What does microbiome mean and what is it about microbiomes that make them so important?
The term microbiome refers to an assemblage of microorganisms that live and interact together in a defined environment. Examples of a microbiome include the networks of soil microorganisms that determine the fertility status of a soil ecosystem, the microorganisms that carry out vital functions in plants and animals, and the communities of microorganisms that impact human nutrition and health. The microorganisms that constitute a microbiome include bacteria, fungi, algae, viruses and other microbes. Microbiomes exist in aquatic and terrestrial environments, where they play crucial roles in determining the state and viability of habitats and the biodiversity that they support.
The state of the microbiome is particularly important in the areas of agriculture and human health, which are interlinked through numerous factors, including environmental health, the state of biodiversity, human nutrition and climate change. These issues represent a focus of discussion in two major international projects, the Earth Microbiome Project and the Human Microbiome Project. Additionally, the new FAO Programme on Bioeconomy for Sustainable Food and Agriculture precisely focuses on issues of responsible consumption and production, using science, technology and innovation to support the transition towards healthier and more sustainable agrifood systems. This is because agrifood systems have a substantial impact on microbiomes from diverse ecosystems, and vice versa.
For example, promoting crop diversity has the potential to enhance soil microbe diversity and the beneficial activities of numerous associated microorganisms. This is relevant in terms of moving away from an extractive agriculture paradigm to more sustainable and ecologically friendly agricultural practices that encourage all aspects of on-farm diversity. Such changes would also have a trickle-down effect on human health in that what is grown in farmers’ fields is eventually consumed and determines ultimately whether a diet is healthy and whether the human gut microbiome is in good shape or not.
Currently, diet is frequently not optimal and has, especially in the case of the “Western Diet”, exerted negative impacts on the human gut microbiome. This microbiome mediates some of the detrimental effects of a poor diet on human health in terms of deficiencies in dietary energy and nutrients, overweight and obesity, and diet-related non-communicable diseases. Within the context of agrifood systems transformation, this points to the need to maintain and restore microbiome biodiversity and functioning in natural and agricultural ecosystems and promote healthy and diverse diets and a sustainable bioeconomy.
In terms of health of the agricultural environment, the soils, water sources, pollinators and biodiversity overall, modern farming practices have often had a damaging effect – land use change, excessive tillage, low plant diversity, and excessive use of harmful agricultural inputs. Environmental health has suffered as key microbiomes have been disturbed or eliminated and crucial ecosystems have been disrupted. Agrifood systems have been identified as a major contributor to climate change, including the loss of key microbiomes that are crucial in carbon cycling. Reduced use of fossil fuel based products to raise agricultural productivity will benefit the entire bioeconomy.
Karel Callens, Senior Advisor to FAO’s Chief Economist, maintains that “at a time where our agrifood systems are facing multiple threats, from climate change, loss of agrobiodiversity and environmental damage, to rising food, energy, and fertilizer prices, new microbiome science, technologies and innovations offer an opportunity to radically redirect our system towards greater sustainability in ways that benefit human health, environmental health and economic revival.”
Parallel game-changing strategies can be used to boost microbiome diversity and functions throughout agrifood systems, and therefore support multiple objectives while reducing trade-offs. For example, dietary diversity and agrobiodiversity link human health and soil health. Similarly, there are parallels between how human health and ecosystem health can be restored by addressing the negative effects on the respective associated microbiomes; in the first instance, through improvements in diet, and in the second, through adoption of less damaging management practices, for example by reducing harmful agrochemical use in favour of expanded use of biopesticides and other bioeconomy products such as biofertilizers. Evidence of interlinkages between microbiomes from different environments in agrifood systems is increasing. Antimicrobial resistance is one case, where excessive, and sometimes unnecessary, use of antimicrobials to manage farm animal and human diseases has resulted in alterations to the respective microbiomes that has in the final analysis been detrimental to health rather than beneficial.
FAO is playing a leading role in microbiome science through encouraging engagement with the scientific community, sharing innovations and solutions to current problems and developing the interface between scientists and policymakers as well as the bio-industry. More specifically, regarding the science of microbiomes, FAO monitors developments, assesses implications of innovations, informs research on developing priorities, promotes debate, and encourages partnerships. Much of this work is done through an informal FAO microbiome working group, in addition to the FAO-led International Sustainable Bioeconomy Working Group (ISBWG).
In the move towards transforming agrifood systems so that they become more sustainable, equitable, inclusive, and environmentally friendly, leapfrogging changes are required. There will inevitably be trade-offs among the social, economic and environmental dimensions of change, but all parts of the bioeconomy – those aspects of the economy that rely on renewable biological resources for the production of food, material and energy – can support in the transition towards sustainability. While many of the costs associated with agrifood systems transformation will be readily apparent, some costs associated with maintaining the status quo or opting for a different approach are hidden.
“For instance, energy-intensive processes for producing agricultural inputs and technologies are not often taken into account,” according to Marta Gomez San Juan, FAO senior bioeconomy expert. “All agrifood systems actors are impacted by input prices and environmental pollution. Microbiome-based fertilizers are a typical bioeconomy example, where more conscious decisions at farm and consumer level can bring about health benefits and ecosystem restoration.” However, Gomez San Juan cautions that “policies should support the competitiveness and quality assurance of biological applications with agrochemical alternatives to ensure efficacy of microbiome products in the field.” Also included among the hidden costs is the damage being done to critical microbiomes through the relentless drive of large-scale agriculture towards increased production and the benefits that would derive from greater recognition of the value of microbiomes and the enormous contributions they make to yields and productivity, the environment and human well-being.
Microbiomes are an unseen ally in agrifood systems transformation and are set to play an increasingly prominent role in many aspects of a healthy bioeconomy.