INRA-Rowett Rumen Microbial Genomics Network workshop
June 20th, 2016 held in Clermont Ferrand
It was a pleasure to welcome over 80 international delegates to the RMG network workshop held in Clermont Ferrand on the 20th June. The sheer number of delates who came to the workshop demonstrates the value of the RMG network in providing opportunities for ruminant scientists to meet and discuss the challenges and future directions for the field.
Dr Sharon Huws (RMG coordinator, IBERS, Aberystwyth University) outlined the past achievements for the RMG in terms of the Hungate 1000, the rumen census and the highly attended past workshops that have been held. In past workshops discussions have centred on the need to choose our methods for assessing the rumen microbiome carefully and applying logic, as concerns have been raised with respect to the fact that next generation sequencing is now standard and the data continues to increase but often the methods applied are not logical and the interpretation perhaps questionable. In an attempt to address these issues the RMG network is coordinating a special research topic on ‘metaomic approaches to study the rumen microbiome: challenges and innovation’ in Frontiers in Microbiology which will allow authors to publish an array of different article types centred around openly discussing our challenges and how we as a community can be more innovative. We encourage you all to consider submitting articles to this special research topic. Articles are reviewed in the standard manner and if accepted will be published online immediately. There are guideline dates for abstract and full manuscript submission which can be found on the Frontiers in microbiology Special edition website, but authors can submit full articles at any point and be published online as soon as an article is accepted. It was also noted that the network is seeking funding to enhance activities. A plea was also made for any help on raising the social media communication of the network, any interested parties please contact Sharon (hnh@aber.ac.uk).
An update on the Hungate 1000 project was given by Dr Chris Creevey (IBERS, Aberystwyth University) and it was great to hear that we now have over 500 bacteria and archaea sequenced as part of this project, this is a highly valuable resource for scientists within the field. Chris also took the audience through accessing the genomic data.
Dr Jan Lassen (Aarhus University, Denmark) also presented an update on the COST Action Program – METHAGENE. METHAGENE aims to agree on protocols to harmonise large-scale methane measurements for implementation in large scale breeding strategies. METHAGENE also aims to enhance scientific cooperation and interactions. An update was given on the stakeholder events, workshops and training that METHAGENE have given to date.
Professor Dewhurst (SRUC, Edinburgh) presented the FACCE-JPI ‘Rumen Stability’ project coordinated by himself with multiple European partners. The project aims to identify and exploit long-term effects of short-duration dietary treatments on methane production, rumen function and responses to methane mitigation interventions at a later stage. There is a focus on manipulations in early life, when the rumen community is developing, but also work on other diet transitions. The idea of this project is to reduce the cost and effort of mitigation strategies by reducing the duration and/or quantity of treatment required and/or to increase the size of responses if treatments have to be reapplied.
Dr Stuart Denman, CSIRO, Australia presented on update on the Rumen Pangenome Program, led by Professor Vercoe, University of Western Australia. The pangenome project focuses on sheep and the extent to which genetics can be used to reduce methane emissions and improve feed efficiency. The program is part of a global network of institutions and organisations using cutting-edge ‘-omics’ technologies to untangle the relationship between the animal and the rumen. Dr Denman showed some interesting data correlating methane emissions to the host genetics and the rumen microbiome.
Dr. Matthew McCabe, Teagasc, Ireland presented data on the use of the Illumina MiSeq for amplicon sequencing of rumen samples. Much discussion was had regarding the usefulness of metataxonomic data and the possible use of PiCRUST software to infer function from such data sets was proposed. This sofware could be a cost-effective means of of obtaining function based data from amplicon sequencing.
Last but not least Dr Milka Popova, INRA, France presented data on the effect of nitrate-supplemented diets on methanogens' diversity and activity in the rumen and Dr Rodolpho Prado Maringa University, Brazil and IBERS, Aberystwyth University, UK presented data on the production and function of membrane vesicles by the rumen microbiome. Specifically he showed the potential that the rumen microbiota excrete membrane vesicles to effectively degrade protein, startch and carboxymethylcellulose.
Following the interesting talks, breakout sessions were conducted to discuss the challenges and the future for ruminant research. The aim of these breakout sessions was to guide what the community would like to see being developed from the RMG network and that which they would like to see being published within the Frontiers in microbiology special edition. Some clear and consistent feedback was obtained from each group:
- A forum on the RMG website allowing exchange of ideas or obtaining advice on technical issues would be of benefit.
- A database which brings together the Hungate 1000 genomes and all published metataxonimc/metagenomic data together into one searchable database that could also serve as a submission point would be an exceptionally valuable resource for the community. We are good at obtaining data and publishing but not necessarily able to look at all data to obtain consensus.
- Standard operating procedures stifle innovation, nonetheless some guidelines are required when applying metataxonims/metagenomics. The EU FP7 RuminOmcs ring test clearly shows the challenge of obtaining consistent metataxonomic data across laboratories. This stifles biological understanding of the rumen microbiome, therefore some guidelines and use of standard (mock community) was deemed as valuable.
- We as a community overlook the rumen eukaryotes and focus on the bacteria. Due to the importance of the protozoa and fungi to ruminant function and subsequently ruminant production and environmental impact, we should not ignore these eukaryotes but should widen our studies to include them
- There was agreement that the RMG network is valuable as it provides opportunities to foster communication and collaboration amongst rumen microbiologists.
