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Timetable (UMCW04)

Engineering and Control of Natural and Synthetic Microbial Communities

Wednesday 26th November 2014 to Friday 28th November 2014

Wednesday 26th November 2014
11:00 to 12:15 Registration
12:30 to 13:20 Lunch at Wolfson Court
13:20 to 13:30 Welcome from John Toland (INI Director)
13:30 to 14:05 H Wang (Columbia University)
Plenary Lecture 1: Engineering syntrophic exchange in synthetic microbial communities
Co-authors: Michael T. Mee (Boston University), James J. Collins (Boston University), George M. Church (Harvard Medical School)

Metabolic crossfeeding is an important process that can broadly shape microbial communities. However, little is known about specific crossfeeding principles that drive the formation and maintenance of individuals within a mixed population. Here, we describe the construction of a series of synthetic syntrophic communities to probe the complex interactions underlying metabolic exchange of amino acids. We experimentally analyzed multimember, multidimensional communities of Escherichia coli of increasing sophistication to assess the outcomes of synergistic crossfeeding. We find that biosynthetically costly amino acids including methionine, lysine, isoleucine, arginine, and aromatics, tend to promote stronger cooperative interactions than amino acids that are cheaper to produce. Furthermore, cells that share common intermediates along branching pathways yielded more synergistic growth, but exhibited many instances of both positive and negative epistasis when these interactions sca led to higher dimensions. In more complex communities, we find certain members exhibiting keystone species-like behavior that drastically impact the community dynamics. Based on comparative genomic analysis of >6,000 sequenced bacteria from diverse environments, we present evidence suggesting that amino acid biosynthesis has been broadly optimized to reduce individual metabolic burden in favor of enhanced crossfeeding to support synergistic growth across the biosphere. These results improve our basic understanding of microbial syntrophy while also highlighting the utility and limitations of current modeling approaches to describe the dynamic complexities underlying microbial ecosystems. This work sets the foundation for future endeavors to resolve key questions in microbial ecology and evolution, and presents a platform to develop better and more robust engineered synthetic communities for industrial biotechnology.

Related links: - Wang Lab at Columbia University
14:05 to 14:40 K Foster (University of Oxford)
Plenary Lecture 2: Cooperation and competition in microbial communities
Since Darwin, evolutionary biologists have been fascinated by cooperative behavior. Honeybee workers labor their whole life without reproducing, birds make alarm calls, and humans often help one another. One major group that remains relatively unexplored, however, is the microbes whose full spectrum of sociality only recently came to light. Microbes often live in large dense groups where one cell can strongly affect the survival and reproduction of others. But do microbes typically help or harm those around them? We study this question using a diversity of systems, including computer simulations, pseudomonad bacteria and budding yeast. We find that single-genotype patches naturally emerge in microbial groups, which creates favorable conditions for cooperation within a particular genotype. Moreover, some microbes actively adjust both genotypic assortment and investment into social traits in a way that promotes cooperation within a genotype. However, our work on interactions be tween different microbial genotypes suggests that, here, the evolution of competitive phenotypes is more likely than cooperation. This leads us to a simple model – the genotypic view – that predicts microbes will evolve to help their own genotype but harm most other strains and species that they meet. We are now moving to understand how our understanding of cooperation and competition in microbial communities can contribute to design principles associated with synthetic and natural systems.
14:40 to 15:15 Plenary Lecture 3: tba INI 1
15:15 to 15:45 Afternoon Tea
15:45 to 16:20 E Trably (INRA - Institut National de la Recherche Agronomique)
Plenary Lecture 4: tba
16:20 to 16:55 B Smets (Technical University of Denmark)
Plenary Lecture 5: Engineering microbial community architecture to set community metabolism
The composition of a microbial community is a major indicator of a community’s metabolic potential. However, the spatial structure of that community, imposed or inherently present, can dictate its extant activity. We are keen to explore how we can steer the spatial structure of open and synthetic microbial communities to select or stabilize a target community metabolism from its constituent members. I will provide experimental and computational insights in our efforts to engineer spatially structured communities to generate redox-stratified biofilms for autotrophic nitrogen removal. These communities can provide test grounds for ecological enquiries and building blocks for technological applications.
16:55 to 17:10 O Croze (University of Cambridge)
Contributed Talk 1: tba
17:10 to 18:00 Welcome Wine Reception and Poster Session INI 1
Thursday 27th November 2014
09:30 to 10:05 V de Lorenzo ([Centro Nacional de Biotecnología])
Plenary Lecture 6: Metabolic conflicts drive multi-scale organization of microbial activities
Biological bottlenecks for microbial biodegradation of recalcitrant compounds in the environment include [i] unfavourable thermodynamics of (bio)chemical reactions at stake, [ii] lack of specificity of existing pathways and enzymes for novel substrates, and [iii] physicochemical stress encountered in polluted sites. Besides these limitations, bacterial cells also experience increased endogenous oxidative stress during metabolism of aromatic compounds, which is exacerbated when enzymes meet suboptimal substrates. Evolving bacterial metabolism is thus shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks -and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. These features suggest that the physical structure of existing biosystems, from operon assemblies to multi-cellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. We have examined oxidative stress brought about by the still-evolving 2,4-dinitrotoluene biodegradative pathway in Burkholderia sp. DNT. The dnt pathway of this bacterium apparently evolved from a precursor naphthalene degradation route and the first enzyme (2,4-dinitrotoluene dioxygenase) maintains some activity towards its earlier substrate. Examination of both in vivo reactions and the associated regulatory system suggests that ROS production is the first bottleneck that evolving pathways have to overcome for dealing with novel compounds. Evolutionary consequences -and some hints and genetic tools for engineering multi-strain biocatalysts- will be discussed.
10:05 to 10:40 G Hernandez-Raquet ([Institut National de la Recherche Agronomique - LISBP INSA, Toulouse])
Plenary Lecture 7: Lignocellulose degradation by enriched microbial consortia from cow rumen and termite gut
Co-authors: Lucas Auer (idem), Adèle Lazuca (idem), Maider Abadie (idem), Gunnar Oelker (idem)

Bioconversion of lignocellulosic biomass into energy and synthons of industrial interest is of current concern to reduce the fossil energy dependence. Lignocellulose can be converted into carboxylates which can be used to produce added-value products (e.g biofuels or bioplastics). Such transformation can be realized by microbial consortia issued from the digestive tract ruminants and phytophage insects. Our aim was to produce microbial consortia displaying stable microbial diversity, high lignocellulolytic potential and high capacity to produce carboxylates using termite gut and cow rumen microbiomes. We also wanted to correlate the functional diversity of these consortia with their enzymatic activity and lignocellulose degradation profiles. To this aim, we studied the lignocellulolytic capacities of cow rumen and gut microbiomes of four species of tropical termites (Termes hospes, Microcerotermes parvus, Nasutitermes lujae and N. ephratae). Lignocellulose transformation was tested in anaerobic reactors (35°C) using wheat straw as sole carbon source. Carboxylate production and residual lignocellulosic substrate were regularly monitored during the incubation period (15 d). Our data showed that gut microbiomes from N. ephratae displayed high capacities to degrade lignocellulose. N. ephratae cow rumen microbiomes were selected to enrich the most active lignocellulolytic spe cies by sequencing batch reactor process. After 10-12 cycles, stable consortia were obtained. Sequencing of 16S rRNA gene showed important differences in the functional species present in these ecosystems compared to the initial communities. The enzymatic activities (endoglucanase, ß-glucosidase, xylanase, ß-xylosidase), mainly associated to the cell biomass, suggested the production of cellulosome-like systems. In this presentation, insights in enzymes activities and diversity will be discussed, providing better understanding of lignocellulose deconstruction by microbial consortia.

10:40 to 10:55 JF Poyatos (Consejo Superior de Investigaciones Cientificas)
Contributed Talk 2: tba
10:55 to 11:25 Morning Coffee
11:25 to 11:55 A Pinto (University of Glasgow)
Plenary Lecture 8: tba
11:55 to 12:30 C Picioreanu (Delft University of Technology)
Plenary Lecture 9: tba
12:30 to 13:30 Lunch at Wolfson Court
14:00 to 14:35 M Asally (University of Warwick)
Plenary Lecture 10: tba
14:35 to 15:10 M Barer (University of Leicester)
Plenary Lecture 11: The good the bad and the irrelevant. Sequential analyses of the sputum microbiome in patients with Chronic Obstructive Pulmonary Disease
Co-authors: Koirobi Haldar (University of Leiceister), Mona Bafadhel (University of Oxford), Chris Brightling (University of Leiceister)

COPD is a chronic respiratory disease associated with progressive deterioration of lung function and eventually death from respiratory failure; chronic exposure to smoke is the major aetiological risk factor and the disease is a major WHO priority. COPD patients have excess production of mucus in their lower airways and this is coughed up as sputum which supports an abundant and diverse microbiome. The course of the disease is characterised by exacerbations in which cough and sputum production increase and lung function worsens. The causes of COPD exacerbations are hotly debated and are likely to be multiple. The view that infections, attributable to one or more microbial pathogen, are the primary cause of exacerbations is widely accepted by physicians and sanctioned by the almost universal use of antibiotics. However, rigorous evidence in support of this view is lacking. We have conducted the first sequential study of the sputum microbiome in COPD patients with samples taken when stable, at the time of exacerbation (prior to antibiotics) then 2 and six weeks later, when all had recovered from the episode. Microbiome profiling was based on Roche 454 sequencing of 16S-rDNA amplicons. With the exception of a small group of virus positive exacerbations the events could not be explained by the arrival or increased abundance of recognised pathogens. Microbiome analyses revealed a high frequency of 20 different phyla in most samples but consistent dominance of Proteobacteria and Firmicutes. No clear pattern with respect to composition or diversity of the microbiome was associated with exacerbations. However, cluster analysis revealed a subgroup of exacerbations in which disturbance of the ratio between Proteobacteria and Firmicutes occurred and subsequently returned to the stable value following therapy. We propose that this subgroup may be patients who need antibiotics while they are unnecessary or even harmful for patients whose microbiomes did not show this pattern.

15:10 to 15:25 R Kleerebezem (Delft University of Technology)
Contributed Talk 3: Flux analysis in microbial ecosystems
Environmental bioprocess modeling has proven as a very useful tool for analysis of natural and man-made ecosystems. Attributing specific redox reactions to specific microbial groups allows for investigating a complex microbial community as the sum of the different reactions in the system. Inclusion of the microbial redox reactions in bioreactor systems and by including thermodynamic equilibria, phase transfer reactions, and spatial distribution of reactions allows for establishment of an overall system description. This kind of models have been used for analysis of numerous wastewater treatment related processes like the activated sludge process, anaerobic digestion, and biofilm processes. In recent years metaproteogenomic methods have become available to investigate microbial ecosystems. To which extent these methods and the corresponding modeling tools are of interest for research in the field of applied environmental microbiology will be the topic of this presentation. First I will present an overview of recent modeling efforts in our research group, and based on that experience I will discuss the potential role of metaproteogenomic tools in the field of environmental microbiology.
15:25 to 15:55 Afternoon Tea
15:55 to 16:30 J Prosser (University of Aberdeen)
Plenary Lecture 12: tba
16:30 to 17:05 A Free (University of Edinburgh)
Plenary Lecture 13: Unpredictability in Microbial Communities and How to Deal With It
Co-authors: Eulyn Pagaling (University of Edinburgh), Fiona Strathdee (University of Edinburgh), Kristin Vassileva (University of Edinburgh), Rocky Kindt (University of Edinburgh), Rosalind J. Allen (University of Edinburgh)

The ability to control and engineer complex microbial communities for particular purposes or functions depends on the reproducibility and stability of community structure and function under controlled conditions. Natural microbial communities contain many low-abundance species, comprising the so-called “rare biosphere”, which may be selected when the environmental parameters governing the system are altered. Current data suggest that the stochastic selection of rare species, together with the complex, non-linear dynamics of these communities, can lead to unpredictability of community structure and function following environmental selection.

We investigate this phenomenon using a simple, replicable laboratory model system, or microcosm, containing diverse microbial ecotypes which cycle nutrients such as carbon and sulphur compounds and generate community function in the form of a redox potential gradient. Variability in the microbial community composition of this model system, studied by 16S rRNA gene-based fingerprinting and sequencing methods, is observed following a selective bottleneck in the system caused by anaerobiosis. Concomitant variation in the development of the redox gradient is also seen. However, stable final communities from this system re-inoculated into the same environment exhibit much less variability than the original communities and a final organisational state which is closely related to their initial state at inoculation. These results suggest that selection under novel environmental conditions can cause unpredictability in microbial community structure and function, but that repeated sele ction can be a means to ensure predictability. We discuss these phenomena with reference to microbial photobioreactor systems containing low microbial diversity which are amenable to engineering by “synthetic ecology”.
17:05 to 17:20 M Ortiz (Harvard University)
Contributed Talk 4: Optimization-based tools for bacterial ecology design
Bacteriophage-based cell-cell communication allows users to create genetically dynamic bacterial ecologies by transmitting DNA molecules between E. coli cells. In previous work, I demonstrated how such a system could be used to transmit DNA messages having different functionalities to develop ecologies over hours-long time courses in liquid or over solid media. If well-designed, such ecologies have the ability to compute, amplify, or report state as a population.

One immediate problem encountered in designing stable bacterial ecologies is that relatively small differences in individual growth rates can impact the resulting population mix in little time. As such, we have focused on developing optimization-based tools for relating the initial and final states of heterogeneous baterial ecologies. We have created a scalable model of the phage-based communication platform to aid development of more complex engineered bacterial ecologies. By inputting few experimental parameters as well as an arbitrary desired output behavior, users can easily obtain the necessary inputs to their engineered system. As phage-based communication via DNA transmission inherently creates genetically distinct species as phage infection proceeds, this tool also enables the user to design and optimize for time-varying behaviors. Overall, it is hoped that such tools will enable greater complexity of heterogeneous bacterial mixtures, help us better understand ec ologies, and allow us to narrow the gap between natural and synthetic systems.

17:20 to 17:35 Contributed Talk 5: tba INI 1
19:30 to 22:00 Conference Dinner at Cambridge Union Society hosted by Cambridge Dining Co.
Friday 28th November 2014
09:30 to 10:05 P Wilmes (Université du Luxembourg)
Plenary Lecture 14: Ecosystems Biology: from data to control of microbial communities
Co-authors: Emilie Muller (University of Luxembourg), Anna Heintz-Buschart (University of Luxembourg), Shaman Narayanasamy (University of Luxembourg), Cédric Laczny (University of Luxembourg)

Mixed microbial communities are complex and dynamic systems. Integrated omics (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum for detailed descriptions of community structure, function and dynamics in situ as well as offering the potential to discover novel functionalities within the framework of Eco-Systems Biology. We have developed an integrative workflow comprising wet- and dry-lab methodologies to enable systematic measurements of microbial communities over space and time, and the integration and analysis of the resulting “multi-meta-omic” data. Two distinct approaches have been developed allowing the deconvolution of integrated omic data either at the population- or community-level. By resolving multi-omic data at the population-level, we have uncovered patterns which suggest that in our model microbial community (lipid accumulating microbial consortia from a biological wastewater treatment tank) t he dominance of a microbial generalist is linked to finely tuned resource usage. Analysis of reconstructed metabolic networks has resulted in the identification of possible “keystone genes”, analogous to keystone species in species interaction networks. Integrated omics will likely become the future standard for the large-scale characterization of microbial consortia within an Eco-Systems Biology framework. In particular, by integrating information from genome to metabolome, integrated omics allows deconvoluton of structure-function relationships by identifying key members and functionalities. For example, identified keystone species and/or genes likely represent driver nodes which may be exploited in view of future control strategies. However, to test emerging hypotheses and formulate predictive models, which support such endeavours, an iterative discovery-driven planning approach is required. This should ultimately allow the manipulation of microbial communities and steer them towards desired outcomes.

10:05 to 10:40 J Rodriguez (Masdar Institute of Science and Technology)
Plenary Lecture 15: Can bioenergetics tell us more about microbial ecosystems activity than community identity?
Co-authors: Rebeca González-Cabaleiro (University of Santiago de Compostela (ES)), Robbert Kleerebezem (Delft University of Technology (NL)), Juan M. Lema (University of Santiago de Compostela (ES))

Bioenergetic considerations appear to play a central role in defining microbial ecosystems activity irrespective of the microbial community identity. Our modelling results suggest that mainly bioenergetics can define the activity of microbial ecosystems at three different levels: (1) When a generalized bioenergy-based model is used to describe the competition between a number of existing and postulated microbial metabolisms, the prevailing successful ones, the reasons behind their success and some syntrophisms are correctly predicted. This has been applied to glucose fermentation and to nitrogen oxidation and reduction ecosystems. Metabolic activities appear to be selected by maximum energy harvest rate. Based on this we postulate that it is primarily energetics who defined the today existing microbial metabolisms, pathway lengths and synergisms among them. (2) When specific anaerobic fermentative reactions of interest are studied under a thermodynamic perspective, conclusions can be drawn out about their potential reversibility. Quasi equilibrium calculations can be used to estimate concentration limits for the feasibility of pathway steps and compares with physiological and kinetic limits. Based on this we postulate that in energy limited microbial ecosystems, thermodynamic limitations can impose unfeasible intermediate metabolite concentrations rendering a metabolic pathway impossible or reversing it. (3) When anaerobic fermentation microbial ecosystems are described as one mass and electron balanced metabolic network, an optimisation of the network for maximum energy yield can provide an accurate prediction of the product formation. This has been successfully applied to the prediction of products and their shifts as a function of the environmental pH. Based on this we postulate that in energy limited microbial ecosystems such as fermentations, a bioenergetic maximum energy harvest rate criteria defines the product spectrum irrespective of the microbial community.

10:40 to 10:55 Contributed Talk 6: tba INI 1
10:55 to 11:25 Morning Coffee
11:25 to 11:55 L Raskin (University of Michigan)
Plenary Lecture 16: Managing microbial communities in anaerobic membrane bioreactors
Anaerobic membrane bioreactor (AnMBR) systems have recently come to the forefront as promising options for mainstream anaerobic treatment of domestic wastewater. Our research has demonstrated with a bench-scale AnMBR that this technology can produce effluent quality comparable to activated sludge treatment at temperatures as low as 6°C. However, we have also demonstrated that this technology can only become competitive as an alternative domestic wastewater treatment option after addressing its high global warming potential due to the presence of dissolved methane in the permeate and the high energy demand for fouling control. While these appear to be typical process engineering problems, we contend that management of the complex anaerobic microbial communities in AnMBR is an essential component of solving these challenges and will show experimental data in support of this statement.
11:55 to 12:30 Plenary Lecture 17: tba INI 1
12:30 to 13:30 Lunch at Wolfson Court
University of Cambridge Research Councils UK
    Clay Mathematics Institute The Leverhulme Trust London Mathematical Society Microsoft Research NM Rothschild and Sons