Determinants of microbe-host responses in the gut across life
Lead Research Organisation:
QUADRAM INSTITUTE BIOSCIENCE
Department Name: UNLISTED
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
To probe specific mechanistic aspects of the gut microbiome's positive influence on health throughout life, we have developed a systems-level experimental approach. We will use innovative in vivo, in vitro, and in silico tools/models in tandem with a key longitudinal cohort (pregnancy and early life) to define and refine novel intervention strategies that will promote gut health. Our multi-disciplinary research theme managed by QIB and university research leaders, maps to three objectives. These objectives will determine how microbes (bacterial, viral, fungal) establish and maintain a balanced community that modulates host homeostatic cross-talk within the gut.
This theme involves a 250-particpant longitudinal population study of pregnancy mothers and their infants, up to 2 years of age.
Theme 1 focusses on the gut during the very first stages of life, and in the elderly, and will seek to unravel: (i) how pioneer/keystone microbial species facilitate healthy development (ii) which microbial mediators modulate microbe-microbe and microbe-host cross-talk and (iii) bi-directional immune system-microbiota interactions within the gut.
Theme 1 Outputs
• identification of critical pre- and post-natal periods for establishing a healthy intestinal microbiome and the contribution that host and environmental factors play
• define molecular mediators of microbe-microbe and microbe-host crosstalk important in microbial ecology and establishing tolerance
Our integrated plan of work will ultimately determine microbiome- and host-associated pathways that could represent key targets for lifestyle changes and therapies that reduce the incidence and burden of infectious, metabolic, and immune-mediated conditions.
This theme involves a 250-particpant longitudinal population study of pregnancy mothers and their infants, up to 2 years of age.
Theme 1 focusses on the gut during the very first stages of life, and in the elderly, and will seek to unravel: (i) how pioneer/keystone microbial species facilitate healthy development (ii) which microbial mediators modulate microbe-microbe and microbe-host cross-talk and (iii) bi-directional immune system-microbiota interactions within the gut.
Theme 1 Outputs
• identification of critical pre- and post-natal periods for establishing a healthy intestinal microbiome and the contribution that host and environmental factors play
• define molecular mediators of microbe-microbe and microbe-host crosstalk important in microbial ecology and establishing tolerance
Our integrated plan of work will ultimately determine microbiome- and host-associated pathways that could represent key targets for lifestyle changes and therapies that reduce the incidence and burden of infectious, metabolic, and immune-mediated conditions.
Planned Impact
unavailable
Organisations
- QUADRAM INSTITUTE BIOSCIENCE (Lead Research Organisation)
- St Mark's Academic Institute (Collaboration)
- University of Toronto (Collaboration)
- University of Oxford (Collaboration)
- Eagle Genomics Ltd (Collaboration)
- UNIVERSITY OF KENT (Collaboration)
- Utrecht University (Collaboration)
- Lanzhou Veterinary Research Institute (Collaboration)
Publications
A James S
(2020)
Preterm Infants Harbour a Rapidly Changing Mycobiota That Includes Candida Pathobionts.
in Journal of fungi (Basel, Switzerland)
Acuna-Gonzalez A
(2023)
Bifidobacterium bacteraemia is rare with routine probiotics use in preterm infants: A further case report with literature review.
in Anaerobe
Adriaenssens EM
(2021)
Phage Diversity in the Human Gut Microbiome: a Taxonomist's Perspective.
in mSystems
Adriaenssens EM
(2020)
Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.
in Archives of virology
Adriaenssens EM
(2021)
Tracing the fate of wastewater viruses reveals catchment-scale virome diversity and connectivity.
in Water research
Adriaenssens EM
(2023)
Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification.
in Nature biotechnology
Alcon-Giner C
(2020)
Microbiota Supplementation with Bifidobacterium and Lactobacillus Modifies the Preterm Infant Gut Microbiota and Metabolome: An Observational Study.
in Cell reports. Medicine
Anany H
(2022)
ICTV Virus Taxonomy Profile: Chaseviridae 2022.
in The Journal of general virology
| Title | Bifidobacterium bronze and perfume sculpture - Wellcome Collection (Being Human) |
| Description | Food historian and artist Tasha Marks of AVM Curiosities has developed a playful bronze and perfume sculpture which suggests the smell of breast milk and celebrates the microbiome and our symbiotic relationship with bacteria. This was in collaboration with Dr Lindsay J Hall |
| Type Of Art | Artwork |
| Year Produced | 2019 |
| Impact | This has enhanced the public's knowledge on the links between certain microbiota members i.e. Bifidobacterium and early life diet - breast milk. |
| URL | https://wellcomecollection.org/pages/XW5QMBEAACUAELBV |
| Title | Guardians of the Gut Exhibit |
| Description | "Guardians of the Gut": 6-meter-long, 2-meter-high gut, with internal game stations which allowed visitors to interact with their 'microbes |
| Type Of Art | Artistic/Creative Exhibition |
| Year Produced | 2018 |
| Impact | This exhbit has been shown at the Royal Society Summer Exhibition and Norwich Science Festivals 2018 |
| Description | • We showed that specific strains of probiotic Bifidobacterium and Lactobacillus species given to preterm babies alongside breast milk beneficially shaped their microbial populations and gut health to levels that matched those of babies born at full-term. The ability of preterm babies to survive, fight infections and derive the full benefits from breast milk were all improved. This is the largest study of this type to date. A corresponding study in collaboration with colleagues at NNUH showed that the same routine probiotic was associated with halving the rates of necrotising enterocolitis (NEC) and sepsis, a deadly illness in preterm babies. • Ruminococcus gnavus is a prevalent human gut symbiont, an early coloniser of the infant gut that persists in adulthood and is disproportionately represented in diseases. There is therefore great interest in understanding the mechanisms by which R. gnavus strains adapt to the gut. We unravelled the molecular pathways underpinning mucin glycan foraging by R. gnavus strains, revealing essential adaptations to the infant and adult gut including the capacity to degrade sialylated, fucosylated glycans and blood group antigens • Using systems biology approaches we have developed a predictive model of the pathways and mediators of microbe-host interactions (the interactome) in the GIT. The interactome model has been validated experimentally and will be of use in identifying and modelling how perturbations through infection, diet, medications etc. impact on the interactome and host health and susceptibility to diseases originating in the GIT. - We discovered that human gut microbiomes can be represented through 5 common (globally present) bacterial guilds, that we call Enterosigantures. These can also be used to predict the health status of the gut microbiome. - Using a large meta-analysis of human gut metagenomes, we discovered that gut bacteria are not only highly persistent, but also often shared among family members and in geographic locations. |
| Exploitation Route | These data form the basis of the next ISP funding and may longer term impact different stakeholders and policies |
| Sectors | Agriculture Food and Drink Healthcare Pharmaceuticals and Medical Biotechnology |
| Description | • A number of studies and collaborations have allowed us to show that specific strains of probiotic Bifidobacterium and Lactobacillus bacteria given to preterm babies with breast milk, beneficially shapes their microbial populations and gut health to levels that match those of babies born at full-term (Cell Reports Medicine, Nature Microbiology, amongst others). This helps vulnerable babies survive, fight infections, derive the full benefits from breast milk, and get the healthiest start in life. We showed a 50% reduction in the devastating disease necrotising enterocolitis and late onset sepsis due to routine administration of probiotic in at-risk preterm infants (BMJ Arc Dis Neonatology). Less than 20% of UK neonatal wards were using routine probiotics on premature babies, but as a result of our work, other Neonatal Intensive Care Units have already changed their policies to use probiotic supplementation in at-risk infants as standard. This work has also been cited in WHO preterm care guidelines • Our work on R. gnavus glycoside hydrolases (involved in mucin glycan degradation) has led to a Commercial Agreement between QIB and Ludger Ltd for commercialisation of fucosidase as a diagnostic, leading to the development of a diagnostic kit for the detection of those at risk of Maturity Onset Diabetes of the Young type 3 (MODY). • Patients with FAP require pre-emptive colectomy. The mucosal immune cell markers that we identified indicated the likelihood of CRC development in individuals with FAP; not only will monitoring these markers negate the requirement for colectomy in some FAP patients, but studies in FAP and CRC also indicate ways in which resetting the immune system could be used both as a preventative treatment for FAP and for beneficial therapeutics in CRC patients. • We have designed an integrated systems genomics workflow termed iSNP, to layer patient data from population-wide genomics with network biology and transcriptomics using UC as a model of a complex genetic disease. We identified pathways regulating the cellular response to stress, cell motility and calcium homeostasis as being overrepresented in the UC-associated signalling network; establishing the potential for iSNP to stratify patients based on patient-specific genetics for precision therapy. • Our data in humans are the first to show that mucosal immune dysfunction contributes to the development of genetically driven cancers; it provides critical evidence for the aetiology of colorectal cancer (CRC). In Inflammatory Bowel Disease (IBD) there are changes in the gut microbiota (dysbiosis) and an increased incidence of CRC. We evaluated interactions between the microbiota and mucosal immunity to determine whether any changes promoted tumorigenesis and demonstrated that dysbiosis in pre-cancerous familial adenomatous polyposis (FAP) is a driver for immune dysfunction. • We have also had 30k+ installs for the LotuS2 software for microbiome analysis |
| First Year Of Impact | 2020 |
| Sector | Agriculture, Food and Drink,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Cultural Societal Economic Policy & public services |
| Description | Membership of R&D Executive Committee influencing educational and research policy updated annually |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Membership of a guideline committee |
| Description | UK Government PostNote |
| Geographic Reach | National |
| Policy Influence Type | Citation in other policy documents |
| URL | https://researchbriefings.parliament.uk/ResearchBriefing/Summary/POST-PN-0574 |
| Description | Written response to government inquiry on bacteriophages |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| URL | https://committees.parliament.uk/writtenevidence/114423/pdf/ |
| Description | BBSRC IAA |
| Amount | £10,377 (GBP) |
| Funding ID | BB/S506679/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 05/2021 |
| Description | BBSRC IAA The Quadram Institute |
| Amount | £300,000 (GBP) |
| Funding ID | BB/S506679/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2022 |
| Description | BBSRC ITAS International Travel Award Scheme |
| Amount | £3,000 (GBP) |
| Organisation | Quadram Institute Bioscience |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 10/2021 |
| Description | Bacterioph00ages for gut health |
| Amount | £614,467 (GBP) |
| Funding ID | BB/W015706/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2022 |
| End | 10/2025 |
| Description | CLRN Flexibility & Sustainability Research Funding |
| Amount | £55,975 (GBP) |
| Funding ID | RDFSF025 |
| Organisation | London North West Healthcare NHS Trust |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2018 |
| End | 07/2019 |
| Description | Clinical seedcorn |
| Amount | £40,000 (GBP) |
| Organisation | Quadram Institute Bioscience |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 12/2024 |
| Description | Diätetische Beeinflussung des Darm-Mikrobiomes bei der Parkinson Krankheit |
| Amount | € 11,200 (EUR) |
| Organisation | Hilde-Ulrichs-Stiftung für Parkinsonforschung |
| Sector | Charity/Non Profit |
| Country | Germany |
| Start | 05/2019 |
| End | 03/2020 |
| Description | EXPLORING THE HUMAN BRAIN MICROBIOME IN PARKINSON'S DISEASE |
| Amount | € 16,000 (EUR) |
| Organisation | ParkinsonFonds Deutschland |
| Sector | Charity/Non Profit |
| Country | Germany |
| Start | 03/2019 |
| End | 03/2020 |
| Description | EkoEvo Collaboration |
| Amount | £1,000 (GBP) |
| Organisation | Ecology and Evolutionary Biology Community of Turkey |
| Sector | Learned Society |
| Start | 05/2020 |
| End | 06/2020 |
| Description | Evolution of pro- and eukaryotic commensals within the human gut |
| Amount | € 1,500,000 (EUR) |
| Funding ID | 948219 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 02/2021 |
| End | 02/2026 |
| Description | Exploration of mucosal microbiomes |
| Amount | £8,900 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2023 |
| End | 03/2023 |
| Description | Immune Response to Q-fever |
| Amount | £99,990 (GBP) |
| Organisation | Defence Science & Technology Laboratory (DSTL) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 03/2021 |
| Description | Integrated Models of the Human Gut- Capital Grant Award for 2021/22 Investment Gateway Panel Business Cases. |
| Amount | £1,152,556 (GBP) |
| Organisation | Quadram Institute Bioscience |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 07/2021 |
| End | 03/2022 |
| Description | KEC PoC grant New human colon-intestine-chip model |
| Amount | £15,000 (GBP) |
| Organisation | Quadram Institute Bioscience |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 06/2021 |
| End | 03/2022 |
| Description | Mucosal microbiome exploration in patients with intestinal inflammation |
| Amount | £58,371 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2022 |
| End | 03/2023 |
| Description | NRP DTP studentship |
| Amount | £10,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2020 |
| End | 09/2024 |
| Description | NRPDTP Studentship Bacteriophages as key players in bacterial adaptation to the human gut |
| Amount | £105,000 (GBP) |
| Funding ID | 2748665 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2026 |
| Description | NRPDTP VitB12 |
| Amount | £80,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2019 |
| End | 06/2024 |
| Description | New antimicrobials to target gut pathogens |
| Amount | £20,000 (GBP) |
| Funding ID | 2116844 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 09/2023 |
| Description | Norwich Research Park Bioscience Doctoral Training Partnership |
| Amount | £100,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2018 |
| End | 10/2022 |
| Description | Norwich Research Park Bioscience Doctoral Training Partnership |
| Amount | £100,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2016 |
| End | 10/2020 |
| Description | Norwich Research Park Bioscience Doctoral Training Partnership |
| Amount | £100,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2015 |
| End | 09/2019 |
| Description | Phages in the infant gut: good, bad or neutral? |
| Amount | £105,000 (GBP) |
| Funding ID | 2444856 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2020 |
| End | 09/2024 |
| Description | Potential therapeutic effects of engineered Clostridium STp products on immune activity |
| Amount | £86,600 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2019 |
| End | 03/2023 |
| Description | Pushing the frontiers of in vivo microbial strain delineation and nucleotide evolution via metagenomics |
| Amount | £80,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2020 |
| End | 05/2024 |
| Description | QIB Proof of Concept: |
| Amount | £7,000 (GBP) |
| Organisation | Quadram Institute Bioscience |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 07/2019 |
| Description | ReStrain: Discovery of markers of a healthy gut microbiome through computational and experimental means (academic-industry collaboration) |
| Amount | £80,000 (GBP) |
| Funding ID | 2246539 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2019 |
| End | 09/2024 |
| Description | Research contract |
| Amount | £99,990 (GBP) |
| Funding ID | 1000137348 |
| Organisation | Defence Science & Technology Laboratory (DSTL) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 02/2021 |
| Description | Reservoirs of mobile antibiotic resistance genes in the gut microbiome of preterm infants |
| Amount | £588,844 (GBP) |
| Funding ID | BB/S017941/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2019 |
| End | 08/2023 |
| Description | St Marks Foundation Research Grants |
| Amount | £216,138 (GBP) |
| Funding ID | RES209 |
| Organisation | St Marks Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 10/2020 |
| Description | St Marks Hospital Studentship |
| Amount | £20,996 (GBP) |
| Organisation | St. Mark's Hospital Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 12/2022 |
| Description | TROVE Research Project |
| Amount | £12,000 (GBP) |
| Funding ID | RES231 |
| Organisation | St. Mark's Hospital Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 02/2020 |
| Description | Training interdisciplinary glycoscientists to get a molecular- level grip on glycocodes at the human mucosa-microbiota |
| Amount | £466,300 (GBP) |
| Funding ID | 814102 |
| Organisation | European Commission |
| Sector | Public |
| Country | Belgium |
| Start | 01/2019 |
| End | 12/2022 |
| Description | iCASE doctoral training programme |
| Amount | £69,900 (GBP) |
| Funding ID | Enterprise DTP: MRC iCASE Studentship 2019-20 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2019 |
| End | 03/2023 |
| Description | international partnering award USA |
| Amount | £10,000 (GBP) |
| Organisation | Quadram Institute Bioscience |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 03/2025 |
| Title | Additional file 1 of CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes |
| Description | Additional file 1: Table S1. Barcode sequences. Table S2a. Sample metrics for the Routine dataset. Table S2b. Sample metrics for the Rapid Response dataset. Table S3. The differences between the consensus genomes of each sequencing method, for all samples with differences reported. Table S4. Reagent costs for the three methods when sequencing 96 samples (CoronaHiT-ONT and ARTIC LoCost) or 384 samples (CoronaHiT-Illumina). Table S5. Sample identifiers and accession numbers. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_CoronaHiT_high-throughput_... |
| Title | Additional file 10 of Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson's disease individuals |
| Description | Additional file 9: Suppl. Table 2. Taxonomic classification of off-target amplicons based on ASV clustering. Classification is either based on LotuS-LCA or LotuS-RDP. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_10_of_Much_ado_about_nothing_Of... |
| Title | Additional file 13 of Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson's disease individuals |
| Description | Additional file 12: Suppl. Table 5. Analysis of off-target amplicons in mock samples. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_13_of_Much_ado_about_nothing_Of... |
| Title | Additional file 14 of Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson's disease individuals |
| Description | Additional file 13: Suppl. Table 6. In depth check of putative true bacteria in brain samples with manual Blast n. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_14_of_Much_ado_about_nothing_Of... |
| Title | GeneCatalog.faa |
| Description | proteins for chicken gene catalog |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/GeneCatalog_faa/19582717/1 |
| Title | GeneCatalog.faa |
| Description | proteins for chicken gene catalog |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://figshare.com/articles/dataset/GeneCatalog_faa/19582717 |
| Title | MOESM1 of Genomic analysis on broiler-associated Clostridium perfringens strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis |
| Description | Additional file 1. Supplementary tables. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/MOESM1_of_Genomic_analysis_on_broiler-associated_Clostr... |
| Title | MOESM1 of Genomic analysis on broiler-associated Clostridium perfringens strains and exploratory caecal microbiome investigation reveals key factors linked to poultry necrotic enteritis |
| Description | Additional file 1. Supplementary tables. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/MOESM1_of_Genomic_analysis_on_broiler-associated_Clostr... |
| Title | Strain delineation based on phylogenies |
| Description | Metagenomic based reconstruction of genomes & subsequent delineation at strain resolution. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | This method, implemented in the MATAFILER pipeline, is being used in multiple collaborations and within the group. |
| URL | https://github.com/hildebra/MATAFILER |
| Description | Chemical glycobiology |
| Organisation | Utrecht University |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Contributed to successful multidisciplinary European Training Network Sweetcrosstalk proposal Supervising tow ESRs on the project WP leader |
| Collaborator Contribution | Coordinator of ITN Host of one of my ESRs |
| Impact | Chemistry, Glycobiology, Microbiology |
| Start Year | 2018 |
| Description | Collaboration with EAGLE genomics, Cambridge |
| Organisation | Eagle Genomics Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Engagement with industry, resulting in knowledge sharing |
| Collaborator Contribution | in kind contributions to HPC usage |
| Impact | -shared studentship -shared knowledge & data |
| Start Year | 2019 |
| Description | Gut - microbiome single cell project |
| Organisation | University of Toronto |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | We have sequenced and analysed samples provided by the partner. |
| Collaborator Contribution | These samples were from an experiment the partner have previously carried out. We were not able to generate such samples, and as the cell isolation protocol was the same that we normally use, processing their samples and then compare the different conditions were straightforward for us. |
| Impact | Single-cell sequence data generated (stem cell, Paneth cell, transit amplifying cells) from mouse (germ-free, ex-germ-free, normal). Data analysis and publication is ongoing. |
| Start Year | 2018 |
| Description | Polyposis Team |
| Organisation | St Mark's Academic Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | St Marks Academic Institute for the Study of Colorectal Diseases is a national and international referral centre for colorectal diseases. Partnering with the Polyposis Team is enabling immune profiling of patients with pre-malignent conditions in relation to the gut microbiota. |
| Collaborator Contribution | Provision of clinical expertise and material |
| Impact | Development of a new Ethical Committee approval - 17/LO/16/36 Changes in immune responses to gut microbiota have been identified in pre-malignant cancer patients with APC gene mutations. We are identifying basic immune parameters that may predispose to the development of malignancy raising the possibility of individualised diagnosis / treatment. |
| Start Year | 2018 |
| Description | Structural biology |
| Organisation | University of Oxford |
| Department | Oxford Hub |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Identified and functionally characterised a novel enzyme activity in gut bacteria |
| Collaborator Contribution | Crystallisation of metabolic enzyme involved in carbohydrate utilisation by bacteria |
| Impact | Manuscript in preparation 3D Structure |
| Start Year | 2019 |
| Description | TROVE project |
| Organisation | St Mark's Academic Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We provide laboratory facilities, immunological expertise to inform experimental design, laboratory training, data analysis and student supervision and training. |
| Collaborator Contribution | Clinical expertise and patient profiling and samples |
| Impact | Participation in the TROVE research project with clinical partners has allowed us to explore the relevance of efferent lymph feeding to the establishment of the microbial fauna in the gut and the resultant immune profiles in response to individual bacteria. Preliminary evidence indicates that profiling may be used in diagnosis and potentially in bacterial treatment with designer probiotics in the future. |
| Start Year | 2018 |
| Description | Transfer of mice deficient in LAP |
| Organisation | Lanzhou Veterinary Research Institute |
| Country | China |
| Sector | Learned Society |
| PI Contribution | Mice deficient in LAP generated at UEA/QIB have been sent to Lanzhou Veterinary Research Institute (LVRI). T. Wileman, P. S. Carding, Regis Stentz from Norwich Research Park, and James Stewart from University of Liverpool visited State Key Laboratory of Lanzhou Veterinary Research Institute (LVRI) , and Pasteur Institute Shanghai in June 2016 to discuss research projects and collaboration. T. Wileman, P. Powell, S. Carding, Regis Stentz from Norwich research Park, and James Stewart from University of Liverpool visited three research institutes (Institute of Microbiology, Beijing Academy of Sciences, State Key Laboratory of Lanzhou Veterinary Research Institute, Northwest Agricultural and Forestry University,Yangling, Shaanxi) in October 2018 to discuss further research projects and collaboration. Mice deficient in LAP generated at UEA/QIB have been sent to University of New Mexico, USA, St Judes Medical Centre, Memphis USA, University of South Florida. USA, |
| Collaborator Contribution | LAP deficient mice will be used in infection studies focusing on Foot and Mouth Disease virus at LVRI, and possibly Zika virus at Pasteur Institute in Shanghai. Scientists from the Chinese Academy of Agricultural Sciences (Zhidong Zhang, Yanmin Li, Xiaodong Qin) and Gang Long from Pasteur Institute Shanghai, visited Norwich Research Park 06:2017 to discuss collaborative work. Dr Yang Yang from LVRI has been sent on a six month secondment (October 2018-May 2019) to UEA to learn how to characterise LAP deficient mice. Mice deficient in LAP will be used in studies of infection and age dependent cognitive decline DOI: 10.1126/sciadv.abb9036 |
| Impact | DOI: 10.1126/sciadv.abb9036 |
| Start Year | 2019 |
| Description | Vitamin B12 Biology |
| Organisation | University of Kent |
| Country | United Kingdom |
| PI Contribution | Secured a joint PhD studentship and grant |
| Collaborator Contribution | Input into grant applications and supervisory expertise |
| Impact | Secured a joint PhD studentship and grant |
| Start Year | 2019 |
| Title | Bifidobacterium and compositions thereof for breast cancer treatment |
| Description | Bifidobacterium and compositions thereof for breast cancer treatment |
| IP Reference | GB2118611.9 |
| Protection | Patent application published |
| Year Protection Granted | 2021 |
| Licensed | No |
| Impact | Patent only filed in Dec 2021 so still in early stages |
| Title | Mucosodom cohort |
| Description | This is the creation of a novel cohort researching & cataloguing the mucosa associated microbiome, congruent with transcriptomic profiles at such sites. This is an early stage cohort, that is already ~30% complete currently. We will investigate the healthy microbiome and the microbiome in inflamed gut microbiomes. |
| Type | Diagnostic Tool - Non-Imaging |
| Current Stage Of Development | Initial development |
| Year Development Stage Completed | 2021 |
| Development Status | On hold |
| Impact | -first use of this technology -allows high resolution gut metagenomics in a spatial context |
| Title | Dadaist2 v1.0.0 |
| Description | Dadaist2: highway to R Documentation: https://quadram-institute-bioscience.github.io/dadaist2/ Repository: https://github.com/quadram-institute-bioscience/dadaist2 Standalone wrapper for DADA2 package, to quickly generate a feature table and a set of representative sequences from a folder with Paired End Illumina reads. Dadaist2 is designed to simplify the stream of data from the read processing to the statistical analysis and plots. Dadaist2 is a highway to downstream analyses: Generation of a PhyloSeq object, for immediate usage in R Possibility to run in the pipeline a custom R script that starts from the PhyloSeq object Generation of MicrobiomeAnalyst-compatible files. MicrobiomeAnalyst provides a web-interface to performgi a broad range of visualizations and analyses. Generation of Rhea-compatible files. Rhea is a standardized set of scripts "designed to help easy implementation by users". In addition to this, Dadaist: Can automatically detect quality boundaries or trim the primers Has a custom mode for variable length amplicons (i.e. ITS), to detect features longer than the sum of the paired-end reads. Ships an open source implementation of UNCROSS2 by Robert Edgar. Has a modular design that allows recycling parts of it in custom workflows. Prepares a MultiQC-enabled overview of the experiment Produces an easy to inspect HTML execution log |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4761407 |
| Title | Dadaist2 v1.0.0 |
| Description | Dadaist2: highway to R Documentation: https://quadram-institute-bioscience.github.io/dadaist2/ Repository: https://github.com/quadram-institute-bioscience/dadaist2 Standalone wrapper for DADA2 package, to quickly generate a feature table and a set of representative sequences from a folder with Paired End Illumina reads. Dadaist2 is designed to simplify the stream of data from the read processing to the statistical analysis and plots. Dadaist2 is a highway to downstream analyses: Generation of a PhyloSeq object, for immediate usage in R Possibility to run in the pipeline a custom R script that starts from the PhyloSeq object Generation of MicrobiomeAnalyst-compatible files. MicrobiomeAnalyst provides a web-interface to performgi a broad range of visualizations and analyses. Generation of Rhea-compatible files. Rhea is a standardized set of scripts "designed to help easy implementation by users". In addition to this, Dadaist: Can automatically detect quality boundaries or trim the primers Has a custom mode for variable length amplicons (i.e. ITS), to detect features longer than the sum of the paired-end reads. Ships an open source implementation of UNCROSS2 by Robert Edgar. Has a modular design that allows recycling parts of it in custom workflows. Prepares a MultiQC-enabled overview of the experiment Produces an easy to inspect HTML execution log |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4761408 |
| Title | LotuS2 |
| Description | Amplicon sequencing pipeline |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Already internationally used by collaborators. Currently (Feb 24) >30,000 installs through BioConda |
| URL | http://lotus2.earlham.ac.uk/ |
| Title | MATAFILER |
| Description | MATAFILER pipeline to process shotgun metagenomics datasets |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | Allows for fast and streamlined analysis of shotgun metagenomics datasets, widely used in group's work and collaborations. The software is constantly being updated, last big release was in 2021 (MATAF3) |
| URL | https://github.com/hildebra/MATAFILER |
| Title | SeqFu - Fastx Sequence Utilities |
| Description | SeqFu A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. SeqFu is available for Linux and MacOS. Documentation: https://telatin.github.io/seqfu2/ Repository: https://github.com/telatin/seqfu2 |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4684491 |
| Title | SeqFu - Fastx Sequence Utilities 1.0 |
| Description | SeqFu 1.0 A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. SeqFu is available for Linux and MacOS. Documentation: https://telatin.github.io/seqfu2/ Repository: https://github.com/telatin/seqfu2 Paper Bioengineering |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4740106 |
| Title | SeqFu - Fastx Sequence Utilities 1.0 |
| Description | SeqFu 1.0 A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. SeqFu is available for Linux and MacOS. Documentation: https://telatin.github.io/seqfu2/ Repository: https://github.com/telatin/seqfu2 Paper Bioengineering |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/4684490 |
| Title | Singularity image: "covtobed" -- a tool to extract coverage information from BAM files |
| Description | Covtobed 0.3 Read one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. https://github.com/telatin/covtobed/ |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/1063493 |
| Title | Singularity image: "covtobed" -- a tool to extract coverage information from BAM files [1.0RC] |
| Description | Covtobed 1.0RC Read one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. https://github.com/telatin/covtobed/
Latest version Since our repository is used to automatically build a Docker container via DockerHub, you can pull the singularity image from there:
|
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/1063492 |
| Title | Singularity image: "covtobed" -- a tool to extract coverage information from BAM files [1.0RC] |
| Description | Covtobed 1.0RC Read one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. https://github.com/telatin/covtobed/
Latest version Since our repository is used to automatically build a Docker container via DockerHub, you can pull the singularity image from there:
|
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| URL | https://zenodo.org/record/3600261 |
| Title | ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways |
| Description | The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralLink: a systems biology workflow which reconstructs and analyses networks representing the effect of viruses on intracellular signalling. These networks trace the flow of signal from intracellular viral proteins through their human binding proteins and downstream signalling pathways, ending with transcription factors regulating genes differentially expressed upon viral exposure. In this way, the workflow provides a mechanistic insight from previously identified knowledge of virally infected cells. By default, the workflow is set up to analyse the intracellular effects of SARS-CoV-2, requiring only transcriptomics counts data as input from the user: thus, encouraging and enabling rapid multidisciplinary research. However, the wide-ranging applicability and modularity of the workflow facilitates customisation of viral context, a priori interactions and analysis methods. Through a case study of SARS-CoV-2 infected bronchial/tracheal epithelial cells, we evidence the functionality of the workflow and its ability to identify key pathways and proteins in the cellular response to infection. The application of ViralLink to different viral infections in a cell-type specific manner using different available transcriptomics datasets will uncover key mechanisms in viral pathogenesis. The workflow is available on GitHub (https://github.com/korcsmarosgroup/ViralLink) in an easily accessible Python wrapper script, or as customisable modular R and Python scripts. |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | ViralLink has been used to study the effect of SARS-CoV-2 infection on lung cells within the publication. Subsequently it is being used for an ongoing project relating to the effect of SARS-CoV-2 infection in the intestines. |
| URL | https://zenodo.org/record/4266585 |
| Description | 17-21 July 2017_2nd Interdisciplinary Signaling Workshop |
| 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 | In this interdisciplinary workshop advanced science was combined with informal summer activities to solve multi-disciplinary scientific questions, by bringing early career scientists together with more established researchers in a relaxing and beautiful location. Invited speakers presented talks on the topics of cell regulation, network modelling, genomics, systems biology, bioinformatics, structural biology, biochemistry, and cheminformatics. Then, selected talks from other participants will be followed by multi-disciplinary teamwork sessions in the afternoon, followed by cultural and social activities, such as medieval team building and handicraft activities in the Visegrad Castle. Poster sessions and plenty of informal opportunities allowed the participants to discuss complex and exciting questions as well as develop new collaborations. The renaissance surroundings of the venue nicely matched with the interdisciplinary nature of the workshop. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://signalingworkshop.org/ |
| Description | 24-25 April 2017_Multiscale analysis of host-microbe interactions in plants, animals and humans |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | The aim of this workshop was to bring together key experts and early-stage scientists working on host-microbe interactions, including pathogen infections, commensals and microbiome level studies, to share novel scientific ideas on the multiscale investigation of host-microbe interactions and to provide an exciting opportunity to establish and improve cross-disciplinary and UK-wide collaborations. After kick off with three keynote speakers on current challenges, the program provides structured study groups to discuss 1) novel methodological approaches; 2) potential future projects requiring participants from different disciplines; 3) the best ways to get funding for such multi-disciplinary projects. We facilitated these goals with short presentations and brainstorming opportunities in coordinated team works, and with panel discussion with representatives of key relevant funding agencies and charities. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.multiscalebiology.org.uk/events/event/multiscale-analysis-of-host-microbe-interactions/ |
| Description | 3 day Numerical ecology training |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | 25 person course organized by the VIB, Belgium with international participants. I organize this 3 day course, including talks and hands-on sessions by Stefano Romano, Ezgi Ozkurt, Rebecca Ansroge, Angela Del Castillo, Nicola Soranzo and Joachim Fritscher. |
| Year(s) Of Engagement Activity | 2021 |
| Description | 3 day Numerical ecology training |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | 30person course organized by the VIB, Belgium with international participants. I organize this 3 day course, including talks and hands-on sessions by Stefano Romano, Ezgi Ozkurt, Rebecca Ansorge, Nicola Soranzo, Duncan Ng and Joachim Fritscher. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://training.vib.be/all-trainings/analysis-16s-rrna-metagenomic-experiments-online-0 |
| Description | 4th Annual European Microbiome Congress |
| 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 | Attendance to 4th Annual European Microbiome Congress. This Conference has a high representation from the Industry: Pharmaceutical companies and Biotechnology companies and provided an excellent opportunity to make contact and discuss work relevant to the Institute Strategic Programmes. The PROMOTING WOMEN IN SCIENCE lunch session was inspiring. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Academia-Industry Networking CarboMet event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | I co-organised and chaired a two day workshop on 'The Role of Carbohydrates in the Gut Microbiome' June 2018 in Brussels attended by 40 delegates from academia and industry as apart of CarboMet. CarboMet (Metrology of Carbohydrates for European Bioindustries) is a four-year Coordination and Support Action (CSA) funded by Horizon 2020 FET-OPEN. It is an European Network that facilitates engagement between key players and stakeholders of the glycoscience community across Europe to identify the current state of the art and in particular future innovation and technological challenges in carbohydrate metrology. I co-wrote and edited the CarboMet positioning paper on 'The Essential Roles of Carbohydrates in Promoting Gut Microbiota Function Through All Stages of Life' which summarises discussions that took place during the workshop. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://carbomet.eu/news/positioning-paper-on-role-of-carbohydrates-in-gut-microbiota-function/ |
| Description | Analysing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions Scientific Advisory Board Meeting Earlham Institute |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Analysing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions Scientific Advisory Board Meeting Earlham Institute |
| Year(s) Of Engagement Activity | 2019 |
| Description | Analyzing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions SYSBIO 2018 - Advanced Lecture Course on Systems Biology |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Analyzing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions SYSBIO 2018 - Advanced Lecture Course on Systems Biology |
| Year(s) Of Engagement Activity | 2019 |
| Description | Annual Aberdeen University Microbiology Schools Lecture |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Talk to approx 150 17-18 year old school children about important of the gut microbiome and also gave a career talk. Feedback received was very positive with students thinking about microbiology as a degree. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Article for the 'Microbiologist' |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Third sector organisations |
| Results and Impact | Article written for SfAM magazine 'Microbiologist': First Contact: The importance of the early life microbiota |
| Year(s) Of Engagement Activity | 2018 |
| Description | BBC Radio Leeds (Gayle Lofthouse show). |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | BBC Radio Leeds (Gayle Lofthouse show). Interview about You Are What You Eat TV show and also wider questions about diet and the gut microbiota. |
| Year(s) Of Engagement Activity | 2022 |
| Description | BIA Webinar |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Arjan Narbad, Lindsay Hall and Alan Walker gave a live BIA webinar to industry members. the webinar was then published on You tube that everyone can access. The title of the Webinar was Developing, feeding and restoring the human microbiome' where Dr Lindsay Hall explained 'Early Life Microbiota' , Dr Alana Walker presented 'Diet and the gut microbiota' and Professor Arjan Narbad gave a presentation on 'Restoring the gut microbiome using FMT' more than 370 people have now seen the webinar. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.youtube.com/watch?v=OtcoxvQvG34 |
| Description | BIA Webinar: Developing, feeding and restoring the human microbiome |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | BIA Webinar: Developing, feeding and restoring the human microbiome. In an interactive webinar with questions from industrial representatives. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Bioinformatics workshop at the Evergreen Phage Meeting |
| 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 | 30 postgraduate students and early career researchers attended a workshop on the use of command-line tools in the analysis of virome data, as part of the Evergreen International Phage Biology meeting in Olympia, WA, USA |
| Year(s) Of Engagement Activity | 2019 |
| Description | British Science Week activity - Guardians of the Gut |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | We contributed an activity to British Science Week 2021 based on our own Guardians of the Gut. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.britishscienceweek.org/plan-your-activities/activity-packs/ |
| Description | CLIMB computing workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | I thought bioinformatics at a CLIMB workshop in Edinburgh organized by Mark Pallen. |
| Year(s) Of Engagement Activity | 2019 |
| Description | CRUK-led workshop |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | CRUK Tumour explants workshop |
| Year(s) Of Engagement Activity | 2021 |
| Description | Comparative analysis of Paneth cell and enteroendocrine cell transcriptomics: organoid and signalling network based approaches Research in progress talk at Quadram Institute. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Comparative analysis of Paneth cell and enteroendocrine cell transcriptomics: organoid and signalling network based approaches Research in progress talk at Quadram Institute. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Computational Systems Biology 2: Analysing and visualising networks |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Training for local PhD students: Computational Systems Biology 2: Analysing and visualising networks |
| Year(s) Of Engagement Activity | 2019 |
| Description | Cytokine responsive transcriptional networks in inflammatory bowel disease |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation to ~50 scientists and clinicians at the 6th Young European Crohns and colitis organisation basic science program in Vienna, Austria. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.ecco-ibd.eu/discover-the-programme-2020/educational-programme-2020/6th-y-ecco-basic-scie... |
| Description | Defining Person-specific Microbiomes with high-resolution Metagenomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Festival of Genomics presentation |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.festivalofgenomics.com/ |
| Description | Dept Seminar APC |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | APC Microbiome Ireland invited Department Seminar, title: From 16S to high-resolution metagenomics |
| Year(s) Of Engagement Activity | 2021 |
| Description | Dialogue event with Older People's Community (public) Group about the microbiome and potential idea for future clinical trial |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Dialogue with Broadland Older People's Partnership Group about the microbiome and its impact on health and immunity in older age. Discussion of the components of the microbiome and what and how this can be affected - and the implications for other organ systems. Plenty of discussion with many opinions and questions expressed. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Dialogue events with Patient Participation Groups (PPGs) about the microbiome and potential idea for future clinical trial |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Patients, carers and/or patient groups |
| Results and Impact | Seven (separate) dialogue events with Patient Participation Groups (PPG) at GP practices across Norfolk to discuss the microbiome with patients and a potential idea for a future clinical trial. Discussions included: composition of microbiome, importance of gut health and impact on immunity and effect on other organs, FMT, gut-brain link, changes in microbiome throughout the life course, probiotics, prebiotics and superfoods, immunosenescence, antibiotics. Plenty of discussion and debate at each event with opinions often expressed as changing by the end of each dialogue. |
| Year(s) Of Engagement Activity | 2019,2020 |
| Description | EI LotuS training |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | I organized the session (lecture + hands-on training) for amplicon sequencing, that was part for the EI metagenomics workshop. |
| Year(s) Of Engagement Activity | 2019 |
| Description | EI innovate talk & panel discussion |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Talk at EI Innovate: High-resolution metagenomics without the need for reference genomes member of the subsequent panel discussion |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/ei-innovate-2021-linking-datasets-and-bioscience |
| Description | ELSA 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 | 3 part ELSA virtual workshop, this was organized by Colin Murrell, Alison Matther and myself. |
| Year(s) Of Engagement Activity | 2020,2021 |
| Description | Earlham Institute open day |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Talk to ~50 members of the public sparking questions and discussion about probiotics and a healthy gut microbiome. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/open-day-2019 |
| Description | Earlham Institute open day |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Discussions with variety of audiences about gut bacteria and probiotics. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/open-day-2019 |
| Description | Evidence for microbiome alterations in Parkinsons disease |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Leiden University Medical Center Departmental seminar, virtual |
| Year(s) Of Engagement Activity | 2022 |
| Description | Evolution and ecological interactions of gut bacterial taxa in challenged ecosystems |
| 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 to give a talk "Evolution and ecological interactions of gut bacterial taxa in challenged ecosystems" at the SMBE conference in Manchester, 2019 |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://smbe2019.org/ |
| Description | Evolution and persistence of human associated microbiomes |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Short talk at ELSA virtual workshop |
| Year(s) Of Engagement Activity | 2020 |
| Description | Expert reaction via Science Media Centre |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Expert reaction to study looking at neonatal antibiotics and growth and BMI in children, as published in Nature Communications* via Science Media Centre. Quotes taken up by press associtaion and used in multiple online newspaper articles and print (Mail, Times and Telegraph) |
| Year(s) Of Engagement Activity | 2021 |
| Description | Guardians of the Gut Classroom Pack |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | Guardians of the Gut is an exciting new resource for children to learn about the importance of their gut microbes. It is a teacher-led online resource that is freely available. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://guardiansofthegut.org/ |
| Description | IBCarb |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Contributed to the final IBCarb workshop Glycobiotechnology 2018. IBCarb (Glycoscience Tools for Biotechnology and Bioenergy) is a growing network of glycoscientists from academia and industry. IBCarb was one of the Networks in Industrial Biotechnology and Bioenergy funded by the BBSRC. The workshop was very successful and attracted around 150 attendees (international audience from academia and industry) . This was an opportunity to showcase the Glycosciences carried out in the UK and in partnership with industrial/business partners. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://ibcarb.com/events/ |
| Description | Identification of master regulators in goblet cells and Paneth cells using transcriptomics profiling of gut organoids and multi-layered networks. QIB Research in Progress |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Identification of master regulators in goblet cells and Paneth cells using transcriptomics profiling of gut organoids and multi-layered networks. QIB Research in Progress |
| Year(s) Of Engagement Activity | 2019 |
| Description | Identifying signalling pathways regulating antimicrobial peptide production in the gut using network biology and organoid transcriptomics Modularity of signaling proteins and networks |
| 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 | Identifying signalling pathways regulating antimicrobial peptide production in the gut using network biology and organoid transcriptomics Modularity of signaling proteins and networks |
| Year(s) Of Engagement Activity | 2018 |
| Description | Interview for Radio 4 |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Invited interviewee for Radio 4 programme: Inside Health. Numerous followups for further information and also engagement from Industry for new collaborations has resulted from broadcast. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.bbc.co.uk/programmes/m000dpky |
| Description | Interviewed and quoted in BBC Future article |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Was interviewed and quoted in BBC Future article: What we and don't know about gut health |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.bbc.com/future/story/20190121-what-we-do-and-dont-know-about-gut-health |
| Description | Introduction to Multiomics Data Integration |
| 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 | Tamas Korcsmaros delivered a talk on the nature of different data types, and provided a training on Cytoscape |
| Year(s) Of Engagement Activity | 2009,2018 |
| URL | https://www.ebi.ac.uk/training/events/2018/introduction-multiomics-data-integration-0 |
| Description | Investigating regulation of intestinal function by Bifidobacteria using network biology and organoid approaches, Microbes in Norwich |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Investigating regulation of intestinal function by Bifidobacteria using network biology and organoid approaches, Microbes in Norwich |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited Lecture - St Mark's Frontiers in Intestinal failure, Royal Society of Medicine, November 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited Lecture presented by member of Antigen Presentation Research Group at St Mark's Frontiers in Intestinal failure, Royal Society of Medicine, November 2019. International conference open to clinical staff, researchers and the general public - successfully reaching new/wider audiences. Potential for new research activity. Presenter won John Nichols prize. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited lecture 23rd Biennial Evergreen International Phage Biology Meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Invited lecture on phage taxonomy. The audience reported increased understanding of the importance of phage taxonomy in data analysis and changing behaviours. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited oral presentation at mini symposium on viruses and their classification, Utrecht University, The Netherlands, March 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited oral presentation at mini symposium. Title "Detection of food- and waterborne viruses using viromics: Will eating shellfish make you sick?" |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited talk Microbiome Virtual International Forum |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited talk at virtual seminar: Dispersal strategies shape persistence and evolution of human gut bacteria (Microbiome Virtual International Forum) |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.microbiome-vif.org/ |
| Description | Invited web seminar for the NASA Astrobiology Institute "Astrovirology Virtual Workshop Without Walls" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Web seminar on Virus Taxonomy: What is it and why should I care? for the NASA Astrobiology seminar series |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://nai.nasa.gov/seminars/featured-seminar-channels/workshops-without-walls/2019/9/18/astrovirol... |
| Description | Jolly good fellows: building a career at Earlham Institute - 20/02/2020 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Website article showcasing fellowship programmes at EI including Tamas Korcsmaros, whose five year fellowship which has led to a large and successful group investigating computational and network-based approaches to understanding complex systems such as the gut. Dr Korcsmaros is the CSP WP2 Lead. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/jolly-good-fellows-building-career-earlham-institute |
| Description | Latitude Music Festival: Exhibited Guardians of the Gut |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | We exhibited our Guardians of the Gut Exhibit at Latitude Festival in July 2019 over 3 days to members of the public (over 5000), We also had several specific school visits (~60 children in total). We received excellent feedback and strong engagement and questions. |
| Year(s) Of Engagement Activity | 2019 |
| Description | LotuS 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 | I co-organized (with VIB, Belgium) and led a 1 day workshop on the usage of the lab developed LotuS, teaching about 20 participants in Leuven, Belgium. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://wiki.bits.vib.be/index.php/NGS_data_analysis#Training_5:_metagenomics |
| Description | Lotus tutorial: website |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Training website for the LotuS software that is under active development in my lab |
| Year(s) Of Engagement Activity | 2019,2020 |
| URL | https://github.com/telatin/lotus-tutorial |
| Description | Member of expert working group for design of new permanent exhibit 'Being Human' at the Wellcome collection. |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | This a large permanent exhibit housed in the Wellcome Collection (London) that was opened in September 2019. Wellcome are collecting feedback on exhibit. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://wellcomecollection.org/pages/XW5QMBEAACUAELBV |
| Description | Metagenomic analysis of the impact of antibiotics on soil and gut bacteria, and their interaction networks |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Undergraduate students |
| Results and Impact | I was invited to give a Department Seminar at the UEA entitled "Metagenomic analysis of the impact of antibiotics on soil and gut bacteria, and their interaction networks" |
| Year(s) Of Engagement Activity | 2019 |
| Description | Microbiology Society 2018 selected talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Third sector organisations |
| Results and Impact | Dr Zoe Schofield was selected to give an oral short talk talk at the annual Microbiology Society Meeting (Birmingham 2018): Bifidobacterium breve stimulates immune development in germ-free mice |
| Year(s) Of Engagement Activity | 2018 |
| Description | Norwich Science Festival |
| 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 | Members of QIB, including from the Narbad group, were present for the whole day of a week long program. As well as discussions with participants, manning tables and displays, there were also hands-on activities, games, and crafts |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://norwichsciencefestival.co.uk/ |
| Description | Norwich Science Festival |
| 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 | Earlham Institute Bee trail at the Norwich science festival |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://norwichsciencefestival.co.uk/about/norwich-science-festival-2019/ |
| Description | Norwich Science Festival 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Took our Guardians of the Gut exhibit to Norwich Science festival for 2-day event (26th-27th October). |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://norwichsciencefestival.co.uk/events/science-without-borders-day/ |
| Description | Oral presentation at 3rd Annual Meeting of the European Virus Bioinformatics Center, Glasgow, March 28-29 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Oral presentation at scientific conference. Title Genome-resolved metaviromics for the detection of pathogenic viruses in the environment: will eating shellfish make you ill? |
| Year(s) Of Engagement Activity | 2019 |
| 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 | Organoid transcriptomics to study cell regulation Internal research presentation at the Earlham Institute |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Organoid transcriptomics to study cell regulation Internal research presentation at the Earlham Institute |
| Year(s) Of Engagement Activity | 2019 |
| Description | PHAVES: Ask Me Anything |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Virtual Debate in the Ask Me Anything format organised by the international non-profit organisation Phage Directory in order to promote phage research and international collaboration across the globe. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine Stem Cells @ Lunch, a fortnightly lunchtime seminar series, hosted by Dr. Davide Danovi at the Centre for Stem Cells & Regenerative Medicine at Guy's Hospital, King's College London, UK. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine Stem Cells @ Lunch, a fortnightly lunchtime seminar series, hosted by Dr. Davide Danovi at the Centre for Stem Cells & Regenerative Medicine at Guy's Hospital, King's College London, UK. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Parkinson's Disease and gut microbial alteration |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Global webinar on Alzheimers and Dementia |
| Year(s) Of Engagement Activity | 2022 |
| Description | Pathway Analysis to Study the Effect of Bifidobacteria on Autophagy in the Intestine 2nd Interdisciplinary Signaling Workshop |
| 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 | Pathway Analysis to Study the Effect of Bifidobacteria on Autophagy in the Intestine 2nd Interdisciplinary Signaling Workshop |
| Year(s) Of Engagement Activity | 2017 |
| Description | Patient group workshop |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Patients, carers and/or patient groups |
| Results and Impact | The research area and potential future directions were presented to the local hospital patient forum, in order to involve patients and public in the design of the research for a future grant proposal. There was a lot of feedback and suggestions from patients which were incorporated into the proposal, and volunteers for a future steering committee were recruited. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Podcast for Economist |
| 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 | Public/other audiences |
| Results and Impact | Podcast with the 'Economist' about the gut microbiome and celiac disease |
| Year(s) Of Engagement Activity | 2018 |
| Description | Policy publication by Microbiology Society |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Contributed to the publication of the Policy document by The Microbiology society. The aim was to To help the microbiology community to consider how it might best take advantage of the opportunities stemming from microbiome research. but at the same time the document woul dbe useful to the wider audience. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://microbiologysociety.org/policy/microbiome-policy-project/unlocking-the-microbiome-report.htm... |
| Description | Populating preterms with probiotics - Clasado online seminar day (QIB hosted event - virtual) |
| 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 | Online workshop and talks about the gut microbiome and diet - for healthcare professionals |
| Year(s) Of Engagement Activity | 2022 |
| Description | Poster presentation: SignaLink 3, a tissue specific and extended multi-layered signaling network resource 2nd Interdisciplinary Signalling Workshop 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Fazekas D., Kadlecsik T., Sudhakar P., Modos D., Turei D., Csabai L., Gul L., Korcsmaros T. (2017) SignaLink 3, a tissue specific and extended multi-layered signaling network resource 2nd Interdisciplinary Signalling Workshop 2017 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://signalingworkshop.org/ |
| Description | Public Debate |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | I was involved in a public debate at Dragons Hall in Norwich (October 2019) as part of the Norwich Science Festival. There was very strong engagement form the audience with lots of follow up questions and results for further information. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://norwichsciencefestival.co.uk/events/dragon-hall-debates-guts/ |
| Description | Public Dialogue Event on Lifelong Health - gut microbes and how they interact with the food we eat to promote health |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Quadram Institute Bioscience held a public dialogue event at the new Quadram Institute when we were joined by 35 members of the public for an open discussion about gut microbes and how they interact with the food we eat to promote health. Simon Carding and Cat Edwards canvassed the group for their opinions using interactive voting technology and there was plenty of lively discussion. The event was illustrated live by Rebecca Osborne who documented the discussion, including questions and debate, in graphical form. Topics discussed included the microbiome and its role in health and disease, the gut-brain connection, prebiotics and probiotics, faecal microbiota transplantation (FMT), healthy and diverse diets, carbohydrates, glycaemic index and our research to investigate the development of healthier food products and future foods designed to counter health problems such as Type 2 diabetes and cardiovascular disease. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Public Talk (Richmond Scientific Society) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | 'Gut bacteria': how microbes influence our health - talk to Richmond Scientific Society, London. There was very strong engagement form the audience with lots of follow up questions and results for further information. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Radio Interview for BBC Radio Norfolk |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Radio interview about our Guardians of the Gut exhibit and the microbiome - in response to the interview we had additional people visit the exhibit during the science festival |
| Year(s) Of Engagement Activity | 2018 |
| Description | Royal Society Summer Exhibition 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Royal Society Summer Science Exhibition 2018 - Guardians of the Gut. Week long engagement with ~10,000 visitors. We are fascinated about understanding how our resident gut microbes (i.e. the microbiota) impact our health, and we are particularly interested in what happens during early life. In our Guardians of the Gut exhibit we explore the amazing variety of microbes that colonise the gut right from the start, from their initial 'seeding', and where we get them from (exploring natural vs. C-section birth), and how specific types, e.g. Bifidobacterium, our favourite bacteria(!), act as Guardians of the Gut. We discuss how microbes play a key role in healthy development; helping to digest components of our food (breast or formula milk), and also how these microbes 'talk' to our immune cells. As these bacteria are so important for our wellbeing, we also explore how disturbing these early life microbial communities through e.g. antibiotics, can have short- and long-term consequences, and may predispose us to chronic diseases such as Ulcerative Colitis. Finally, we showcase some of the approaches and therapies, we and others, are developing to promote healthy early life microbial ecosystems with the aim of maintaining health and treating disease. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://royalsociety.org/science-events-and-lectures/2018/summer-science-exhibition/exhibits/guardia... |
| Description | Save Money: Good Health ITV 1 |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Discussed the role of the gut microbiota on health and associated 'products' on the market including self-testing kits with Sian Williams (August 2019). |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.itv.com/presscentre/ep4week35/save-money-good-health |
| Description | Signalling Networks: From Data to Modelling |
| 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 | Contributed to a training course run at the Earlham institute entitled 'Signalling Networks: From Data to Modelling'. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/signalling-networks-data-modelling |
| 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 | TV interview - BBC Look East |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | TV interview on BBC Look East about our Guardians of the Gut exhibition - people specifically attended the exhibit after they had watch the interview. |
| Year(s) Of Engagement Activity | 2018 |
| Description | TV interview for Jiangsu Association for Science and Technology |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Gave TV Interview for Chinese television on the importance of my research and the value of long term collaboration with Jiangnan University in Jiangsu province. The interview was follow of my keynote lecture at the international conference in Wuxi. The interview resulted in wider awareness in Jingsu province about the science collaboration between UK and China. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Teaching population genetics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Undergraduate students |
| Results and Impact | I was invited to the EMBL, Heidelberg, to teach a course on population genetics and participate in student discussions for EMBL first year PhD candidates. |
| Year(s) Of Engagement Activity | 2019 |
| Description | The Human Microbiome MOOC |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Learn how a healthy microbiome can combat disease Contributed to new MOOK: The Human Microbiome. The microbiome - the microbes that live within the human body - can have a huge impact on human health. As such, it's vital to understand the complexity of the microbiome, and how it can impact on disease and wellbeing. On this course, you'll go on a fascinating journey into the human body - down to the gut - where the ecology and roles of the human microbiome will be narrated. You'll explore how your microbiome changes throughout your life, reflect on the role of food in its modulation, and explain the functions the microbiome has in the gastrointestinal tract in daily life. Over 4000 people registered and completed 3 week course. There was lots of engagement via the FutureLearn MOOK platform. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.futurelearn.com/courses/the-human-microbiome/1 |
| Description | The secret life in our gut and how it influences health and disease |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | ESOF Leiden, virtual conference, Expert panel discussion organized by EMBL including 4 young PIs. Competitive application for this application that we won. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.esof.eu/ |
| Description | Women of the Future in STEM |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Students and postdoctoral research assistants from the Narbad group participated in the Women of the Future event at JIC in November 2019. A number of schools attended with 14-16 year olds to meet women working in STEM. The aim was to present role models, talk enthusiastically about their work and to showcase to female schoolchildren the variety of jobs available in STEM subjects, to increase their interest in this field for future education. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Workshop presentation - Microbiome as medicine |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | An oral presentation for a BBSRC cross-institute microbiome workshop, looking to foster ideas and collaborations which could lead to novel therapeutics to treat or prevent gastrointestinal disorders/side effects. Discussions were positive and many delegates agreed that this area of research holds promise for future applications in human health |
| Year(s) Of Engagement Activity | 2019 |
| Description | You Are What You Eat (Channel 5 - 6 episodes across series running Jan-Feb 2022) |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | You Are What You Eat (Channel 5 - 6 episodes across series running Jan-Feb 2022). I was an the microbiome expert for the TV series. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.channel5.com/show/you-are-what-you-eat |
| Description | oral presentation in Computational Biology workshop at the Keystone Symposium on the Global Virome in Health and Disease |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I presented my work on bacteriophage taxonomy in the context of identifying bacteriophages in microbiome data to a group of experts in viromics. The audience agreed with my assessments and have indicated they will change their practices. |
| Year(s) Of Engagement Activity | 2020 |
| Description | video broadcast on UK-China probiotics centre |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Arjan Narbad gave TV interview to the students of Department of Food Science and Technology, Jiangnan University. The video was distributed via departmental WeChat link. This activity informed the student about the Joint centre and the research links and opportunities for joint collaborations between and UK and China |
| Year(s) Of Engagement Activity | 2018 |