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.

Publications

10 25 50
 
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