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

10 25 50

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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

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Belanche A (2012) Bacterial protein degradation by different rumen protozoal groups. in Journal of animal science

 
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 Unknown
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