Canada Partnering Award: A one health approach to understanding and using bacteriophages in the control of enteric pathogens
Lead Research Organisation:
QUADRAM INSTITUTE BIOSCIENCE
Department Name: Gut Microbes and Health
Abstract
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Publications
Anany H
(2022)
ICTV Virus Taxonomy Profile: Chaseviridae 2022.
in The Journal of general virology
| Description | Using this award, we consolidated a key research partnership between the Quadram Institute Bioscience (UK) and the Agriculture and AgriFood Canada (AAFC). Research capability at the QIB and AAFC was significantly increased through the delivery of specialised training workshops in phage genome annotation and viromics. The award allowed the implementation of viromics protocols developed for the human gut environment to farm soil and water (One Health compartment). This allowed us to build a picture of the bacteriophages that are native to the agricultural system for future biocontrol applications, as well as the other viruses present in the system. Further funding was secured to analyse the viromics datasets that were generated and to expand their scope. Finally, a subset of Canadian bacteriophages were tested for their infectivity on UK bacterial foodborne pathogens as training for the UK researchers. |
| Exploitation Route | The training material and datasets generated by this study will be very useful for further investigations into the virome of the food chain and the connectivity between food and gut. The materials generated here are more broadly applicable to any context or environment where one wants to investigate bacteriophage presence and diversity, as well as the ecology and gene content. |
| Sectors | Agriculture Food and Drink Environment Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| Description | The award gave rise to a new line of investigation in the partner labs in the UK and Canada, involving the presence and diversity of bacteriophages in the food chain and how they can be exploited for biocontrol of foodborne pathogens. The training tools and workflows developed here are of broad use across microbiology and microbiome science, and have received positive feedback from the scientific community. It has increased the global visibility of the BBSRC-funded Quadram Institute Bioscience, and the UK research in general. The travel award has also allowed early career scientists from the UK visit the Canadian partner and exchange knowledge in a personal way that wouldn't have been possible without the award. This opportunity has been extremely useful in their professional development and guiding further career choices. The award also allowed the PIs to jointly attend an Innovate UK Phage Innovation Network meeting where barriers to the use of bacteriophages were discussed and thereby contributed to policymaking on this topic. The award has led to further collaborations both with the Co-Is and other group leaders at the Quadram Institute, leading to new projects being developed and funding for one PhD student being secured. |
| First Year Of Impact | 2022 |
| Sector | Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Policy & public services |
| Description | Canada partnership continuation on bacteriophages in the food chain |
| Amount | £21,500 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2024 |
| End | 06/2024 |
| Title | De novo sequencing of phages T4 and T7 |
| Description | Raw data and assemblies of the de novo sequencing of the "model" phages T4 and T7, performed with Illumina NextSeq 2x150 and Oxford Nanopore, generated for the "Phage Annotation Workshop" held online on November 2021: https://github.com/quadram-institute-bioscience/phage-annotation-workshop/ |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Datasets used as teaching materials and available for any scientist to use. |
| URL | https://zenodo.org/record/5704419 |
| Description | Research visit and partnership with Agriculture and AgriFood Canada |
| Organisation | Agriculture and Agri-Food Canada |
| Country | Canada |
| Sector | Public |
| PI Contribution | Research visit to Agriculture and Agrifood Canada (AAFC), including review of the Bacteriophage lab activities (AAFC). Set of collaborative experiments started, sequencing and data analysis performed at QIB. |
| Collaborator Contribution | Set of collaborative experiments started where lab work is performed as in-kind contribution by AAFC. |
| Impact | Outcomes: 2022 research visit, 2021 phage annotation workshop (see other outputs). |
| Start Year | 2021 |
| Title | Repository for the Phage Genome Annotation Workshop |
| Description | Technical repository with the files and instructions for the Phage Genome Annotation workshop |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Used by the participants to the workshop, but also widely downloaded afterwards thanks to the sharing on social media. The repository received six stars, |
| URL | https://github.com/quadram-institute-bioscience/phage-annotation-workshop/ |
| Title | Software repository for Viromics workshop |
| Description | GitHub repository for the viromics training workshop, including workflow development, tutorial and supporting data. |
| Type Of Technology | Software |
| Year Produced | 2023 |
| Impact | The workflow that was developed as part of the award is being used by other academics, including collaborators at AAFC to analyse their data. |
| URL | https://github.com/adriaenssens-lab/viromics/wiki/Canada-Partnership-Viromics-Workshop-2023 |
| Description | Oral presentation at the African Phage Symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The Africa Phage Forum organised a virtual symposium "African Phage Symposium 2021" for all stakeholders (students, academics and NGOs) on the continent, with invited talks from international stakeholders and academics. I presented a seminar titled "Basics of phage genome annotation & classification - How to get started" which addresses one of the key knowledge gaps for African scientists, sequencing and genomics. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://apf.phage.directory/ |
| Description | Phage Annotation Workshop 2021 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | We organised a 3 half-day workshop on the principles of phage genome annotation. The event was conducted live virtually and attended by researchers from the Quadram Institute, Agriculture and AgriFood Canada and the University of Guelph, Canada. Teaching materials were made available to the general public through GitHub and YouTube. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://github.com/quadram-institute-bioscience/phage-annotation-workshop/wiki |
| Description | Stand at Norwich Science Festival: Bacteriophages, can viruses be good? |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Stand at the Norwich Science Festival where school aged children could do a craft activity to learn about bacteriophages, which are good viruses. Excellent engagement and feedback with children and parents from across East Anglia, estimated 200 children attended the stand. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Viromics Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The Adriaenssens lab at the Quadram Institute Bioscience organised a workshop on viromics methods in Norwich, attended by members of the institute and four visiting scientists from Canada. Further research projects are being designed after this workshop and further funding was acquired. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://github.com/adriaenssens-lab/viromics/wiki/Canada-Partnership-Viromics-Workshop-2023 |
| Description | Youtube playlist: talks and screencasts from the Phage Annotation Workshop |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Video recordings of talks and practicals from the Phage Annotation Workshop. Persistent media enables the re-use of the produced materials and datasets. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.youtube.com/playlist?list=PLTOYPYSmztrdhjh0aVCmPjTKHKV3A5TCa |