

The meeting will feature approx.. 20 invited and 25 contributed talks. On the first day, there will be parallel tutorials focusing on mathematical models and experimental measurements of microbial communities. Selected talks will cover broad and recent topics in microbial community research, including:

Microbial community bioinformatics
Biophysics of spatial communities
Mathematical models of community dynamics
Ecology-Evolution feedbacks in communities
Synthetic community engineering
Applications of microbial communities

The event is additionally supported by Gordon and Betty Moore Foundation.

Fees

Registration Only

Registration Package: £208
Student Registration Package: £158
Virtual Registration Package: £0

The Registration Package includes admission to all seminars, lunches and refreshments on the days that lectures take place (Monday - Friday), wine reception and formal dinner, but does not include other meals or accommodation.

Accommodation

Unfortunately we do not have any accommodation to offer so all successful applicants will need to source their own accommodation.

Please see the Hotels Combined website for a list of local hotels and guesthouses.

Meals

Lunch

Lunch will be held at Churchill College. Timings will be confirmed with the timetable.

Evening Meal

Participants are free to make their own arrangements for dinner.

Formal Dinner

The Formal Dinner will be held at Robinson College on Wednesday 12th October.

The event is a tradition for INI participants and gives you a chance to socialise with your colleagues on a more personal level. It is not one to miss!

Timetable

Monday 10th October 2022
09:00 to 09:55	Registration and Morning Coffee	No Room Required
09:55 to 10:00	Ulrike Tillmann University of Oxford Welcome Talk	Room 1
10:00 to 11:30	Babak Momeni Boston College Tutorial: Spatial and ODE modelling of communities	Room 1
11:30 to 11:45	Morning Coffee	No Room Required
11:45 to 13:15	Stefan Schuster Friedrich-Schiller-Universität Jena Tutorial: FBA and FBA-based modelling of communities	Room 1
13:15 to 14:15	Lunch at Churchill College	No Room Required
14:15 to 14:30	Introduction to workshop by organisers	Room 1
14:30 to 15:05	Otto Cordero Massachusetts Institute of Technology TBA	Room 1
15:05 to 15:25	Sarah Duxbury University of Warwick Contributed Talk: Robust spatial organisation and community composition of a phototrophic microbial community predicts metabolic interactions	Room 1
15:25 to 15:45	Ruben Garrido-Oter None / Other Contributed Talk: Design and experimental evolution of phototrophic microbial consortia	Room 1
15:45 to 16:15	Afternoon Tea	No Room Required
16:15 to 16:50	Amelia Barber Friedrich-Schiller-Universität Jena; Leibniz Institute for Natural Product Research and Infection Biology A global survey of host, aquatic, and soil microbiomes reveals ecological properties shared between bacterial and fungal generalists	Room 1
16:50 to 17:10	Ashish George University of Illinois at Urbana-Champaign Contributed Talk: Functional universality in slow-growing microbial communities arises from thermodynamic constraints	Room 1
17:10 to 17:30	Shreya Arya University of Illinois at Urbana-Champaign Contributed Talk: Predicting microbial community compositions using compressive sensing	Room 1
17:30 to 19:30	Welcome Wine Reception & Poster Session at the INI	No Room Required
17:30 to 19:30	Poster Session	Discussion Room

Tuesday 11th October 2022
09:00 to 09:35	Kiran Patil University of Cambridge Xenobiotic-Microbiome Interactions	Room 1
09:35 to 10:10	Stefanie Widder Medical University of Vienna Antagonistic microbial community processes demarcate different pulmonary exacerbation types in Cystic Fibrosis	Room 1
10:10 to 10:30	Stefan Schuster Friedrich-Schiller-Universität Jena Studying microbial communities by evolutionary game theory	Room 1
10:30 to 11:00	Group Photo and Morning Coffee	No Room Required
11:00 to 11:35	Sunil Laxman Biochemical logic for extreme metabolic specialization driving division of labor within clonal cell communities	Room 1
11:35 to 11:55	Lukas Eigentler University of Dundee Contributed Talk: Competition and coexistence in bacterial range expansion: the role of founder cells and spatial heterogeneities	Room 1
11:55 to 12:15	Daniel Garza KU Leuven Contributed Talk: Exploring the dynamic metabolic strategies of a gut bacterial consortium	Room 1
12:15 to 14:30	Lunch at Churchill College	No Room Required
14:30 to 14:50	Glen Dsouza ETH Zürich; Swiss Federal Institute of Aquatic Science and Technology (Eawag) Interspecies interactions determine growth dynamics of biopolymer degrading populations in microbial communities.	Room 1
14:50 to 15:10	Lluís Hernández-Navarro University of Leeds Contributed Talk: Eco-evolutionary dynamics of cooperative antimicrobial resistance	Room 1
15:10 to 15:45	Angus Buckling University of Exeter Antibiotics as drivers of bacteria-plasmid network structure	Room 1
15:45 to 16:15	Afternoon Tea	No Room Required
16:15 to 16:50	Kirsty Wan University of Exeter Microscale motility: challenges, opportunities, ecological considerations	Room 1
16:50 to 17:10	Astrid Stubbusch ETH Zürich The role of contact-dependent antagonism in marine communities	Room 1
17:10 to 17:30	Simon Van vliet Universität Basel Predicting global dynamics of microbial communities from the molecular properties of cell-cell interactions	Room 1
17:30 to 19:30	Poster Session	Discussion Room

Wednesday 12th October 2022
09:00 to 09:35	Thomas Curtis Newcastle University; University of Newcastle upon Tyne TBA	Room 1
09:35 to 10:10	James Chong University of York Making sense of sewage	Room 1
10:10 to 10:30	Michael Manhart ETH Zurich Evolution of nutrient co-limitation in microbial communities	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 11:35	Katherine Coyte University of Manchester Understanding the impact of microbial interactions on early-life microbiome dynamics	Room 1
11:35 to 11:55	Jamie Lee Imperial College London Contributed Talk: Designing novel microbial therapies for atopic dermatitis using mechanistic modelling	Room 1
11:55 to 12:15	Knut Drescher Universität Basel Contributed Talk: Unicellular and multicellular stress responses in bacterial biofilms	Room 1
12:15 to 14:00	Lunch at Churchill College	No Room Required
14:00 to 15:30	Todd Parson Sorbonne Université Tutorial: Stochastic/statistical modelling of communities	Room 1
15:45 to 17:45	Chris Quince University of Warwick Tutorial: Metagenomics analyses	Discussion Room
19:30 to 22:00	Formal Dinner at Robinson College	No Room Required

Thursday 13th October 2022
09:00 to 09:35	Thomas Bell Imperial College London Ecosystem functioning in miniature	Room 1
09:35 to 10:10	Jef Huisman Universiteit van Amsterdam Molecular vibrations of water predict global distributions of phototrophic organisms in lakes and oceans	Room 1
10:10 to 10:30	Marco Mauri Friedrich-Schiller-Universität Jena Contributed Talk: Dynamics of algae-bacteria interactions in artificial plankton communities	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 11:35	David Johnson None / Other Microbial spatial self-organization and the spread of plasmid-encoded functional novelty	Room 1
11:35 to 11:55	Maaike Sangster INRIA Grenoble - Rhône-Alpes Analysis and control of an E.coli cross-feeding consortium on an automated experimental platform	Room 1
11:55 to 12:15	Amir Mitchell University of Massachusetts Contributed Talk: Systematic mapping of the cross-feeding networks in E. coli uncovers ideal shared goods for mutualistic communities	Room 1
12:15 to 14:30	Lunch at Churchill College	No Room Required
14:30 to 14:50	Miaoxiao Wang ETH Zürich Contributed Talk: Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor	Room 1
14:50 to 15:10	Sonal . University College London Contributed Talk: Deciphering a novel response to hydrogen sulfide in budding yeast	Room 1
15:10 to 15:45	Marcel Kuypers Max Planck Institute for Marine Microbiology Microbial nitrogen cycling networks in the changing ocean	Room 1
15:45 to 16:15	Afternoon Tea	No Room Required
16:15 to 18:10	Open Discussion Sessions	Room 1

Friday 14th October 2022
09:00 to 09:35	Karoline Faust KU Leuven Application of microbial community models to human gut bacteria – challenges and insights	Room 1
09:35 to 10:10	Wenying Shou University College London TBA	Room 1
10:10 to 10:30	Alex Yuan University of Washington; Fred Hutchinson Cancer Research Centre Contributed Talk: Rigorous and general statistical tests for correlations between time series	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 11:35	Leo Lahti University of Turku Techniques & tools for microbiome data integration in longitudinal profiling studies	Room 1
11:35 to 11:55	Todd Parson Sorbonne Université Contributed Talk: TBA	Room 1
11:55 to 12:15	Jimmy Gonzalez Nunez Johns Hopkins University Contributed Talk: The Role of Quenched Noise in the Evolution of Populations undergoing Range Expansions	Room 1
12:15 to 14:30	Lunch at Churchill College	No Room Required
14:30 to 14:50	Babak Momeni Boston College In vitro communities of nasal bacteria as a model for studying community dynamics and intervention	Room 1
14:50 to 15:10	Guilhem Sommeria-Klein University of Turku Contributed Talk: Modelling host-associated microbiota over host evolutionary time	Room 1
15:10 to 15:45	Chris Barnes University College London Design and control of microbial communities	Room 1

Understanding microbial communities; function, structure and dynamics

Microbial communities: current approaches and open challenges

Organisers

Rosalind Allen University of Edinburgh
Marco Polin University of Warwick; Mediterranean Institute for Advanced Studies (IMEDEA)
Chris Quince University of Glasgow
Wenying Shou University College London
Orkun Soyer University of Warwick
Carsten Wiuf Københavns Universitet (University of Copenhagen)

Speakers

Sonal . University College London
Shreya Arya University of Illinois at Urbana-Champaign
Amelia Barber Friedrich-Schiller-Universität Jena; Leibniz Institute for Natural Product Research and Infection Biology
Chris Barnes University College London
Thomas Bell Imperial College London
Angus Buckling University of Exeter
James Chong University of York
Otto Cordero Massachusetts Institute of Technology
Katherine Coyte University of Manchester
Thomas Curtis Newcastle University; University of Newcastle upon Tyne
Knut Drescher Universität Basel
Glen Dsouza ETH Zürich; Swiss Federal Institute of Aquatic Science and Technology (Eawag)
Sarah Duxbury University of Warwick
Lukas Eigentler University of Dundee
Karoline Faust KU Leuven
Ruben Garrido-Oter None / Other
Daniel Garza KU Leuven
Ashish George University of Illinois at Urbana-Champaign
Jimmy Gonzalez Nunez Johns Hopkins University
Lluís Hernández-Navarro University of Leeds
Jef Huisman Universiteit van Amsterdam
David Johnson None / Other
Marcel Kuypers Max Planck Institute for Marine Microbiology
Leo Lahti University of Turku
Sunil Laxman
Jamie Lee Imperial College London
Michael Manhart ETH Zurich
Marco Mauri Friedrich-Schiller-Universität Jena
Amir Mitchell University of Massachusetts
Babak Momeni Boston College
Todd Parson Sorbonne Université
Kiran Patil University of Cambridge
Chris Quince University of Glasgow
Maaike Sangster INRIA Grenoble - Rhône-Alpes
Stefan Schuster Friedrich-Schiller-Universität Jena
Wenying Shou University College London
Guilhem Sommeria-Klein University of Turku
Astrid Stubbusch ETH Zürich
Ulrike Tillmann University of Oxford
Simon Van vliet Universität Basel
Kirsty Wan University of Cambridge
Miaoxiao Wang ETH Zürich
Stefanie Widder Medical University of Vienna
Alex Yuan University of Washington; Fred Hutchinson Cancer Research Centre

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Participants

Georgina Alabone None / Other
Rosalind Allen University of Edinburgh
Ben Allen University of Newcastle upon Tyne
Shreya Arya University of Illinois at Urbana-Champaign
Matthew Asker University of Leeds
Vironika Bahat University of Glasgow
Basak Bahcivanci None / Other
Amelia Barber Friedrich-Schiller-Universität Jena; Leibniz Institute for Natural Product Research and Infection Biology
Chris Barnes University College London
Megan Barnett British Geological Survey
Fiona Bate University of York
Thomas Bell Imperial College London
Angus Buckling University of Exeter
Freya Bull University of Edinburgh
Fatima Ceballos Rodriguez-Conde University College London
Marianna Cerasuolo University of Portsmouth
James Chong University of York
Otto Cordero Massachusetts Institute of Technology
Katherine Coyte University of Manchester
Thomas Curtis Newcastle University; University of Newcastle upon Tyne
Knut Drescher Universität Basel
Glen Dsouza ETH Zürich; Swiss Federal Institute of Aquatic Science and Technology (Eawag)
Sarah Duxbury University of Warwick
Lukas Eigentler University of Dundee
Jesus Mauricio Encinas Riveros ICTP-SAIFR/IFT-UNESP, Sao Paulo; Universidade de São Paulo
Karoline Faust KU Leuven
Daniel Garza KU Leuven
Ashish George University of Illinois at Urbana-Champaign
Jimmy Gonzalez Nunez Johns Hopkins University
Alyssa Henderson ETH Zürich
Lluís Hernández-Navarro University of Leeds
Jef Huisman Universiteit van Amsterdam
Matthias Hülsmann ETH Zürich
Mani Sai Suryateja Jammalamadaka Massachusetts Institute of Technology
David Johnson None / Other
Ciara Keating University of Glasgow
Isaac Klapper Temple University
Marcel Kuypers Max Planck Institute for Marine Microbiology
Pierre D.M. Lafont University of Edinburgh
Leo Lahti University of Turku
Sunil Laxman
Jamie Lee Imperial College London
Renee Martha Llamas Ramirez University College London
Rachel Los Technische Universiteit Delft
Tatjana Malycheva Friedrich-Schiller-Universität Jena
Michael Manhart ETH Zurich
Thierry Marti ETH Zurich
Marco Mauri Friedrich-Schiller-Universität Jena
Amir Mitchell University of Massachusetts
Mauro Mobilia University of Leeds
Babak Momeni Boston College
Coralie Muller INRIA Bordeaux - Sud-Ouest
Said Munoz montero Imperial College London
Todd Parson Sorbonne Université
Kiran Patil University of Cambridge
Ellen Piercy King's College London
Marco Polin University of Warwick; Mediterranean Institute for Advanced Studies (IMEDEA)
Chris Quince University of Warwick
Sebastien Raguideau Earlham Institute (formerly The Genome Analysis Centre)
Divvya Ramesh ETH Zürich
Serina Robinson Swiss Federal Institute of Aquatic Science and Technology (Eawag)
Camila Rojas Villalobos Universidad San Sebastián, Santiago, Chile; Centro Científico y Tecnológico de Excelencia Ciencia & Vida
Jerko Rosko University of Warwick
Chandler Ross University of Turku
Pallabita Saha KU Leuven
Derryk Schieck University of Warwick
Olga Schubert ETH Zurich
Stefan Schuster Friedrich-Schiller-Universität Jena
Xiang Shi University of Glasgow
Wenying Shou University College London
Guilhem Sommeria-Klein University of Turku
Orkun Soyer University of Warwick
Astrid Stubbusch ETH Zürich
Philipp Tandler Swiss Federal Institute of Aquatic Science and Technology (Eawag); ETH Zürich
Pablo Ugalde INRIA Bordeaux - Sud-Ouest
João Pedro Valeriano Miranda UNESP
Simon Van vliet Universität Basel
Thomas Vinestock King's College London
Kirsty Wan University of Exeter
Miaoxiao Wang ETH Zürich
Robert West University of Warwick
Stefanie Widder Medical University of Vienna
Carsten Wiuf Københavns Universitet (University of Copenhagen)
Xueqin Yang University College London; Sun Yat-sen University
Alex Yuan University of Washington; Fred Hutchinson Cancer Research Centre
Haris Zafeiropoulos KU Leuven
Sophie Zhu University College London; Imperial College London
Agustina Ziliani ETH Zürich; None / Other