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Integrative microbiome research


Microbiome research involves the investigation of the complex community of microorganisms associated with a particular organism or environment. It is a rapidly developing research field, spurred by technologies that allow detailed exploration of the composition of microbial communities that can include bacteria, fungi, archaea, protists and viruses). Such studies are revealing evidence for the influence of microbiomes on a broad range of biological systems and processes, many of which are relevant to BBSRC's mission and strategic research priorities.

Despite recent advances, many fundamental questions about the dynamics, function and influence of microbiomes remain unresolved. Answering these questions will require integrative approaches: research that combines the skills, methodologies and expertise from a range of disciplines from within the biosciences and beyond. Through building UK research capability and capacity in integrative microbiome research, BBSRC ultimately expects to establish the knowledge and evidence needed to enable scientifically robust management and utilization of these complex microbial communities in a range of contexts.


To promote research that advances our understanding of the biological function and influence of microbiomes across challenges spanning BBSRC's portfolio.

Scientific scope

Applicants addressing this priority area should seek to move beyond descriptive characterisation of microbial community structure to tackle biologically significant questions. Investigation of the function and influence of microbiomes is expected to require application of a range of complementary approaches and collaborative multidisciplinary proposals are encouraged.

Key challenges relevant to the priority area include:

  • Exploring the significance of variation in microbiome composition within and between individual organisms (e.g. humans, farm animals, plants), and how this relates to host genotype, phenotype and health status
  • Determining principles governing the assembly, dynamics, stability and vulnerability to disturbance of the microbiome, including the influence of key biotic and abiotic factors (microbial, host, environmental)
  • Identifying and characterising functional properties of the microbiome, including key microbial players and processes, relationships between rare and abundant microbial species, the microbial metabolic and signalling interactions taking place, and the genes and molecules driving the microbiome-host relationship
  • Building a mechanistic understanding of the influence of the microbiome on host physiological processes, immune systems and developmental changes through the life course

Within this challenge context, we would particularly welcome proposals that:


Proposals should seek to address well defined biological questions about the role and function of the microbiome, or develop new methods and approaches that are relevant to microbiome research. It is expected that applicants will provide evidence of robust study design and sampling strategies, as well as a clear strategy describing how data will be analysed and managed.

BBSRC is uniquely positioned to advance understanding of microbiomes associated with a broad range of biological organisms, from underpinning through to strategic and applied studies. Proposals to study microbiomes in the context of animals, plants, soils, humans, industrial processes, model systems, or other environments are welcome where the research questions address BBSRC's mission and remit.

Outputs and impacts

Proposals should comply with our data sharing policy, which promotes the adoption of community standards and sharing of metadata (see related links). Where a novel technology or methodology is developed during a project, researchers should consider its potential applications within the broad biosciences research community and beyond, including steps necessary to make them accessible and user friendly. The translation of research outputs into practice through partnerships, application by industry, or by informing policy-making is encouraged.

BBSRC considers impacts on training and the skills base to be particularly important for the development of UK microbiome research capability.


The priority area encourages research ranging from underpinning through to strategic and applied studies. End-user engagement is encouraged to promote translation of research findings to practical applications. Applicants should explain how, during the course of the project, they will take steps to maximize the broad impact of their research. Resources can be requested for appropriate activities.

UKRI-BBSRC Microbiome Capability Workshop

The workshop was held on March 4 2020 and designed to help understand the current and future capability needed for microbiome research and enable UKRI-BBSRC to support the continuing development of Integrative Microbiome Research in the UK. The workshop uniquely brought together disciplines from across UKRI-BBSRC’s remit and beyond along with Industry, Networks and Learned Societies. Experienced community members provided UKRI-BBSRC with advice around the opportunities for microbiome capability across the breadth of UKRI-BBSRC’s microbiome research areas, covering areas including skills, infrastructure, and emerging research approaches. It also enabled a forum to promote the exchange of knowledge across the sector. This downloadable document is a summary of the workshop and not a strategy, it is located here alongside UKRI-BBSRC’s Integrative Microbiome Research priority area as a resource for the microbiome community.