Food Microbiome and Health: The impact of plant-rich diets on the gut microbiome keystone species and food-borne pathogens
Lead Research Organisation:
QUADRAM INSTITUTE BIOSCIENCE
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 define GIT microbiome signatures associated with plant-based foods with metabolic intermediates key to host health and with resilience to food-borne pathogens.
Planned Impact
unavailable
Publications
Adriaenssens EM
(2025)
ICTV Virus Taxonomy Profile: Duplodnaviria 2025.
in The Journal of general virology
Anwar S
(2025)
DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study
in mSystems
Ariaeenejad S
(2024)
Precision enzyme discovery through targeted mining of metagenomic data.
in Natural products and bioprospecting
Bedarf JR
(2025)
A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease.
in NPJ Parkinson's disease
Bell A
(2023)
Biochemical and structural basis of sialic acid utilization by gut microbes.
in The Journal of biological chemistry
Bindels L
(2025)
A blueprint for contemporary studies of microbiomes
in Microbiome
Bisht A
(2026)
Gut microbial diversity impacts carbohydrate fermentation by children with severe acute malnutrition
in iScience
| Description | The overarching aim of FMH Theme 2 is to connect different data layers across Themes 1, 3, and 4 in FMH. Specifically, the evaluation of biotic interactions of microorganisms in the gut microbiome upon changes in diet, and how the microbial ecosystem as a whole will be affected, how it can sustain colonization resistance (against potentially pathogenic organisms) and the metabolic pathways most likely affected through diet changes. Significant achievements • We developed a new ML algorithm that can partition gut microbiomes in 5 recurrent and globally present "Enterosignatures". These signatures differ in their capacity to metabolise plant-derived macro- and micronutrients, providing a new framework for linking diet to microbiome function. The approach has been generalised (cvaNMF, published in Nucleic Acids Research 2025) to other microbial ecosystems, implemented as a publicly available web tool (>30 active users), a patent application was submitted(PCT/GB2024/051033). • Mechanistic work on keystone taxa has identified how Bilophila wadsworthia - a sulphur-reducing bacterium responsive to dietary fat and protein - colonises the gut via specialised bacterial microcompartments and energy metabolism pathways (Nature Communications 2025). Cross-feeding interactions between B. wadsworthia and Bacteroides thetaiotaomicron were identified, enhancing hydrogen sulphide production, have been characterised (Gut Microbes 2024), directly addressing Objective 2.2. • Multiple diet intervention datasets have been analysed. A prebiotic dietary intervention in Parkinson's Disease patients restored faecal metabolite profiles, including short-chain fatty acids, with preliminary evidence of neuroprotective effects (npj Parkinson's Disease 2025). Studies on bioactive plant micronutrients found that while host and bacterial metabolism are substantially affected, overall microbiome composition remains resilient - an important finding for understanding the stability of the gut ecosystem under dietary change. In collaboration with F&NNBRI we investigated the impact of bioactive micronutrients, discovering that while host and bacterial metabolism a strongly impacted, the overall microbiome remains stable. Cross-cutting bioinformatics infrastructure developed under this award, including: • MG-TK (a general-purpose metagenomics pipeline deployed across QIB and the Earlham Institute), • LotuS2 (an amplicon sequencing pipeline with >50,000 BioConda installations), • ARG-Sniper (a FAIR workflow to detect AMR genes in metagenomes) • readfx (a high-performance sequence parsing library used to process >200 Tb of sequencing data). • clusterMAGs (automated MAG-based species clustering) • protal (strain-resolved species profiling) • metaMDBG (assembler of long read metagenomes) An improved archaeal reference database (KSGP 3.1) has been released to address the multi-kingdom coverage required by Objective 2.1. Extent to which objectives were met Objectives 2.1 (community shifts and strain-level changes) and 2.2 (keystone taxa and metabolic mechanisms) are progressing well, with published outputs directly addressing the core research questions. The Enterosignatures framework and associated tools provide the analytical foundation for spatiotemporal and cross-feeding network analyses (O2.1.1, O2.1.2). Mechanistic characterisation of sulphur-reducing bacteria and Bifidobacterium-diet interactions is underway (O2.2.1). Objective 2.3 (colonisation resistance to food-borne pathogens) is at an earlier stage, as planned. In vitro colon model experiments examining phage-microbiome interactions have been initiated (dataset deposited: ENA PRJEB96854). Full experimental pathogen exclusion assays (O2.3.2) are planned for Years 4-5. Mucosal metagenomics protocols have been developed, manuscript in progress. |
| Exploitation Route | The Enterosignatures framework and associated software provide an immediately usable tool for classifying gut microbiome states in clinical and population cohorts and are being explored for commercial application. Mechanistic findings on keystone taxa such as B. wadsworthia and Bifidobacterium spp. provide candidate targets for next-generation dietary interventions and personalised probiotics. The bioinformatics pipelines and databases developed are publicly available and in active use by the wider metagenomics community. Findings are being disseminated through international training workshops (EBAME, 2022-2025), conference presentations, and peer-reviewed publications, ensuring uptake by academic, clinical, and industry partners. Leverage funding secured to date - including MRC and BBSRC studentships and a DSIT-funded phage regulatory sandbox project - demonstrates the downstream research agenda being built on this award. |
| Sectors | Education Environment Healthcare |
| Description | The metagenomic pipelines developed have been widely used across UK research groups, has been highlighted by sequencing providers (PacBio and ONT) and public installations are often >10,000. The developed software and practices have been used in international training courses (Belgium, France), and datasets (gut, soil) are being made available to the wider research community. Work by researchers has informed public outreach activities, such as "Pint of Science" of "Norwich Science festival", research blogs have been featured in the "The Independent" (https://www.independent.co.uk/life-style/health-and-families/pancreatic-cancer-symptoms-survival-rate-cause-b2890943.html) . Further, our work has informed policy makers, such as answering a Parliamentary inquiry (2023), work from Hildebrand has been cited 54 times by policy makers (SAGE report). Enterosignature work has been discussed with several companies and an initial patent application was filed; currently we are evaluating interest. It has been highlighted by "Frontier Strategy" as emerging technique (https://www.frontier-innovation.com/signals/silent_signals/). Based on this novel concept we developed the cvaNMF package (>350 installations), that is available across multiple platform and has garnered interest from both academic and industrial (e.g. Danone) partners. |
| First Year Of Impact | 2023 |
| Sector | Agriculture, Food and Drink,Education,Environment,Healthcare |
| Impact Types | Societal Economic Policy & public services |
| Description | Answered Soil health Parliament inquiry |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | Advice given to UK parliament (SH0045) |
| URL | https://committees.parliament.uk/writtenevidence/117557/pdf/ |
| Description | Bacteriophages in the ageing gut as targeted therapeutics |
| Amount | £115,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2023 |
| End | 09/2027 |
| Description | Clinical seedcorn |
| Amount | £40,000 (GBP) |
| Organisation | Quadram Institute Bioscience |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 12/2024 |
| Description | Clinical seedcorn-VALET study: Vaginal virome AnaLysis in Endometriosis and Termination of pregnancy patients. |
| Amount | £34,000 (GBP) |
| Organisation | Quadram Institute Bioscience |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 01/2026 |
| End | 01/2028 |
| Description | Detecting and tracking low abundant pathogens using 3rd gen sequencing |
| Amount | £110,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2024 |
| End | 10/2028 |
| 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 | Multi-Agency Regulatory Groundwork for Engineered Phage Regulatory Sandbox |
| Amount | £921,246 (GBP) |
| Organisation | Department for Science, Innovation and Technology |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2025 |
| End | 10/2027 |
| Description | NRPDTP CASE |
| Amount | £80,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2024 |
| End | 09/2028 |
| Description | NUTRIMIND |
| Amount | € 5,000,000 (EUR) |
| Organisation | European Commission |
| Sector | Public |
| Country | Belgium |
| Start | 05/2026 |
| End | 06/2030 |
| Description | QI Clinical SeedCorn Award "Bacteriophages for chronic lung infections" |
| Amount | £34,949 (GBP) |
| Funding ID | 20440 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2024 |
| End | 03/2025 |
| Description | Rapid metagenomic strain profiling of Inflammatory bowels disease patients via Nanopore sequencing |
| Amount | £110,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2023 |
| End | 09/2027 |
| Description | Unleashing the flavour potential of plant-based foods via fermentation |
| Amount | € 4,600,000 (EUR) |
| Funding ID | 101181661 |
| Organisation | European Commission |
| Sector | Public |
| Country | Belgium |
| Start | 11/2024 |
| End | 04/2028 |
| Description | international partnering award Spain |
| Amount | £10,000 (GBP) |
| Organisation | Quadram Institute Bioscience |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 02/2024 |
| End | 06/2024 |
| Title | Soil Metagenome ONT |
| Description | This protocol describes the sample collection to sequence acquisition workflow for Oxford Nanopore long-read sequencing of a complex soil sample using a ligation sequencing kit kit LSK-114 and R10.4.1 FLO-PRO114M flowcells. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | This protocol has enabled ONT sequencing of soil microbiomes. |
| URL | https://www.protocols.io/view/soil-metagenome-ont-j8nlk8nmwl5r/v1 |
| Title | Soil Metagenome PacBio V2 V.2 |
| Description | This protocol describes the sample collection to sequence acquisition workflow for PacBio Revio long-read sequencing of a complex soil sample using SMRT Bell library prep kit 2.0 and Revio SMRT cells. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | Enabled HiFi sequencing of soil microbiomes. |
| URL | https://www.protocols.io/view/soil-metagenome-pacbio-v2-rm7vzjqo8lx1/v2 |
| Title | Bioproject PRJNA1144839 Desulfovibrio piger isolates from human faecal samples |
| Description | Sequencing data of Desulfovibrio piger isolates |
| Type Of Material | Database/Collection of data |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | Expanding the diversity of Desulfovibrio phages |
| Title | Control samples for ITS1 Metabarcoding of the Cynomolgus Macaque Intestinal Mycobiome |
| Description | Library and Sequencing controls used for the Metabarcoding ITS1 analysis of intestinal content of the Cynomolgus Macaque |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | ITS1 sequencing is widely adopted for the analysis of fungal communities, yet the majority of metabarcoding tutorials are based on the 16S marker. This dataset was used to deliver ITS specific training, focusing on the sequencing controls to adopt in such studies. |
| URL | https://zenodo.org/record/6881353 |
| Title | Dataset to test the Nextflow Tutorial |
| Description | Tutorial: https://telatin.github.io/microbiome-bioinformatics/Nextflow-start/ Repository: https://github.com/telatin/nextflow-example |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Using CLIMB infrastructure, we delivered the first DSL2-native tutorial for Nextflow, using this dataset to build an example pipeline |
| URL | https://zenodo.org/record/5931662 |
| Title | De novo sequencing of phages T4 and T7 |
| Description | Raw data and assemblies of the de novo sequencing of the "model" phages T4 and T7, performed with Illumina NextSeq 2x150 and Oxford Nanopore, generated for the "Phage Annotation Workshop" held online on November 2021: https://github.com/quadram-institute-bioscience/phage-annotation-workshop/ |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Two widely known genomes sequenced de novo to provide valuable training datasets for bioinformatics tutorials and phage annotation workshops |
| URL | https://zenodo.org/record/5704419 |
| Title | Host removal database: Homo sapiens, Sars-Cov-2, PhiX174 |
| Description | cleanup-db Kraken2 database, built upon a viral sequence masked human reference from: Handley, Scott A. (2020). Virus+ Sequence Masked Human Reference Genome (hg19) (1.0) [Data set]. Zenodo. [10.5281/zenodo.4116107] but separating chromosomes as artificial taxa to allow for QC, and includes Sars-Cov-2 and PhiX 174 gutcheck-db A very small DB containg some common gut bacteria and Human and Murine mitochondrial genome: Akkermansia muciniphila Bacteroides fragilis Bifidobacterium longum Blautia obeum strain Escherichia coli Enterococcus faecium Prevotella copri See: https://github.com/telatin/cleanup |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | custom database to remove common contaminants from metagenomics samples (Homo, Sars-Cov-2 and PhiX-174); by splitting the human genome in individual chromosomes, this database enable a quality check against reads wrognly classified as human. |
| URL | https://zenodo.org/record/7050266 |
| Title | Sequence data for phage cocktail colon model study (BioProject: PRJEB96854) |
| Description | Raw sequence reads for experiments performed. Preprint describing dataset publicly available: https://doi.org/10.64898/2026.01.28.702202 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2026 |
| Provided To Others? | Yes |
| Impact | Pilot study to test the effect of phage treatment on the healthy human microbiome. The use of in vitro models of the human gut allowed us to bypass the use of animal models as per 3Rs. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB96854 |
| Description | Machine Learning applied to microbial datasets |
| Organisation | University of Turin |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | Our research team worked with Dr. Giovanni Birolo during his visit to the Quadram Institute, focusing on the application of machine learning techniques to microbial genomics. Together, we embarked on a project that integrated Dr. Birolo's background in mathematics and computer science with our team's ongoing research in microbial genomics and metabarcoding datasets. Our contributions: 1) Data Preparation and Provision: We provided comprehensive metabarcoding datasets, which included a wide variety of microbial genomic sequences. Our team was responsible for collecting, curating, and pre-processing these datasets with in-house developed pipelines to ensure they were suitable for machine learning analysis, which was crucial for the success of the workshop and subsequent research activities. 2) Expertise in Microbial Genomics: We offered insights into the biological significance and potential applications of the machine learning models developed during the collaboration. This allowed for a more targeted approach in the analysis and interpretation of the data, leading to more biologically meaningful outcomes. 3) Technical Support and Infrastructure: We facilitated access to the necessary computational resources and infrastructure required for the intensive computational tasks associated with machine learning and data analysis. This included high-performance computing facilities and software tools tailored for bioinformatics research and our own QIB Cloud infrastructure. 4) Workshop Organization and Participation: Our team organized a workshop titled "Random Forests and Cross-Validation on a Metabarcoding Dataset," delivered by Dr. Birolo. We contributed to the workshop's content by providing case studies and examples from our research. Furthermore, our team actively participated in the workshop, engaging in discussions, sharing insights, and fostering a collaborative learning environment for all participants. See https://github.com/quadram-institute-bioscience/datasciencegroup/blob/main/4_machine_learning/Prediction-notes.ipynb |
| Collaborator Contribution | 1) Expertise in Machine Learning: Dr. Birolo introduced advanced machine learning techniques, particularly random forests and cross-validation methods, tailored for the analysis of complex metabarcoding datasets. His deep understanding of these computational approaches enabled our team to adopt more sophisticated analytical strategies, significantly enhancing our ability to decipher microbial genomic data. 2) Workshop Delivery: Dr. Birolo delivered an insightful workshop titled "Random Forests and Cross-Validation on a Metabarcoding Dataset," which was instrumental in upskilling our research team. This workshop provided theoretical knowledge and included practical sessions on applying these machine-learning techniques to real-world datasets, fostering a hands-on learning environment. 3) Novel Analytical Frameworks: By integrating his mathematical and bioinformatics expertise, Dr. Birolo contributed to the development of novel analytical frameworks that improved the accuracy and efficiency of identifying and classifying microbial species from metabarcoding data. This advancement has the potential to greatly impact the field of microbial genomics, opening up new avenues for research and application. |
| Impact | 1) Workshop material (see link) 2) Engagement with researchers to define the application of Machine Learning on microbial genomics datasets 3) Primed a collaboration on software development (ongoing) |
| Start Year | 2024 |
| Description | Prebiotic SME |
| Organisation | Clasado BioSciences |
| Country | Jersey |
| Sector | Private |
| PI Contribution | Testing of prebiotic compounds on gut microbiota and gut barrier function |
| Collaborator Contribution | Provided study product, human resource, expert knowledge |
| Impact | INFORM grant (BIV) on going |
| Start Year | 2024 |
| Description | Working Group 1 Member - Microorganism Discovery, Characterisation and Optimisation for Microbial Food Applications, COST Action CA24132 |
| Organisation | European Cooperation in Science and Technology (COST) |
| Department | COST Action |
| Country | Belgium |
| Sector | Public |
| PI Contribution | Contributed expertise in microbial discovery and characterisation to WG1 of COST Action CA24132, supporting strain evaluation and optimisation for food applications. Engaged in cross-institutional collaboration, data exchange, and development of shared research objectives within the network |
| Collaborator Contribution | With the rapid population growth, demand for food is quickly increasing and meeting protein supply requirements is becoming a global problem. Plant proteins have been proposed as alternatives to animal proteins, but their production needs big extensions of arable land and demands huge volumes of freshwater which results in considerable environmental issues. A promising solution are microbial protein for food and feed applications. This COST action, entitled Accelerating Innovation and Development of European Microbial Foods (Mic2Food), aims to facilitate the development of new microbial foods for the European market. Mic2Food will create a unique network with a balanced geographic distribution to tackle scientific and technological challenges to make microbial food substitutes a reality. Collectively, Mic2Food aims to: (1) isolate and identify new, non-pathogenic microorganisms with desired properties for their application as microbial foods, including their protein content and lipid composition, and micronutrient content, and optimise their production properties in line with food regulations. (2) develop and upscale their production processes from lab scale over pilot scale to industrial scale. (3) establish downstream processing (DSP) (e.g. removal of RNA) and formulations to produce appealing products that can be commercialised. (4) monitor regulatory changes for microbial food and facilitate commercialisation of microbial food products in Europe and worldwide. (5) quantify the nutritional and mechanical properties of the microbial strains and food products in a standardised way throughout the development. (6) accelerate the translation from academic research to tangible products through close collaboration with established industrial partners. |
| Impact | N/A |
| Start Year | 2025 |
| Title | Method of Characterisation of Microbiomes |
| Description | Enterosignature typing of human gut microbiomes |
| IP Reference | |
| Protection | Patent / Patent application |
| Year Protection Granted | 2024 |
| Licensed | Commercial In Confidence |
| Title | 'readfx' a high-performance Nim library to parse FASTX files |
| Description | High-performance FASTA & FASTQ parsing for Nim. Wraps Heng Li's battle-tested kseq.h and adds a native Nim parser, gzip support, paired-end reads, and a rich suite of sequence utilities. A library built for 1) Maximum throughput: Built on Heng Li's kseq.h C library via FFI. The pointer-based readFQPtr iterator reuses a single buffer across records for near-zero allocation overhead. 2) Transparent gzip: Pass .fastq.gz or plain .fastq - the library decompresses on the fly. Stdin is also supported by passing "-" as the filename. 3) Paired-end reads: readFQPair reads two FASTQ files in lockstep, yielding an FQPair record for each mate pair. Optional name validation catches mismatched files. 4) Sequence utilities: Reverse complement, GC content, nucleotide composition, quality trimming, low-quality masking, and subsequence extraction - all in one import. 5) IUPAC primer matching - findPrimerMatches finds primer binding sites using IUPAC ambiguity codes, with configurable mismatch thresholds. |
| Type Of Technology | Software |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | This library allowed low-memory and high-speed pre-processing of 500 Tb of raw sequencing output produced at the Quadram institute |
| URL | https://corebio.info/readfx/ |
| Title | ARG_Sniper |
| Description | ARG-Sniper is a Nextflow DSL-2 pipeline designed for metagenomic analysis that processes paired-end FASTQ files to detect antibiotic resistance genes using multiple bioinformatics tools. The pipeline runs five different analysis tools in parallel: GROOT, ARIBA, KMA (adopted from ARGprofiler), KARGA, and SRST2, each requiring their respective databases. Users can selectively skip any of the five tools using command-line flags (--skip_groot, --skip_ariba, etc.), allowing for customized analysis workflows. The pipeline takes FASTQ and processes them through the selected tools. After individual tool execution, the pipeline collects all results and generates a summary report that consolidates findings from each analysis. The workflow outputs separate directories for each tool's results along with a final summary directory containing the integrated analysis. Note: This pipeline focuses on detecting antibiotic resistance genes and does not report SNP-based resistance mechanisms. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Allowed a FAIR workflow for a benchmark on AMR detection in metagenomes, and the publication of the benchmark. |
| URL | https://github.com/quadram-institute-bioscience/ARG-Sniper |
| Title | KSGP |
| Description | New reference database for 16S amplicon sequencing, with a focus on so far unnamed Archaea |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | The database was included in our LotuS2 pipeline and has prompted several researchers to contact me with follow up questions. |
| URL | https://ksgp.earlham.ac.uk/ |
| 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 | MG-TK |
| Description | MG-TK is the follow up pipeline, derrived from MATAFILER. It is a general purpose tool for processing metagenomes. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Enables processing metagenomes across the QIB and EI. |
| URL | https://github.com/hildebra/mg-tk |
| Title | MetaPilot |
| Description | MetaPilot is an software platform designed to automate and optimize complex metaproteomics workflows. It was developed as a specialized research tool to bridge the gap between raw mass spectrometry data and functional microbiome insights. |
| Type Of Technology | Software |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | MetaPilot has been adopted by the international metaproteomics community to automate complex microbiome workflows. This technology has accelerated the transition from raw mass spectrometry data to actionable biological insights, streamlining researches in the field of gut microbiome studies. |
| URL | https://metapilot-web.vercel.app/ |
| Title | adhesiomeR |
| Description | adhesiomeR is a tool to detect adhesion related genes in E. coli genomes. Based on detected genes, an adhesion profile is created. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | While we made the product already available, we are still in the process of submitting an accompanying publication. |
| URL | https://adhesiomer.quadram.ac.uk/app/adhesiomeR |
| Title | anvi-script-reformat-bams |
| Description | A contribution to the Anvi'o package to allow reformatting of BAM files used to create coverage tracks |
| Type Of Technology | Software |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | Anvi'o is a world-class package used by thousands of projects, with more than 1000 citations. Anvi'o model is open-source with a vibrant community that accepts contributions. This package was accepted and officially added to the Anvi'o repository. |
| URL | https://anvio.org/help/main/programs/anvi-script-reformat-bam/ |
| Title | clusterMAGs |
| Description | C++ program to cluster MAGs into de novo species clusters. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Central part of the MATAFILER pipeline developed in the Hildebrand group, this software allows for completely automated species definitions in metagenomes. |
| URL | https://github.com/hildebra/clusterMAGs |
| Title | cvaNMF |
| Description | cvaNMF enables the discovery of signatures within high dimensional datasets, that enable a more intuitive description. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | We are currently writing a research paper with outputs from this tool |
| URL | https://github.com/apduncan/cvanmf |
| Title | enterosignatures |
| Description | This webtool allows to calculate enterosignatures from any uploaded genus table. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | Presented software recently at conference, with vivid interest by audience. We have registered >30 active users so far |
| URL | https://enterosignatures.streamlit.app/?utm_medium=oembed |
| Title | metaprokka, codon aware |
| Description | Prokka is a very famous package for predicting genes in bacterial genomes. We noticed that viral genomes can undergo codon repurposing (https://pubmed.ncbi.nlm.nih.gov/38187747/) and thus we created a modified version of Prokka that is optimised for metagenomics dataset and evaluates the ideal genetic code to be used automatically. |
| Type Of Technology | Software |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The package is available from Bioconda https://bioconda.github.io/recipes/metaprokka/README.html and was downloaded >2000 times. |
| URL | https://bioconda.github.io/recipes/metaprokka/README.html |
| Title | nim-abif |
| Description | Op |
| Type Of Technology | Software |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | Modern and fast parsing of Sanger chromatograms is still used to validate SNPs and plasmids. Allows ultrafast screening of hundreds of mutations in seconds. |
| URL | https://quadram-institute-bioscience.github.io/nim-abif/ |
| Title | sdm |
| Description | sdm (simple demultiplexer) is a general applicable, fast and scalable software, that can demultiplex, quality filter and dereplicate input read sequences, transfer file formats and be used for various utility functions related to raw reads. Ongoing developments, last major release in 2021 |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | Central part in group's pipelines, e.g. LotuS2 (https://github.com/hildebra/lotus2) and MATAFILER (https://github.com/hildebra/MATAFILER). |
| Description | 9th Ebame 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 | Taught metagenome bioinformatics and molecular methods as part of the 9th Ebame workshop in Brest. The team teaching included myself but also Seb Raguideau and Rob James,. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://maignienlab.gitlab.io/ebame/ |
| Description | Anvi'o Workshop 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | 40 researchers at different career stage engaged with the authors of Anvi'o to learn how to curate and explore pangenomes, metagenomes and metabolic pathways datasets. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://corebio.info/workshops-2024/anvio |
| Description | BBSRC Fellow Meeting in London, from 25-26th of June 2025 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Gave a talk at the BBSRC Fellow meeting entitled: "The role of sulfur and nitrogen metabolism within the human gut" |
| Year(s) Of Engagement Activity | 2025 |
| Description | Dept seminar at U Essex |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Undergraduate students |
| Results and Impact | talk title: The human gut microbiome explored at single nucleotide resolution |
| Year(s) Of Engagement Activity | 2023 |
| Description | EBAME 10 (2025) 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 | Microbial Ecology is undergoing rapid evolution and dramatic progresses thanks to the combined advances of next-generation DNA sequencing technologies and computational approaches for data analysis and visualization. As a result, microbial ecogenomics has become an essential part of investigations of marine or terrestrial habitats, or host-microbe interactions. The aim of the workshop on Emerging Bioinformatics Approaches for Microbial Ecogenomics is to bring together researchers who generate complex 'omics datasets to investigate biological, ecological and evolutionary questions with researchers who develop new concepts and computational methods to analyze such datasets. The workshop will have lectures on new methods and their applications on real-world datasets, and tutorials for hands-on experience. |
| Year(s) Of Engagement Activity | 2022,2023,2024,2025 |
| URL | https://maignienlab.gitlab.io/ebame/ |
| Description | EPSRC AMR focused One Health - Trusted Research Environment (OH-TRE) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This project is a part of the EPSRC-funded Digital Health Hub for Antimicrobial Resistance (AMR) which focuses on bringing together outstanding interdisciplinary teams across academia, government, the NHS, industry, and charities to harness emerging digital technologies to transform antimicrobial stewardship and one-health surveillance. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Evolve, Survive, Thrive! 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 | An activity for children to 'evolve' playdough microbes to understand niche adaptation |
| Year(s) Of Engagement Activity | 2026 |
| URL | https://norwichsciencefestival.co.uk/ |
| Description | Introduction to LLMs: training for researchers and students |
| 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 | Introduction to LLMs and their intrinsic limitations, in an open format suitable for general audience (including admin staff and other staff) |
| Year(s) Of Engagement Activity | 2025,2026 |
| URL | https://quadram-institute-bioscience.github.io/ai-training |
| Description | Invincible Invisibles |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Schools |
| Results and Impact | Invincible Invisibles was a two-day science outreach event conducted during August 2025 aimed to teach microbiology for Koothanoor Higher Secondary School, Tamil Nadu, as an native of the same village. This project was planned for sparking curiosity and showing students that science isn't just something in textbooks-it's in their food, their health, and their everyday lives. In a place where access to science resources is limited, we hope this hands-on experience plants the seed for lifelong interest and learning.The primary aim of "Invincible Invisibles" is to help students understand the importance of the microbial world around and within them. We want to spark curiosity and build foundational knowledge about how microbes impact health, food, hygiene, and the environment. Roughly 100 students participated in the event, and the impact it created was recorded in a blog (https://quadram.ac.uk/blogs/inspiring-the-next-generation-exploring-the-invisible-microbial-world-with-students-in-koothanoor-india/). Kids view in their local language with sub titles can be seen here: https://youtu.be/qdM9z6RHw6w |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://quadram.ac.uk/blogs/inspiring-the-next-generation-exploring-the-invisible-microbial-world-wi... |
| Description | Microbes Zoo at 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 | Outreach event showcasing the excellence of microbiology at the Norwich Research Park |
| Year(s) Of Engagement Activity | 2026 |
| Description | Microbiology Society Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I gave a selected talk with the title: "Bacterial microcompartments and energy metabolism drive gut colonization by Bilophila wadsworthia" |
| Year(s) Of Engagement Activity | 2025 |
| Description | Presentation for BBSRC project officers |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Policymakers/politicians |
| Results and Impact | 5 minute presentation for BBSRC project officers |
| Year(s) Of Engagement Activity | 2025 |
| Description | Quadram Institute KimJang Konnection |
| 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 | Hands On Fermented Foods - KimJang Event. Quadram Institute hosted a KimJang event to celebrate the Korean, communal, tradition of Kimjang. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Talk at Pharmabiotics, Lille |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Speaking to industry/startup about recent developments from Quadram and my group. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Talk at Pint of Science |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Talk at Pint of Science about the importance of healthy nutrition |
| Year(s) Of Engagement Activity | 2024 |
| Description | Workshop on fermented foods |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | workshop to discuss the analysis of microbiomes and whole genome sequencing of of fermented foods |
| Year(s) Of Engagement Activity | 2024 |
| Description | invited talk at 3rd Visegrad Interdisciplinary Signaling Workshop, Hungary |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Gut Metagenomics: finding good descriptors of bacterial communities and their members |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://2023.signalingworkshop.org/ |
| Description | invited talk at Exploring the Microbiome, ELSA workshop, Norwich |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Undergraduate students |
| Results and Impact | talk title: PacBio metagenomics: blessing or blemish? |
| Year(s) Of Engagement Activity | 2023 |
| Description | invited talk at PacBio Roadshow London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | talk title: Exploring the personalized human gut microbiome |
| Year(s) Of Engagement Activity | 2023 |
| Description | nf-core hackathon 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Local site of "nf-core" hackathon to improve the open source pipelines and documentation from the nf-core organization |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://corebio.info/workshops-2024/nf-core |
| Description | talk at 13th Gut Micro. Symp, Aberdeen |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | talk title: igh-resolution metagenomics in human gut microbiome studies |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.abdn.ac.uk/events/conferences/gutmicro2023/ |
| Description | talk at Conference Microbiome Interactions in Health and Disease |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | talk title: Enterosignatures allow for generalized classification of abnormal gut microbiomes |
| Year(s) Of Engagement Activity | 2024 |
| Description | talk at FNS-cloud meeting, Belgium |
| 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 | Talk title: Gut Metagenomics: finding good descriptors of bacterial communities and their members |
| Year(s) Of Engagement Activity | 2023 |
| Description | virtual talk at GRDI-AMR2, Canada |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Talk title: From assemblies to MAGs to MGS: genome-centric short- and long-read metagenomics |
| Year(s) Of Engagement Activity | 2024 |