Microbial cultures for increased yield and efficiency of production systems in developing countries
Lead Research Organisation:
ABERYSTWYTH UNIVERSITY
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
Ruminant production is an important component of human nutrition, especially in developing countries, but there is no single answer to issues of sustainable improvement as climates, feed sources and breeds of animals vary across the globe. Building on international collaborations and world-leading expertise in rumen microbiology, we will generate a biological and data resource that can be used by researchers in DAC-listed countries to increase productivity by developing animal feeding strategies tailored to location.
Planned Impact
unavailable
Publications
Abecia L
(2018)
Analysis of the Rumen Microbiome and Metabolome to Study the Effect of an Antimethanogenic Treatment Applied in Early Life of Kid Goats.
in Frontiers in microbiology
Davoudkhani M
(2024)
Integrating microbial abundance time series with fermentation dynamics of the rumen microbiome via mathematical modelling.
in PloS one
Dimonaco NJ
(2022)
No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study.
in Bioinformatics (Oxford, England)
Dimonaco NJ
(2023)
StORF-Reporter: finding genes between genes.
in Nucleic acids research
Friedersdorff JCA
(2020)
The Isolation and Genome Sequencing of Five Novel Bacteriophages From the Rumen Active Against Butyrivibrio fibrisolvens.
in Frontiers in microbiology
Hitch TCA
(2018)
Spherical: an iterative workflow for assembling metagenomic datasets.
in BMC bioinformatics
Huws SA
(2018)
Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future.
in Frontiers in microbiology
Muñoz-Tamayo R
(2023)
Review: Towards the next-generation models of the rumen microbiome for enhancing predictive power and guiding sustainable production strategies.
in Animal : an international journal of animal bioscience
| Description | This grant provided an initial 10 months of funding to establish the groundwork for a Biological and Bioinformatic Resource that would support Rumen microbial research globally. The successful outcomes were: 1) Establishment of infrastructure for a rumen microbe Biological Resource. This included purchase of the freezers and purchase of cultures all commercially available rumen microbial isolates. This represented the initial phase of the establishment of a permanent biological collection of rumen microbial cultures for researchers from countries in receipt of ODA to request for research. 2) Establishment of infrastructure for a Bioinformatic Resource for integration of Rumen microbe genomic data and development of a proof of concept for a tool that would allow cross referencing of microbial genomic information with environmental sequencing data and providing users with an easy-to-use graphical interface for carrying out queries across an entire microbial community. 3) Data generation from understudied rumen microbes. This resulted in the generation of novel sequence data from anaerobic fungi and ciliates both which are under-represented rumen organisms. These findings are being applied to leverage novel funding to develop the resource further and to generate more interactions with the research community. |
| Exploitation Route | These findings demonstrated the feasibility of data integration and novel data generation for the rumen microbial community, providing a prototype for knowledge generation. These findings can be taken forward through the further development of the prototypes into a system containing all available rumen genomic information. |
| Sectors | Agriculture Food and Drink Education |
| Description | (METH-ABATE) Development and validation of novel technologies to reduce methane emissions from pasture based Irish agricultural systems |
| Amount | € 1,249,005 (EUR) |
| Organisation | Northern Ireland Department of Agriculture, Environment and Rural Affairs (DAERA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 01/2023 |
| Description | HoloRuminant - Healthy terrestrial livestock microbial ecosystems for sustainable production |
| Amount | € 11,000,000 (EUR) |
| Funding ID | H2020-SFS-2020-2 Project 101000213 - HoloRuminant |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 08/2021 |
| End | 08/2026 |
| Description | MASTER: Microbiome Applications for Sustainable food systems through Technologies and EnteRprise |
| Amount | € 11,000,000 (EUR) |
| Funding ID | H2020-SFS-2018-202 |
| Organisation | EU-T0 |
| Sector | Public |
| Country | European Union (EU) |
| Start | 01/2019 |
| End | 12/2022 |
| Description | SeaSolutions: Seaweeds and seaweed-ingredients to reduce enteric methane emissions from pasture-based sheep, cattle and dairy cows (FACCE-ERA NET GAS) |
| Amount | € 1,969,000 (EUR) |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 01/2020 |
| End | 01/2023 |
| Title | RumenMine |
| Description | This database in alpha closed release brings together all the genomic data from the hungate 1000 with a meta-transcriptomic dataset to allow users to search for genes across 500 organisms, and check the expression level at different time points during the early colonisation of grass in the rumen of cattle. |
| Type Of Material | Database/Collection of data |
| Provided To Others? | No |
| Impact | This database has allowed in-house investigation of the genomic factors unique to the rumen organisms, we have also hosted visiting staff from Brazil who have used it as part of their research into species groups of rumen bacteria. |
| URL | http://rumenmine-dev.ibers.aber.ac.uk/rumenmine-dev/begin.do |
| Description | Collaboration for linking rumen mechanistic models to microbial metabolic networks |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | We have brought our metabolic networks reconstructed from microbial metatranscriptomic and metagenomic data from the rumen to this collaboration to investigate ways that these could be linked to mechanistic models of the rumen from INRA |
| Collaborator Contribution | INRA have brought their mechanistic models of the rumen system to investigate ways that these could be linked the microbial metabolic networks we have developed from the rumen. |
| Impact | https://doi.org/10.1371/journal.pone.0298930 https://doi.org/10.1016/j.animal.2023.100984 |
| Start Year | 2019 |
| Title | CowPI: A Rumen microbiome focussed version of the PICRUST functional inference software |
| Description | "CowPI," is a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. It consists of a set of pre-calculated files that can be used with an installation of PICRUSt to allow functional predictions to be made from 16S rRNA samples from the rumen microbiome. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Since release this tools have been cited 7 times and is now used regularly for the prediction of the functional capacity of a rumen microbiome sample from 16S data. |
| URL | https://www.cowpi.org |
| Company Name | AMPLY |
| Description | AMPLY uses machine learning and bioinformative approaches to discover new antibiotics that are effective against multi-drug resistant (MDR) pathogens, as well as operating a database of bioactive compounds. |
| Year Established | 2021 |
| Impact | In 2025 the company closed its second round of investment. |
| Website | https://amplydiscovery.com/ |
| Description | Interview on Naked Scientists about the importance of ruminants in agriculture. |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | This was a live interview on the Naked Scientists show, where they were investigating the contribution of microbes "from farm to fork". I was asked to contribute to the discussion on the importance of microbes to agricultural animals, particularly those microbes in the rumen. This was initially broadcast live on BBC radio Cambridgeshire, with followup broadcasts on BBC Radio 5 Live and internationally on ABC Radio National in Australia. The show was also made into a podcast which id distributed globally. following the show there were many comments from both colleagues and the general public on the content (for instance on twitter), particularly on myths that had been dispelled about methane from agricultural animals and general greater awareness that had been raised on the topic. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.thenakedscientists.com/articles/interviews/digesting-science-ruminants |