Area of investment and support

Area of investment and support: Integrative microbiome research

Through building UK research capability in integrative microbiome research, the Biotechnology and Biological Sciences Research Council (BBSRC) expects to establish knowledge and evidence to enable management and usage of complex microbial communities in contexts relevant to our research priorities.

BBSRC’s standard research grant provides up to £2 million for projects in this priority area.
The standard research grant is an ongoing scheme. Projects can last up to five years.
Partners involved:
Biotechnology and Biological Sciences Research Council (BBSRC)

The scope and what we're doing

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

There are several key challenges relevant to the priority area.

Variation in microbiome composition

We are interested in exploring the significance of variation in microbiome composition within and between individual organisms, for example, humans, farm animals and plants. We are interested in how this relates to host genotype, phenotype and health status.

Disturbance of the microbiome

We are interested in determining principles governing the assembly, dynamics, stability and vulnerability to disturbance of the microbiome. This includes the influence of key biotic and abiotic factors (microbial, host, environmental).

Functional properties of the microbiome

We are interested in 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
  • the genes and molecules driving the microbiome-host relationship.

Influence of the microbiome on host physiological processes

We are interested in building a mechanistic understanding of the influence of the microbiome on:

  • host physiological processes
  • immune systems
  • developmental changes through the life course.

Proposals we welcome

Within this challenge context, we would particularly welcome proposals that are relevant to other priority areas, seek to resolve technological challenges, or employ novel approaches.

Other BBSRC priority areas

We would welcome proposals that are relevant to other BBSRC priority areas, for example:

Resolving methodological and technological challenges

We welcome proposals that seek to resolve methodological and technological challenges, such as closing the gap in our ability to measure phenotypic characteristics of the microbiome and its constituents. We also welcome proposals with improved methods to analyse and manage microbiome data.

Modelling approaches

We are interested in proposals that employ modelling approaches to understand and predict the dynamics and systems properties of the microbiome and microbiome-host or environment interactions.

Advance biotechnological methods

We are interested in proposals that advance biotechnological methods to control, modify or engineer the microbiome for beneficial purposes.


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 you 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.


Proposals should comply with our data sharing policy, which promotes the adoption of community standards and sharing of metadata.

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 policymaking 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. You should explain how, during the course of the project, you will take steps to maximise the broad impact of your research.

Resources can be requested for appropriate activities.

Why we're doing it

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

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. These 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.

Opportunities, support and resources available

This is one of BBSRC’s priority areas for our standard research grant. You can apply at any time.

Standard (sometimes known as ‘responsive’) funding opportunities are open to a wide range of research and approaches within BBSRC’s remit.

Find out more about applying for funding and what to include in your application.

Past projects, outcomes and impact

Microbiome Capability Workshop

The workshop was held on 4 March 2020 and designed to help understand the current and future capability needed for microbiome research and enable BBSRC and UK Research and Innovation (UKRI) to support the continuing development of Integrative Microbiome Research in the UK.

The workshop uniquely brought together disciplines from across UKRI’s and BBSRC’s remit and beyond along with industry, networks and learned societies. Experienced community members provided UKRI and BBSRC with advice around the opportunities for microbiome capability across the breadth of UKRI’s and BBSRC’s microbiome research areas. These covered areas including skills, infrastructure, and emerging research approaches. It also enabled a forum to promote the exchange of knowledge across the sector.

Read the BBSRC Microbiome Capability Workshop 2020 Report

Who to contact

Freya Varden


Last updated: 27 July 2023

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