Rational design of microbial community mixtures for biogas production
Lead Research Organisation:
University of York
Department Name: Biology
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
We have recently shown that biogas production can be enhanced through mixing multiple microbial communities together. We propose to improve this process and assess its practical application in industrial settings. We will combine high throughput laboratory experiments, genetic and metabolomic profiling and modelling to identify community combinations and invasion conditions that will enhance reactor performance. We will use this information to conduct an industrial-scale trial, the results of which will be used to assess and refine the predictive power of lab-scale measures for improving the efficiency of industrial ADs. In addition to the clear applied benefits, the results will provide fundamental and novel insights into the dynamics of microbial "community coalescence", which are likely to have relevance for the enhancement of other biotechnological, remediation and agricultural processes
Planned Impact
The project seeks to enhance the efficiency of methane production from anaerobic digestion (AD) in industrial contexts through bio-augmentation. The work will have significant direct impact for the AD industry. Impact will primarily be realised through our industrial partner, Amur, who offer services to improve the efficiency of AD throughout the UK. Amur has been closely engaged in the co-design of the proposal and exploitation of the results thereof. They will conduct a controlled, replicated trial (objective 4) and offer advice and the bio-augmentation service to their clients. To this end, we will hold regular workshops in partnership with Amur to communicate our findings to participants in the industrial trial and the wider customer base and identify IP assets and products for exploitation. Most impact will occur towards the end of the grant, when the industrial trial is complete, yet Amur, and where relevant their client base, will provide input and guidance into the earlier experimental phases of the project. There is likely to be Intellectual Property (IP) associated with the project, notably the ability to select synergistic community combinations, and identifying and protecting this will be crucial for the application of the more refined methods. We will establish IP protection (by agreement with all partners) if the lab-based results are promising. The general approach could improve a range of biotechnologies involving microbial communities (e.g. bioremediation of contaminated soils and water), hence we will communicate the results through a broader stakeholder workshop involving existing contacts (notably water industries). Finally, we will communicate the work to the general public via a range of established activities through the Universities of Exeter and York.
People |
ORCID iD |
| James Chong (Principal Investigator) |
Publications
Ibarra-Esparza F
(2023)
Implementation of anaerobic digestion for valorizing the organic fraction of municipal solid waste in developing countries: Technical insights from a systematic review
in Journal of Environmental Management
Innard N
(2022)
The challenges of monitoring and manipulating anaerobic microbial communities.
in Bioresource technology
Saye LMG
(2021)
The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production.
in Microorganisms
Shahi F
(2022)
Case Report: The effect of intravenous and oral antibiotics on the gut microbiome and breath volatile organic compounds over one year
in Wellcome Open Research
Shahi F
(2022)
Case Report: The effect of intravenous and oral antibiotics on the gut microbiome and breath volatile organic compounds over one year.
in Wellcome open research
Shahi F
(2022)
Case Report: The effect of intravenous and oral antibiotics on the gut microbiome and breath volatile organic compounds over one year
in Wellcome Open Research
Walker R
(2021)
Facilitating peer-led group research through virtual collaboration spaces: an exploratory research study
in Research in Learning Technology
| Description | Collaboration with University of Exeter |
| Organisation | AB Agri Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | MS analysis of samples plus resulting data analysis |
| Collaborator Contribution | Collection of relevant experimental samples for analysis |
| Impact | Collaborative research |
| Start Year | 2020 |
| Description | Collaboration with University of Exeter |
| Organisation | University of Exeter |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | MS analysis of samples plus resulting data analysis |
| Collaborator Contribution | Collection of relevant experimental samples for analysis |
| Impact | Collaborative research |
| Start Year | 2020 |
| Description | EBnet Collaboration |
| Organisation | UK Environmental Biotechnology Network |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | James Chong and Sarah Forrester are active members within the EBnet Working Group. Through their work with EBnet they are able to publicise the Cloud-SPAN project, via sharing information and delivering talks at webinars. |
| Collaborator Contribution | EBnet support and promote the training opportunities created through the Cloud-SPAN project. The collaboration also allows members to exchange expertise in the field of HPC driven microbial genomics research, which in turn improves the quality of the Cloud-SPAN training resources. |
| Impact | James Chong and Sarah Forrester are active members within the EBnet Working Group. Through their work with EBnet they are able to publicise the Cloud-SPAN project, via sharing information and delivering talks at webinars. |
| Start Year | 2021 |
| Description | EBNet Webinar: Using Big Data Approaches to Understand Microbial Communities |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | EBNet Webinar: Using Big Data Approaches to Understand Microbial Communities Thursday, 10th February 2022 at 13.00 - 14.15. The SESSION RECORDING is available here https://www.youtube.com/watch?v=1QH0JK0X0Xw EBNet are hosting a series of specialist webinars to support knowledge exchange amongst members. "Using Big Data Approaches to Understand Microbial Communities". Hear the latest developments from top speakers and participate in the online chat to engage with questions. This fascinating session is brought to you by the Chairs: Dr Sarah Forrester, the Chong Group, Dept. of Biology, University of York & Dr Bing Guo. Dr Sarah Forrester is a PDRA within James Chong's group within the Biology department at the University of York. She gained her PhD at the University of Liverpool in 2016 using multi 'omic approaches to analyse parasite genomic data, and has worked since then on a range of microbial systems and used a variety of bioinformatic methods. She performs HPC driven microbial genomics research and delivers bioinformatics training. As a 2022 Software Sustainability fellow and a certified Software Carpentry instructor, she is passionate about instilling good bioinformatic practises into her training. She is also involved in the preparation and delivery of the material for Cloud-SPAN: Specialised analyses for environmental 'omics with Cloud-based High Performance Computing , see https://cloud-span.york.ac.uk/. TALK TITLE: INTRODUCTION TO THE EBNET BIOINFORMATICS WORKING GROUP Prof James Chong is a Royal Society Industry Fellow and Professor in the Department of Biology at the University of York, where he runs a research group exploiting a range of 'omics techniques to understand microbial community dynamics, as well as leading the EBNet Working Group "Bioinformatics Training for Microbial Environmental Biotechnologies". His group is involved in generating microbial community metagenomics, meta-transcriptomics and metabolomics datasets. His group use established analytical pipelines, but also develop their own bespoke scripts for data analysis. Insight into the application of 'omics techniques, and the ways in which they can be applied to environmental biotechnology use cases to greater understand microbial community dynamics, has driven his desire to develop bioinformatic training resources. This is currently being supported by the UKRI Grant Cloud-SPAN: Specialised analyses for environmental 'omics with Cloud-based High Performance Computing, and is co-led by James, see https://cloud-span.york.ac.uk/. Impact: enables the dissemination of the project details to a wider audience and generates registrations to current activities |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://ebnet.ac.uk/ebnet-rc22-bigdata/ |
| Description | EBNet Working Group Coordinator |
| 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 | James Chong is the Working Group Chair for EBnet. This WG aims to create Bioinformatics training for microbial Environmental Biotechnologies. In this role James is able to make new connections and publicise the work of Cloud-SPAN. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://ebnet.ac.uk/about/wg-details/wg-bioinformatics/ |
| Description | European Biosolids and Bioresource Conference 2022. 22nd and 23rd of November in Birmingham James Chong and Sarah Forrester |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | James Chong and Sarah Forrester delivered Bioinformatics session, 40 minute Q & A on metagenomics and bioinformatics and access to training European Biosolids and Bioresource Conference 2022. 22nd and 23rd of November in Birmingham , ~40 people attended 13:35 - 13:50 Bioinformatics-based diagnostics for monitoring AD - Professor James Chong, University of York, UK 13:50 - 14:05 Using multi-omic approaches to understand the co-digestion of wheatstraw and sewage sludge - Dr. Sarah Forrester, Senior Post Doc, University of York, UK |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://european-biosolids.com/wp-content/uploads/2022/11/European-Biosolids-Bioresources-Conference... |
| Description | Metagenomics online training course April 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A training course was organised online comprising online lectures, drop in help sessions, and a slack channel for support for 30 participants. Following completion of this course, learners will be trained to : explain the hierarchical structure of a file system and describe the files and file structure used in the course explain what is meant by a working directory, a path and a relative path and write down paths that they will need for the course start a Terminal (Mac) or Git Bash Terminal (Windows) navigate a file system using the command line log in to and exit their AWS instance (the cloud) use common commands such as ls, pwd and cd, on the command line know the difference between genomics and metagenomics describe the steps in a metagenomic workflow perform quality control on reads and assemble them into a metagenome perform polishing to improve an assembly use binning to separate the metagenome into different species or MAGs (Metagenome-Assembled Genomes) use Kraken 2 to assign taxonomy to reads and contigs and phyloseq in R to analyse taxonomic diversity |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://sites.google.com/york.ac.uk/cloud-span/train-with-us/specialised-skills#h.jqgzsdc8hbla |
| Description | Participation in an activity, workshop or similar - Training Course: Genomics - 6-7 December 2022 - University of York |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Training course for 14 participants from 6 different institutions. Participants completed the interactive workshop and developed practical skills and increased their knowledge in the area of data management and analytical skills for genomic research. All participants connected to the Cloud-SPAN community via the slack channel and in person. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://cloud-span.github.io/00genomics/ |