Call for action to foster microbiome research: a driver for future-proof food systems & circular economy innovations
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Call for action to foster microbiome research: a driver for future-proof food
systems & circular economy innovations
Microbiomes (a.k.a. microbial communities) consist engagement of decision-makers in governments,
of trillions of bacteria, viruses and fungi. They exist parliaments and funding institutions. By now, the
within and on humans, animals and plants in both human microbiome has been characterised in great
terrestrial and aquatic environments, and play a key depth; however, considering the whole food system
role in shaping life on our planet. Microbiome from primary production to waste management, as
research will significantly influence innovations in described under the FOOD 2030 policy1, the potential
health and disease management, food system safety of microbes to improve environments benefitting
and productivity, and ecosystem health. Therefore, health and well-being is still mostly untapped.
microbiomes have the potential to play a crucial part
in the 21st century’s circular economy. Despite this, Priority improvements suggested
awareness and support for this promising field are
still to be enhanced. • Better regulation: A One Microbiome concept
comparable to the One Health approach
Globally, knowledge about the microbiome is (protecting the integrity of human, animal,
expanding rapidly. Europe is taking part in a plant, soil, food, feed and environmental health)
worldwide race to unearth the best available is suggested as an appropriate policy vision to
discoveries and develop scientific techniques for provide guiding principles for safety and
understanding and managing the microbiome for the registration rules — ideally, a single
benefit of society. These gains in knowledge reveal microbiome-based food law.
that microbiome-based solutions may be key for the • More, and more coherent, research funding:
development of a modern circular economy and a Microbiome research needs to become a
sustainable, fair and healthy food system. For research field on its own. Aligned funding
instance, microbial communities might play a leading programmes in the fields of food, agriculture
role in fighting diseases and infections with and the environment (e.g. within the upcoming
microbiome modulation through pro- or prebiotics, Horizon Europe programme), will avoid costly
potentially increasing health benefits; they may duplication. EU funding should include large
better control plant pests through bio-based agents, infrastructures such as biobanks and easy-to-
or degrade and revalourise waste and wastewater use open science platforms.
through catalytic bioprocesses and protect • Harmonised rules: Concise safety standards and
environments by acting as bio-sensors. Overall, evaluation requirements (including the
innovative microbiome applications have the clarification of legal frameworks) concerning
potential to create sustainable high-value different microbes used in food, feed,
alternatives to conventional approaches in health and biocontrol and biopreserving are a prerequisite
food system management whilst reducing burdens on for the safe production, application and
soils and waters and decreasing greenhouse gas consumption of microbiome-based products.
emissions. These should also be communicated to the
public to build their trust.
To support and encourage this upcoming field,
microbiome researchers are asking for the
1Microbiome research attracts great interest This paper can be used to raise awareness amongst
private funders, stakeholders in higher education,
The microbiome is a hot topic in both national and science communicators, associations and citizens
international media. Though much of what we know that are affected by the outcomes of microbiome
about microbiomes remains relativel obscure, the research activities. Above all, the publication is a call
ongoing discovery of the microbial potential to for political decision-makers at various levels to
provide societal challenge-oriented solutions is seen improve regulations so that they consider the
as a chance by key global players. complexity of microbial communities and emphasise
microbiomes as an integral part in research funding
Bill Gates, the founder of Microsoft and co-chair of — and an appeal for investment in both the necessary
the Bill & Melinda Gates Foundation, points to the infrastructure and the relevant start-ups working on
microbiome as central to solving the challenge of efficient, innovative efforts. This is elaborated on in
malnutrition, obesity and many inflammatory the ‘Action is needed!’ section below.
diseases. Funding from the foundation may, in the
future, target a better understanding of nutrition for Several legislative proposals that will affect the future
the gut microbiome that could help, within the next starting position of microbiome-related discoveries
10-20 years, to save the lives of millions. According to and developments are underway at EU and at
Gates, ‘that deeper understanding is why I predict national levels. This paper provides an overview of
we’re going to solve malnutrition.’2 the opportunities and challenges involved, with an
emphasis on food systems and the circular economy.
The Organisation for Economic Cooperation and The initial improvements suggested are listed in the
Development (OECD) characterises microbiome current brief, and more details are to be provided as
research as a most promising scientific field that can the projects develop.
help solve major challenges. Yet to have real impact,
advances are required in five areas: science policy, The challenges: widespread fragmentation
the enabling of applied science, public–private
cooperation, regulatory frameworks, and skills, Microbiome R&I is widely fragmented, not only
communication and public awareness.3 across scientific disciplines but also within regulatory
contexts, which is posing barriers to the efficient
The International Bioeconomy Forum, a worldwide deployment of viable microbiome products and
platform for scientific and governmental exchange on therapies. Currently, microbiome research is a sub-
bioeconomic developments, regards the microbiome set of, or an appendix to, research within the fields of
and the knowledge about it as one of the key factors agriculture, food, health and the environment. Rarely
in the fight against climate change and ensuring food is the microbiome considered as an active and
and nutrition security as well as global health.4 prominent member of the environment.
The policy brief presented here, issued by the EU- Within funding programmes, food safety legislation
funded project MicrobiomeSupport and its or other management cycles the microbiome is
Innovation Actions (see fact sheet), aims at bringing usually not taken into consideration at a top level.
attention to the needs of, and deficiencies and This leads to dispersed and often incomplete results,
bottlenecks in, microbiome research and innovation leaving microbiome research in a disadvantaged
(R&I). position compared to major research sectors.
2Research fragmentation that needs to be
overcome • Clarity in safety and efficacy standards,
therefore, is crucial. However, divergent
• Different research languages, methods, standards between the coverage and scope of
protocols and technologies and incoherent or the evaluation of food microbes, for example of
inexistent rules for data sampling, collection, those traditionally used as probiotics
use and storage hinders the comparison of (lactobacilli or bifidobacteria), and those for
research results across disciplines, labs and major commensal bacteria living with us, are
fields. confusing.
• There are no standardised classifications and • Classifications and definitions of new
definitions for microbiome-based products and microbiome products are not harmonised.
processes. Sometimes they are even contradictory, as is the
• Microbiome issues are dispersed across various case with, for example, probiotics, and
policy fields (intellectual property rights; biocontrol and biopreserving products.
registration procedures, including data • Every second new pesticide registered in the EU
requirements for product applications; safety is a biopesticide. However, the registration
protocols in production processes and end-user procedures for what are known as ‘biocontrol
safety). agents’ (including both pest and soil control),
are expensive and unclear. They also vary across
To validate research, and concurrently foster the individual countries. Current data requirements
development of regulations that facilitate the for their registration are often still designed for
commercialisation of applications, common standard conventional chemicals and are unfit to be
operating practices need to be defined. They need to applied to new microbiome-based product
be robust and flexible, leaving provision for protocols. This leads to expensive and time-
adaptation in response to the rapid advances in consuming procedures. In the US the time to
technology. register a biocontrol agent does not exceed one
year, while in the EU it takes more than five.
The industry will not implement methods and
protocols if they are not standardised. Research may Overall, this is resulting in uncertainty for
not advance if basic EU research infrastructures entrepreneurs and investors, and consequently
(such as biobanks or IT-infrastructure including causes fragmented marketplaces within the same
support for, and retainment of highly qualified and classes of produce or within classes of biocontrol
trained personal are not established. agents while being non-compliant to the EU’s
internal market rules. Guidelines need to be
Regulative gaps to be avoided updated and assessment bodies must integrate
microbiome considerations within their work.
Trusted relationships among researchers, industry,
suppliers, consumers and the public are the sine qua
non condition for introducing innovative microbiome-
based medical and nutritional applications. This is
equally true for improving the performance of the
food system, which may imply microbial release into
environment.
3Action is needed! Initiatives, to coordinate national funding and
programming with that on an EU level.
Policy and funding coherence: Modernising existing
policies, such as the Common Agricultural Policy Consistent food microbes’ legislation: One single
(CAP), is needed to support the transition towards a source of food microbe laws for food (production,
sustainable agri-food sector that can integrate the processing and consumption) might overcome the
principles of a circular economy. This in turn is current incoherencies and gaps. The same applies for
expected to stimulate microbiome R&I, which is probiotic legislation and legislation regarding
fragmented across disciplines. biocontrol agents. There is a demand for minimum
requirements to legally define a probiotic or prebiotic
A coherent and aligned policy approach considering in the microbiome context to advance innovation.
the interdependencies between different
microbiomes in humans, animals, plants and Common standards: The coverage and scope of the
environments demands a One Microbiome concept safety assessment of taxonomic microbe units used in
(protecting the integrity of human and other food, feed, biocontrol and biopreserving agents lack
microbiomes) as a guiding principle in law and as a the harmonisation needed to ensure the overall safe
policy vision (comparable to the One Health production, application and consumption of
approach). This would allow more coherent microbiome-based produce across the EU. Pre-
policymaking within the CAP, food laws, and feed product-launch safety and efficacy data provisions
additive regulations and innovation policies, as it should be updated regularly to reflect new
would also result in a more integrated and coherent technologies and food safety techniques. Registration
funding of microbiome research in the fields of procedures for biocontrol products need to be
agriculture, health, food and the circular economy, simplified and harmonised.
particularly in the light of the HorizonEurope research
programme (2021-27). The EU should take a front- Microbiome research and the Nagoya Protocol:
runner role in pursuing an integrated approach, to Existing concerns about the Diversity Nagoya
end confusion and uncertainty for all actors. Protocol on Access and Benefit Sharing may lead to
issues around securing intellectual property and
Better research coordination: To support the conducting research that will adversely affect
urgently needed transformation of food systems, investment and translation. European countries have
microbiome research requires upgrading and highly diverse practices in applying this protocol:
alignment on an international level, including more from very restrictive to no application at all.
long-term funding for large-scale trials, better International agreement should be sought on the
infrastructures (e.g. biobanks for storing samples and implementation of the Nagoya Protocol in relation to
isolates, bioinformatic databases, computing power microbiome research. The rising loss of biodiversity
for large-scale analyses of microbiome data as well as also affects the microbiome and may lead to
for storing and sharing data efficiently and considerations and dialogues about whether key
transparently), human resource and maintenance elements of human (maybe also animal, plant and soil
support. Excellent and collaborative microbiome microbiomes in the context of specific cultures)
research under HorizonEurope demands the should be recognised as part of our global heritage.
completion of initiatives, such as thematic networks
within the European Research Area (the ERA-Nets Platforms: EU-wide knowledge exchange platforms
Cofund scheme) and the Joint Programming need to be established through workshops, expert
4panels and clear, transparent and openly available The rewards: healthy guts, nutritious food,
reference documents (facilitating coordination clean and sustainable environments
between industry stakeholders or associations and
policy institutions) about regulatory needs and According to the OECD, a global food increase of 70 %,
adaptations of, among other things, safety standards especially for protein and fibre, is needed by 20503.
and registration rules. Academia needs to be actively This raise in agricultural productivity needs to be
involved via coordination and support actions, which obtained under changing climate conditions and with
have, alongside other initiatives, a responsibility to declining soil and water quality. At the same time
contribute to the future strategic programming of there is a strong need to improve European food
agri-food microbiome research and innovative systems in terms of sustainability, quality, nutritional
actions. They can also ensure better coordinated value, safety and international competitiveness.
feedback from microbiome research to policy.
MicrobiomeSupport project partners are currently
Microbiome literacy and technology assessment: mapping all ongoing microbiome research
Microbiome literacy efforts require clear public- internationally, from basic to applied research (i.e.
awareness messages about the benefits, risks and product development activities) including available
misconceptions of microbiome innovations. Serious infrastructures and facilities in the field of food- and
investment is demanded for adequate school and health-related microbiome research. The goal is to
adult education as well as for science communication gain a clearer picture of potential future funding
to ensure microbiome literacy. Given the current pathways in Europe and beyond.
hype on the microbiome in the mediam there is a
danger of overselling the scope of microbial According to the Microbiology Society,5 current
innovation. Unexpected detrimental consequences general approaches to managing and modulating the
(or side effects) and long-term impacts of optimising microbiome for increased benefits range from
microbiomes need to be carefully investigated, as do introducing beneficial microbes into existing
the GMO aspects of microbiome R&I. Improved microbiomes, to promoting beneficial microbiome
technology assessment capacities at national and EU- diversity and functionality by managing
level can help manage expectations. environmental conditions. Other approaches include
the development of diagnostics, predictive models
Consumer rights and citizen participation: To ensure and biomarkers (incl. applications for the prediction
transparency for consumers, microbiome products of diseases, enhancing food safety and monitoring
must be clearly labelled. Further, models of citizen environments), the prospecting of microbiomes as
participation, allowing co-creation for addressing sources for new products, and the design of synthetic
potential risks and issues, need to be adopted for microbiomes with particular function(s).
microbiome applications that may influence lifestyles
and food consumption patterns through new forms Advancements will aim at the best available
of environmental management or waste and applications for better health and well-being, clean
wastewater treatments. Both, labelling and and sustainable environments, disease-resistant
participation will enable informed choices and crops and soils, the degradation and revalourisation
democratic decisions for citizens. Public authorities of waste and wastewater, climate mitigation and
and scientists need to initiate and lead the process of multi-billion-euro markets.
education, communication, expectation
management and participation to foster trust.
56
MicrobiomeSupport: projects, partners and stakeholders
The Horizon 2020-funded coordination and support Four Innovation Actions (IAs), funded under Horizon
action MicrobiomeSupport 2020 and including academic and industrial
(www.microbiomesupport.eu) has been financed partners, are focused on applied research to trigger
with EUR 3.5 m for 36 months (2018-2021). The innovative development. They collaborate with
action is a close collaboration of 36 academic and MicrobiomeSupport.
governmental partners (including two associated
partners) from 13 EU countries and 7 international The four Innovation Actions are:
partners from non-EU countries. The consortium is
working together with over 100 Advisory Group MASTER (www.master-h2020.eu): Development of
members, ranging from government agencies to knowledge and commercial products for the safety of
academic institutions and industry stakeholders food across multiple food chains, to include marine,
(including the support of the IBF working group Food plant, soil, rumen, meat, brewing, vegetable waste,
System Microbiome). and fermented foods. The focus is on technologies
and enterprise.
MicrobiomeSupport’s objectives are to:
SIMBA (www.simbaproject.eu): Development of
• Harmonise the methods, approaches and microbial product solutions, including viable
standards used in microbiome research in terrestrial and aquatic microbiomes for soils, plants
different environments (e.g. soil, plants, and waters to foster food security through
aquatic, animals, humans, etc.) to ensure robust sustainable agro- and aquacultures.
data for economic and public health;
• Support international efforts to align funding (to CIRCLES (www.circlesproject.eu): Development of
avoid the unnecessary duplication of research knowledge of food system microbiomes to
and maximise existing/previous projects and implement a vast panel of smart microbiome
data, specifically through coordinating with the modulators (SMMs), such as pro/prebiotics,
IBF’s working group Food Microbiomes); fermentative agents, and energy and waste
• Raise public awareness on the potential of management cultures.
microbiome applications;
• Map ongoing international research and HOLOFOOD (www.holofood.eu): The focus is on
facilities to draft a joint R&I strategy and agenda understanding the host (animal) and associated
in the context of the wider bioeconomy and microbiome interplay and impact in response to
circular economy research. natural feed additives within two popular food
systems, salmon and chicken, resulting in optimised
and sustainable food production systems.
7Selection of governments, councils & References
research agencies as advisors to 1
European Commission (2018) FOOD 2030: Future-
MicrobiomeSupport proofing our food systems through research and
innovation. DOI: 10.2777/188064.
Federal Ministry for Sustainability and Tourism
2
(previously BMLFUW), Austria Paul Brackley (2019) Bill Gates makes two big
Council for Agricultural Research and Analysis of predictions for global healthcare in Cambridge Union
Agricultural Economics, Italy speech. Cambridge Independent, 7 October.
Ministry of Higher Education and Science, 3
Denmark OECD (2017) The microbiome, diet and health:
Department of Agriculture, Food and the Marine, Towards a science and innovation agenda. OECD
Ireland Science, Technology & Innovation Policy Paper 42.
Estonian Research Council, Estonia 4
Agriculture and Agri-Food Canada (2019)
Ministry of Higher Learning, Research and International Bioeconomy Forum. Website.
Innovation, France
5
Standing Committee on Agricultural Research, Microbiology Society (2017) Unlocking the
France microbiome: opportunities and challenges of
International Scientific and Technological microbiome research for health and agriculture.
Cooperation Directorate at the General Secretariat Website.
for Research and Technology, Greece
Spanish Foundation for Science and Technology,
Spain
National Centre for Research and Development,
Poland
Microbial Research Resource Infrastructure,
MIRRI, Portugal
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