Policy: Connecting microbiome research stakeholders

Issue: The Microbiome

09 May 2017 article


Participants at the Society’s Microbiome Research Stakeholder Workshops discussed opportunities and challenges for microbiome research and innovation. 

Microbiomes aren’t just receiving attention from microbiologists. Internationally, governments, funders, regulators and other science policy stakeholders are also increasingly interested in the potential impacts, implications and innovations arising from microbiome research. 

Responding to the need for accessible expert information on this rapidly growing area, the Society’s Microbiome Expert Working Group is producing a science policy report on microbiome research and its relevance to health, agriculture and food, biotechnology and the environment. 

Stakeholder workshops

To inform the policy report and to facilitate interdisciplinary networking and knowledge exchange, the Society organised five workshops in the UK and Ireland. 

Collectively, these multidisciplinary workshops involved around 160 participants, including researchers and representatives from government, research funders, industry, regulators and science communicators.

Discussions highlighted cross-cutting opportunities and challenges for microbiome research relevant to health, agriculture and food, biotechnology and the environment. 


Participants identified wide-ranging current and future opportunities for science, society and the bioeconomy from our growing knowledge of microbiomes, and the development and application of novel tools and biotechnologies to characterise, manage and exploit them. Opportunities included precision microbiome-based diagnostics and biotherapeutics, bioprospecting microbiomes for natural products, and novel tools and technologies for increased agricultural productivity and sustainability or for bioenergy and bioremediation.

The relevance and opportunities of research investigating linkages between different host and environmental microbiomes for a One Health agenda and tackling antimicrobial resistance was also emphasised. 

However, participants were clear about the early-stage nature of much microbiome research and challenges that need to be addressed to deliver on these opportunities. 

Hype and engagement

Hype around microbiomes is a key challenge, but also an opportunity to engage policy-makers and the public about the importance of microbiome research and microbiology generally. Misinformation, poorly-evidenced products and applications, and perceived overselling of research could risk public confidence and safety, and affect future investment in the field. Building the evidence base, clearly communicating research, and public engagement are vital. 

Public and stakeholder engagement was also highlighted as important in relation to social and bioethical considerations, for example, around synthetic biology and implications of research for behaviour, lifestyle and health (e.g. diet, childbirth).

Research and knowledge gaps

The early-stage nature of microbiome research also means that there are knowledge gaps and challenges common to host and environmental research. Participants highlighted the inherent complexity and diversity of microbiomes as a broad challenge for the field, for example, making establishing baselines and biomarkers for ‘healthy’ versus ‘disturbed’ microbiomes challenging. Support for big data and longitudinal studies will be key. 

While studies characterising microbiome diversity are important, the need for more focus on and support for mechanistic and functional research was emphasised, for example, to move from correlation to causation in microbiome disease studies, and facilitate development of robust interventions. 

The importance of increasing focus on the non-bacterial members of microbiomes such as viruses and fungi, as well as undetected microbes, was also highlighted. 

Lack of fundamental and long-term understanding about the consequences of manipulating host and environmental microbiomes was also a concern.

Knowledge integration and capacity building 

Increasing interdisciplinary working was a key theme. Microbiome research is inherently multidisciplinary, requiring improved collaboration and integration of skills and expertise across informatics, microbiology, biochemistry, systems biology and other disciplines, and communication between researchers working on different microbiomes. Better collaboration between academia, industry, regulators and end-users is also needed to facilitate translation.

Skills and expertise gaps in bioinformatics and microbiology, and the need for more integrated training of these and other skills, were also repeatedly raised as issues.

Improving the reproducibility and comparability of studies, and access to samples and datasets was also seen as key. Development and adoption of standards and best practice for sampling, analysis and data will be important; the inadequacy of metadata (e.g. clinical, environmental information), for example, was a commonly cited issue. Development of infrastructures, including microbiome biobanks, accessible and interoperable databases and cloud-computing platforms are also needed.

Making progress

Importantly, participants suggested community-led activities and support from funders, learned societies and other stakeholders that could help, or are already helping, to progress microbiome research and translation. Ideas and examples broadly included improving informatics and technology platforms; targeted funding and training to meet needs; and interdisciplinary networks, meetings and initiatives to strengthen collaborations and focus efforts. 

Outputs and next steps

Feedback from participants was very positive, with many valuing the opportunity for interdisciplinary knowledge exchange and discussion. Information and perspectives gathered have been used to inform the Society’s microbiome policy report, consultation responses and subsequent meetings with policy stakeholders. 

The Society will launch the policy report later this year when Expert Working Group members will present findings to policy-makers and other stakeholders. The Society will also focus on other activities to disseminate the report and facilitate engagement to help progress and inform about microbiome research and microbiology. 

For more information about the stakeholder workshops and our Microbiome Policy Project visit our website or contact the Policy team

Paul Richards

Policy Officer

Isabel Spence

Head of Public Affairs