We are hosts in a microbial World… · MICROBES KEEP THE GREAT MAJORITY OF THE PLANET GENETIC DIVERSITY, ... Nutrition for sustainable and healthy diet Climate smart and env. sustainable

We are hosts in a microbial World…

…there are 100 million times as many bacteria on Earth (13x1028) as stars in the universe, and virus are even more (13x1031)

https://www.micropia.nl/en/

MICROBES KEEP THE GREAT MAJORITY OF THE PLANET GENETIC DIVERSITY,

METAGENOMICS IS MICROBIAL!

The astonish level of diversity of shapes and functions of the µ_crobial (10-3 mm = µ) world

VIRUS – BACTERIA - FUNGI

BACTERIA INHABIT OUR PALNET SINCE 3.5 BILLION OF YEARS

microbial evolution past 3.5 billion of years has produced an immense biological diversity in genetic and phenotypic variation

MICROBES RAPRESET 60% OF THE PLANET BIOMASS

2/3 OF THE PLANET LIFE IS MICROBIAL

MICROBES ARE THE BASEMENT OF EUCARIOTIC (VISIBLE) LIFE ON EARTH

MICROBES IN NATURE LIVE IN COMMUNITIES OF DIFFERENT SPECIES, THE MICROBIOMES

environmental microbiomes are the basement of life on earth,

being responsible of the biogeochemical cycles (C, N, P

and S), C recycling and food transformation

all the macroorganisms are holobionts, defined as animals or plants together with associated microorganisms living on them.

The holobionts microbiomes contribute to the host physiology

MICROBES IN NATURE LIVE IN COMMUNITIES OF DIFFERENT SPECIES, THE MICROBIOMES

CLASSICAL METHODS FOR STUDYING MICROBES ARE GROWTH DEPENDENT

metagenomics is the only approach for unlocking and exploiting the immensity of

microbiomes diversity

cultivable microorgansimsconstitute much less than 1% of

the total microbial population (12.000 vs 4 M)

METAGENOMIC THE BEST SEARCHING TOOL FOR MICROBIAL BIOPROSPECTING

INTRODUCTION

metagenomics is the untargeted sequencing of the genetic material present in a given sample

MICROBIOMES CENTRALITY

environmental microbiomes

host associated

soilwaterair humananimalplant

biogeochemical cycles

physiology and health planet health

earth microbiomes

AIR MICROBIOME

8x10 CFU Exp4 ml-1

primary biological aerosols (PBA) are directly released from the biosphere

PBA undergo to mixing with other aerosols, including biogenic secondaryaerosols (SOA) formed upon oxidation of volatile organic compounds (VOC)

AIR MICROBIOME ESTABLISHMENT

https://youtu.be/Ye45DGkqUkE?t=122

Joan Cáliz et al., PNAS 2018

BIODIVERSITY AND VARIABILITY OF AIBORNE MICROBIAL COMMMUNITIES

provenience and seasonal variability

terrestrial ecosystems are the major source of ice nucleation

active microrgansisms which influence the evolution of clouds

and precupitation

ICE NUCLEATION

MICROBIAL ECOLOGY IN THE OCENAS Sunagawa et al., Science 2015

analysis of 243 ocean microbiome samples, collected at 68 locations representing all main oceanic regions (except for the Arctic) from three depth layers,

ocean microbiomes contains the largest microbial reservoir from

the planet. At least 35.000 prokaryotes species and 40 M non

redundant novel genes

temperature and oxygen are dominant drivers of

variation in surface water microbiomes

SOIL

soils harbor some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage.

global distribution patterns and functional gene repertoires of soil microorganisms

both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, the relative contributions of these microorganisms to global nutrient cycling varies spatially.

fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH

Bahram et al., Nature 2018

BIOGEOCHEMICAL CYLES

the biogeochemical cycles put into connection biotic and abiotic components in an ecosystem

All macro-organisms populating our planet exist as holobionts

Holobionts are defined as animals or plants together with associated microorganisms living on them (known as microbiomes)

HOLOBIONTS EXIST WITHIN A RANGE OF SYMBIOSIS

OBLIGATORY SYMBIOSIS

e.g. herbivores, termites, corals, sponges, legumes …

WEAK SYMBIOSIS

e.g. carnivores, omnivores, non-human primates and human beings …

HOLOBIONTS AND HOLOGENOME

THE ANIMAL MICROBIOMES

each animal has its peculiar microbiome whose structure depends on host

genetics and dietary niche, seminal animals share similar microbiomes

Fitness contribution of microbiomes to their host

• NITROGEN FIXATION IN LEGUMINOSES

• CELLULOSE DEGRADATION IN RUMINANTS

• PHOTOSYNTHESIS BY MICROALGAE IN CORALS

• OXIDATION OF ORGANIC COMPOUNDS IN SPONGES

• ESSENTIAL AMINO ACID SYNTHESIS IN MAMMALIAN OMNIVORES

• MODULATION OF THE IMMUNE FUNCTION IN MAMMALIAN OMNIVORES

• PROTECTION FROM PATHOGEN ATTACK IN MAMMALIAN OMNIVORES

OB

LIG

ATO

RYW

EAK

human beings and all other animals host complex and specific microbial communities in different body sites, eg. skin, mouth, gut, esophagus …

HUMAN AND ANIMAL MICROBIOMES

THE HUMAN INTESTINAL MICROBIOTAwe are 90% bacteria, 1013–1014 habits our body and the great majority

of these microorganisms is hidden in the gastrointestinal tract

• 1012 CFU/g• up to 1.5 kg

the most dense bacterial ecosystem on our planet

organized in a ecosystem of highly

interconnected microbes

HUMAN INTESTINAL MICROBIOTA

• enhancement of the digestive efficiency and modulation of energetic homeostasis

• vitamin synthesis

• competitive barrier against colonization/invasion

• development, education and function of the immune system• strengthening of the GIT epithelium impermeability

• detoxification of xenobiotics

• central nervous system modulation

• endocrine system modulation

our bacterial counterpart provides essential features we have not evolved

WE MEET OUR MICROBIOME QUITE EVERY DAY

rhizosphere microbiota, microbes population the layer of soil adhering to the root

root/endophytic microbiota, microbiota within the host tissue

phyllosphere microbiome, microbes population living of leaf surface

THE PLANT MICROBIOME

rizodeposition, photosynthesis derived organic compounds secreted to the rozosphere sustain and

selecting for the plant microbiomes

rozosphere and root microbiomes protect plant from pathogens, enhance mineral acquisition, regulate energy

metabolism and support growth

ROZODEPOSITION AND GROWTH, THE MUTUAL INTERACTION

the Earth Microbiome Project is a systematic attempt to characterize global microbial taxonomic and functional diversity

for the benefit of the planet and humankind

1x10-20 % OF THE TOTAL DNA OF EARTH HAVE BEEN SEQUENCED

METAGENOMES EXPLOITATION FOR ONE HEALTH

human health Sustainability

food security

holistic and integrative vision of health, were the health of the planet ecosystems and all organisms living on it are strongly interconnected

MICROBIOMES AND CLIMATE CHANGE

WORLD MICROBIOME DAY – JUNE THE 27TH

communicate and disseminate the microbiome importance for the human beings and the planet life

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 818290.

uses 70% of H2O Food production

now uses 30% of energydelivers 25% of GHG

9 billion by 2050 60% more food

Sustainable food production is now a EU priority

Nutrition for sustainable and healthy diet

Climate smart and env. sustainable food systems

Circularity and resource efficiency food systems

Innovation and empowerment of communities

Prioritize sustainable food production

current food systems exert a

strong pressure on natural resources

climate change is occurring faster than expected

Given the increasing planet

population, we need to further

boost food production by 2050

The perfect storm

We need to change the paradigm for food production

We must reduce the footprint of food systems on natural resources, while keeping the

production of secure and safe food for the future

Microbiomes ecological services for food systems

MICROBIOMES

PLANTSANIMALS

HUMANS ENVIRONMENT

ONE HEALTHQUALITY SUSTAINABILITY

SAFETY PRODUCTIVITY

CIRCLES

CIRCLES

CIRCLES aims to discover, translate and communicate innovative microbiome-based

applications to improve EU food systems

QUALITY SUSTAINABILITY

SAFETY PRODUCTIVITY

The Circles aims

CIRCLES will provide Smart Microbiome Food Systems (SMFSs) for 7 food chains relevant to

the EU market

Spinach – TomatoesRomania, Italy, Spain

Poultry – PigsItaly

Atlantic salmon; Seabream; Fisheries Ireland, UK, Norway; Spain, Italy,

Greece

The real-world approach, our labs are real-world food systems

A new paradigm of food production based on microbiomes biotechnology

SMFSs are defined as food systems where microbiomes circulation and dynamics are optimized for better performances

in terms of productivity, quality, safety and sustainability

MICROBIOMES BIOTECHNOLOGY

design of microbiomes-tailored circular actions based on the integrative usage of Smart Microbiome Modulators (SMMs) for optimizing the food system microbiomes

Integrative microbiomes biotechnology

A CONCRETE EXAMPLE, AMR REDUCTION

Microbiomes to combat the spread of antibiotic resistances

antibiotic-free food systems

microbiomes impact on

animal helath

SMFS value chain

SMFS

ExploitationCommunication

business models

IPR protection

brought to the marketlicensing private equity investments

fund raisingcommunication plan (internal)involvement (stakeholders) engagement (citizens)

SMFS ManagerSMFS Certifier

Smart Microbiomes Food Products (SMFPs) spinach, tomato, chicken meat, pork meat, flesh of salmon, flesh of seabream Microbiome Transparent Labels (MTLs)

Drone sampling platforms for env. measuring in food systemsSMMs for plants/animals

SMMs for wastewaters SMMs for litters

SMMs for sediments

Sampling kit for SMFS biomarkers

Sampling kit for worker microbiomes

jobs

agro biotech

tools

foodsproducts

v

food safety

SMFS expected impacts

SMFS

SHORT TERM LONG TERMbetter C footprint Sustainability

nutrition security

new products new

marketsnew jobs

new services

How will we create the SMFSs in the real world?

Current food systems are far from being microbiomes optimized

domestication has forced the loss of microbiomes-dependent probiotic functions in food systems

probiotic functions internal to the food system microbiomes have never been optimized

food system microbiomes are depleted in their probiotic potential

we have no holistic and ecological vision of the food system microbiomes, the hubs at the connection with food system co-variates,

their dominant dynamics and circulations

• Observe wild microbiomes (holobionts and environment) to discover hubs as providers of probiotic functions lost in the current food systems

• Observe current food system microbiomes to search for hubs as providers of internal probiotic functions

• Observe the dominant dynamics across food system microbiomes to understand the ecological rules (dominant dynamics and circulations) governing these ecosystems

In SMFSs, we aim to reintroduce lost microbiome functionalities, as well as to enhance internal probiotic functions

SMFS, a new paradigm for a microbiome-optimized food system

soil/feed

d

Food system microbiomes and their connections are longitudinally assessed across each food system actor in parallel with key co-variates for evaluating sustainability, safety, quality and productivity

plant/animal processing food

waste

workers

Observe food system microbiomes with a holistic approach

available data from public databases

Learn from nature

poll. env.

feed

animals plantswild life assessment

microbiomes from the wild counterparts of the food system actors

soil

food system microbiomes from different production sites in the real world

Observational phase

wild microbiomes from correspondingholobionts and environments

1.

2.

n.

Conceptual framework of the modelling phase

ECOLOGICAL RULES

FOOD SYSTEM MICROBIOMES AND

CO-VARIATES

WILD MICROBIOMES

HUBS AS PROVIDERS OF INTERNAL PROBIOTIC

FUNCTIONS

HUBS AS PROVIDERS OF LOST PROBIOTIC

FUNCTIONS

SELECTION OF SMMs AS PROVIDERS OF LOST

PROBIOTIC HUBS

SELECTION OF SMMs TO ENHANCE INTERNAL

PROBIOTIC HUBS INTEGRATIVE CIRCULAR ACTIONS

SMFS MODELS

Internal and lost probiotic hubs and functions

longitudinal sampling across the food system

network architecture

correlationsmicrobiomes - covariates

probiotic hubs

SMFS model, network architecture and probiotic hubs

soil/feed

d

SMMs will be used in integrative microbiomes-tailored circular actions for the optimization of the food system microbiomes

plant/animal processing food

waste

workers

Circular actions, innovative applications for microbiomes-optimized food systems

SMMsagricultural biologicals

SMMsbioactivators/biopromoters

SMMsfeed

supplements

Intervention phase

food system microbiomes from different production sites in the real world

1.

2.

n.

MODULATION

MONITORING

VALIDATION

SMFS VALUE CHAIN

VEGETABLES MEAT FISH

sustainable production of secure, safe and high-quality foods

Commercial exploitation of new products and services