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AgResearch

GRA-A2 Workshop Report

1

Global Research Alliance

Rumen Microbial Genomics

Network Workshop Report

May 2011

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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

global research alliance rumen microbial genomics network ... · gra-a2 workshop report 8 table 1....

Documents