Understanding microbiology to combat malnutrition

Lead Research Organisation: QUADRAM INSTITUTE BIOSCIENCE
Department Name: UNLISTED

Abstract

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Technical Summary

This deliverable is directly relevant to GCRF’s key challenge ‘Systems that deliver safe and nutritious food for all’. The current rise in the world population places greater pressure on food safety and security in LMICs, where there is high incidence of malnutrition, particularly in children. Globally, childhood undernutrition causes the death of ~5.6 million children each year. This project will deliver microbiological resources and genomic data to ultimately address the need to deliver sustainable, locally produced, fermented foods derived from locally grown agriculture products that will be safer and have an improved nutrient composition. It will also further the understanding of commensal strains which may have the capacity to function as probiotics to supplement poor diets. The approach is readily translated to other LIMCs where natural fermentation of agricultural products is widely practiced, and will assist local food industries to develop improved products, with a positive impact on the economy

Planned Impact

unavailable
 
Description 1. Using DNA based sequencing technology we were able to assess the diversity and microbial composition of naturally fermented foods in Africa. For some of the samples derived from a food called Kunu Saki we demonstrated the changes in microbial composition during the fermentation process. Our results indicated that that many of the products contained potential pathogenic bacteria highlighting the need for improving the microbiological safety of these foods.
2. Several hundred strains of bacteria and yeasts were isolated from a large variety of naturally fermented from 9 different African countries. We then sequenced the entire genomes of all the bacteria. These sequences will shortly be placed in public databses so they are freely available to all researchers in Africa and elsewhere
3. Via workshop held in Ghana we provided training to 15 African students/postdoctoral researchers and technicians in using molecular profiling of the fermented foods relevant to their countries as well as in whole genome sequencing of bacterial isolates.
4. We identified a number of bacterial strains with useful properties such as production of vitamins and antimicrobial activities that could be developed as started cultures in Africa to improve the nutritional quality and safety of these foods that are consumed daily by millions of consumers in Africa
Exploitation Route The sequencing data published online will be available by all researchers in Africa for comparison with their own findings. The data and resources generated within this project may pave the way for developing new starter cultures for application in African fermented foods to improve the shelf life of these products and improve food safety.
Sectors Agriculture

Food and Drink

Healthcare

Manufacturing

including Industrial Biotechology
 
Description BBSRC IAA
Amount £10,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 06/2019
 
Description Marie Curie CLARÍN-COFUND
Amount € 65,000 (EUR)
Funding ID ACA 17 - 16 
Organisation Foundation for the Promotion of Applied Scientific Research and Technology in Asturias 
Sector Public
Country Spain
Start 03/2018 
End 02/2020
 
Description Collaboration with Dr Damaris Odeny (ICRISAT, Kenya) and the Technical University of Kenya 
Organisation International Crops Research Institute for the Semi-Arid Tropics
Country India 
Sector Charity/Non Profit 
PI Contribution Our group provided training to a technician from the Technical University of Kenya on DNA extraction from fermented foods and DNA extraction from bacterial isolates. William Onyango Chienjo was trained in QIB on 29 and 30 January 2018. Our group also provided intellectual input in the design of the experiments.
Collaborator Contribution Dr Odeny and his team provided the samples to be studied in this project and the expertise on fermented foods. His group also undertook the DNA extraction from the fermented foods and bacterial isolates which will be sequenced in QIB.
Impact Metagenomic and genomic datasets that will be used in future publications.
Start Year 2017
 
Description Collaboration with Dr Damaris Odeny (ICRISAT, Kenya) and the Technical University of Kenya 
Organisation Technical University of Kenya
Country Kenya 
Sector Academic/University 
PI Contribution Our group provided training to a technician from the Technical University of Kenya on DNA extraction from fermented foods and DNA extraction from bacterial isolates. William Onyango Chienjo was trained in QIB on 29 and 30 January 2018. Our group also provided intellectual input in the design of the experiments.
Collaborator Contribution Dr Odeny and his team provided the samples to be studied in this project and the expertise on fermented foods. His group also undertook the DNA extraction from the fermented foods and bacterial isolates which will be sequenced in QIB.
Impact Metagenomic and genomic datasets that will be used in future publications.
Start Year 2017
 
Description Collaboration with Prof. Anteneh Tesfaye 
Organisation Addis Ababa University
Country Ethiopia 
Sector Academic/University 
PI Contribution Our group provided bioinformatics support to the PhD student Guesh Mulaw.
Collaborator Contribution Our partner Prof. Anteneh Tesfaye provided bacterial strains to be studied in this project and the expertise on fermented foods.
Impact Genomic datasets that will be used in future publications.
Start Year 2017
 
Description Collaboration with Professor Folarin Oguntoyinbo (University of Lagos, Nigeria) 
Organisation University of Lagos
Country Nigeria 
Sector Academic/University 
PI Contribution Our group provided training to students from the University of Lagos on DNA extraction from fermented foods, DNA extraction from bacterial and yeast isolates and bioinformatic analysis of metagenomic and whole genome sequencing data. PhD student Nwanneka Akinyemi was trained in IFR from October 2016 - February 2017 and PhD student Oluwaseun Juliana Areh was trained at QIB from 22/11/2017 to 27/12/2017.
Collaborator Contribution Professor Oguntoyinbo and his team provide the samples to be studied in this project and the expertise on fermented foods. His group also undertook the DNA extraction from the fermented foods which were later sequenced in QIB.
Impact As result of this collaboration one publication has arisen (doi:10.1128/genomeA.00481-16) and two publications are in preparation.
Start Year 2014
 
Description Collaboration with Professor Wisdom Amoa-Awua (CSIR-Food Research Institute, Ghana) 
Organisation Council of Scientific and Industrial Research (CSIR)
Department Food Research Institute (CSIR-FRI)
Country South Africa 
Sector Charity/Non Profit 
PI Contribution Our group provides training to one student from the University of Lagos on DNA extraction from fermented foods, DNA extraction from bacterial and yeast isolates and bioinformatic analysis of metagenomic and whole genome sequencing data. PhD student Amy Atter is being trained in QIB from 19/02/2018 to 16/07/2018.
Collaborator Contribution Professor Amoa-Awua and his team provide the samples to be studied in this project and the expertise on fermented foods. His group also undertook the DNA extraction from the fermented foods which will be sequenced in QIB.
Impact As a result of this collaboration metagenomic and genomic datasets were obtained. The results will be included in future publications.
Start Year 2017
 
Description Collaboration with professor Amit Rai India 
Organisation National Agri-Food Biotechnology Institute
Country India 
Sector Public 
PI Contribution We hosted the visit of prof Amit Rai to QIB and In March 20204 Arjan Narbad visited NABI-DTP institute and gave a presentation and discussed further collaboration.
Collaborator Contribution Prof Rai visited QIB in February 2024 and this resulted in further planned collaboration grant applications to extend the link between QIB and NABI-DBT institute. Joint experimental work is planned.
Impact Further short term funding to undertake collaboration experimental work via staff exchange from NABI to QIB.
Start Year 2024
 
Description Wokshop Uganda 
Organisation University of Los Lagos
Country Chile 
Sector Academic/University 
PI Contribution We organised the workshop in Kampla that brought together 12 researchers form Africa and elsewhere elsewhere who have interest in development and safety of African fermented foods.
Collaborator Contribution Professor Ogutoyinbo was instrumental in helping to organise this workshop, gave a presentation and contributed to discussions.
Impact Further research collaborations are planned between Research group of Professor Oguntoyinbo and my research group.
Start Year 2018
 
Description Analysis of the Microbiomes of Naturally Fermented Foods Training Course 
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 15 postgraduate students and postdoctoral researchers attended the workshop in which they acquired hands-on practical of molecular-based methods for assessing the microbial composition of naturally fermented foods. The attendees provided samples which led to a joined publication which has been submitted to the International Journal of Food Microbiology.
Year(s) Of Engagement Activity 2018
 
Description Talk at Wymondham College 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Talk at Wymondham College for 15 students on the topic of "improvement of food and health using bacteria" and the objectives of our project. The students were interested in the talk and there were questions and discussion about the topic.
Year(s) Of Engagement Activity 2018