Microbial Communities in the Food Chain
Lead Research Organisation:
Quadram Institute Bioscience
Department Name: Contracts
Abstract
We will explore the chicken gut microbiome using culture-based and sequence-based approaches. We will document the microbial ecology of Salmonella and E. coli in the food chain to prime novel ecological and synthetic biology strategies for preventing the spread of pathogens and AMR.
Organisations
- Quadram Institute Bioscience, United Kingdom (Lead Research Organisation)
- University of Surrey, United Kingdom (Collaboration)
- Public Health England, Salisbury (Collaboration)
- Earlham Institute, NORWICH (Collaboration)
- University of Sydney, Australia (Collaboration)
- Imperial College London, United Kingdom (Collaboration)
- London Sch of Hygiene and Trop Medicine, United Kingdom (Collaboration)
Publications
Baker D
(2021)
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes
in Genome Medicine
Callanan J
(2021)
Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses.
in Microbial genomics
Chewapreecha C
(2019)
Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei.
in Communications biology
Crossfield M
(2022)
Archaeal and Bacterial Metagenome-Assembled Genome Sequences Derived from Pig Feces
in Microbiology Resource Announcements
Foster-Nyarko E
(2021)
Genomic diversity of Escherichia coli from healthy children in rural Gambia.
in PeerJ
Foster-Nyarko E
(2020)
Genomic diversity of Escherichia coli isolates from healthy children in rural Gambia
Foster-Nyarko E
(2022)
The microbial ecology of Escherichia coli in the vertebrate gut
in FEMS Microbiology Reviews
Foster-Nyarko E
(2020)
Gambian poultry isolates from hyperendemic group of AMR Escherichia coli strains in sub-Saharan Africa
in Access Microbiology
| Description | Results. We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n=582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes This represents the most comprehensive view of the chicken gut associated microbiome to date, encompassing dozens of novel candidate bacterial genera and hundreds of novel candidate species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from faeces, documenting thirty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. Conclusions. Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provides a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome. |
| Exploitation Route | Identification of novel species in the chicken gut will inform all future studies on this microbiome; might allow identification of novel probiotics Smart probiotics could perhaps be developed incorporating enhanced flagellar display |
| Sectors | Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology |
| Description | Health and Social Care Committee |
| Geographic Reach | National |
| Policy Influence Type | Gave evidence to a government review |
| Description | Hosting PHE students |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Have hosted multiple students working with Public Health England at my institute for training in bioinformatics. |
| Description | POSTnote on AMR |
| Geographic Reach | National |
| Policy Influence Type | Gave evidence to a government review |
| URL | https://researchbriefings.parliament.uk/ResearchBriefing/Summary/POST-PN-0595 |
| 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 | S. Typhi and protozoa in contaminated water in Zimbabwe |
| Amount | $100,000 (USD) |
| Funding ID | OPP1217121 |
| Organisation | Bill and Melinda Gates Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 11/2019 |
| End | 04/2021 |
| Title | Creation of Golden Gate constructs for Gene Doctoring |
| Description | 4 plasmids assembled for the publication "Creation of Golden Gate constructs for Gene Doctoring" (submitted, 2020). The sequences and plasmid DNA have been submitted to the Addgene repository and will be accessible following sequence verification and QC approval by Addgene. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | The plasmids are available to other researchers through the Addgene repository and may prove useful for future work. |
| URL | https://www.addgene.org/depositing/78058/ |
| Description | Characterisation of large flagellins |
| Organisation | Imperial College London |
| Department | Imperial College Business School |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Laboratory and bioinformatics work on large flagellins |
| Collaborator Contribution | Laboratory and bioinformatics work on large flagellins |
| Impact | http://pubmed.org/30462661,29258714 |
| Start Year | 2018 |
| Description | Chicken gut metagenome |
| Organisation | London School of Hygiene and Tropical Medicine (LSHTM) |
| Department | Department of Pathogen Molecular Biology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have agreed to perform metagenomic sequencing of chicken samples |
| Collaborator Contribution | They have agreed to supply the chciken samples |
| Impact | None yet. |
| Start Year | 2018 |
| Description | Chicken gut microbiome investigations |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have performed metagenome sequencing on chicken faecal samples |
| Collaborator Contribution | Roberto La Ragione and his team have provided us with chicken faecal samples |
| Impact | Generation of metagenome sequences and metagenome-assembled genomes from chicken faeces |
| Start Year | 2019 |
| Description | Chicken gut microbiome investigations |
| Organisation | University of Surrey |
| Department | School of Veterinary Medicine |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have performed metagenome sequencing on chicken faecal samples |
| Collaborator Contribution | Roberto La Ragione and his team have provided us with chicken faecal samples |
| Impact | Generation of metagenome sequences and metagenome-assembled genomes from chicken faeces |
| Start Year | 2019 |
| Description | Collaboration with Dr Aaron Jenkins - University of Sydney |
| Organisation | University of Sydney |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | We will provide expertise in nanopore sequencing and Salmonella Typhi epidemiology to help build capacity in Fiji to better understand the persistence of S. Typhi in the environment. |
| Collaborator Contribution | Our partners provide access to a field site and specimens from patients with strong epidemiological and geographical metadata. |
| Impact | Grants awarded from BMGF - Gemma Langridge (QIB) as PI - two other grants with QIB Co-Investigators with PIs from Canada and Australia |
| Start Year | 2018 |
| Description | Gambian Chicken metagenomics |
| Organisation | London School of Hygiene and Tropical Medicine (LSHTM) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Metagenomic sequencing of chicken and guinea fowl caecal samples |
| Collaborator Contribution | Harvesting and supply of relevant samples. |
| Impact | No publication outputs so far, but sequences have been generated |
| Start Year | 2018 |
| Description | Investigation of antibiotic resistance in Salmonella Infantis |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Both partners have had several discussion meetings around the reporting of S. Infantis and risk assessment. QIB have supplied informatics support through Gemma Langridge and Microbiology through John Wain. The first paper has been submitted |
| Collaborator Contribution | PHE provide public health intervention experience, several genome sequences and a route to change the reporting guidelines. |
| Impact | Salmonella nomenclature in the genomic era: a time for change. MA Chattaway, GC Langridge, J Wain. Scientific reports 11 (1), 1-8 Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica Infantis isolates in England and Wales. WWY Lee, J Mattock, DR Greig, GC Langridge, D Baker, S Bloomfield, ... Microbial genomics 7 (10) |
| Start Year | 2018 |
| Description | AMR workshop Canada |
| 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 | "Towards a Human and Animal Health Risk Assessment for Foodborne and Environmental Antimicrobial Resistance", International Expert Workshop, 3-7 March 2019. The workshop comprised 40 international experts on AMR; projected outcomes include a publication. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Campylobacter research discussion with 2 Sisters Food Group |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion with Directors of 2 Sisters about potential areas of collaboration with the aim to investigate the diversity and spread of Campylobacter in poultry and food. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Comment for Sci DEv Network. Bringing science and development together through news and analysis. |
| 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 | Media (as a channel to the public) |
| Results and Impact | Provided comment within an article called "Focus piece on: Antibiotics resistance breaks global boundaries " |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.scidev.net/global/health/opinion/antibiotics-resistance-breaks-global-boundaries.html |
| Description | Engagement with New Zealand Food Safety Science & Research Centre |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I visited the New Zealand Food Safety Science & Research Centre and gave a presentation entitled "Whole genome sequencing and metagenomics for the investigation of food safety and antimicrobial resistance". A roundtable discussion with students and researchers then followed. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Interface event with researchers and clinicians |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Interface/network meeting between researchers and Norfolk and Norwich University Hospital Trust clinicians to facilitate joint projects |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited speaker at Microbes in Norwich event |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | I was an invited speaker at the 2019 Microbes in Norwich symposium, giving a talk entitled "Bugs, drugs and evolution: Genomic epidemiology of drug-resistant infections" |
| Year(s) Of Engagement Activity | 2019 |
| Description | Invited speaker to University of Liverpool |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | I was an invited speaker to the University of Liverpool's Institute of Integrative Biology's Genomes, Systems and Therapeutic Targeting Seminar Series, with a title entitled "Seeking sources and reservoirs of Salmonella using whole genome sequencing" |
| Year(s) Of Engagement Activity | 2018 |
| Description | Invited speaker to afternoon symposium, Department of Veterinary Medicine, University of Cambridge |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Presentation was "Mining (meta)genomics for meaningful microbial matters: pathogen and AMR transmission across the One Health spectrum" delivered at an afternoon symposium |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited speaker to give a seminar at the Norwegian Veterinary Institute, Oslo, Norway |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Presentation on "Whole genome sequencing and metagenomics to understand bacterial transmission and antimicrobial resistance" on 24 February 2020 |
| Year(s) Of Engagement Activity | 2020 |
| Description | London International Youth Science Forum |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Schools |
| Results and Impact | I spent the day with the participants involved with this forum, which involves 500 students aged 16-21 from 70 different countries. I gave a lecture entitled 'Antimicrobial resistance - an evolving and international problem' to 40-50 of the participants, and then discussed key areas of debate around this issue. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.liysf.org.uk/ |
| Description | MRC-CLIMB workshop in The Gambia, 2018 |
| 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 | A CLIMB delegation ran a bioinformatics workshop in The Gambia, in collaboration with the MRC Unit in Fajara (The Gambia), that hosted the course. One day (Jan.22) was dedicated to set up the course (computer performance test, virtual machine, workshop simulation), then 21 students attended the three-day workshop (January 23-25) and were introduced to bioinformatics, cloud computing, Illumina and Nanopore sequencing, microbial genomics and metagenomics, phylogenesis and phylogenetic trees. Aims of the course were defined with Gambian tutors, and the activities were planned accordingly. The success of the workshop is well documented in a survey filled by participants at the end of the course: quality of presentations, assistance during the workshop, relevance for their research were reported to be very good or excellent. The MRC-CLIMB Unit in The Gambia is interested in making it an annual appointment. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation at a virtual conference on Pathogen Genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Gave a presentation at the "Pathogen Genomics Conference - Connecting Science to Patient Care", Public Health Wales, Cardiff. The talk was entitled "Application of shotgun metagenomics to document loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients". |
| Year(s) Of Engagement Activity | 2020 |
| Description | Presentation at a virtual conference on metagenomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Gave a presentation at the Earth & Life Sciences Alliance Workshop on Metagenomics on 20/12/20; approximately 140 people attended. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Presentation at the Food Standards Agency Scientific Advisory Committees Discovery Day, London, UK, Jun 13, 2019 |
| 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 presentation entitled "Antimicrobial resistance in the food chain" to new and existing members of the Food Standards Agency's (FSA) Scientific Advisory Committees and FSA employees |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation at the Food Standards Agency's Antimicrobial Resistance Workshop |
| 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 presentation to employees of the Food Standards Agency on antimicrobial resistance at the FSA AMR workshop |
| Year(s) Of Engagement Activity | 2020 |
| Description | Presentation at the Unit Seminar at the Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine on 16th October 2020 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A PhD student gave an external presentation entitled: Genomic diversity of Escherichia coli isolates from non-human primates and backyard poultry in the Gambia |
| Year(s) Of Engagement Activity | 2020 |
| Description | Presentation to government working group on AMR |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Presentation on antimicrobial resistance to the Defra Antimicrobial Resistance Coordination (DARC) Group meeting, Jun 8, 2021 |
| Year(s) Of Engagement Activity | 2021 |
| Description | Seminar speaker at the Doherty Institute, University of Melbourne |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I gave a seminar at the Doherty Institute, University of Melbourne entitled "Adventures in Salmonella sequencing: genomic epidemiological investigations of outbreaks and antimicrobial resistance" |
| Year(s) Of Engagement Activity | 2018 |
| Description | UK AMR Funders Forum workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | I was an invited participant in this workshop, where the objective was to consider the evidence on antimicrobial workshop from a human, animal, agricultural/ food, and environmental perspective to identify research gaps and opportunities, and to help inform and better achieve policy objectives. The outcomes of the workshop informed the refresh of the UK AMR strategy and how it can be best delivered. |
| Year(s) Of Engagement Activity | 2018 |