MICROBIOME:

THE MISSING LINK?

SCIENCE AND INNOVATION FOR HEALTH, CLIMATE
AND SUSTAINABLE FOOD SYSTEMS
HOW CAN WE TRANSFORM OUR DIETS THESE ARE BIG QUESTIONS!
AND FOOD SYSTEMS TO SOLVE HARD-CORE The world is afloat with views on
PROBLEMS OF UNDERNOURISHMENT, how best to go about these issues.
Unfortunately, the fact is that we have so
WHILE AT THE SAME TIME TACKLING THE
far not been very successful in resolving
EMERGING PANDEMIC OF OBESITY AND any of these issues in a significant way.
DIET-RELATED NON-COMMUNICABLE Beyond the point of lack of political
DISEASES? commitment, this fact also begs the
question whether there is maybe
something amiss in our understanding
of the causes of these problems.
HOW WILL WE BE ABLE TO FEED
Are we overlooking something?
10 BILLION PEOPLE BY 2050
WITHOUT DESTROYING OUR
NATURAL RESOURCE BASE?

CAN WE STOP AND

POSSIBLY EVEN REVERSE
THE LOSS OF BIODIVERSITY,
ENVIRONMENTAL DEGRADATION, The views expressed in this document are those of the author(s)

AND CLIMATE CHANGE? and do not necessarily reflect the views or policies of the Food
and Agriculture Organization of the United Nations (FAO).

2
In search for answers, an informal group The group has since evolved in an inter-
of people got together first to look into the disciplinary team that is focusing on
question about alternative explanations for a systematic review of transformative
the obesity and non-communicable diseases scientific research into the role of the
(NCDs) pandemic. A review of recent microbiome in nutrition and health,
scientific literature showed how gut dysbiosis, agriculture and food systems, and
an imbalance in the gut microbiome, is the bioeconomy at large. This note
a common factor in obesity and various outlines some preliminary findings,
diet-related NCDs. A further search for implications and opportunities with the
factors that can cause dysbiosis led to idea of stimulating further thinking and
the identification of a variety of possible exploration.
causative factors, including lifestyle factors,
The team currently consists of:
use of antibiotics, diet composition, the
Karel Callens, bio engineer by training and
presence of various chemical compounds in
Deputy Strategic Programme Leader, Food
our food, etc. Some of these compounds can
Security and Nutrition; Catherine Bessy,
enter our food as agro-chemicals used during
agronomist and food scientist and Food
production, or additives used in processing
Safety officer; Anne Bogdanski, biologist
and transformation. Others, like mycotoxins
by training and Natural Resources officer;
are the result of poor practices.
Fanette Fontaine, Associate professor of
This finding led the group to expand its microbiology; Ceren Gurkan, economist
exploration to the role of the microbiomes by training and Programme Officer; Sarah
of for example animals, plants, soils, rivers, Nájera Espinosa, Food Safety consultant,
oceans, etc. and how their disturbance with a background in environmental
could affect for example soil fertility, carbon science; Dylan Warren Raffa, plant and soil
sequestration, plant and animal growth and expert and PhD Fellow on Agrobiodiversity;
health, etc. and Susan Grooters, epidemiologist.

3
 CHALLENGES

DEMOGRAPHIC
MALNUTRITION SHIFTS
Obesity and NCDs

NATURAL RESOURCE
CLIMATE DEGRADATION
CHANGE

BIODIVERSITY
LOSS
SHIFTS
IN DIETS

4
 LOOKING FOR THE BEST PATH TOWARDS
NOURISHING 10 BILLION PEOPLE
Unhealthy diets now pose a greater risk to Even though we waste roughly over a third of
morbidity and mortality than unsafe sex, all food produced worldwide, there remains
alcohol, and drug and tobacco use combined. enough to feed everyone. Yet hunger persists
They are at the root of the global obesity and and malnutrition is on the rise. While poverty
diet-related non-communicable disease (NCD) and inequality play a big part, something even
pandemic. The ways of food production that more fundamental is amiss. The natural world,
lead to these unhealthy diets also pose a the bedrock of poor people’s livelihoods, and
major threat to climate stability and ecosystem arguably our global economy, is under severe
resilience, and constitute the most important pressure. This is likely the biggest challenge
driver of environmental degradation and natural defining the twenty-first century. Climate
resources depletion. change, biodiversity loss, soil degradation,
and other forms of manmade environmental
Malnutrition comes in different forms. While
damage demonstrate how our food system is
nearly a third of the world’s population is
mining nature, and in the process undermining
overweight or obese, one out of nine people
its very foundation. While the poor are the first
remains undernourished, and more than one out
to experience the consequences, there is a
of three suffers from micronutrient deficiencies.
growing ripple effect throughout the global food
Three quarters of all deaths globally are due
system and society.
to NCDs, and three quarters of all NCD-related
deaths occur in low- and middle-income Although poverty levels have steadily gone
countries. People often suffer from multiple down, we are on a trajectory where poverty
forms of malnutrition and diet-related health reduction risks following the same path as
problems over their lifetime and sometimes malnutrition, slowing down after a period
even at the same time. of relative improvement. Inequality, a key

5
determinant of poverty, is already on the services. It entails the sustainable use of
rise. A major factor in this relapse are the renewable biomass and efficient bioprocesses
hidden environmental and health costs to achieve sustainable production. In some
of the economic growth and agricultural instances, it might also mean to conserve the
intensification that have supported growth in biological resource base rather than using it.
food supplies and incomes. It relies on the use of enabling and converging
technologies, including biotechnology; and it
We are on a path where we are degrading our
requires integration of policies and actions
natural resource base, including its biological
across agriculture, health and other sectors
resources, to the point where major disruptions
and industries.
in our food system and in the socio-economic
fabric of society will inevitably force the In the short term, there is little that we can
system to change. We are at a crossroads: the do to curb the global demand for food and
choice is between doing nothing, risking our other products that depend on biological
future food security and health, or deciding to resources. Demand will continue to rise as
take action, whereby action means radically the world population grows to ten billion
rethinking our food system from a sustainable before eventually shrinking again. However,
bioeconomy perspective. by taking a bioeconomy approach, we can
alter the nature of this demand and the
Bioeconomy is about exploiting synergies
processes through which the food system and
and considering hard trade-offs between the
bioeconomy meet that demand. This approach
food system and other parts of the economy
could accommodate the necessary increases
that depend on biological resources and
in agricultural production, without continuing
processes for the production of goods and
to degrade our natural resource base.

6
 SMALL THINGS CAN MAKE
A BIG DIFFERENCE
Bioscience is uncovering the pathways and live. Perhaps the most critical discovery to
common drivers behind the triple challenge date is that microbiome diversity, rather than
of obesity and NCDs, climate change, and any particular microorganism, is at the root of
biodiversity loss. In the process, microbiology microbiome ecosystem resilience, including
and the inter-disciplinary study of the the resilience of the human body to withstand
microbiome have rediscovered microorganisms stress and disease.
as a vast and untapped natural resource with
Within the sphere of human health, gut
great potential to shift the balance of the
dysbiosis, or the loss of microbiome
‘nature – food systems – people’ equation back
diversity and shifts in the composition of the
into the healthy zone.
microorganisms populating the gut, can result
The microbiome refers to the combined in loss or alteration of a healthy microbiome.
genetic material of all microorganisms living Dysbiosis affects various functions, including
in a given ecosystem, including in the human digestion, energy metabolism, immunity,
body. Current estimates put the total number intestinal permeability and brain function. The
of different microbial species at one trillion, link between gut dysbiosis and obesity and
of which we currently only know about 0.001 food related NCDs like diabetes, cancer, heart
percent. Because of the convergence of disease, allergy, irritable bowel syndrome, etc. is
techniques across computing, bio-engineering now established.
and genomics, we are now able to detect and
Microbiome research is adding depth to our
study this wealth of microbial species that, up
understanding of nutrition, and of how diets and
until very recently, were undetectable.
food products, mediated by the gut microbiome,
The diversity of microorganisms surpasses by affect human health. The gut microbiome
far the diversity of all the other living organisms metabolizes certain food components not
on earth. They perform many, often critical, digested by the human gut, making a large
functions in the ecosystems in which they variety of metabolites available for human

7
cells to digest further, or for other microbes and in the continuous regeneration of the
to use. Much of this process, including the natural resource base. Agriculture and natural
presence and function of bacterial metabolites resource management practices that protect
were unknown until recently. This research and enhance microbiome diversity are the
shows that in addition to genetic factors diet foundation of sustainable food systems. For
composition directly affects the ecology of example, we now understand the negative
the gut microbiome and thus its functionality impacts of agrochemicals on soil fertility, of
and this may result in adverse health effects. fertilizer runoffs on algal blooms in lakes, rivers
In addition, recent research suggests that the and oceans, and the positive impacts that
presence in food of certain compounds can various bacteria and fungi, living in association
influence the microbiome ecology: this appears with plants, can play on nutrient absorption,
to be the case for some pesticide residues, metabolism and plant health.
certain additives and veterinary drug residues,
From a climate change perspective, the
for example. What emerges is that we need
recent Intergovernmental Panel on Climate
to consider the microbiome as a functional
Change (IPCC) Report on Climate Change
part of our body and look at how our diet over
and Land highlights the important role of
time, starting from the first thousand days of a
soil microbiome in climate change, from the
person’s life, affects nutrition and health.
perspective of impact as well as adaptation
Similar to what we are learning about the and mitigation. A soil’s microbiome plays
human gut microbiome, we are now also an essential role in major natural cycles
discovering how the microbiomes of on earth (like nitrogen and carbon cycles)
soils, rivers, lakes and oceans are key to which underpin the functioning of soils and
environmental health. The microbiome plays their ability to capture and store carbon. The
a central role in agricultural production and microbiome of oceans, lakes and rivers play a
productivity, forestry, fisheries and aquaculture, similarly important role in climate change.

8
 POSITIVE SERVICES
Development
OF THE MICROBIOME Feed
of the immune conversion
system

Resistance Resistance
to pathogens to pathogens

HUMANS ANIMALS
Detoxifying
Fat storage hazardous
regulation ingesta
Vitamins
synthesis Nutrient
absortion

PLANTS Soil
fertility
WATER AND SOILS
Carbon
sequestration BODIES

Resistance
Feed for to pests and
Carbon diseases
other animal sequestration
species

9
 POTENTIAL APPLICATIONS
OF THE LATEST DISCOVERIES ON THE

MICROBIOME
CREATING
SUSTAINABLE BUSINESS REDUCING
OPPORTUNITIES ANTIMICROBIAL GROWTH
PROMOTERS USE

REPLACING INORGANIC IMPROVING

FERTILIZERS AND WASTE TREATMENT
PESTICIDES

PREVENTION
AND TREATMENT
IMPROVING OF DIET-RELATED
SOIL CARBON NON-COMMUNICABLE
SEQUESTRATION DISEASES
PREVENTION
AND TREATMENT OF OPPORTUNITIES
INFECTIOUS DISEASES FOR BIOFUEL
PRODUCTION

10
 FROM THE MICROBIOME
TO THE BIOECONOMY
Microbiome research holds one of the keys health several decades later. Similarly, climate
to the intertwined goals of food system change has been in the making for many
sustainability and healthy diets for all. It decades. This cause-effect time lag is not a
provides insights into how to produce more great formula for accountability.
with less, reduce external input use, regenerate
The public sector has a great responsibility
the fertility and health of our soils and
towards people, and especially towards
water bodies, enhance food production and
future generations, to lower this burden and
productivity, and help people prevent and treat
to hold those who generate the hidden costs
various NCDs, as well as infections that have
accountable for covering and, where possible,
become resistant to antibiotics.
reducing them. This is indeed challenging not
From biological and ecological perspectives, in the least because it may not be politically
the case of the microbiome is clear. However, attractive to do so. While there is scope to
does it also make social and economic improve efficiency by cutting food loss and
sense? The burden of ill health, environmental waste, this will not be enough. It also does not
degradation and climate change are massive, solve health issues. We will not be able to face
and the associated costs are largely up to this complex challenge without major
unaccounted for in the prices of food and new investments, both public and private, in
other products and services that depend on renewability and the efficiency with which we
nature. Hidden costs often only materialize in use our natural resources.
the distant future, well beyond the time when
An important aspect of the bioeconomy
the actions that led to these costs took place.
approach is to look towards science, technology
For example, exposure to antibiotics and
and innovation for new ways of producing not
malnutrition in early childhood may only affect
only more, but also better and healthier food

11
with much fewer natural resources, while at methane production by ruminants; increasing
the same time regenerating our degraded biofuel production; enhancing waste treatment;
natural resource base. Microbiome science development of new antimicrobials; and
has opened up an important window of prevention and treatment of various diet-
opportunity for this type of radical change related communicable diseases, antimicrobial
through very practical solutions that also hold resistant infections, etc. In fact, many of these
great business potential and are therefore applications are already being tested or applied.
politically attractive. The European Union,
Public sector investment in microbiome
for example, is investing heavily in national
research and innovation is rapidly gaining
and regional bioeconomy strategies and the
traction in a growing number of countries.
cross-disciplinary research and innovation
Private sector interest is large and also growing
that go with such strategies. Other countries
as microbiome research is leading to new
are also making major inroads – for example,
products and services and opening up new
through collaborative research platforms like
markets. Scientific discovery and innovation
the Human Microbiome Project and the Earth
are taking place ever more rapidly. However, the
Microbiome Project, which bring together
speed at which this new knowledge leads to
research centres, universities, companies, as
policy debate and change remains painstakingly
well as scientists, consumers, farmers, food
slow. Developing countries also run the risk
processors and health practitioners.
of staying behind. The fact that microbiome
Some of the latest microbiome discoveries science cuts across traditional borders of
and innovations have demonstrated a potential scientific domains, technical disciplines and
to rethink the way we produce our food, while economic sectors adds to the complexity of the
preserving and leveraging our natural resources, policy, regulatory and institutional implications
for example: replacing antimicrobial growth of these developments. It is, however, time to
promoters, inorganic fertilizers, and pesticides; look thoroughly at this myriad of tiny beings
improving plant nutrition; promoting soil that may explain the missing links between our
carbon sequestration and soil remediation; biggest challenges.
enhancing animal feed conversion; reducing

12
 WHAT IS FAO’S ROLE?

Unpacking complex issues, engaging with multiple stakeholders and bridging boundaries
between science and policy are core functions in which the Food and Agriculture
Organization of the United Nations (FAO), has a comparative advantage. Faced with the
challenges and opportunities described above, FAO needs to engage with the scientific
community worldwide to identify and share innovative ideas and solutions that can bring
rapid and tangible food systems change. From a microbiome science perspective, this
entails investing in a dedicated science-policy interface, the purpose of which would be to:

• monitor the latest scientific research in the microbiome domain as it pertains to healthy
diets, agriculture, climate, the environment, and food systems and the bioeconomy more
broadly. This would also include assessing which evidence is solid enough to inform
sound policy and technical advice (e.g. scientific literature and systematic reviews,
expert consultations);

• assess the implications arising from the combination of innovations in the food
system and research on the role of microbiome in human health for policy, legislation,
standards and other normative instruments at national, regional and global levels (e.g.
implications for food safety risk assessments and standards, implications for food-
based dietary guidelines);

• inform research on issues that need further investigation from a microbiome perspective
(e.g. related to the impact of specific compounds on the gut microbiome, country
assessments of factors that drive NCDs through gut dysbiosis);

• promote debate among the scientific community, policy-makers, private sector actors
and consumers; and

• promote long-term partnership with centres for scientific research and innovation, including
south-south and other forms of cross-country cooperation, as a means of promoting
greater uptake of new science, innovation, development and application by end-users.

13
 FAO’S ROLE
B OUN D A R I E S B
NG

ET
GI

WE
BRI D

EN
UNPACKING SCIENCE AND POLICY
COMPLEX
ISSUES ENGAGING
WITH DECISION MAKERS
AND MULTIPLE STAKEHOLDERS

BRINGING DIFFERENT
SCIENTIFIC DISCIPLINES IDENTIFYING
TOGETHER AND SHARING
INNOVATIVE IDEAS

14
 REFERENCES
Blaser, M.J. 2014. The Microbiome Revolution. J Clin Locey, K.J. & Lennon, J.T. 2016. Scaling laws predict
Invest. 124(10):4162-5 global microbial diversity. Proc Natl Acad Sci U S A.
113(21):5970 -5975.
Clemente, J.C., Ursell, L.K., Parfrey, L.W. & Knight, R.
2012. The impact of the gut microbiota on human Lynch, S.V. & Pedersen, O. 2016. The Human Intestinal
health: An integrative view. Cell. 148(6):1258 -1270. Microbiome in Health and Disease. N Engl J Med.
375(24):2369 -2379.
Domínguez Bello, M.G., Knight, R., Gilbert, J.A. & Blaser,
M.J. Preserving microbial diversity. 2018. Science. Sheth, R.U., Cabral, V., Chen, S.P. & Wang, H.H. 2016.
362(6410): 33-34. Manipulating Bacterial Communities by in situ
Microbiome Engineering. Trends Genet. 32(4):189 -200.
Doré, J., Multon, M.C., Béhier, J.M., Affagard, H.,
Andremont, A., Barthélémy, P., et al. 2017. The human Tamburini, S., Shen, N., Wu, H.C. & Clemente, J.C. 2016.
gut microbiome as source of innovation for health: The microbiome in early life: Implications for health
Which physiological and therapeutic outcomes could outcomes. Nat Med. 22(7):713 -722.
we expect? Therapies. 72(1):21 -38. Tsiaoussis, J., Antoniou, M.N., Koliarakis, I., Mesnage,
Flandroy, L., Poutahidis, T., Berg, G., Clarke, D., et. Al. R., Vardavas, C.I., Izotov, B.N. & Tsatsakis, A. 2019.
2018. The impact of human activities and lifestyles on Effects of single and combined toxic exposures on
the interlinked microbiota and health of humans and the gut microbiome: Current knowledge and future
ecosystems. Sci. Total Environ. 627:1018-1038. directions. Toxicology Letters. 312:72-97.

Gentile, C.L. & Weir, T.L. 2018. The gut microbiota at Wallace, R.J., Sasson, G., Garnsworthy, P.C., Tapio, I.,
the intersection of diet and human health. Science. Gregson, E., Bani, P., et al. 2019. A heritable subset
362(6416): 776-780. of the core rumen microbiome dictates dairy cow
productivity and emissions. Sci Adv. 5(7):eaav8391.
Golonka R.M., Yeoh, B.S. & Vijay-Kumar, M. 2019.
Dietary Additives and Supplements Revisited: the Willett, W., Rockström, J., Loken, B., Springmann,
Fewer, the Safer for Gut and Liver Health. Current M., Lang, T., Vermeulen, S. et al. 2019. Food in the
Pharmacology Reports. 5(4): 317-317. Anthropocene: the EAT-Lancet Commission on
healthy diets from sustainable food systems. Lancet.
Hadrich D. 2018. Microbiome Research Is Becoming 393(10170):447-492.
the Key to Better Understanding Health and Nutrition.
Front Genet. 9:212 Zmora, N., Suez, J. & Elinav, E. 2019. You are what
you eat: diet, health and the gut microbiota. Nat Rev
Jin, Y. X., Wu, S. S., Zeng, Z. Y. & Fu, Z. W. 2017. Gastroenterol Hepatol. 16(1):35-56.
Effects of environmental pollutants on gut microbiota.
Environmental Pollution. 222:1-9.
HUNGER ERADICATION, FOOD SECURITY AND NUTRITION PROGRAMME MANAGEMENT TEAM (SP1)
[email protected]
www.fao.org

FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS (FAO)

Viale delle Terme di Caracalla
00153 Rome, Italy

CA6767EN/1/10.19
© FAO, 2019
Some rights reserved. This work is available
under a CC BY-NC-SA 3.0 IGO licence