Functional dynamics of the microbiome
Lead Research Organisation:
Aberystwyth University
Department Name: IBERS
Abstract
The aim of this sub-programme is to identify the microbial functionalities associated with efficient fermentation of fresh forage and how they can be promoted. The use of non-culture based technologies has revealed the complexity and diversity of the rumen microbial ecosystem. These approaches have shown that microbial profile can vary over remarkably short time periods as a result of different forage diets and as a result of duration of colonisation events. A change in diversity may not necessarily result in an altered functional phenotype, so sequence-based results (metagenomics and RNA-seq) will be mapped to metabolic pathways (e.g.., KEGG, GO) to characterise the microbial functionality associated with succensional microbial colonisation and degradation of fresh forages representing desirable and poor fermentation outcomes. Proteomics (2-D gel electrophoresis, differential fluorescent labelling, orbitrap-MS) will be used to confirm the effect of gene expression change on protein/enzyme abundance. Visible (fluorescence microscopy) and spectral imaging (FTIR, Raman spectroscopy) techniques will be used to determine chemio-spatial aspects of attachment and colonisation pertaining to both the plant and microbial components.
Publications
A Huws S
(2014)
Differential Colonization of Plant Parts by the Rumen Microbiota is likely to be due to Different Forage Chemistries
in Journal of Microbial & Biochemical Technology
Abecia L
(2014)
Feeding management in early life influences microbial colonisation and fermentation in the rumen of newborn goat kids
in Animal Production Science
Abecia L
(2014)
An antimethanogenic nutritional intervention in early life of ruminants modifies ruminal colonization by Archaea.
in Archaea (Vancouver, B.C.)
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
Akanni WA
(2015)
Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis.
in Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Alcaide M
(2012)
Gene sets for utilization of primary and secondary nutrition supplies in the distal gut of endangered Iberian lynx.
in PloS one
Ann Huws S
(2012)
Effects of feeding Mediterranean buffalo sorghum silage versus maize silage on the rumen microbiota and milk fatty acid content.
in The Journal of general and applied microbiology
Belanche A
(2016)
Effects and mode of action of chitosan and ivy fruit saponins on the microbiome, fermentation and methanogenesis in the rumen simulation technique.
in FEMS microbiology ecology
Belanche A
(2013)
Comparison of ryegrass and red clover on the fermentation pattern, microbial community and efficiency of diet utilisation in the rumen simulation technique (Rusitec)
in Animal Production Science
Belanche A
(2016)
An Integrated Multi-Omics Approach Reveals the Effects of Supplementing Grass or Grass Hay with Vitamin E on the Rumen Microbiome and Its Function.
in Frontiers in microbiology
| Description | This work was at the cutting edge of understanding the relationships between complex microbial communities. Based on our hypothesis of successional colonisation of ingested feed by the rumen microbiota coupled with the increased opportunity provided by next generation sequencing (16S profiling) we have developed in vitro and in vivo approaches confirming that feed degradation occurs through multiple waves of colonisation by differing species and phyla of rumen bacteria. Furthermore by applying metatranscriptomic sequencing plus custom computational interpretation it has been possible to reveal the functional activities that are required at different stages of colonisation, as provided by the different groups of colonising organisms. This has primarily shown that there is likely to be a mis-match between the "key activities" of many of the characterised cultured rumen bacteria with what their in vivo role may be. These data have been published. |
| Exploitation Route | Most of the key researchers involved in this project have moved to alternative employment. Their continued academic interest in the functional microbial ecosystem is therefore contributing to research and teaching in many organisations and will help disseminate the novel findings. |
| Sectors | Agriculture, Food and Drink,Environment |
| Description | Our work has informed the Advanced training partnership in sustainable and efficient food production. Specifically the modules in Ruminant Nutrition and Ruminant Gut Microbiology. To date some 160 student have enrolled on the ATP with students reporting that it has made a material difference to this business practices: Example Student Comments: "Learning about rumen manipulation has given me plenty of ideas for potential areas for R&D/product development that my company could start to investigate" Liz Norton, Nutritionist for Miron Bio-Systems "I was very interested in the work surrounding potential methane mitigation techniques, and the role sequencing can potentially play in reducing the environmental impact of ruminant production through manipulation of the rumen microbial populations." Current data in this module will be used to inform decisions regarding trials using Alltech solutions, as well as to answer technical and scientific queries from sales force and customers.' Helen Warren, Alltech |
| First Year Of Impact | 2012 |
| Sector | Agriculture, Food and Drink,Education,Environment |
| Impact Types | Societal |
| Description | Chair in Rumen Systems Biology |
| Amount | £600,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2013 |
| End | 12/2017 |
| Description | Climate KIC RuMeClean |
| Amount | £218,042 (GBP) |
| Organisation | BioHorizons |
| Sector | Private |
| Country | United States |
| Start | 01/2014 |
| End | 12/2015 |
| Description | Doctoral Career Development Scholarship |
| Amount | £68,889 (GBP) |
| Organisation | Aberystwyth University |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 10/2014 |
| End | 09/2017 |
| Description | FACCEJPI Rumenstability |
| Amount | £25,200 (GBP) |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 02/2014 |
| End | 01/2017 |
| Description | GCRF-IAA |
| Amount | £300,000 (GBP) |
| Funding ID | BB/GCRF-IAA/09 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2016 |
| End | 03/2017 |
| Description | Global Challenges Research Fund Data and Resources |
| Amount | £942,900 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2016 |
| End | 07/2017 |
| Description | International Partnering Award Brazil |
| Amount | £41,531 (GBP) |
| Funding ID | BB/L026716/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2014 |
| End | 03/2018 |
| Description | KESS studentship |
| Amount | £56,000 (GBP) |
| Organisation | European Social Fund (Welsh Government/ EU) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2016 |
| End | 09/2019 |
| Description | NERC-SARIC translation |
| Amount | £197,442 (GBP) |
| Funding ID | NE/P007996/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2017 |
| End | 07/2018 |
| Description | NRN LCEE Cluster |
| Amount | £435,721 (GBP) |
| Organisation | The Sêr Cymru National Research Network for Low Carbon, Energy and Environment (NRN-LCEE) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2015 |
| End | 12/2018 |
| Description | NRN antimicrobials from bovine metagenomes |
| Amount | £49,970 (GBP) |
| Organisation | National Research Network, Life Sciences and Health |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2014 |
| End | 09/2015 |
| Description | SARIC Club Translation Award |
| Amount | £248,000 (GBP) |
| Funding ID | NE/P007996/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2017 |
| End | 01/2018 |
| Description | TSB beef supply chain |
| Amount | £386,672 (GBP) |
| Funding ID | 101407 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2013 |
| End | 02/2016 |
| Description | Teagasc ruminant methane |
| Amount | £72,728 (GBP) |
| Organisation | Teagasc |
| Department | Teagasc Food Research Centre |
| Sector | Academic/University |
| Country | Ireland |
| Start | 01/2014 |
| End | 01/2018 |
| Description | WG Land use review |
| Amount | £13,000 (GBP) |
| Organisation | Welsh Assembly |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2014 |
| End | 07/2014 |
| Description | BBSRC UK-Brazil Partnering Award |
| Organisation | Federal University of Minas Gerais |
| Country | Brazil |
| Sector | Academic/University |
| PI Contribution | Members of research team have travelled to Brazil to share knowledge of characterising and exploiting novel antimicrobials within the rumen microbiola |
| Collaborator Contribution | Members of the receiving organisation in Brazil hosted the visit and shared in their understanding of exploiting novel antimicrobials within the rumen microbiola |
| Impact | Knowledge sharing |
| Start Year | 2014 |
| Title | Compounds for novel use in ruminants (recently filed) |
| Description | The present invention relates to the field of synthetic compounds and their use in ruminants to improve ruminant growth performance, reduce rumen methane emission, reduce urine ammonia excretion, and/or to reduce rumen acetate to propionate ratio. Moreover, it also relates to a feed composition for ruminants comprising these compounds. |
| IP Reference | 32402-EP-EPA |
| Protection | Patent application published |
| Year Protection Granted | 2017 |
| Licensed | Yes |
| Impact | Recently filed patent application. Licensed to DSM. |
| Title | Methods and Compositions for Improving Feed Outcomes (Recently filed) |
| Description | The present invention relates to a method of improving outcomes in ruminant feeding. The improved outcome may be selected from inhibiting protozoal activity in a rumen of a ruminant; and/or improving feed efficiency of a ruminant; and/or improving growth performance of a ruminant; and/or reducing greenhouse gas emissions from a rumen of a ruminant. The present invention further relates to a composition comprising a saponin and a glycosidase inhibiting iminosugar. |
| IP Reference | P33635GB1 |
| Protection | Patent application published |
| Year Protection Granted | 2017 |
| Licensed | No |
| Impact | Recently filed patent application of relevance to livestock industry. |
| Title | New bis ester of ivy sapogenins for ruminants |
| Description | The present invention relates to the field of synthetic bis esters of ivy sapogenins, and their use in ruminants to improve ruminant growth performance, reduce rumen methane emission, reduce urine ammonia excretion, and/or to reduce rumen acetate to propionate ratio. More particularly, it relates to bis esters of hederagenin and their use. Moreover, it also relates to a feed composition for ruminants comprising bis esters of hederagenin, and 10 to novel bis esters of hederagenin. |
| IP Reference | WO2016193309 |
| Protection | Patent application published |
| Year Protection Granted | 2016 |
| Licensed | Yes |
| Impact | Licensed to DSM. Application relevant to agricultural industry. |
| Title | Novel use of compounds in ruminants (recently filed). |
| Description | The present invention relates to the field of synthetic compounds and their use in ruminants to improve ruminant growth performance, reduce rumen methane emission, reduce urine ammonia excretion, and/or to reduce rumen acetate to propionate ratio. Moreover, it also relates to a feed composition for ruminants comprising these compounds. |
| IP Reference | 32401-EP-EPA |
| Protection | Patent application published |
| Year Protection Granted | 2017 |
| Licensed | Yes |
| Impact | Recently filed patent application. Licensed to DSM. |
| Description | "Y Bol Buwch" (All Things Rumen) exhibit at Royal Welsh Show, July 2015 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | • Initiated and oversaw "Y Bol Buwch" (All Things Rumen) exhibit at Royal Welsh Show, July 2015 including "Live lab" deonstrations of DNA extraction and fermentation and "Bug bashing" (type of coconut shy). |
| Year(s) Of Engagement Activity | 2015 |
| Description | AKS Invited to give seminar at Oxford Brookes |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Talked to a group of bioscience postgraduates and supervisors. Wide ranging discussions on practicalities and ethics associated with livestock and the environment. New potential research contacts made. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Exhibition at Royal Welsh Show 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Exhibits and quizzes used to alter awareness of grass quality and how it is digested in the rumen under the general heading "Not all grasses are the same". The enabled more detailed discussions with adults and livestock practitioners about determination of quality traits and IBERS breeding directions. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Public engagement (Royal Welsh Show) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Demonstration of interactive rumen over four days of national agricultural show, leading to discussion with members of the public and prospective students. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Sparking Impact Meeting - Waitrose Supply Chain/IBERS |
| 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 | With British producers facing ever-increasing expectations - to deliver traceability, meet higher environmental standards and maintain the countryside - Waitrose, IBERS and suppliers have been working together to share experiences on topics such as animal and plant diseases, food security issues and strains on productivity. This event gave suppliers, large and small, direct access to Waitrose buyers, food technologists and scientists and helped smaller producers, in particular, to understand food legislation. The outcome of the event was a sharing of best practice throughout Waitrose's supply chain and beyond. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Visit to WHEB, EU, Brussels |
| 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 | Visit of 7 researchers to Welsh Higher Education Brussels, organised by National Research network (Wales) in Low Carbon Energy and Environment. Objective was to engage with Research Programme Directors and managers of platforms related to agriculture. |
| Year(s) Of Engagement Activity | 2016 |
| Description | information for SoB poster |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | Dr Kingston-Smith collaborated with Society of Biology during their preparation of a poster for schools titled "What goes in to a cow?" aimed at GCSE level students. Posters used by Society of Biology Staff during National Science week. Posters available to schools. |
| Year(s) Of Engagement Activity | 2013 |
| Description | information request: Becoming a goat. |
| 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 | Public/other audiences |
| Results and Impact | Initial enquiry for information by telephone, followed by visit March 2014 relating to Wellcome Trust Grant to artist Thomas Thwaites on "Becoming a goat". During visit it was possible to attend a relevant lecture, talk with several research staff. Followed up by questions by email. Aim of grant was to produce exhibition (planned to be in London and possibly Aberystwyth) and book of the experience. Awaiting final outcome. |
| Year(s) Of Engagement Activity | 2014 |