Understanding microbial communities; function, structure and dynamics

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Programme theme

The importance of microbial communities for health, industry and the natural environment cannot be overstated. Despite this, there is an enormous gap between the levels of our empirical knowledge of microbial communities composition and experimental and theoretical understanding of their function, structure, and dynamics. Developing and advancing mathematical and computational approaches for the study of microbial communities has huge potentials for this field. The aim of this programme is to build an interactive community of theoretical and empirical scientists that can provide these developments.

Click here to download the programme's final scientific report

Preprints

Title	Year	Programme
Lyapunov functions, stationary distributions, and non-equilibrium potential for chemical reaction networks Authors: DF Anderson, G Cracium, M Gopalkrishnan, C Wiuf Download PDF	2014	UMC
Finding the positive feedback loops underlying multi-stationarity Authors: E Feliu, C Wiuf Download PDF	2014	UMC
Saccharomyces cerevisiae: a nomadic yeast with no niche? Authors: Matthew R Goddard, D Greig Download PDF	2014	UMC

Title

Year

Programme

Lyapunov functions, stationary distributions, and non-equilibrium potential for chemical reaction networks

Authors: DF Anderson, G Cracium, M Gopalkrishnan, C Wiuf

Download PDF

2014

UMC

Finding the positive feedback loops underlying multi-stationarity

Authors: E Feliu, C Wiuf

Download PDF

2014

UMC

Saccharomyces cerevisiae: a nomadic yeast with no niche?

Authors: Matthew R Goddard, D Greig

Download PDF

2014

UMC

Workshops

UMCW01

Seminars

Sunday 21st August 2011
15:00 to 16:00	Chaos in biology: Experiments, implications and mathematical tools	Room 2

Tuesday 12th August 2014
14:00 to 15:00	Modelling interactions between hydrodynamics and dispersal that help shape biofilm community composition across a range of scales.	Room 2
15:00 to 16:00	A Non-exchangeable Coalescent Process Arising In Phylogenetics	Room 2

Thursday 14th August 2014
14:00 to 15:00	Bacterial migration in porous media: new statistical physics with implications for soil bioremediation and microbial ecology	Room 2
15:00 to 16:00	Superbugs vs communities in environmental bioremediation	Room 2

Tuesday 19th August 2014
14:00 to 15:00	Methanogenic Communities	Room 2
15:00 to 16:00	Modelling Biochemical Pathways	Room 2

Thursday 21st August 2014
14:00 to 15:00	Cooperation, cheating and collapse in microbial populations	Room 2
15:00 to 16:00	Chaos in biology: Experiments, implications and mathematical tools	Room 2

Tuesday 26th August 2014
14:00 to 15:00	Catalytic origami: Genetic tools and strategies for assembling 3D bacterial consortia	Room 2

Thursday 28th August 2014
14:00 to 15:00	Life on the edge - microbial evolution in the presence of drug gradients	Room 2

Tuesday 2nd September 2014
14:00 to 15:00	Understanding reactions of introduced bacteria in natural and engineered environments	Room 2
15:00 to 16:00	Metabolic interactions in microbial communities	Room 2

Thursday 4th September 2014
14:00 to 15:00	Representing microbial communities in Earth system models	Room 2
15:00 to 16:00	Theory of adaptive evolution informed by microbial experiments	Room 2

Friday 5th September 2014
14:00 to 17:00	UMC Discussion Group	Discussion Room

Monday 8th September 2014
10:30 to 12:00	Welcome meeting	Room 2
16:00 to 17:00	On the (un)reasonable (in)effectiveness of mathematics in biology: Rothschild Distinguished Visiting Fellow Lecture	Room 1
17:30 to 18:30	Wine Reception following Rothschild Lecture	No Room Required

Tuesday 9th September 2014
09:30 to 10:30	UMC Discussion Group	Room 1

Wednesday 10th September 2014
11:00 to 12:30	Registration	No Room Required
12:30 to 13:20	Lunch at Wolfson Court	No Room Required
13:20 to 13:30	Welcome from John Toland (INI Director)	No Room Required
13:30 to 14:05	Plenary Lecture 1: Contingency and convergence in microbial population dynamics	Room 1
14:05 to 14:40	Plenary Lecture 2: Cancer-like overgrowths and genomic regulatory design in microbes	Room 1
14:40 to 15:15	Plenary Lecture 3: Simple Theory and the Microbial World	Room 1
15:15 to 15:45	Afternoon Tea	No Room Required
15:45 to 16:20	Plenary Lecture 4: Phage and Origins of the Immune System	Room 1
16:20 to 16:55	Plenary Lecture 5: Survival of the unfit - how demographic noise can create suboptimal species	Room 1
16:55 to 17:10	Contributed Talk 1: Computational models of spatial behaviour of microbial communities	Room 1
17:10 to 18:00	Wine Reception and Poster Session	No Room Required

Thursday 11th September 2014
09:30 to 10:05	Plenary Lecture 6: Mixed and Hierarchical Utilization of Carbon Substrates by Bacteria	Room 1
10:05 to 10:40	Plenary Lecture 7: Numerical modelling, an interdisciplinary bridge in studying microbial biofilms	Room 1
10:40 to 10:55	Contributed Talk 2: The Initiative for the Critical Assessment of Metagenome Interpretation (CAMI)	Room 1
10:55 to 11:25	Morning Coffee	No Room Required
11:25 to 11:55	Plenary Lecture 8: Algal-bacterial consortia and evolution of mutualism	Room 1
11:55 to 12:30	Plenary Lecture 9: Structure and functions of the bacterial phyllosphere microbiota	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 14:35	Plenary Lecture 10: Phylogeny and functionality in anaerobic microbial communities: making sense of metabolite outputs and population dynamics	Room 1
14:35 to 15:10	Plenary Lecture 11: Modelling the emergent dynamics of human colonic microbiota	Room 1
15:10 to 15:25	Contributed Talk 3: A functional population model of fiber degradation by the human intestinal microbiota	Room 1
15:25 to 15:55	Afternoon Tea	Room 1
15:55 to 16:30	Plenary Lecture 12: Determining the microbial population dynamics of anaerobic digestion using metagenomics	Room 1
16:30 to 17:05	Plenary Lecture 13 (teleconference): tba	Room 1
17:05 to 17:20	Contributed Talk 4: Metabolic Modelling in an Evolutionary Framework Predicts Phenotypic Diversification of E.coli growing on Glucose as the Single Carbon Source	Room 1
17:20 to 17:35	Contributed Talk 6: Metaproteomics of algal blooms	Room 1
19:30 to 22:00	Conference Dinner at Gonville and Caius College	No Room Required

Friday 12th September 2014
09:30 to 10:05	Plenary Lecture 14: Development and Evolution in Environmental Biofilms	Room 1
10:05 to 10:40	Plenary Lecture 15: Geomicrobial kinetics: bridging the gap between laboratory and nature	Room 1
10:40 to 10:55	Contributed Talk 5: Uptake levelling in chemotactic bacteria measured by the Gini index	Room 1
10:55 to 11:25	Morning Coffee	No Room Required
11:25 to 11:55	Plenary Lecture 16: Collective Functionality Through Microbial Individuality	Room 1
11:55 to 12:30	Plenary Lecture 17: Micro-scale biological interactions shape microbial community dynamics on marine particles	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required

Monday 15th September 2014
10:30 to 12:00	UMC Get Together	Room 2

Tuesday 16th September 2014
14:00 to 15:00	Biology of Integrative and Conjugative Elements (special agents of bacterial evolution)	Room 2
15:00 to 16:00	Mathematical aspects of growing colonies	Room 2

Thursday 18th September 2014
14:00 to 14:30	Metagenome, metatranscriptome and single cell genome sequencing of biogas-producing microbial communities from production-scale biogas plants	Room 2
14:30 to 15:00	Computational tools for the taxonomic analysis of shotgun metagenome samples	Room 2
15:00 to 15:30	Gaining Insights into the Uncultured Microbial World by Computational Metagenome Analysis	Room 2
15:30 to 16:00	Toward resolving the fine scale genetic structure of microbial populations: a metagenomic Hi-C approach	Room 2

Monday 22nd September 2014
10:30 to 12:00	UMC Get Together	Room 2

Thursday 25th September 2014
14:00 to 15:00	Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a hierarchical Dirichlet process	Room 2

Monday 29th September 2014
10:30 to 12:00	UMC Get Together	Room 2

Tuesday 30th September 2014
14:00 to 15:00	Colorful niches of phototrophic microorganisms shaped by vibrations of the water molecule	Room 2

Thursday 2nd October 2014
14:00 to 15:00	The construction and use of bacterial bioreporters	Room 2
15:00 to 16:00	Modelling electrochemically-active biofilms	Room 2

Monday 6th October 2014
10:30 to 12:00	UMC Get Together	Room 2

Tuesday 7th October 2014
14:00 to 15:00	Predictability and Unpredictability in nutrient-cycling microbial ecosystems	Room 2
15:00 to 16:00	Impacts of rising CO2 on harmful cyanobacterial blooms	Room 2

Thursday 9th October 2014
09:30 to 12:30	PhreeqC tutorial session	Room 2

Monday 13th October 2014
10:30 to 12:00	UMC Get Together	Room 2

Tuesday 14th October 2014
14:00 to 15:00	TBA	Room 2
15:00 to 16:00	Microbial communities and the structure-function twins	Room 2

Thursday 16th October 2014
14:00 to 15:00	Speculation about Quantum Isolation in Biology	Room 2
15:00 to 16:00	Game-theoretical approaches in microbiology	Room 2

Monday 20th October 2014
15:00 to 16:00	Experimentally Quantifying Patterns in Microbial Eukaryote Populations	Room 2
16:00 to 17:00	The Evolution of Multicellularity	Room 1

Tuesday 21st October 2014
14:00 to 15:00	Outstanding Questions in the Ecology and Evolution of Coral Reef Microbes	Room 2

Thursday 23rd October 2014
15:00 to 16:00	TBA	Room 2

Monday 27th October 2014
12:00 to 12:30	Registration	No Room Required
12:30 to 13:20	Lunch at Wolfson Court	No Room Required
13:20 to 13:30	Welcome from John Toland (INI Director)	No Room Required
13:30 to 14:30	Plenary Lecture 1: Understanding bacterial communication and cooperation: combinatorial quorum-sensing	Room 1
14:30 to 14:45	Contributed Talk 1: The Crabtree effect and its influences on fitness of yeast populations from natural isolates	Room 1
15:00 to 15:15	Contributed Talk 2: Less is more: Selective advantages can explain the loss of biosynthetic functions in bacteria	Room 1
15:15 to 15:30	Afternoon Tea	No Room Required
15:30 to 16:30	Plenary Lecture 2: Theoretical principles of virus-host population dynamics	Room 1
16:30 to 17:30	Plenary Lecture 3: Are simple models more general?	Room 1
17:30 to 18:30	Wine Reception and Poster Session	No Room Required

Tuesday 28th October 2014
09:30 to 10:30	Plenary Lecture 4: Biofilms, particularly Biofilm Models	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 12:00	Plenary Lecture 5: Biogeochemical Reaction Modeling: Theory and Application	Room 1
12:00 to 12:15	Contributed Talk 3: The role of metabolic and immunological competition in structuring pneumococcal populations and the effects of vaccination	Room 1
12:15 to 12:30	Contributed Talk 4: How the coexistence of specialist and generalist species is influenced by the size of environmental graining	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 15:00	Plenary Lecture 6: Resolving microbial community structure and function using next generation sequencing	Room 1
15:00 to 15:15	Contributed Talk 5: Successive range expansions of interacting microbial populations promote spatial diversity	Room 1
15:15 to 15:30	Contributed Talk 6: Carbon source-dependent metabolic costs of amino acid biosynthesis in Escherichia coli	Room 1
15:30 to 16:00	Afternoon Tea	No Room Required
16:00 to 17:00	Discussion Session: Different approaches to the modelling of microbial communities	Room 1

Wednesday 29th October 2014
09:30 to 10:30	Plenary Lecture 7: Mathematics of social behavior	Room 1
10:30 to 10:45	Contributed Talk 7: Social evolution of toxic metal bioremediation in P.aeruginosa	Room 1
10:45 to 11:30	Morning Coffee	No Room Required
11:30 to 12:30	Plenary Lecture 8: Game theory for modelling microbial communities	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 15:00	UMC Discussion Session	Room 1
19:30 to 22:00	Conference Dinner at Emmanuel College	No Room Required
19:30 to 22:00	Conference Dinner at Emmanuel College	No Room Required

Thursday 30th October 2014
09:00 to 09:20	Registration	No Room Required
09:20 to 09:30	Welcome from Christie Marr (INI Deputy Director)	No Room Required
09:30 to 10:05	Plenary Lecture 1: Non-Equilibrium Dynamics in Ecological Communities	Room 1
10:05 to 10:40	Plenary Lecture 2: tba	Room 1
10:40 to 10:55	Contributed Talk 1: Structure and functions of the bacterial root microbiota in wild and domesticated barley	Room 1
10:55 to 11:25	Morning Coffee	No Room Required
11:25 to 11:55	Plenary Lecture 3: Individual-level models, demographic stochasticity and spatio-temporal variations in microbial populations	Room 1
11:55 to 12:30	Plenary Lecture 4: Modeling Ocean Viruses: From Infections to Ecosystems	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 14:35	Plenary Lecture 5: Neutral models on island chains: biodiversity measures, and the 'everything is everywhere' problem.	Room 1
14:35 to 15:10	Plenary Lecture 6: Ecology and the evolution of multicellularity	Room 1
15:10 to 15:25	Contributed Talk 2: Structure, Function and Dynamics in Microbial Communities	Room 1
15:25 to 15:55	Afternoon Tea	No Room Required
15:55 to 16:30	Plenary Lecture 7: Spatio-temporal dynamics of microbial ecosystem metabolism	Room 1
16:30 to 17:05	Plenary Lecture 8: An Economic Framework of Microbial Trade	Room 1
17:05 to 17:20	Contributed Talk 3: Metabolic Network Approaches for delineating functional division within Bacterial Communities	Room 1
17:20 to 18:30	Wine Reception and Poster Session	No Room Required

Friday 31st October 2014
09:30 to 10:05	Plenary Lecture 9: tba	Room 1
10:05 to 10:40	Plenary Lecture 10: Feedback between microevolution and community structure	Room 1
10:40 to 10:55	Contributed Talk 4: Understanding microbial networks driving nitrogen cycling in soil	Room 1
10:55 to 11:25	Morning Coffee	No Room Required
11:25 to 11:55	Plenary Lecture 11: The evolution of groups and microbial collectives	Room 1
11:55 to 12:30	Plenary Lecture 12: The causes and consequences of metabolic specialization	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required

Monday 3rd November 2014
09:00 to 17:00	COMSOL tutorial	Discussion Room
10:30 to 12:00	UMC Get Together	Room 1

Tuesday 4th November 2014
10:00 to 10:05	Welcome from Orkun Soyer	Room 1
10:05 to 10:20	Taking a bottom-up approach: using metabolic models to study how interactions shape natural-occurring microbial communities	Room 1
10:20 to 10:35	tba	Room 1
10:35 to 10:50	Issues in Flux Balance Analysis	Room 1
10:50 to 11:15	Morning Coffee and Discussions	No Room Required
11:15 to 11:30	Importance of Standardising Genome-Scale Stoichiometric Models	Room 1
11:30 to 11:45	Standardisation of stoichiometric models: how and why	Room 1
11:45 to 12:00	Constraint-based modeling of microbial communities and their interaction with the host	Room 1
12:00 to 13:00	Sandwich Lunch at INI	No Room Required
13:00 to 13:15	Exchanging stoichiometric models: interoperability at genome scale	Room 1
13:15 to 13:30	tba	Room 1
13:30 to 13:45	Optimal metabolic dynamics resolved by cyclic FBA	Room 1
13:45 to 14:00	Implementing Trade-offs in FBA	Room 1
14:00 to 14:30	Afternoon Tea and Discussions	No Room Required
14:30 to 17:00	Discussions (suggested topics): Limitations of SM, Optimisation function, Standardisation of SM models	Room 1

Wednesday 5th November 2014
14:00 to 15:00	Energetic feedback on chromatin state defines a system-wide reset point	Room 1
15:00 to 16:00	Interaction driven spatial patterning in microbial communities	Room 1

Thursday 6th November 2014
14:00 to 15:00	Controlling chaos in population models	Room 2
15:00 to 16:00	How microbial communities drove the evolution of the genetic code more than 3.8 billion years ago	Room 2

Monday 10th November 2014
10:30 to 12:00	UMC Get Together	Room 2
14:00 to 15:00	Understanding the structure and function of microbes involved in cycling of trace gases in the environment	Room 1

Thursday 13th November 2014
14:00 to 15:00	Why are there so few microbial species?	Room 2
15:00 to 16:00	Omics approaches reveal how chemistry governs the biology of cystic fibrosis lung infections	Room 2

Friday 14th November 2014
11:00 to 12:00	Modelling Macro Ecological Patterns: Neutral Theory and Beyond	Room 2

Monday 17th November 2014
10:30 to 12:00	UMC Get Together	Room 2

Tuesday 18th November 2014
14:00 to 15:00	Sexual signals between yeast cells	Room 2

Friday 21st November 2014
14:00 to 15:00	Life at High Reynolds Number	Room 2

Monday 24th November 2014
10:30 to 12:00	UMC Get Together	Room 2
17:00 to 18:00	Wine Reception to follow Robert May's Seminar	No Room Required

Tuesday 25th November 2014
14:00 to 17:00	Informal discussion	Room 1
14:00 to 15:00	The role of immune selection on the population structure of metabolic genes in pathogenic bacteria	Room 2
15:00 to 16:00	Spiralling patterns in models inspired by bacterial games with cyclic competition	Room 2

Wednesday 26th November 2014
11:00 to 12:15	Registration	No Room Required
12:30 to 13:20	Lunch at Wolfson Court	No Room Required
13:20 to 13:30	Welcome from John Toland (INI Director)	No Room Required
13:30 to 14:05	Plenary Lecture 1: Engineering syntrophic exchange in synthetic microbial communities	Room 1
14:05 to 14:40	Plenary Lecture 2: Cooperation and competition in microbial communities	Room 1
14:40 to 15:15	Plenary Lecture 3: Bacterial interactions in synthetic communities and in the wild	Room 1
15:15 to 15:45	Afternoon Tea	No Room Required
15:45 to 16:20	Plenary Lecture 4: Eco-engineering of fermentative microbial communities: the role of keystone species	Room 1
16:20 to 16:55	Plenary Lecture 5: Engineering microbial community architecture to set community metabolism	Room 1
16:55 to 17:10	Contributed Talk 1: Synthetic microbial systems as ecosystems simulators	Room 1
17:10 to 18:00	Welcome Wine Reception and Poster Session	Room 1

Thursday 27th November 2014
09:30 to 10:05	Plenary Lecture 6: Metabolic conflicts drive multi-scale organization of microbial activities	Room 1
10:05 to 10:40	Plenary Lecture 7: Lignocellulose degradation by enriched microbial consortia from cow rumen and termite gut	Room 1
10:40 to 10:55	Contributed Talk 2: Long distance relationships between algae and bacteria	Room 1
10:55 to 11:25	Morning Coffee	No Room Required
11:25 to 11:55	Plenary Lecture 8: Towards a predictive framework for microbial community dynamics in drinking water systems	Room 1
11:55 to 12:30	Plenary Lecture 9: Computation and Polymer Synthesis for Designer Quorum Sensing Behaviour	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 14:35	Plenary Lecture 10: tba	Room 1
14:35 to 15:10	Plenary Lecture 11: The good the bad and the irrelevant. Sequential analyses of the sputum microbiome in patients with Chronic Obstructive Pulmonary Disease	Room 1
15:10 to 15:25	Contributed Talk 3: Flux analysis in microbial ecosystems	Room 1
15:25 to 15:55	Afternoon Tea	No Room Required
15:55 to 16:30	Plenary Lecture 12: The paradox of nitrification in acid soils and lessons for microbial community ecology	Room 1
16:30 to 17:05	Plenary Lecture 13: Variability and Alternative Community States in Microbial Communities	Room 1
17:05 to 17:20	Contributed Talk 4: Optimization-based tools for bacterial ecology design	Room 1
17:20 to 17:35	Contributed Talk 5: Numerical Continuation of Equilibria of Cell Population Models with Internal Cell Cycle	Room 1
19:30 to 22:00	Conference Dinner at Cambridge Union Society hosted by Cambridge Dining Co.	No Room Required

Friday 28th November 2014
09:30 to 10:05	Plenary Lecture 14: Ecosystems Biology: from data to control of microbial communities	Room 1
10:05 to 10:40	Plenary Lecture 15: Can bioenergetics tell us more about microbial ecosystems activity than community identity?	Room 1
10:40 to 11:25	Morning Coffee	No Room Required
11:25 to 11:55	Plenary Lecture 16: Managing microbial communities in anaerobic membrane bioreactors	Room 1
11:55 to 12:30	Plenary Lecture 17: Modeling biofilm formation in porous media and fouling in membrane processes	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required

Monday 1st December 2014
10:30 to 12:00	UMC Get Together	Room 2

Wednesday 3rd December 2014
16:30 to 17:00	Informal discussion	Discussion Room

Thursday 4th December 2014
13:30 to 13:45	Welcome & Introduction	Room 1

Monday 8th December 2014
10:30 to 12:00	UMC Get Together	Room 2

Understanding microbial communities; function, structure and dynamics

Organisers

Rosalind Allen University of Edinburgh
Thomas Curtis Newcastle University
Thomas Pfeiffer Massey University
William Sloan University of Glasgow
Orkun Soyer University of Warwick
Carsten Wiuf Københavns Universitet (University of Copenhagen)

Understanding microbial communities; function, structure and dynamics

Programme theme

Preprints

Lyapunov functions, stationary distributions, and non-equilibrium potential for chemical reaction networks

Finding the positive feedback loops underlying multi-stationarity

Saccharomyces cerevisiae: a nomadic yeast with no niche?

Workshops

Summer school

Microbial communities: the unknown unknowns

Understanding natural microbial communities

Engineering synthetic microbial communities

Microbial communities: current approaches and open challenges

Seminars

Organisers

Supported By

Understanding microbial communities; function, structure and dynamics

Programme theme

Preprints

Lyapunov functions, stationary distributions, and non-equilibrium potential for chemical reaction networks

Finding the positive feedback loops underlying multi-stationarity

Saccharomyces cerevisiae: a nomadic yeast with no niche?

Workshops

Summer school

Microbial communities: the unknown unknowns

Understanding natural microbial communities

Engineering synthetic microbial communities

Microbial communities: current approaches and open challenges

Seminars

Organisers

Supported By

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