Unlocking the Microbiome Launch Event Summary
On 15 November 2017, the Microbiology Society launched its science policy report ‘Unlocking the Microbiome’, at an event held at The Royal Society in London. The event connected over 60 representatives from academia, industry, research funding and government to discuss opportunities and challenges of rapidly emerging field of microbiome science for health, agriculture and food, environment and biotechnology. The event was chaired by Dr Peter Cotgreave, Chief Executive at the Microbiology Society.
Professor Julian Marchesi (Professor of Human Microbiome Research, University of Cardiff, and Professor of Clinical Microbiome Research, Imperial College London), Chair of the Society’s Microbiome Expert Working Group, provided the keynote address. He outlined opportunities for microbiome research, including for human health, sustainable agriculture and biotechnology, and recommendations from the Society’s report to progress microbiome science to deliver on these opportunities. Professor Marchesi emphasised how interdisciplinary working and new tools were enabling scientists to better explore and exploit communities of microbes in their environments as whole systems. Professor Marchesi noted the document was extremely timely given the excitement around microbiome science, but would also help to address the challenge of hype around this science.
Dr Cotgreave chaired a multidisciplinary panel discussion about the report and the issues it raises with Professor Marchesi, Professor Jim Prosser (Chair in Environmental Microbiology, University of Aberdeen), Dr Fiona Brennan (Research Officer, Soil and Environmental Microbiology, Teagasc), Dr Rob Finn (Team Leader, Sequence Families, European Bioinformatics Institute – EMBL-EBI) and Dr Lena Ciric (Senior Lecturer, Department of Civil, Environmental and Geomatic Engineering, UCL).
Professor Prosser highlighted that while new techniques and initiatives to understand microbiomes were exciting, caution was needed; a key scientific challenge and need is moving the focus from descriptive and correlation-based microbiome studies to mechanistic, hypothesis-driven research, something that would require a change in how microbial ecology was being done.
Dr Ciric highlighted how microbiome research in the context of the built environment and engineering was opening up opportunities to monitor and build more healthy environments, for example reducing transmission of disease in hospitals, through better design and cleaning of surfaces and air quality. Dr Ciric noted that she already worked with infectious control specialists in hospitals, although a challenge is ensuring scientific guidance on hospital design is correctly communicated and implemented at the design stage.
Dr Finn discussed data and bioinformatics challenges and opportunities for microbiome science, noting that the TARA Oceans Project has generated sequence data equivalent to 135 Human Genome Projects, and that EBI’s databases held 200 billion annotations from microbiome research. He also highlighted how microbiome data analysis encompassed a broad range of expertise, including microbiologists, bioinformaticians and software engineers, and that dialogue between these groups was improving to enable provision of required data services. A key challenge is making use of all the metagenomic sequence data being generated from microbiomes. Microbial reference genomes, which are used to assemble and annotate the functions of metagenomic data, are biased towards the relatively small number of culturable microbes, meaning much data can't be effectively analysed.
Dr Brennan noted that there was interest from the farming community in soil and plant microbiology, including the potential to reduce fertiliser and pesticides inputs and sustainable intensification. A challenge is that current knowledge of plant and soil microbiomes is often insufficient to meet interest from the farming sector in practical applications. Agricultural microbiome systems are also large and complex so understanding enough of these systems to appropriately inform interventions is also difficult.
The panel and audience discussed a range of other issues, including:
- The need to improve standards for data collection and analysis. Dr Finn highlighted that the bioinformatics community had a key role to play in driving up standards and were proactively trying to do this.
- Needs to facilitate a shift from association to causation when studying links between diseases or environmental conditions and the microbiome, such as to enable longitudinal studies. Professor Marchesi suggested that while we ideally want to identify causation and mechanisms, in some cases very strong association data between the microbiome and disease may be enough to support microbiome-based interventions such as Faecal Microbiota Transplantation, although investigating data other than genomics, including metabolites was important.
Dr Brennan added that in an agricultural and environmental context comprehensive and longitudinal studies were important to understand complex interactions between microbiomes, plant genetics and environmental factors, as well as different temporal and global points. An audience members emphasised that environmental longitudinal studies were important, but alongside cross-sectional studies.
In terms of the key bottlenecks limiting progress in microbiome research:
- Professor Marchesi called for dedicated interdisciplinary funding in the UK to capture microbiome research that might fall through the gaps of current programmes, as well as building capacity to annotate sequence data so that data and money used to generate it was not being wasted. Related to this, participants highlighted the need to build infrastructure, including culture collections and microbial taxonomy to progress microbiome research.
- Capturing the interest and investment from industry and other stakeholders to work with the scientific community to help development and translation of microbiome research. A funder representative noted that the UK had a well-established track record of developing emerging areas of science, and that it may be beneficial for the academic community and industry to work together to develop a roadmap for progressing microbiome research and innovation. The need to be careful about overhyping microbiome research, whilst pointing to tangible opportunities was also noted.
Participants also discussed how collaboration between learned societies and research funders could collaborate to help facilitate interdisciplinary microbiome research skills. The inclusion of microbiome science on degree courses was also noted as a potential route to ensure future skills capacity.
Advancing Microbiome Science: A BBSRC Perspective
Peter Burlinson (Strategy and Policy Manager at the Biotechnology and Biological Sciences Research Council [BBSRC]) outlined BBSRC’s priorities and investments in microbiome research, and work investigating how they could add value across the research base, including collaborative activities with other funders and exploring industrial interest. Peter spoke about a recent review of BBSRC’s microbiome activities, noting that this topic cut across their portfolio, including responsive and strategic priorities relating to food nutrition, health, and agriculture and food security. Peter highlighted that facilitating interdisciplinary partnerships, and exploiting and expanding new ways of working would be important, noting BBSRC database funding support and the BBSRC-supported ComMet metagenomics community as existing positive examples. A BBSRC responsive mode priority on Integrative Microbiome Research promoting building fundamental knowledge, and future work looking at ‘T-shaped skills’ and how BBSRC could help bring the community together to build capability were highlighted.
UK Plant Microbiome Initiative
Dr Matthew Ryan (Research Leader, Biological Resources, CABI) and Professor Penny Hirsch (Research Scientist, Rothamsted Research) introduced the UK Plant Microbiome Initiative. The objective of the initiative is: “Developing an infrastructure to unlock the potential of the Plant Microbiome, placing the UK at the forefront of research, facilitation and policy, through the establishment of a Secretariat to coordinate and foster collaboration by bringing together academics, industry and other stakeholders through an ‘open innovation approach’”. Issues identified by the initiative, with which they would like to engage, include: improving the agri-tech innovation pipeline; promoting greener and sustainable agri-tech solutions; addressing legislation and regulatory issues; promoting a multidisciplinary approach; promoting support for infrastructure so that it is less fragmented; and addressing resource provision by improving capacity from Biological Resources Centres and UK National Culture Collections to underpin microbiome research and development.
The Microbiome – Social Science Perspectives
Dr Beth Greenhough (Associate Professor of Human Geography) and Dr Carmen McLeod (Postdoctoral Researcher) discussed the work of the Oxford Interdisciplinary Microbiome Project. They highlighted an agenda-setting project to identify key questions social scientists could address about the microbiome, and the Good Germs, Bad Germs Project, a participatory metagenomics project seeking to engage the public with microbiome science. The project aimed to develop a method for making microbes visible and to allow people to design experiments on the domestic microbiome; and to see the effects of this method on how they think about and ensure kitchen hygiene.
Microbiome and their Significance in Animal Production: Diet, Health and Antibiotics
Professor Martin Woodward (Professor of Human Gut Microbiome Studies, University of Reading) highlighted some of the opportunities of microbiome research in relation to animal health and livestock production. Focusing on research in chickens, Professor Woodward outlined opportunities to look at how the microbiome interacted with diet and production, as well as potential to increase sustainability by investigating the use of waste products as sources of food and dietary fibre. Professor Woodward also highlighted that reducing the use of antibiotics was a major challenge, and as well as being an issue as antimicrobial resistance could also be important in terms of the quality of livestock products. Professor Woodward concluded by discussing the potential of focusing on how we can alter microbiomes to improve health and sustainable production in the future, for example the possibility of self-repairing microbiomes using technologies such as genome editing.
The Human Microbiome – Opportunities for Translation
Dr Lindsay Hall (Research Leader, Quadram Institute) discussed opportunities for translating research on the human microbiome, including using improved understanding of how diet and other interventions can modulate the gut microbiome; utilising the microbiome to modulate immune therapies; and mining the microbiome for novel anti-microbials, e.g. bacterocins, which might be usable as alternatives to antibiotics. Dr Hall suggested that translation to address some infections and gut disorders could occur within the next five years, while targeted interventions to modulate the gut microbiome for metabolic syndrome and cancer were likely to be much further off. Increasing understanding of the maternal microbiome and those in an aging population also present opportunities for potential interventions to promote development and life-long health, such as probiotics to promote microbiome development in pre-term babies. Understanding mechanisms and optimising potential interventions are key challenges. Dr Hall noted the importance of multidisciplinary research, including the involvement of ecologists, and the importance of working with policy-makers, regulators and clinicians to promote translation and update clinical practice. A question from the audience highlighted the potential to collect multiple microbiome samples from longitudinal cohorts to facilitate collaborative work.
The full programme for the Unlocking the Microbiome event can be viewed on our website.
Image: The panel discussion at the Unlocking the Microbiome event. Microbiology Society.