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AgResearch
GRA-A2 Workshop Report
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Global Research Alliance
Rumen Microbial Genomics
Network Workshop Report
May 2011
AgResearch
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Date and location of workshop
25th-26th February 2011
Travelodge Hotel, Palmerston North, New Zealand
Organised by:
AgResearch Limited &
New Zealand Agricultural Greenhouse Gas Research Centre
Funding source
New Zealand Ministry of Agriculture and Forestry, as part of its support for the Global
Research Alliance on Agricultural Greenhouse Gases
Acknowledgements
This report was prepared primarily by Dr Sinead Leahy and Dr Adrian Cookson. Input
has also been provided by Dr Graeme Attwood, Dr Peter Janssen, Dr Bill Kelly, Dr
Christina Moon, Dr Gemma Henderson, Dr Ron Ronimus and Dr Eric Altermann.
Disclaimer
This report has been commissioned by the New Zealand Government to support the
goals and objectives of the Global Research Alliance on Agricultural Greenhouse Gases.
While every effort has been made to ensure the information in this publication is
accurate, the Global Research Alliance does not accept any responsibility or liability for
error of fact, omission, interpretation or opinion that may be present, nor for the
consequences of any decisions based on this information. Any view or opinion
expressed does not necessarily represent the view of the Global Research Alliance.
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Contents Executive summary ........................................................................................................... 5
Introduction ...................................................................................................................... 6
Background ................................................................................................................... 6
Participants ................................................................................................................... 7
Overview of the workshop ............................................................................................. 10
Day 1 ........................................................................................................................... 10
Keynote scientific presentations ............................................................................ 10
Day 2 ........................................................................................................................... 10
Rumen Microbial Genomics Network Session ....................................................... 10
Collaborative Projects Session ................................................................................ 10
Author: Professor Bryan White (USA) .................................................................... 11
Author: Professor Jamie Newbold (UK) .................................................................. 11
Author: Dr Yas Kobayashi (Japan) ........................................................................... 11
Author: Associate Professor Athol Klieve (Australia) ............................................. 11
Author: Dr Silvio Cravero (Argentina) ..................................................................... 12
Author: Dr Alexandre de Menezes (Ireland) .......................................................... 12
Author: Dr Chris McSweeney (Australia) ................................................................ 12
Author: Dr Diego Morgavi (France) ........................................................................ 12
Author: Professor Mark Morrison (Australia) ........................................................ 12
Author: Dr Eddy Rubin (USA) .................................................................................. 12
Author: Professor Tim McAllister (Canada) ............................................................ 13
Author: Dr Bill Kelly (New Zealand) ........................................................................ 13
Author: Professor Greg Cook (New Zealand) ......................................................... 13
Author: Associate Professor Vic Arcus (New Zealand) ........................................... 13
Workshop Minutes ......................................................................................................... 14
Day 1 ........................................................................................................................... 14
Keynote scientific presentations ............................................................................ 14
Day 2 ........................................................................................................................... 14
Rumen Microbial Genomics Network Session ....................................................... 14
Collaborative Projects Session ................................................................................ 15
Action Points and Recommendations ............................................................................ 15
Appendix 1 ...................................................................................................................... 17
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RMG Network “Straw-man” (as sent to workshop participants in advance of the
session) ....................................................................................................................... 17
Rumen Microbial Genomics (RMG) Network ......................................................... 17
Network Benefits .................................................................................................... 17
What the Network would do .................................................................................. 17
Structure ..................................................................................................................... 18
Network Structure and Funding ............................................................................. 18
Network Guidelines .................................................................................................... 18
Network membership ............................................................................................. 18
Data deposition and sharing ................................................................................... 19
Publication guidelines ............................................................................................. 19
Intellectual property protection ............................................................................. 19
Protection/sharing of protocols, tools and algorithms .......................................... 19
Ethical considerations ............................................................................................. 19
Appendix 2 ...................................................................................................................... 20
Summary of questionnaire responses: ....................................................................... 20
Appendix 3 ...................................................................................................................... 22
Author Powerpoint presentations .............................................................................. 22
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Executive summary
The purpose of the Global Research Alliance Rumen Microbial Genomics Network
workshop was to initiate support for the establishment of a global collaborative
network of researchers, working with a common set of principles and guidelines, to
underpin the development of methane mitigation technologies using a microbial
genomics approach.
The two-day workshop involved participants from New Zealand (15), Australia (3),
Europe (3), North America (3), South America (1) and Japan (1). All the overseas
participants and four from New Zealand gave presentations on their current (and
planned) Rumen Microbial Genomics research programmes.
There was universal acceptance of a proposed ‘straw-man’ structure for a Global
Research Alliance-Rumen Microbial Genomics (Alliance -RMG) Network and agreement
and enthusiasm from all the participants that the Alliance-RMG Network should be led
and co-ordinated by AgResearch, New Zealand. Refer to Appendix 1 for the ‘straw-
man’.
Three collaborative projects (Hungate 1000 – a reference microbial genome collection;
deep sequencing of rumen microbial communities from high/low methane emitting
ruminants; functional microbial genomics) stemming from a series of break-out
sessions were endorsed by the workshop participants as being projects which would
generate data that would have far-reaching positive impacts on the ability of the
international Rumen Microbial Genomics research community to develop methane
mitigation technologies.
Workshop participants endorsed the organisers lead role in efforts to secure funding
opportunities both for the formation of the Alliance -RMG Network, and for the three
collaborative research programmes.
A white paper will be developed that identifies a way forward for the RMG Network
and details the priority collaborative projects.
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Introduction
Background
Enteric methane (CH4) emissions from livestock constitute 32% of New Zealand’s
greenhouse gas (GHG) emissions. Consequently, livestock have been targeted as a
major focus area for research into potential GHG mitigation methods in New Zealand
and as an area where New Zealand science can make a major contribution to the
Global Research Alliance (Alliance). New Zealand has a high international profile in
livestock-related GHG research through its efforts to develop a comprehensive
national agricultural GHG inventory and its ground-breaking research programme to
develop targets for GHG mitigation based on both microbial and animal genomic
information.
Methane production arises as a result of microbial activity within the rumen and there
are a number of on-going Rumen Microbial Genomics and Rumen Microbial Ecology
programmes led by AgResearch which aim to further our understanding of the
complex rumen microbial ecosystem and to deliver new tools for methane mitigation.
Consequently AgResearch has the largest concentration of scientists in the world in
this area with significant capabilities in both the growth of rumen micro-organisms and
microbial genomics capabilities. Despite local strengths, the complexity of the rumen
microbial community means that more rapid progress can be made in developing
mitigation technologies if an internationally co-ordinated and collaborative approach is
taken to improving our understanding of rumen microbial ecology. The development
of a co-ordinated international strategy with a global approach, based on Rumen
Microbial Genomics (RMG) applications, involving engagement with other groups
having common interests, will facilitate better use of existing resources. It will also
help build critical mass into research projects so that novel strategies which can be
utilised to mitigate methane production, have a greater prospect of being developed.
Under the auspices of the Alliance, a network workshop, organised by AgResearch, was
therefore initiated to bring the main researchers and organisations involved in
worldwide efforts to mitigate methane using an RMG approach.
The purpose of the network workshop was to gain support for the establishment of a
global collaborative network of researchers with a common set of principles and
guidelines to underpin the development of worldwide methane mitigation and rumen
adaptation technologies through a microbial genomics approach.
The goals of the workshop were to:
(i) determine whether there was support for a Rumen Microbial Genomics (RMG)
Network from workshop participants
(ii) if support was forthcoming, achieve consensus on how a RMG Network would
be structured and
(iii) identification of projects for future collaborative research.
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Participants
Invitations to attend the workshop were sent to key scientists working in rumen
microbial genomics, with some consideration given to achieving an even geographic
spread of participants across countries. A further opportunity to nominate
participants after the meeting was extended to all member countries of the Alliance.
In total, 21 rumen microbial scientists from nine countries participated in the two-day
workshop.
Prior to the workshop all international participants (Table 1) were required to fill out a
pre-workshop questionnaire (see Appendix 2) which sought feedback on whether
there was a need for an RMG Network, and if so, what its function, scope and structure
should be.
The questionnaire results were used by the organizing committee to construct a
‘straw-man’ design of an RMG Network (see Appendix 1).
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Table 1. Participants of the Global Research Alliance-Rumen Microbial Genomics Network Workshop.
Local Organising Committee Specialism Institute/University
Dr Graeme Attwood* Rumen Microbial Genomics AgResearch Ltd.
Dr Bill Kelly* Rumen Microbial Genomics AgResearch Ltd.
Dr Eric Altermann# Rumen Microbial Genomics AgResearch Ltd.
Dr Christina Moon Rumen Microbial Genomics AgResearch Ltd.
Ms Kate Parlane Workshop organiser New Zealand Agricultural Greenhouse Gases Research Centre.
Dr Sinead Leahy Rumen Microbial Genomics AgResearch Ltd.
Workshop Participants
Associate Professor Vic Arcus* Protein Structure & Function University of Waikato, New Zealand
Mark Aspin Pastoral Greenhouse Gas Research Consortium, New Zealand
Dr Silvio Cravero* Rumen Microbial Genomics Instituto de Biotecnologia, Instituto Nacional de Tecnologia
Agropecuaria, Argentina
Dr Harry Clark* Novel GHG mitigation strategies & co-
ordinator of NZ GHG inventory
Director, New Zealand Agricultural Greenhouse Gas Research
Centre, New Zealand
Professor Gregory Cook*# Microbial Genomics & Protein Structure
& Function
University of Otago, New Zealand
Dr Adrian Cookson# Rumen Microbial Ecology AgResearch Ltd., New Zealand
Dr Alexandre de Menezes * Rumen Microbial Metagenomics Teagasc, Irish Agriculture and Food Development Authority &
University College Dublin, Ireland
Dr Gemma Henderson Rumen Microbial Ecology AgResearch Ltd., New Zealand
Dr Peter Janssen* Rumen Microbial Ecology AgResearch Ltd., New Zealand
Associate Professor Athol Klieve* Rumen Nutrition & Microbial Ecology University of Queensland, Australia
Professor Yas Kobayashi* Rumen Microbial Ecology University of Hokkaido, Japan
Dr Shaun Lott Protein Structure & Function University of Auckland, New Zealand
Professor Tim McAllister* Rumen Nutrition & Microbial Ecology Agriculture & Agri-Food Canada, Canada
Dr Chris McSweeney* Rumen Microbial Ecology CSIRO Livestock Industries, Australia
Dr Diego Morgavi* Rumen Microbial Ecology Institute National de la Recherche Agronomique, France
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Professor Mark Morrison* Rumen Microbial Genomics CSIRO Livestock Industries, Australia
Professor Jamie Newbold* Rumen Nutrition & Microbial Ecology Institute of Biological, Environmental and Rural Sciences,
Aberystwyth University, Wales
Dr Ron Ronimus Rumen Microbial Ecology and Protein
Structure & Function
AgResearch Ltd., New Zealand
Dr Eddy Rubin* Rumen Microbial Metagenomics Department of Energy, Joint Genome Institute, USA
Dr Gerald Rys Policy & Strategy Development Ministry of Agriculture and Forestry, New Zealand
Professor Bryan White* Rumen Microbial Genomics Institute for Genomic Biology, University of Illinois, USA
* keynote speaker
# session facilitator
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Overview of the workshop
Day 1
Keynote scientific presentations Strong collaborative research is a prerequisite in the development of universal
methane mitigation and rumen adaptation technologies. Therefore Day One involved
scientific presentations by fifteen of the workshop participants (Appendix 4) which
provided a view of the current state of international rumen microbial genomic
research. Key strengths, synergies and possible gaps in our present knowledge were
identified from the presentations as a whole, which facilitated the identification of
clear areas for collaboration within a potential Network structure. The information in
these presentations laid the foundation for Day Two discussions on the formation and
optimum structure of the RMG Network and the scoping of future ground breaking
collaborative research projects that the establishment of the RMG network would
facilitate.
Day 2
Rumen Microbial Genomics Network Session The workshop questionnaire results and the ‘straw-man’ design were presented as a
basis for discussion. This was followed by presentations by other workshop
participants who have had experience with international collaborative networks. An
open forum followed, resulting in consensus that the formation of a network would be
highly beneficial to the rumen microbial research community and would promote rapid
progress in understanding the research necessary for development of universal
methane mitigation and rumen adaptation technologies.
Collaborative Projects Session
The session began with a presentation of potential collaborative projects that had
been agreed on by the workshop organising committee as a way to initiate dialogue.
An open discussion followed and the four topics below were selected for further
analysis by break-out groups.
1. Reference microbial genomes (Hungate 1000).
2. Deep sequencing of rumen metagenomes.
3. Functional genomics.
4. Tools and resources for exploiting existing datasets.
Each break-out group was asked to evaluate the four projects according to the
following criteria:
• Aim/Strategy – linked to methane mitigation/hydrogen producers/fibre
utilization
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• Identify collaborators
• Discuss existing programmes
• Identify resources required
• Funding opportunities
• Gap issues
Each break-out group nominated a leader who presented their findings and an open
discussion followed which resulted in three key potential collaborative research areas
being identified by the workshop participants.
Presentations
Author: Professor Bryan White (USA) Title: Systems biology approaches to analysing the rumen
Summary: Presentation discussed the following research areas – metagenomics of
cows fed different diets and of different microbial fractions, genome sequencing of
rumen Ruminococcus species, cellulosome systems of rumen Ruminococcus species,
viromics and CRISPR’s of the rumen environment and investigation of gnotobiotic
lambs using metagenomics, RNAseq and metabolomics.
Author: Professor Jamie Newbold (UK) Title: Manipulating rumen fermentation
Summary: Presentation discussed the manipulation of the rumen microbiome using
dietary yeast. In terms of the environment the key message was related to
understanding how the rumen microbiome interacts with its substrate. Work on
colonising microbes and high sugar grasses with respect to sheep farming was
presented.
Author: Dr Yas Kobayashi (Japan) Title: Methane reduction from ruminants by feeding cashew nut shell liquid containing
rare phenolic compounds
Summary: Presentation discussed the use of a cashew by-product for the reduction of
methane. Results were shown in-vitro and both in sheep and cattle. Bacterial and
archaeal populations were examined and were found to have changed significantly.
Author: Associate Professor Athol Klieve (Australia) Title: Rumen microbial genomics; University of Queensland and Queensland
Government perspective
Summary: Presentation highlighted the work, both past and present of the University
of Queensland and Queensland Government with respect to the area of microbial
genomics. The future work of the Queensland Enteric Methane Hub was also
discussed.
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Author: Dr Silvio Cravero (Argentina) Title: Gene prospecting in ruminal bacteria: looking for molecules with
biotechnological applications
Summary: This presentation described the genome sequencing of a CLA-producing
Butyrivibrio strain from the rumen, and Butyrivibrio and Pseudobutyrivibrio strains
isolated from the C1 compartment (forestomach equivalent to the rumen) of farmed
llamas. Research on characterizing the microbiota from the C1 compartment of wild
llamas and vicunas was also described.
Author: Dr Alexandre de Menezes (Ireland) Title: Rumen methane mitigation in Ireland: current research in microbial ecology and
genomics
Summary: Research was presented on rumen microbial genomic activities occurring in
Ireland. Microbial community analysis was used to study the bacterial and
methanogen communities in cows with either high or low feed efficiency, the addition
of dietary oils and different pasture versus total mixed rations diets.
Author: Dr Chris McSweeney (Australia) Title: Recent insights into hydrogenotrophic populations in the rumen
Summary: Presentation discussed hydrogenotrophic alternatives to methanogenesis
with respect to reductive acetogenesis and rumen microbial responses to methane
inhibition including elevated hydrogen concentrations.
Author: Dr Diego Morgavi (France) Title: Rumen microbiota & methane production
Summary: Presentation gave a background to livestock and methane emissions in
France. Research was presented regarding methane-methanogen relationships
including diet, inhibitory microbial compounds and microbial manipulation. The
presentation also discussed metagenomics and the construction of a reference
catalogue of the bovine rumen metagenome.
Author: Professor Mark Morrison (Australia) Title: Differences Down under: Methane, Macropods, and Metagenomics
Summary: Presentation discussed metagenomics as a means to understand structure-
function analyses of gut microbiomes. Research regarding the tammar wallaby was
presented including work surrounding its archaeal population. Metagenomic analyses
of feed utilization and hydrogen balance in Australian livestock for lower methane
emissions was also discussed.
Author: Dr Eddy Rubin (USA) Title: Metagenomic discovery of biomass-degrading genes and genomes from cow
rumen
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Summary: Presentation highlighted the Joint Genome Institute’s research in the area
of genomics and cellulosic biofuels. Work was presented showcasing the cow rumen as
a highly efficient system at biomass deconstruction. Deep sequencing technique was
presented as a means to understand the rumen environment, improve the genomics
of uncultured organisms and enhance the identification of useful cellulolytic rumen
enzymes for the biofuel industry. The presentation’s message was that trawling deep
metagenomic data is a successful strategy to add to the diversity of enzymes with
desired activities.
Author: Professor Tim McAllister (Canada) Title: Functional genomics: Discovering novel bio-catalysts from gastrointestinal
microbiomes
Summary: Presentation discussed the identification of novel lignocellulolytic enzymes
from rumen fungi and their enzyme characterizations. Analysis was presented on the
musk ox rumen microbiome.
Author: Dr Bill Kelly (New Zealand) Title: “To pastures new” AgResearch’s Rumen Microbial Genomics programme
Summary: Presentation highlighted the research of the AgResearch Rumen Microbial
Genomics Team. It showcased the rumen methanogen genomics programme and the
work of the NERF (New Economy Research Fund) isolation, genomics and
metagenomics programmes.
Author: Professor Greg Cook (New Zealand) Title: Methanogen ATP synthases as targets to control methane production in the
rumen
Summary: This presentation focused on the A1A0 ATP synthase from M. ruminantium
as a potential target for chemogenomic or vaccine-based methane mitigation
strategies.
Author: Associate Professor Vic Arcus (New Zealand) Title: Mining enzymes from rumen microbes
Summary: This presentation described the work done on the cloning, expression,
biochemical analysis and structural determination of carbohydrate-degrading enzymes
identified from the genome of B. proteoclasticus B316. Four enzymes have been
studied in detail: Est1E (feruloyl esterase), Est2A (acetyl esterase), Xsa43E
(arabinosidase) and Cel5C (a multifunctional enzyme with activity against cellulose and
arabinoxylan).
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Workshop Minutes
Day 1
Keynote scientific presentations
• Internationally, there are few groups as comprehensive in coverage as the NZ
ruminant microbiology group which currently has funding for ecology,
genomes, function etc. NZ has both a comprehensive and co-ordinated
programme compared with other international rumen microbial genomic
research groups.
• A significant group of researchers are involved in low depth metagenomics
work. The Joint Genome Institute’s recent metagenomics study1 using deep
sequencing of the rumen microbiome is a significant development in the rumen
metagenomics field; low depth metagenomic work is only scratching the
surface of the diversity and density of microbes present in the rumen.
• A need was recognized to study animals on different diets to obtain a global
perspective on the diversity of methanogen colonisation of ruminant animals.
• There is a clear need for reference rumen microbial genomes. This point was
re-iterated many times by several researchers. The metagenomic work cannot
be sensibly or effectively interpreted without a reference genome dataset.
• It is apparent that although a variety of research programmes are being
undertaken on a variety of worldwide ruminant species, there is no global co-
ordination and many gaps remain within current research efforts.
Day 2
Rumen Microbial Genomics Network Session
• With the largest concentration of rumen microbial scientists in the world, New
Zealand was nominated to lead the RMG network.
• Membership of the Network will be open to all/any individual, country or
organisation that is can contribute in some way.
• Committed and effective leadership was recognized as being instrumental in
the success of large, collaborative networks.
• There must be clear goals with quality science being the driver.
• There must be on-going commitment to the network and the scientific benefits
it brings - it must be more than a funding opportunity.
1 Hess, M., Sczyrba, A., Egan, R., Kim, T.W., Chokhawala, H., Schroth, G., Luo, S., Clark, D.S., Chen, F.,
Zhang, T., Mackie, R.I., Pennacchio, L.A., Tringe, S.G., Visel, A., Woyke, T., Wang, Z. and Rubin E.M. 2011.
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331: 463-
467.
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• Inclusiveness: it is apparent that each country/group has slightly different
ruminant production systems which complement the research of each group,
thus largely avoiding direct duplication.
• Data generated within the network will be a large resource that will
significantly move rumen microbiology science forward.
• Regular communication will be critical to the success of the network. The work
of the network must be transparent to all members.
• IP discussions should be held upfront. It is important to be proactive with this
issue.
Collaborative Projects Session
The following three areas were seen as being suitable as collaborative projects among
the network members. The fourth area, ‘Tools and resources for exploiting current
datasets’ was discarded as it was agreed that this area would be developed in parallel
with data emerging from all the other three prospective projects. The following bullet
points are only a summary of the discussions that occurred and a subsequent ‘white
paper’ will cover the rationale behind the three chosen areas in more detail.
1. Reference microbial genomes (Hungate 1000).
2. Deep sequencing of rumen metagenomes.
3. Functional genomics.
This part of the meeting was followed by a discussion led by Eddy Rubin, JGI Director
where he described how the JGI is enthusiastic in supporting genome and
metagenome sequencing projects which have a clearly defined rationale with
international impact. There is an excellent fit between the JGI mandate and the
methane mitigation research area that the Network targets. JGI have considerable
expertise in large-scale genome and metagenome sequencing projects and the analysis
of large sequencing data sets. Eddy Rubin expressed a willingness to work with our
network members, and to assist with the development and submission of project
proposals to the JGI. The JGI, as a Network partner, can generate and provide (through
‘in kind’/co-funding) the initial analysis of hundreds of gigabases of sequence
information which can be used by Network members to assist in our understanding of
rumen microbial metabolism and interactions.
Since the workshop finished, the JGI has released their 2011 call for their Community
Sequencing Program (CSP). This year “Microbial emission and capture of greenhouse
gases” has been identified as an area of special interest. This provides an excellent
opportunity for the Network to submit collaborative proposals which fit under the
Alliance-RMG Network principles and guidelines.
Action Points and Recommendations
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• AgResearch scientists, led by Dr Adrian Cookson, Dr Graeme Attwood and Dr
Peter Janssen will identify funding opportunities for the initial and on-going co-
ordination activities of the RMG Working Group/Network.
• AgResearch scientists, Cookson, Attwood and Janssen shall initially take the
lead in the organisation and co-ordination of the Alliance -RMG network and its
preliminary activities. Thereafter leadership will be expanded to an
international Working Group encompassing other international members.
• In order to publicise the Alliance -RMG network, AgResearch scientists will
identify funding opportunities to set up a RMG Network webpage within the
Alliance website (http://globalresearchalliance.org) outlining its aim of
developing methane mitigation and rumen adaptation technologies using a
microbial genomics approach. Regular contact through newsletters, email
updates and an annual workshop will be used to keep the network members
informed. Transparency was identified as an important attribute for the
network.
• The identified collaborative projects will be developed by AgResearch and
Network members and will be open to all Network members for critique and
input. AgResearch will take the lead in identifying funding sources for these
projects from within the RMG network members.
• A summary document from the Alliance -RMG Workshop will be prepared.
• AgResearch representative to attend the JGI User group meeting in March to
discuss the JGI’s support of the sequencing components of the identified
network projects.
• Co-ordinated planning of future work with the Alliance -A5 (Survey of rumen
microbial diversity) funded programme.
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Appendix 1
RMG Network “Straw-man” (as sent to workshop participants in advance of the session)
Rumen Microbial Genomics (RMG) Network
The RMG network will represent a global collaborative network of researchers with a
common set of principles and guidelines in rumen microbial genomics to underpin the
development of worldwide CH4 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 (or of parts 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”.
Network Benefits
• Enhance communication and collaboration between research groups
• Improve ability to attract funding with international, integrated studies
• Streamline future rumen microbial genomics research i.e. prevention of
duplication
• Raise public awareness of present and future research activities
• Sharing of knowledge and technologies i.e. protocols, cultures, primer sets,
sequence information, analysis tools
• Training –exchange of students, technicians, staff, particularly with developing
countries
• Improve scientific robustness of current research, enhanced stature and
credibility of rumen microbiology research
• Worldwide perspective of rumen microbial genomics
What the Network would do
• Foster collaborations
• Share cultures
• Sequence reference genomes
• Establish a central data repository for the rumen microbiome
• Pan-genome analyses
• Metagenomic/metatranscriptomic analyses of the rumen microbiome
• Facilitate collaborative funding applications
• Publish findings from collaborative projects
• Enhance stature and credibility of rumen microbiology research
• Provide training opportunities for developing countries
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• Annual meetings, linked with major gut microbiology conferences, to map out
collaborative research and discuss progress in the field of rumen microbial
genomics
• Exchange staff and knowledge/technologies
• Establish standardised guidelines/protocols for data acquisition, analysis and
storage
• Develop a web portal to display and promote the research activities of its
members
Structure
Network Structure and Funding
The Network should be inclusive and open to membership for all that are willing to
effectively contribute in some way. Its structure would be modelled on the
international human microbiome projects (http://commonfund.nih.gov/hmp/).
The organisational structure for the network could take various forms however, we
propose the network would initially be established, co-ordinated and maintained by
AgResearch.
At a minimum, the Network will be a forum for discussion of what members are
working on. In this case the operational rules would be relatively relaxed and members
would make independent contact with each other outside of the network if they wish
to share data and other information. The preferred status of the Network would be a
central database for members to share genomic and metagenomic information and
techniques directly with the other members. Accordingly, there would be a need for
firm guidelines about how that information could be used. The comments below
contemplate a central database model (extracts taken from the HMP websites) and
raise some areas of debate that may impinge on the functioning of the network.
Network Guidelines
Network membership
Two membership types are envisioned: full members and associate members. Full
members would be eligible to access all data, protocols and tools without any
restrictions. Associate members would access only part of the data shared in the
Network relevant to their respective projects. Both types of membership would come
with a set of obligations and privileges that would be decided upon by the Network.
The Network would be open at all times to new full and associate members provided
they carry out research at the expected high standard and contribute materially to the
Network. Exceptions may be granted on a case-by-case basis depending on the merits
of the applicant (e.g. supporting science development relevant to the GRA mission in
developing countries).
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Data deposition and sharing
Data will be deposited in a format agreed upon in the Network. Depositors agree to
verify data (for technical accuracy) and maintain/adhere to high scientific standards for
protocols and algorithms. Data and tools will be freely accessible exclusively within the
network. Unpublished data cannot be released outside the Network or published
without the consent of the original contributor.
Publication guidelines
It is expected that users of the pre-publication data will act responsibly to recognize
the scientific contribution of the RMG Network data producers by following normal
standards of scientific etiquette and fair use of unpublished data. Data can be
published at any time by the original contributors.
Intellectual property protection
General consideration needs to be given to who owns the information contributed to
the Network. Consideration also needs to be given to the entitlement to any future
benefit, revenue or otherwise, from information on the Network. For example, who
owns, or has rights to use of, improvements to other members’ IP? A wider discussion
around the rules relating to confidentiality needs to be held, and will include
consideration of what members will be permitted to do with the information on the
Network.
Protection/sharing of protocols, tools and algorithms
Verified in vitro/in vivo protocols and guidelines will be deposited into the network
and can be accessed and utilised freely. Data and information created from these
protocols implies authorship/acknowledgment/reference of the original
contributors/network in subsequent publications, according to normal standards of
scientific etiquette. Careful consideration needs to be given to the risks relating to
accuracy, storage and security of information.
Ethical considerations
Participating members would be expected to operate under the appropriate scientific
and animal ethics guidelines relevant to their own countries.
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Appendix 2
Summary of questionnaire responses:
Q1. Do you think there is a need for an International Rumen Microbial Genomics
Network?
• It will prevent duplication of sequencing effort, particularly of specific bacterial
genomes.
• It will lead to a standardisation of research techniques, extend the lines of
communication and allow for worldwide perspectives and broad ecological
studies to be undertaken.
• It will advance science and improve knowledge.
• Encourage the sharing of information.
• It will be mutually beneficial for a number of research groups.
• It will provide more benefits than relying on informal and personal contacts.
Q2. What do you believe the function and scope of the network should be?
• To generate comprehensive reference genome and metagenome sequence
libraries for relevant microbial communities including the bovine rumen,
hindgut, and production environment.
• Provide access to data that will serve as the foundation for subsequent
translational research.
• Sharing information about the suite of molecular tools that are presently
available for defining and characterizing the nature and function of rumen
microbial communities.
• Sharing technological solutions/advances to align approaches.
• To avoid duplication
• Promote collaboration.
• Lobbying for funding to promote integrated studies.
• Enable inter-agency access to and comparisons of datasets.
• Serve as a forum for the exchange of technical expertise (technical workshops).
• Enable the uploading of genome data for use as scaffolding by others with
similar but different genome sequencing projects.
• To exchange protocols, to optimize techniques, to standardize methods, to
exchange material, to connect people
Q3. What do you think is an appropriate structure for such a network?
• A small-sized network may be appropriate at first. Once targets are fixed, the
network can grow with scientists from developing country.
• Should be modelled on similar, existing international networks.
• A virtual group or network supported through a web-based platform.
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• Good management/leadership and strong support from the Alliance.
• A structure that included government representatives from member countries
may ensure greater engagement and new funding opportunities
• There should be a board that looks for funding opportunities.
• Funding from member countries would likely initiate a working group of
participants who are actively involved in a shared outcome.
• A process needs to be established to identify all participants and research areas
within countries.
• Needs to allow for wide scale involvement.
• A structure similar to that of the NIH HMP (http://nihroadmap.nih.gov/hmp/)
and Metasted, a working public international consortium for the complete
sequencing of the metagenome of a reference soil (http://www.metasted.ec-
lyon.fr/).
• Results should be disseminated in accord with the NHGRI Policy for the Release
of Large-Scale Genomic DNA Sequence Data
• Provision of a good road map based on basic genomic science.
Q4. What would you want to get out of such a network?
• Linkages with regard to gene function and variability.
• Collaboration and access to leaders in this field, techniques, data and samples.
• Satisfaction to see this research area continue and make significant
contributions to society.
• The ability to obtain/exchange data and information, and have approval to use
and apply this information to projects.
• Training in different techniques.
• Opportunities to leverage international funding.
• The possibility to standardize quantitative techniques
Q5. What would you be willing to contribute to such a network?
• Sequencing and analysis.
• Our experience in microbiology and molecular biology techniques.
• We can offer people to annotate genomes.
• Host meetings.
• Contribute data where appropriate.
• Enter into collaborative and cooperative ventures with other participants.
• Exchange strains of microbes and contribute to a database of strains that are
available to the network
• Providing technical information.
• Personal time and effort
“We must come to the realization that with the amount of information generated by
metagenomic and metatranscriptomic approaches that none of us will live long
enough to interpret it all. Thus sharing of such information will maximize returns on
research investment and accelerate the rate of advancements in the field”.
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Appendix 3
Author Powerpoint presentations
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