‘Roots are but as guts inverted’: an exploration of microbiomes

Microbiomes are ubiquitous and critical to the world as we know it. They are essential for the functioning and health of natural ecosystems, both terrestrial and aquatic. Microbiomes underpin agricultural systems and therefore our food supply, they play crucial roles in production of greenhouse gases and the sequestration of carbon. Microbiomes are critical for lifelong health in humans and animals, from early development to old age.

We find microbiomes in water, soil, on plants, in human/animal guts, oral cavity, on the skin and even in clouds. It is becoming clear that plants, animals and humans exist as holobionts, that is biological individuals made up of a host organism and the microorganisms that live on or in it. Microbiomes are the foundation of planetary health, underpinning the ecosystems that humans depend on.

Innovative research addressing the challenges facing planetary and human health

The study of microbiomes is critical, and while it continues at a pace, it is clear that different disciplines are working in isolation from each other and that there is limited integrated understanding of host-microbiota interactions across kingdoms.

It is our belief that breaking down these barriers and taking a cross-disciplinary approach will deliver quicker, better and more innovative solutions to some of the most pressing challenges facing humankind, including climate change mitigation, biodiversity crisis, agricultural sustainability and human ill-health.

With this in mind, and with support from the Rank Prize Funds, in October 2024 we brought together leading experts with the next generation of researchers from three key disciplines, plant science, invertebrate science and human biology, all working on microbiomes to facilitate inter-disciplinary discussions.

Inspiration from conceptual and methodological advances in other disciplines

Our goal was for the participants to share experience and ideas, and to break the disciplinary barriers in microbiome research. It was clear that there was plenty to learn from each other, and participants from the different disciplines identified important parallels as well as connections in how microbiomes link plant, soil, animal and human health.

Each discipline recognised conceptual and methodological advances being used in the other systems and the opportunity to use these to change the way they work. For example, invertebrate researchers were inspired by the ecological relevance of plant microbiome research, which uses synthetic microbiomes isolated from soil. An increased use of ecologically relevant synthetic microbiomes for the widely used model organism C. elegans would enable the study of e.g. developmental biology, neurobiology and ageing in the context of natural microbiota interactions. Researchers studying human health were interested in how microbes in the soil impact on the human gut microbiota by altering the nutritional composition of common crops. Plant researchers were struck by the potential of using of C. elegans models to explore bacterial adaptations relevant to root soil interactions and impacts on function.

New insights from interdisciplinary microbiome research programmes

The main take-home message was that the different disciplines should come out of their silos and work together with a more integrated approach to consider the whole system. By breaking disciplinary boundaries between researchers working on plant, invertebrate and mammalian microbiomes new insights may emerge through coordinated research programmes, for example:

• Understanding of interactions across kingdoms (microbes, plants, invertebrates) in the soil that underpin soil ecology, contributing to soil health and the resilience of plants and soil animals to stressors related to climate change and human activity (drought, heat, salinity, pollution)
• Understanding of how interactions across kingdoms in the soil affects human health e.g. through metabolite production, quality and composition of food crops, degradation of soil toxins and pollutants
• Understanding similarities of microbial communities across systems e.g. in the mucosa and rhizosphere

Innovative research addressing knowledge gaps in microbiome research

The symposium identified opportunity for innovative and important interdisciplinary research  addressing important knowledge gaps in how microbiomes affect human, animal, plant and soil health

• One health: Considering the collective impact of microbes on roots, plants, animals and humans (a microbe-soil-root-plant-human health axis)
• Use of the model organism C. elegans, a free-living soil nematode, to understand cross-kingdom interactions relevant to soil health and important food crops
• Further develop and make better use of ethical, inexpensive invertebrate model systems as pre-clinical models that leverage mechanisms for human research
• Investigate the similarities of microbiome communities and functions in the human gut mucosa and the plant rhizosphere mucilage
• Use of prebiotics and probiotics to improve plant health
• Exploration of plant diversity as a means of enhancing microbiome diversity and health in humans

By bringing these themes together we can accelerate research through using a different approach to develop new novel ideas from the synergies that exist across the fields.

Dr Marina Ezcurra (University of Kent)

Professor Timothy George (The James Hutton Institute)

Professor Peter Gregory (University of Reading)

Professor Sue Ozanne (University of Cambridge)

Dr Gemma Walton (University of Reading)