Engineering Synthetic Microbial Communities for Biomethane Production
Lead Research Organisation:
University of Warwick
Department Name: School of Life Sciences
Abstract
Complex microbial communities underlie natural processes such as global chemical cycles and digestion in higher animals, and are routinely exploited for industrial scale synthesis, waste treatment and fermentation. Our basic understanding of the structures, stabilities and functions of such communities is limited, leading to the declaration of their study as the next frontier in microbial ecology, microbiology, and synthetic biology. Focusing on biomethane producing microbial communities (BMCs), we will undertake a two-tiered approach of optimising natural communities and designing synthetic communities with a focus on achieving robust, high-yield biomethane production. Within this biotechnological framework, our proposal will address several fundamental scientific questions on the link between the structure and function of microbial communities.
To ensure success in this challenging project, we assembled the strongest possible interdisciplinary research team that combines significant practical and scientific expertise in microbial ecology and evolution, systems modelling, molecular microbiology, bioengineering, genomics, and synthetic biology.
We are confident that this team will deliver and that this project will result in significant impact in the scientific and industrial domains. Through our work, described in detail below, we will; significantly improve the current understanding of the structure-function relation in microbial communities, provide the scientific community with a systematic, temporal genomics and transcriptomics dataset on complex microbial communities, develop novel computational tools for microbial community (re)design, and experimentally build synthetic BMCs that will act as model ecosystems in different research fields. These scientific developments, in turn, will accumulate in the development of more sustainable bioenergy solutions for the UK economy by optimising the communities underlying biomethane production. This will help to drive the efficiency of biomethane as an alternative fuel source.
To ensure success in this challenging project, we assembled the strongest possible interdisciplinary research team that combines significant practical and scientific expertise in microbial ecology and evolution, systems modelling, molecular microbiology, bioengineering, genomics, and synthetic biology.
We are confident that this team will deliver and that this project will result in significant impact in the scientific and industrial domains. Through our work, described in detail below, we will; significantly improve the current understanding of the structure-function relation in microbial communities, provide the scientific community with a systematic, temporal genomics and transcriptomics dataset on complex microbial communities, develop novel computational tools for microbial community (re)design, and experimentally build synthetic BMCs that will act as model ecosystems in different research fields. These scientific developments, in turn, will accumulate in the development of more sustainable bioenergy solutions for the UK economy by optimising the communities underlying biomethane production. This will help to drive the efficiency of biomethane as an alternative fuel source.
Technical Summary
We will employ both top-down (directed evolution) and bottom-up (synthetic biology) engineering of biomethane producing microbial communities (BMCs) with improved functionality. These two approaches are connected via the resulting BMCs, which will be further analysed in mid-scale reactors with the aim to impact biotechnological application of microbial communities.
Directed evolution of BMCs. We will combine our expertise in experimental evolution with applied expertise in biomethane production to use group selection on naturally derived BMCs to improve their biomethane productivity. Using the expertise and the infrastructure at TGAC, we will employ next generation sequencing to determine how communities change in response to selection, and whether significant evolutionary change has occurred in the transcriptomes of focal species. Our core experimental evolution setup will use 60 mini reactors to set up independent batch cultures, where biomethane production can be measured in real-time by automated monitoring of gas volume.
Rational engineering of synthetic BMCs. We will combine our expertise in kinetic modelling and flux balance analysis (FBA) with molecular biology to rationally design and experimentally implement synthetic BMCs. The starting point for both FBA and experimental work will be an existing co-culture that is capable of converting lactate into methane. The engineered communities and their temporal behaviour will be analysed using genomics and transcriptomics approaches.
Testing and scaling up of (re)engineered BMCs. We will test the performance and stability of evolved and synthetic BMCs under industrially realistic conditions in mid-scale reactors using our expertise and lab infrastructure in process engineering. For this task, we will use both anaerobic membrane reactors (AnMBRs), which allow for the maintenance of BMCs in the reactor without "washout" and more commonly used continuously stirred tank
Directed evolution of BMCs. We will combine our expertise in experimental evolution with applied expertise in biomethane production to use group selection on naturally derived BMCs to improve their biomethane productivity. Using the expertise and the infrastructure at TGAC, we will employ next generation sequencing to determine how communities change in response to selection, and whether significant evolutionary change has occurred in the transcriptomes of focal species. Our core experimental evolution setup will use 60 mini reactors to set up independent batch cultures, where biomethane production can be measured in real-time by automated monitoring of gas volume.
Rational engineering of synthetic BMCs. We will combine our expertise in kinetic modelling and flux balance analysis (FBA) with molecular biology to rationally design and experimentally implement synthetic BMCs. The starting point for both FBA and experimental work will be an existing co-culture that is capable of converting lactate into methane. The engineered communities and their temporal behaviour will be analysed using genomics and transcriptomics approaches.
Testing and scaling up of (re)engineered BMCs. We will test the performance and stability of evolved and synthetic BMCs under industrially realistic conditions in mid-scale reactors using our expertise and lab infrastructure in process engineering. For this task, we will use both anaerobic membrane reactors (AnMBRs), which allow for the maintenance of BMCs in the reactor without "washout" and more commonly used continuously stirred tank
Planned Impact
In line with national and international policy, this research aims to produce a step change in the efficient production of biomethane, a key renewable energy source. This, in turn, will impact on government and industrial end users, who have clearly articulated their requirements for improvements in yield and reliability of biomethane production. At the scientific level, the relations between structure, composition and function in microbial communities is at the heart of several unresolved questions in the fields of microbial ecology and evolution, microbiology and synthetic biology.
1. Academic Communities
Impact on Existing Communities. This research will benefit systems microbiologists by generating a more complete understanding of the interactions found in complex microbial communities and synthetic biologists by developing improved tools and approaches for the manipulation of microbial communities. These tools will be applicable to biomethane production but will also be of interest for the production of biofuels or bio-products by accommodating bacteria into a stable productive community. In addition, our proposed research will provide the scientific community with an unprecedented data set on the composition and structure of complex microbial communities and provide novel computational tools for their study.
Educational Impact. Today's scientific challenges require bringing together scientists from diverse fields and educating younger scientists in a genuinely cross-disciplinary fashion. Being a truly integrative project that amalgamates theory and experiment towards achieving a better understanding of complex microbial communities, the proposed research will provide an ideal setting for the development of the participating staff and PhD students, and will excite a new generation of scientists.
2. Industrial Communities
The innovative nature of this project and the economic and regulatory drivers related to biomethane production have already created strong interest from industry. We have engaged end users in the development of this proposal, primarily through an industrial liaison workshop held in Exeter in December 2011. Most attendees of this workshop, as well as several other industrial companies are now members of our advisory board (AB); major users of biomethane production, SME technology development companies, and a regional industry network. There is strong interest in the potential for future commercial exploitation of the proposed basic research, and we will actively seek to pursue opportunities for commercial industrial collaborations during and post-project.
3. Policy and Society
Impact on Policy. The close link between government priorities on renewable energy and greenhouse gas emission, and biomethane production through anaerobic digestion is explicitly recognised in the DECC Strategy and Action Plan, 2011. The Government has set targets to recycle 50% of household waste by 2020, reduce greenhouse gas emissions to 34% below 1990 levels by 2020 and by 80% by 2050, and achieve greater energy security. The related regulations and innovation stimulation packages developed by the Government, heavily influences the anaerobic digestion bioindustry. Recognising this link, we have already sought advice on engagement with DECC, and following this advice, we will provide them with research briefing papers as results are made available.
Social Impact. The proposed research is extremely timely and of significant social relevance since it addresses an important aspect of a "daily" challenge, namely eco-friendly and sustainable energy production. We will capitalise on this and use the project as a way to engage with the public and funding bodies and offer collaborative opportunities to think in innovative and informed ways about systems biology, synthetic biology and microbial biotechnology.
1. Academic Communities
Impact on Existing Communities. This research will benefit systems microbiologists by generating a more complete understanding of the interactions found in complex microbial communities and synthetic biologists by developing improved tools and approaches for the manipulation of microbial communities. These tools will be applicable to biomethane production but will also be of interest for the production of biofuels or bio-products by accommodating bacteria into a stable productive community. In addition, our proposed research will provide the scientific community with an unprecedented data set on the composition and structure of complex microbial communities and provide novel computational tools for their study.
Educational Impact. Today's scientific challenges require bringing together scientists from diverse fields and educating younger scientists in a genuinely cross-disciplinary fashion. Being a truly integrative project that amalgamates theory and experiment towards achieving a better understanding of complex microbial communities, the proposed research will provide an ideal setting for the development of the participating staff and PhD students, and will excite a new generation of scientists.
2. Industrial Communities
The innovative nature of this project and the economic and regulatory drivers related to biomethane production have already created strong interest from industry. We have engaged end users in the development of this proposal, primarily through an industrial liaison workshop held in Exeter in December 2011. Most attendees of this workshop, as well as several other industrial companies are now members of our advisory board (AB); major users of biomethane production, SME technology development companies, and a regional industry network. There is strong interest in the potential for future commercial exploitation of the proposed basic research, and we will actively seek to pursue opportunities for commercial industrial collaborations during and post-project.
3. Policy and Society
Impact on Policy. The close link between government priorities on renewable energy and greenhouse gas emission, and biomethane production through anaerobic digestion is explicitly recognised in the DECC Strategy and Action Plan, 2011. The Government has set targets to recycle 50% of household waste by 2020, reduce greenhouse gas emissions to 34% below 1990 levels by 2020 and by 80% by 2050, and achieve greater energy security. The related regulations and innovation stimulation packages developed by the Government, heavily influences the anaerobic digestion bioindustry. Recognising this link, we have already sought advice on engagement with DECC, and following this advice, we will provide them with research briefing papers as results are made available.
Social Impact. The proposed research is extremely timely and of significant social relevance since it addresses an important aspect of a "daily" challenge, namely eco-friendly and sustainable energy production. We will capitalise on this and use the project as a way to engage with the public and funding bodies and offer collaborative opportunities to think in innovative and informed ways about systems biology, synthetic biology and microbial biotechnology.
Organisations
- University of Warwick (Lead Research Organisation)
- Syngenta International AG (Collaboration)
- Joseph Fourier University (Collaboration)
- Polish Academy of Sciences (Collaboration)
- Soehngen Institute of Anaerobic Microbiology (Collaboration)
- UNIVERSITY OF YORK (Collaboration)
- University of Washington (Collaboration)
- Green Biologics (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
Publications
Benarroch JM
(2020)
The Microbiologist's Guide to Membrane Potential Dynamics.
in Trends in microbiology
Chen J
(2019)
Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer.
in Journal of the Royal Society, Interface
De Souza-Guerreiro TC
(2021)
Seeking Insights into Aging Through Yeast Mitochondrial Electrophysiology.
in Bioelectricity
Delattre H
(2020)
Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis.
in Journal of the Royal Society, Interface
Dolfing J
(2013)
Syntrophic propionate oxidation via butyrate: a novel window of opportunity under methanogenic conditions.
in Applied and environmental microbiology
Dolfing J
(2014)
Syntrophy in microbial fuel cells.
in The ISME journal
Dolfing J
(2014)
Thermodynamic constraints on syntrophic acetate oxidation.
in Applied and environmental microbiology
Du Lac M
(2017)
Predicting the Dynamics and Heterogeneity of Genomic DNA Content within Bacterial Populations across Variable Growth Regimes.
in ACS synthetic biology
Ghasimi DSM
(2015)
Microbial population dynamics during long-term sludge adaptation of thermophilic and mesophilic sequencing batch digesters treating sewage fine sieved fraction at varying organic loading rates.
in Biotechnology for biofuels
Grosskopf T
(2014)
Synthetic microbial communities.
in Current opinion in microbiology
Großkopf T
(2016)
Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.
in BMC evolutionary biology
Großkopf T
(2016)
A stable genetic polymorphism underpinning microbial syntrophy.
in The ISME journal
Großkopf T
(2016)
Microbial diversity arising from thermodynamic constraints.
in The ISME journal
Herrero M
(2015)
Bioaugmentation and its application in wastewater treatment: A review.
in Chemosphere
Hesse E
(2018)
Ecological selection of siderophore-producing microbial taxa in response to heavy metal contamination.
in Ecology letters
Jiang X
(2018)
Impact of spatial organization on a novel auxotrophic interaction among soil microbes.
in The ISME journal
La Edwards C
(2020)
Rapid Detection of Proliferative Bacteria by Electrical Stimulation.
in Bio-protocol
Laver T
(2015)
Assessing the performance of the Oxford Nanopore Technologies MinION.
in Biomolecular detection and quantification
Lu Y
(2013)
Reply to "syntrophic propionate oxidation via butyrate: a novel window of opportunity under methanogenic conditions".
in Applied and environmental microbiology
Morcrette H
(2020)
Campylobacter jejuni 11168H Exposed to Penicillin Forms Persister Cells and Cells With Altered Redox Protein Activity.
in Frontiers in cellular and infection microbiology
O'Brien S
(2013)
The interplay between microevolution and community structure in microbial populations.
in Current opinion in biotechnology
Oko BJ
(2017)
Dynamics of two methanogenic microbiomes incubated in polycyclic aromatic hydrocarbons, naphthenic acids, and oil field produced water.
in Biotechnology for biofuels
Petropoulos E
(2019)
High rate domestic wastewater treatment at 15 °C using anaerobic reactors inoculated with cold-adapted sediments/soils - shaping robust methanogenic communities
in Environmental Science: Water Research & Technology
Petropoulos E
(2021)
Sewage treatment at 4 °C in anaerobic upflow reactors with and without a membrane - performance, function and microbial diversity
in Environmental Science: Water Research & Technology
Quince C
(2021)
STRONG: metagenomics strain resolution on assembly graphs.
in Genome biology
Raguideau S
(2021)
Novel microbial syntrophies identified by longitudinal metagenomics
Sambles C
(2017)
Metagenomic analysis of the complex microbial consortium associated with cultures of the oil-rich alga Botryococcus braunii.
in MicrobiologyOpen
Sari T
(2017)
Generalised approach to modelling a three-tiered microbial food-web.
in Mathematical biosciences
Schofield Z
(2020)
Bioelectrical understanding and engineering of cell biology
in Journal of The Royal Society Interface
Sierocinski P
(2017)
A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities.
in Current biology : CB
Sierocinski P
(2018)
Biodiversity-function relationships in methanogenic communities.
in Molecular ecology
Sirec T
(2019)
Electrical Polarization Enables Integrative Quality Control during Bacterial Differentiation into Spores.
in iScience
Stilwell P
(2018)
The effect of cheats on siderophore diversity in Pseudomonas aeruginosa.
in Journal of evolutionary biology
Stratford J
(2019)
Electrically induced bacterial membrane-potential dynamics correspond to cellular proliferation capacity
in Proceedings of the National Academy of Sciences
Studholme DJ
(2015)
Some (bacilli) like it hot: genomics of Geobacillus species.
in Microbial biotechnology
Studholme DJ
(2016)
Genome sequences of six Phytophthora species associated with forests in New Zealand.
in Genomics data
Tao Y
(2020)
Biogas productivity of anaerobic digestion process is governed by a core bacterial microbiota
in Chemical Engineering Journal
Wade M
(2016)
Perspectives in mathematical modelling for microbial ecology
in Ecological Modelling
Wade MJ
(2016)
Emergent behaviour in a chlorophenol-mineralising three-tiered microbial 'food web'.
in Journal of theoretical biology
Wade MJ
(2017)
MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions.
in PloS one
Westerholm M
(2019)
Growth Characteristics and Thermodynamics of Syntrophic Acetate Oxidizers.
in Environmental science & technology
Widder S
(2016)
Challenges in microbial ecology: building predictive understanding of community function and dynamics.
in The ISME journal
Zerfaß C
(2019)
Interrogating metabolism as an electron flow system.
in Current opinion in systems biology
Zerfaß C
(2018)
Engineering microbial communities using thermodynamic principles and electrical interfaces.
in Current opinion in biotechnology
Zerfaß C
(2019)
Manganese Oxide Biomineralization Provides Protection against Nitrite Toxicity in a Cell-Density-Dependent Manner.
in Applied and environmental microbiology
| Title | Research on synthetic microbial communities explained |
| Description | A 3-minute video explaining our research on microbial communities in an accesible way. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2014 |
| Impact | The video was featured on BBSRC home page and twitter. |
| URL | http://osslab.lifesci.warwick.ac.uk/adLola_rsrcs.html |
| Title | sLola Project Film |
| Description | A short film describing the sLola project 'Engineering Synthetic Microbial Communities for Biomethane Production'. Filming took place at all participating institutes in order to capture the work being done on AD minimal communities, community mixing and evolution, cold-adapted communities and reactor design. The film was tailored for use with a wide audience including future collaborators, funders, industry members, academics and students. The film is still at the editing stage, we will post the URL as soon as we can. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| Impact | None |
| Description | 1. We have shown that Anaerobic digestion (AD)-adapted communities produce more biogas compared to natural, methanogenic communities and that this is underpinned by changes in community composition following adaptation to AD conditions. We demonstrated for the first time the importance of diversity of rare species in the starting inoculum and that AD performance can be enhanced by having a mixed community inocula. 2. We have established minimal methanogenic communities at the lab scale and identified a genetic polymorphism that underpins the required syntrophy. 3. We have developed mathematical models to analyse and predict microbial community dynamics, stability and diversity by taking into account thermodynamic inhibitions. 4. We have developed a metabolic modelling platform to model ecological and evolutionary dynamics in a microbial community, allowing biologically important predictions to be made. This will help us to extend the minimal communities we are creating. 5. We have published a series of review and opinion papers, with a large number of co-authors in some cases. These have established that microbial communities, as complex dynamical systems with intertwined ecological and evolutionary processes, present themselves as the new integrated research frontier. Additional review and opinion papers highlight research priorities, such as the development of synthetic microbial fuel cells, as well as the application of synthetic biology approaches to communities, and commented on potential biotechnological routes, such as bioaugmentation, for increased biomethane generation. |
| Exploitation Route | Our work on mixed communities (key finding 1) raises the possibility to use a large volume inoculum from a well performing AD plant to save another failing AD plant, thus reducing large costs associated with failures. Our work on creating minimal communities (key finding 2) has provided important insights into understanding and engineering methanogenic communities. Models developed for Key finding 3 and 4, can be extended to any microbial community to allow predictive conclusions to be drawn on their stability, dynamics and diversity, thus, facilitating the (re)engineering of microbial communities. |
| Sectors | Agriculture, Food and Drink,Energy,Environment |
| URL | https://warwick.ac.uk/fac/sci/lifesci/research/slola |
| Description | We have contributed to a report (prepared by the BBSRC) to the House of Lords, and relating to renewable energy We have engaged with growers and suppliers at the annual Waitrose science event, of which many use AD as part of their business. Some of our findings have been taken up by industry. In particular, results on the impact of community mixing on methane production in AD settings has been utilised by a company for the initiation of their first reactor. Further talks with this company are ongoing to explore additional applied research. |
| First Year Of Impact | 2014 |
| Sector | Agriculture, Food and Drink,Energy,Environment,Other |
| Impact Types | Economic |
| Description | BEE BBSRC spotlight area 2022 |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://www.ukri.org/news/bbsrc-launches-new-responsive-mode-spotlight-pilot/ |
| Description | Anaerobic Digestion Network |
| Amount | £705,651 (GBP) |
| Funding ID | BB/L013835/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2014 |
| End | 01/2019 |
| Description | Anaerobic Digestion Network BIV |
| Amount | £10,000 (GBP) |
| Funding ID | BIV2018008 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2018 |
| End | 02/2019 |
| Description | BBSRC AD Network BIV |
| Amount | £10,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Department | Anaerobic Digestion Network (AD Network) |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 03/2017 |
| End | 07/2017 |
| Description | BBSRC AD Network POC |
| Amount | £59,970 (GBP) |
| Funding ID | POC2016012 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Department | Anaerobic Digestion Network (AD Network) |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 02/2018 |
| Description | BBSRC Impact Acceleration Account (IAA) |
| Amount | £149,790 (GBP) |
| Funding ID | BB/S506783/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2018 |
| End | 03/2021 |
| Description | BBSRC Impact Acceleration Account (IAA) |
| Amount | £3,000 (GBP) |
| Funding ID | BB/S506783/1 |
| Organisation | University of Warwick |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 05/2018 |
| End | 05/2018 |
| Description | Isaac Newton Institute for Mathematical Sciences research programme |
| Amount | £200,000 (GBP) |
| Organisation | Isaac Newton Institute for Mathematical Sciences |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 08/2014 |
| End | 12/2014 |
| Description | SPARKS - engineering synthetic communities for algae-to-bio-methane conversion |
| Amount | £20,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | |
| Description | Technology and Resource Development Fund |
| Amount | £151,448 (GBP) |
| Funding ID | BB/N023285/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2016 |
| End | 09/2017 |
| Description | Understanding the origin and evolution of metabolic interactions using synthetic microbial communities |
| Amount | £939,000 (GBP) |
| Funding ID | BB/T010150/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2019 |
| End | 09/2023 |
| Title | MI-Sim |
| Description | A MATLAB package for the numerical analysis of microbial ecological interactions |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | The publication has had over 3000 views and has been cited twice. |
| URL | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0173249#ack |
| Title | MetQy |
| Description | MetQy is a R package to ease interfacing with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to query metabolic functions of genes and genomes |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | None to report |
| URL | https://academic.oup.com/bioinformatics/article/34/23/4134/5033387 |
| Title | Micodymora |
| Description | Micodymora is a python package allowing to simulate Ordinary Differential Equations (ODE) models of microbial population dynamics, while providing gas/liquid transfer and acide/base equilibria as additional features |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | None as yet |
| URL | https://github.com/OSS-Lab/micodymora |
| Title | UK AD Microbiome website |
| Description | A project website has been created where all sequencing and metadata is stored and made available for public use: http://anaerodynamics.com. 2022 update, new website created: https://warwick.ac.uk/fac/sci/lifesci/research/osslab/research/past/anaerodynamicsproject |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | None |
| URL | http://anaerodynamics.com |
| Description | David Stahl |
| Organisation | University of Washington |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Visited University of Washington to collaborate and discuss research findings relating to synthetic cultures. |
| Collaborator Contribution | Hosted visit to set up collaboration and discuss research findings of overlapping interest. |
| Impact | Submitted publication on EvoFBA |
| Start Year | 2015 |
| Description | Dominique Schneider |
| Organisation | Joseph Fourier University |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Hosted a visit in order to finalise joint publication on evoFBA manuscript |
| Collaborator Contribution | Hosted a visit in order to set up collaboration on FBA technique |
| Impact | Manuscript ready for submission |
| Start Year | 2014 |
| Description | Green Biologics |
| Organisation | Green Biologics |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Carried out a 3-month pilot project funded by the AD Network: BIV2018008. The project title was 'Bioelectrochemical conversion of cellulosic biomass into methane and organic acids'. |
| Collaborator Contribution | provision of expertise and samples for the project. |
| Impact | None to report yet. |
| Start Year | 2018 |
| Description | INRA-Narbonne |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | The research team were involved in the instigation and organisation of a bilateral meeting held in Narbonne. The group travelled to Narbonne and gave a total of four presentations of their research. Update: In 2018, the slola group traveled again to Narbonne to meet with the INRA group to exchange research ideas. |
| Collaborator Contribution | The INRA-Narbone group were involved in the organisation of the bilateral meeting. They contributed nine research presentations and a training session for PhD students. |
| Impact | As a result of this meeting, overlaps in research interests were identified. One PDRA made an additional visit to INRA Montpellier and Narbonne to carry out specific mathematical analyses. Another PDRA hosted a follow-on meeting with scientists from INRA-Narbonne to discuss experimental results of common interest. A joint paper was published as a result of this collaboration: Pawel Sierocinski,et al (2017) Current Biology 27(21):3390-3395. |
| Start Year | 2014 |
| Description | INRA-Narbonne 2018 |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Members of the sLola team traveled to Narbonne, France, to attend a two day workshop organised by Kim Milferstedt on 'Bridging theory and practice in ecological engineering'. The sLola group contributed to the scientific discussions and gave 6 presentations. |
| Collaborator Contribution | Organisation and participation of the workshop 25-26 June 2018 |
| Impact | Previously reported publications. No new outputs to report. |
| Start Year | 2014 |
| Description | James Chong |
| Organisation | University of York |
| Department | Department of Biology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Visited collaborator for training and discussions |
| Collaborator Contribution | Provided training and discussions on microbe cultivation techniques |
| Impact | development of cultivation techniques for methanogens. |
| Start Year | 2013 |
| Description | Piotr Garstecki |
| Organisation | Polish Academy of Sciences |
| Department | Institute of Physical Chemistry |
| Country | Poland |
| Sector | Public |
| PI Contribution | Visited collaborator to exchange ideas on microfluidic devices for growing microbes. |
| Collaborator Contribution | Hosted visit to exchange ideas on microfluidic devices for growing microbes. |
| Impact | Identified common interests and potential for future experiments. |
| Start Year | 2014 |
| Description | SIAM |
| Organisation | Soehngen Institute of Anaerobic Microbiology |
| Country | Netherlands |
| Sector | Private |
| PI Contribution | The sLola research team plus other PDRAs from the Soyer group visited the Netherlands for a research exchange workshop with researchers from the SIAM research program. Research talks and poster presentations were given at the workshop as well as participation in round table discussions on Anaerobic digestion microbiology topics and potentials for future collaboration. |
| Collaborator Contribution | The SIAM group hosted the workshop and also gave research talks and poster presentations and participated in round table discussions on Anaerobic digestion microbiology topics and potentials for future collaboration. |
| Impact | None to report yet. |
| Start Year | 2017 |
| Description | Syngenta 2019 |
| Organisation | Syngenta International AG |
| Country | Switzerland |
| Sector | Private |
| PI Contribution | Members of the BEE innovator team visited Syngenta to discuss future project collaboration. |
| Collaborator Contribution | Hosted the meeting. |
| Impact | None Yet. |
| Start Year | 2019 |
| Title | MicrobeMeter |
| Description | MicrobeMeter is a high-resolution photometer with continuous measurement and wireless capabilities. It allows measuring of microbial growth dynamics, as used in many disciplines of life sciences, such as molecular biology, systems biology and synthetic biology. |
| IP Reference | |
| Protection | Copyrighted (e.g. software) |
| Year Protection Granted | 2018 |
| Licensed | No |
| Impact | more than 50 units sold. Manuscript describing the blueprint of the MicrobeMeter on bioRxix has been downloaded 2373 (https://www.biorxiv.org/content/10.1101/407742v1.article-metrics). |
| Title | EvoFBA |
| Description | Source Code for Simulating Evolution of Constraint Based Models of Cellular Metabolism. This is a MATLAB implementation of the evolutionary and ecological dynamics simulations of growing E.coli populations as presented in "Grosskopf T, et al, BMC Evol Bio, 2016". These simulations involve mimicking growth dynamics of E.coli cells using dynamical constraint-based modeling of cellular metabolism and mimicking ecological dynamics through differential equations describing concentrations of media components. See the associated paper for further details. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Impact | None |
| Title | MI-Sim |
| Description | MI-Sim is a MATLAB graphical user-interface whose main function is the numerical analysis of dynamical systems describing ecological interactions (motifs) as presented in "Wade M, et al, PLoS ONE, 2017" |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Impact | None |
| Company Name | HUMANE TECHNOLOGIES LIMITED |
| Description | Humane Technologies Limited is a spin-out company from the University of Warwick. It focuses on design and development of life sciences research equipment. Besides a growing in-house product range, the company offers consultancy and turn-key prototype and device engineering solutions for small and large companies, universities, schools, and individuals. Our focus areas cover biomedical devices, biotechnology microbial processes and life sciences fundamental research. Within each field, we can help you implement your device and platform ideas into reality, from prototyping all the way to mass production stages. |
| Year Established | 2018 |
| Impact | Provision of affordable lab equipment. |
| Website | https://humanetechnologies.co.uk/products/ |
| Description | 'Doing Engineering' workshop |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Doing Engineering' was the first of Engineering Life's experimental, interdisciplinary meetings. Our project is inspired by and focuses on the relationship between engineering and biology in young fields like synthetic biology. Because synthetic biologists express great admiration of and a desire to emulate traditional engineering fields, we care about what engineering itself is. 'Doing Engineering' was intended to explore this type of discipline and work from a variety of perspectives. Most importantly, we brought engineers and synthetic biologists to discuss their personal experiences of engineering. Seventeen practitioners, including social scientists, philosophers of technology, policy experts, synthetic biologists and engineers came together and used novel methods to study the nuances of being an engineer and practicing engineering. We began the day by introducing ourselves using images that for each person represented engineering. Those included wooden propellers, a Saturn V rocket blasting off, a champagne glass filled with raspberries, and a make-believe image of bacteria filled with electronics. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.doingeng.sps.ed.ac.uk |
| Description | AAAS annual meeting - invited talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited speaker at the annual meeting of the American Association of the Advancement of Science (AAAS). |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.aaas.org/events/2020-aaas-annual-meeting |
| Description | AD Monitoring Project Stakeholder Meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | An online meeting was held with key industrial participants of this project. Results of the project were clearly presented together with plans to publish the data. Also discussed were options for applying for future funding with industrial support. |
| Year(s) Of Engagement Activity | 2021 |
| Description | AD Science meets Industry 2016 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | We hosted a one-day workshop to bring together anaerobic digestion (AD) practitioners and scientists. The event consisted of both science and industry focussed talks, a session from an expert on AD and an open discussion forum. We also launched a new (BBSRC) project on monitoring AD microbiomes, with 10 companies coming forward to take part. In total 68 people attended the meeting, representing 26 companies and 13 academic institutions. |
| Year(s) Of Engagement Activity | 2016 |
| Description | BEE workshop 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Representatives from 8 Universities and 3 Industries came together for the 1st BEE workshop.The attendees expertise covered; Microbiology, Plant biology, Synthetic biology, Physics, Environmental Engineering, Chemical Engineering, Biochemistry, Chemistry, Electrochemistry, Robotics, Electrical Engineering, and Biophysics. The BEE workshop covered a wide range of areas, with the focus on electrical processes at the cellular and organism levels. The workshop allowed BEE innovators to link up with other researchers in the UK. Following on the enthusiasm of the participants and also the BEE innovators, we are now starting to organise the 2nd workshop. This will be an international meeting, particularly with colleagues from the US. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://warwick.ac.uk/fac/sci/lifesci/research/beehive/beeworkshop_program/ |
| Description | BEE workshop 2019 'Electrical Cell Biology' |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | 48 people attended the Bio-Electrical Engineering workshop 28-29 March 2019 at Warwick University, organised by the BBSRC IAA awarded 'BEE innovation hub'. This workshop brought together an interdisciplinary group of researchers with expertise in microbiology, plant science, biophysics, electrical engineering, neuroscience, and cell biology to exchange ideas and results relating to 'electrical forces in cell biology'. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://warwick.ac.uk/fac/sci/lifesci/research/beehive/2nd_bee_workshop/ |
| Description | Edinburgh Science Festival |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | Yes |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Interest and questions from the public Possible participation in the 2015 festival |
| Year(s) Of Engagement Activity | 2014 |
| URL | http://www.sciencefestival.co.uk |
| Description | Isaac Newton Institute Workshop on Microbial communities: current approaches and open challenges |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This is a 4-month residential workshop we have organised at the Isaac Newton Institute. It aimed to assess the state of the microbial communities research field and resulted in significant impact on the development of the field. The 2022 follow on workshop took place over four days and included 20 invited and 25 contributed talks that covered broad and recent topics in microbial community research. |
| Year(s) Of Engagement Activity | 2014,2015,2022 |
| URL | https://www.newton.ac.uk/event/umc/ |
| Description | Monitoring AD Microbiomes September 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | We organised a 1-day workshop to disseminate the results from the AD Monitoring project 'BBSRC POC2016012' (Predictive Temporal Analysis of Functional Microbiomes in UK's Anerobic Digestion Reactors). The event was attended by 35 people, comprising a mix of academics and AD industry members, all with an interest in Anaerobic Digestion microbiology. Many of the industry attendees have been taking park in the AD monitoring project. As well as disseminating and discussing the findings from the AD monitoring project we presented our future plans for the project and made contact with new industry members who would be willing to participate in any future activities. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Penny College talk 2015 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | 40 min talk explaining biogas production and microbial ecology to grade 9 students. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Royal Cornwall show 2015 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | 3 h demonstration session on biomethane producing microbial communities and how it can improve a farmer's business. Approximately 60 people attended. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Summary for House of Lords inquiry |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | Yes |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | summary formed part of the inquiry report None as of yet |
| Year(s) Of Engagement Activity | 2013 |