Network Chronicles The

The Rumen Microbial Genomics Network is a global collaborative network of researchers with a common set of principles and guidelines in rumen microbial genomics to underpin the development of methane mitigation and rumen adaptation technologies.

The Network's efforts are focused on generating a shared comprehensive data resource that will enable investigators to characterize the relationship between the composition of the rumen microbiome and the efficient bioconversion of fibrous feedstuffs, leading to a more environmentally acceptable production of nutritious foods in all parts of the world.

Welcome to the first Rumen Microbial Genomics Network newsletter. Contributions and suggestions

for future RMG Network newsletters and items for inclusion on the RMG Network website (www.rmgnetwork.org.nz) are most welcome, as is permission to include links to your own websites that outline your research areas. Items for posting may include short reports on conference visits, workshops, more general news items or publicity for future meetings. For example, the website currently has links to several conferences, that cover various aspects of microbiology, genomics etc. due to be held in 2013. Links to publications can also be suggested and posted on the website.

Origins of the Rumen Microbial Genomics Network The Rumen Microbial genomics Network operates under the umbrella of the Livestock Research Group of the Global Research Alliance on Greenhouse Gases (p.2). The network is the outcome of a meeting hosted in Palmerston North, New Zealand in February 2011. There are now 183 members on the RMG Network mailing list who are participants in the underpinning Global Rumen Census (www.globalrumencensus.org.nz) and/or Hungate 1000 (www.hungate1000.org.nz) projects, also funded by the New Zealand Government. Members originate from 30 countries and are affiliated to 80 different research institutes, universities, government departments etc.

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of which was to promote the importance of research in this area. Dr. Gemma Henderson represented the Rumen Microbiology Team and AgResearch as a keynote speaker at the ISIMB. Several areas where Prof. Hilario Mantovani (UFV) and AgResearch could collaborate were identified. For example, Prof. Hilario Mantovani and his team will provide AgResearch with rumen samples that are representative of typical ruminant housing and dietary situations found in Brazil for inclusion in the Global Rumen Census project (www.globalrumencensus.org.nz). They will also provide rumen bacterial isolate cultures for inclusion in the Hungate 1000 project (www.hungate1000.org.nz) (• Gemma Henderson, AgResearch).

International Symposium on Microbiology and Biotechnology (ISIMB), The Federal University of Viçosa, Brazil The Federal University in Viçosa (UFV) is one of the best agricultural and technological universities in Brazil. It is located in the state Minas Gerais, the main region to produce of milk and coffee. The university maintains several hundred ruminants on its farms that are used for both teaching and research purposes. Prof. Hilario Mantovani, and colleagues at the UFV, hosted the inaugural International Symposium on Microbiology and Biotechnology (ISIMB, www.simb.ufv.br/), the aim

View of the main campus of the Federal University of Viçosa.

The newsletter of the Rumen Microbial Genomics Network

Newsletter #01, December 2012

The programme is now approaching the end of its first year, where the focus so far has primarily been on the development of methods to be used in the programme. Thus, the workshop enabled the participants to share their progress in developing and assessing methods, mainly focusing on those associated with the main trial which involves the analysis of rumen microbiomes and animal genotype of 1,000 dairy cows. Considerations had to be made for the many steps involved in analysing the rumen microbiome, including how the rumen should be sampled (taking into account the availability of fistulated animals), rumen sample preservation, DNA extraction methods, and the genetic loci and sequencing methods to use to most accurately reflect the rumen microbial community.

The RuminOmics Microbial Genomics Workshop Planning the logistics of any sizeable animal trial involving rumen sampling is no easy feat, but when this involves 1,000 dairy cows across four different countries, each using different sampling teams and resources, the challenge is significant, and the co-ordination and harmonisation of methods is imperative. Such considerations were the subject of the recent RuminOmics workshop, held in late November in the tiny village of Pinsot in the Rhône-Alpes region of France.

RuminOmics is a European Union-funded international programme led by Prof. John Wallace of the University of Aberdeen in Scotland, which unites researchers from 11 different institutes across Europe with the aim of connecting the animal genome, gastrointestinal microbiomes and nutrition to improve digestion efficiency and the environmental impacts of ruminant livestock production.

A wintry day in Pinsot, with the local ruminants passing through (top).

Perspectives from related international projects, including the Global Rumen Census and Hungate1000, which are currently being undertaken by the GRA Rumen Microbial Genomics Network members, were also presented, providing further food for thought on approaches that the consortium could take. By the end of the workshop, a strategy for sampling and analysis was decided upon, enabling the next exciting phase of this significant project to be undertaken. To learn more about the RuminOmics programme, please visit www.ruminomics.eu/ (• Christina Moon, AgResearch).

Harmonisation of techniques associated with ruminal genome, microbiome and metagenome analysis. The analysis of how the ruminal microbial community influences methanogenesis depends on a set of techniques that are used to characterize the genome, microbiome and metagenome. The outcome of the analysis often depends on the details of the techniques used. How should samples of ruminal digesta be taken? And when? How should they be stored? How should DNA be extracted? Following extraction, several methods are available for analysing the community, but are they all valid? How best can we use NGS to achieve our objectives in this respect? And how does metagenomic sequence data from massively parallel sequencing help us to analyse the structure and activity of the community? This workshop is sponsored by the EC Framework 7 consortium, RuminOmics, and the Rumen Microbial Genetics Network. Its aim is to explore the various techniques that are being used and if possible, to make them consistent, in order to facilitate comparisons between the

Next RMG Network Workshop: 22nd June 2013, Dublin, Ireland The next meeting of the RMG Network is scheduled to be held in Dublin, Ireland on 22nd June 2013 immediately prior to the Greenhouse Gases and Animal Agriculture (GGAA) meeting. It will be a one-day workshop jointly organised with the RuminOmics consortium.

results of experiments carried out by the many international groups working on rumen microbial ecology as it relates to methane and N emissions from ruminant livestock production. For further information on pre-conference workshops see www.ggaa2013.ie/workshops.html

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The Greenhouse Gases and Animal Agriculture Conference

2013 will take place in Dublin, Ireland 23rd - 26th June 2013 GGAA 2013 will attract speakers and delegates from throughout the globe and will build on previous successful meetings in the series. The meeting will focus on advancements in the areas of animal derived GHG mitigation since the last meeting in Banff, 2010. The programme has been designed to address topics that are relevant to delegates from both developed and developing countries. We hope to be able to provide limited financial support for some delegates from least developed countries who have Summaries accepted for presentation at the meeting. Please visit www.ggaa2013.ie for more information about the conference venue, accommodation, social programme, sponsorship opportunities and contact details.

Call for One-page Summaries Now Open You are invited to submit a one-page summary for review by the Scientific Committee. An example and template for the summary are available to download on the Greenhouse Gases & Animal Agriculture website – http://www.ggaa2013.ie/abstracts.html

Format and content guidelines are also available, along with a checklist for review. We strongly advise you to study this carefully before you start preparing your submission. Summary Submission Deadline: Friday 18th January 2013

Please go to https://teagasc.conference-services.net/authorlogin.asp?conferenceID=3391&language=en-uk to enter the online submission system.

Note, summaries will be published in the Cambridge University Press series ‘Advances in Animal Biosciences’ and must be suitable for use as a scientific reference. Submission of a summary is deemed a commitment to present the paper. The Scientific Committee will review all summaries submitted and contact you regarding your submission by Monday 4th March 2013.

The Scientific Programme will run from Monday 24th to Wednesday 26th June 2013, including a mix of invited and offered theatre presentations, as well as poster session presentations. You can review the preliminary scientific programme at http://www.ggaa2013.ie/programme.html

Pre-Conference Workshops Saturday 22nd June 2013: For more information go to: http://www.ggaa2013.ie/workshops.html

1 Joint RuminOmics/Rumen Microbial Genomics Network Workshop. Harmonization of techniques associated with ruminal genome, microbiome and metagenome analysis

2 Measurement Techniques for Methane Emissions and Use of Methane Energy 3 Techniques for Measuring GHG from Soil and Manure

Post-Conference Workshops and meetings: The joint RuminOmics/Rumen Microbial Genomics Network Workshop will take place on Saturday 22nd June 2013. Registration for these workshops is through the main registration form. The LRG will meet on the 28th - 29th June

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RMG Network and the Global Research Alliance The Global Research Alliance on Agricultural Greenhouse Gases, which was launched in December 2009, is founded on the voluntary, collaborative efforts of more than 30 member countries.

The focus of the Alliance is research, development and extension of technologies and practices that will help deliver ways to grow more food (and more climate-resilient food systems) without growing greenhouse gas emissions.

The Alliance promotes an active exchange of data, people and research to help improve the ways that agricultural greenhouse gas research is conducted and to enhance participating countries’ scientific capability. Alliance members work with farmers and farmer organisations, the private sector, international and regional research institutions, foundations and non-governmental organizations to improve the sharing of research results, technologies and good practices, get these out on the ground.

The Alliance aims to deepen and broaden mitigation research efforts across the agricultural sub-sectors of livestock, paddy rice, cropping and the cross-cutting themes of soil carbon and nitrogen cycling. The RMG Network is one of several networks and associated projects set up under the umbrella of the Livestock Research group.

Agriculture plays a vital role in food security, poverty reduction and sustainable development. The sector is particularly vulnerable to the impacts of climate change and faces significant challenges in meeting a dramatic increase in global food demand, while reducing its contribution to greenhouse gas emissions.

Agriculture currently produces 14 percent of the world’s annual greenhouse gas emissions. Agricultural emissions are expected to rise by about 30-40% above 2005 levels by 2050.

Many countries already have research underway to better understand, measure, and manage agricultural greenhouse gases emissions. By linking these efforts through the Alliance, faster progress can be made towards the solutions needed for improving agricultural productivity and reducing its contribution to climate change.

The RMG Network is a network for all persons (scientists, industry representatives, policy makers) who are interested in rumen microbial genomics to underpin the development of CH4 mitigation and rumen adaptation technologies.

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RMG Network Working Group takes shape The RMG Network is currently coordinated by New Zealand, but to ensure that the RMG Network will represent a global collaborative network of researchers with a common set of principles and guidelines, international representation is a prerequisite. Therefore several active researchers in the Rumen Microbial Genomics area have been offered the opportunity to join the RMG Network Working Group (WG). The RMG Network WG will:

• promote and endorse the goals and auspices of the Network through collaboration and publication of

high quality/impact research programmes • agree a co-ordinated Network communication strategy • be open and transparent in the support of underpinning projects • oversee the research areas which underpin the RMG Network • commit to publicising the activity of the Network in their respective region/countries to generate

interest for all projects • explore opportunities for developing new collaborative projects or enhancing RMG Network-aligned

projects with shared staff/students, training etc. Individual RMG Network WG members have been identified who may be able to lead specific research areas that are endorsed by the RMG Network and will be responsible for progressing the Network’s work plan in these areas. They will report back to the Network co-ordinator with news on new collaborative projects, RMG Network-aligned projects, staff/student exchanges, training etc. which can be included in quarterly newsletters.

The current RMG Network WG consists of

Dr Adrian Cookson Network Co-ordinator, AgResearch Limited, New Zealand Dr Cecile Martin INRA, France Dr Stuart Denman CSIRO, Australia Dr Sharon Huws University of Aberystwyth, Wales Prof Yasuo Kobayashi University of Hokkaido, Japan Dr Itzhak Mizrahi Volcani Research Center, Israel Dr Leluo Guan University of Alberta, Canada Dr Andre-Denis Wright University of Vermont, USA

The ASGGN’s more than 200 members come from 40 countries and include researchers, advisers and policy makers. The members are affiliated to 99 different organisations including universities, national research organisations, private research organisations, consultancies and government departments and agencies. The Methane Phenotype Working Group of the ASGGN is currently preparing a positioning paper for publication in a peer reviewed journal. This paper will identify current methodologies and recommend future directions for measuring methane emissions and feed intake in ruminant livestock.

The ASGGN also plays a significant role in a New Zealand funded post-doctoral project. Dr Natalie Pickering will work across multiple countries to combine existing phenotype information and leverage experience with other methane phenotyping groups to develop shared measurement protocols and breeding objectives that will accelerate reductions in emissions intensity via targeted breeding and selection indexes. Existing data from international institutions will be used to determine the correlation between genetic traits and low-emitting phenotypes.

The ASGGN website can be found at www.asggn.org and the primary contact is Grant Shackell: asggn@agresearch.co.nz

Animal Selection Genetics and Genomics Network The science behind genetic and genomic technologies that contribute to animal selection tools to mitigate methane emissions from ruminant livestock, requires a huge resource of animals of different species and breeds, and access to unique skills.

The Animal Selection, Genetics and Genomics Network (ASGGN) offers a forum and environment in which scientists from all over the world can share information and data. The network will facilitate a coordinated international research effort to achieve progress at a much faster rate than possible by a single country working alone.

One of the first areas for WG discussion is to develop a strategy to ensure the RMG Network is self-sustainable beyond June 2013. Potential options will be discussed by the WG and through the wider Network. Thereafter we propose the co-ordination and management of the network will change at the workshop being held before the GGAA conference.

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The RMG Network website

Current information posted on the RMG Network website includes information on future conferences for 2013 including GGAA, but input from RMG Network members is important to make it a valuable information resource. Please send contributions, recent articles of interest, or research methods that will benefit the wider Rumen Microbial Genomics research community to the website administrator Adrian Cookson at rmg.network@agresearch.co.nz. Participants of the NZ Government funded Global Rumen Census and Hungate 1000 projects that underpin the RMG Network who have provided their contact details will be signed up automatically in the very near future. Membership will provide access to the Members only pages where you will find the members directory, Forum option and in time, access to data stemming from the Global Rumen Census and Hungate 1000 projects. If you have colleagues who are not yet members, it would be appreciated if you could encourage them to join by directing them to the Network website.

The Italian Job After starting his Masters in September 2011, Vincenzo Lopreiato started to look at opportunities for an internship overseas. In late 2011, Vincenzo’s supervisor, Professor Paolo Bani, contacted the New Zealand Agricultural Greenhouse Gas Centre (NZAGRC) enquiring whether there were any opportunities for internships where students might focus on greenhouse gas (GHG) emissions from ruminants. This interest in enteric GHG emissions stemmed from Professor Bani’s involvement in the RuminOmics programme led by Professor John Wallace at the University of Aberdeen. The NZAGRC forwarded Professor Bani’s enquiry to Dr David Pacheco (AgResearch, Animal Health Team) and Dr Adrian Cookson (Rumen Microbiology Team) and through a series of further email enquiries, Vincenzo arrived in early September 2012 for a four month internship at AgResearch in Palmerston North. Vincenzo’s interest in the GHG emissions and methane mitigation research areas, the involvement of Catholic University of Piacenza with the RuminOmics programme and the AgResearch capabilities in this area made an internship at the Grasslands campus in Palmerston North a good choice. Vincenzo’s internship has enabled him to assist with a number of different on-going studies. He has been involved in a study involving the measurement of ruminant methane emission studies using SF6, fixing yokes on animal and the background behind this technique.

Vincenzo has also assisted with respiration chamber studies to determine effective combination/sequences of methanogenesis inhibitors to examine the effect of increased hydrogen concentration on production parameters. The SF6 and chamber methane measurement methods that will be assessed for further studies at the Catholic University of Piacenza upon Vincenzo’s return in early 2013.

Vincenzo outside the New Zealand Ruminant Methane Measurement Centre, Palmerston North, NZ0

Vincenzo obtained his Bachelors Degree in Agricultural Sciences and Technologies from the Catholic University of Piacenza, Italy in 2011. His interests in animal nutrition stem from his final year thesis where he undertook a project entitled ‘Changes in ruminal fermentation of corn grain during maturation’. Vincenzo has continued at the Catholic University of Piacenza and is currently studying for his Masters in Animal Sciences. To learn more about the RuminOmics programme, visit www.ruminomics.eu/ (• Adrian Cookson, AgResearch)

The RMG Network website is now live – you can find it at www.rmgnetwork.org.nz

Follow us on www.facebook.com/RumenMicrobialGenomicsNetwork

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Hungate 1000 Kicks Off The first 51 selected bacterial strains for the Hungate 1000 project were dispatched to the US Department of Energy’s Joint Genome Institute (JGI) in October. Genomic DNA was prepared from these strains originate from the AgResearch culture colleaction that include taxonomically novel isolates, both high and low G+C strains, and a group of Butyrivibrio strains that fall into several different, albeit related, taxonomic groups. Annotated draft sequence data is expected from mid-February 2013 and will be made available to RMG Network participants soon thereafter. Further work is on-going to isolate genomic DNA from a second set of cultures that will be submitted to JGI in early 2013. Further updates on this second set of genomic DNA preparations will be made available once they have passed quality control and have been accepted by the JGI.

The Hungate 1000 project is now ready to invite our international participants to nominate cultures they would like to obtain sequence information for under this RMG Network initiative. Many participants have already been contacted by Dr Bill Kelly, (Project Leader), and Dr Sinead Leahy, (Communications Co-ordinator), to gauge interest, and request information regarding cultures that can be contributed. They will work with participants to ensure cultures are prepared according to the Hungate 1000 submission protocols.

The AgResearch Rumen Microbiology Team here will be co-ordinating the culturing and genomic DNA isolation for the Hungate 1000 project using the protocols for DNA isolation that JGI have found to be successful for a range of different bacterial groups.

The Hungate 1000 website, www.hungate1000.org.nz, is currently under construction and will be populated with updates and information in the coming months. In the first instance links will be provided to rumen microbial genome sequences that are already available. For further enquiries regarding the Hungate 1000 project contact Bill (bill.kelly@agresearch.co.nz) or Sinead (sinead.leahy@agresearch.co.nz) or through hungate1000@agresearch.co.nz (• Adrian Cookson, AgResearch).

NK4A124, most closely related to Treponema bryantii, is amongst the first Hungate 1000 strains to be genome sequenced by JGI

2013 Congress on Gastrointestinal Function, Chicago, USA

The 2013 CGIF (15th-17th April 2013) will maintain a tradition established in 1951 to provide academic and industry scientists a forum to present the latest advances in our understanding of gastrointestinal microbiology, (immuno)physiology and nutritional sciences.

The topics presented at the Congress include studies with livestock and poultry species for food production and biomedical research, as well as clinical and nutritional studies relevant to improving human health and well being. Research that addresses the environmental and public health impacts from gastrointestinal microbiology (e.g. the ecology of antibiotic resistance, food safety, and waste management) is also welcome.

The 2013 Congress will be held at the Gleacher Center, located close to Chicago's "Magnificent Mile“. The abstract submissions will be used by the Congress' scientific committee to select oral presentations for the 4 sessions; with dedicated space for poster presentation throughout the Congress and a formal poster session also included in the schedule. Similar to the 2011 Congress, we are in negotiations for the abstracts and plenary presentations to be published in a prominent scientific journal.

Further details on the conference can be obtained from http://congressgastrofunction.org/. Abstract submission deadline is 24th January 2013. Further details on abstract submission can be obtained from the 2013 CGIF website on http://congressgastrofunction.org/abstract.asp

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Global Research Alliance Senior Scientist (GRASS) Award

Supporting research in Agricultural Greenhouse Gases

The New Zealand Government in support of the goals of the Global Research Alliance is funding senior scientists from Alliance member countries to participate in an exchange programme to enhance collaboration and the building of mutually beneficial research partnerships between New Zealand and other Global Research Alliance countries.

Focus areas

Methane emissions from livestock and livestock wastes Nitrous oxide emissions from livestock wastes Enhancement of pastoral soil carbon sinks Integrated whole farming systems impacts at all scales as they relate to livestock emissions. National inventory development as it relates to livestock emissions

Eligibility

To be eligible, you must: Have a PhD or be a scientist with at least 5 years experience participating in/leading major projects that align to the priorities of LEARN, the Alliance or other relevant national strategies.

Demonstrate impact and leadership in your professional field.

Be able to contribute to scientific research and its application in your home region and the larger Alliance network, based on your networking record.

Work in collaboration with a New Zealand research organisation.

Be resident and normally employed on a permanent contract by a research organisation in an Alliance member country.

Funding

The exchange must be between 6 weeks and 6 months duration.

Up to $30,000 for 6 months (pro rata for less than 6 months) will be provided to recipients to cover actual and reasonable living expenses.

Up to $5,000 will be provided for economy airfares and travel/medical insurance.

Up to $5,000 will be awarded for associated research costs.

For more details refer to the LEARN Website: www.livestockemissions.net or email the New Zealand Agricultural Greenhouse Gas Research Centre: enquiry@nzagrc.org.nz

Contact RMG Network Co-ordinator: Adrian Cookson Email: rmg.network@agresearch.co.nz Website: www.rmgnetwork.org.nz

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