TOP TEN IN GASTROENTEROLOGIA ISEO 13 14 MARZO 2015TOP TEN IN GASTROENTEROLOGIA - ISEO 13_14 MARZO 2015

Microbiota intestinale:Microbiota intestinale: un decennio diun decennio di

conquisteconquistemarco candela@unibo itmarco.candela@unibo.it 

HUMAN INTESTINAL MICROBIOTAwe are 90% bacteria (1013–1014) and our bacterial counterpart provideswe are 90% bacteria (10 10 ) and our bacterial counterpart provides

essential features we have not evolved

• enhancement of the digestive efficiency and modulation of energetic homeostasisenergetic homeostasis

• vitamin synthesis

titi b i i t l i ti /i i• 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 modulationendocrine system modulation

WHAT IS MISSING IN GERM-FREE MICE

PHYLOGENETIC DIVERSITY

> 1000 species

6 (out of 100) bacterial phyla• Firmicutes, Bacteroidetes : 90%• Actinobacteria, Proteobacteria, Fusobacteria

and Verrucomicrobia : 10%and Verrucomicrobia : 10%

GUT METAGENOME FUNCTIONAL DIVERSITYDIVERSITY

MICROBIOME 106 GENES

58% KNOWN 42% UNKNOWN58% KNOWN 42% UNKNOWN • carbohydrate metabolism (CAZymes)• energy metabolisme e gy e abo s• amino acid metabolism• biosynthesis of secondary metabolites• metabolism of cofactors and vitamins• metabolism of cofactors and vitamins

SUBSTRATES OF THE GM CAZymes ARSENALthousands of enzymes while we possess only 17thousands of enzymes while we possess only 17

El Kaoutary et al., Nature Rev. 2013

not accessible to the human glycobiome !

The GM possesses a broad glycobiome complexity, complementing the limited diversity of the human glycobiome and enhancing the superorganism capacity

to metabolize complex polysaccharides

WE ARE BORN STERILE IN A MICROBIAL WORLDWORLD

environmental microorganisms

vaginal flora (mother)

fecal flora (mother / father) Lactobacillaceae

Gut microbiota Proteobacteria

skin flora (mother / father)-Streptococcus-Staphylococcus

Streptococcus, Staphylococcus

Proteobacteria

mother’s milkmicroorganisms

mouth flora (mother / father)p y

-Lachnospiraceae-Ruminococcaceae-Bacteroidaceae-Bifidobacteriaceae

Streptococcus, Staphylococcus, Proteobacteria, Actinobacteria, Bacteroidetes

INFANT MICROBIOTAGE

NO

ME - low diversity

- highly dynamic- Bifidobacterium-dominated

f b

mother’s milk-Bifidobacteriaceae-Proteobacteria (dead)

INFANT MICROBIOTA

VID

UA

L G

WEANING - presence of aerobes - Bacteroidetes and Veillonella as minor components

ADULT INDIVIDUAL MICROBIOTA

IND

I p

(from 1st year to all life)

there is a strong selection towards a readily changeable individual microbiome profilechangeable individual microbiome profile

ECOSYSTEM PLASTICITY UNIQUENESS OF OUR HISTORY, PHYSIOLOGY AND LIFESTYLEPHYSIOLOGY AND LIFESTYLE

peculiar structure and temporal dynamics of the individual intestinal microbiota

provide microbiota ecosystem services in the face of personalized physiology, immune system, environmental or dietary exposure and lifestyle

The gut microbiota is a multistable systemCandela M Biagi E Maccaferri S Turroni S and Brigidi P Intestinal microbiota is a plastic factor responding to environmentalCandela M., Biagi E., Maccaferri S., Turroni S. and Brigidi P. Intestinal microbiota is a plastic factor responding to environmental 

changes. Trends Microbiol. 2012 Aug; 20(8): 385‐91.

MUTUALISM

n different compositional layoutsn different compositional layouts

OPTIMIZATION OF SUPERORGANISM’S METABOLIC AND IMMUNOLOGICAL PERFORMANCESIMMUNOLOGICAL PERFORMANCES

LIFESTYLE IMPACTS THE GM ON A DAILY TIMESCALE two subjects, everyday sampling, iOS App to record everyday lifestyle and dietary habits

David et al., Genome Biol. 2014

PERIOD OF STATIONARY GM DYNAMICS

di di t b t l idlmedian distance between samples rapidly reaches the asymptoterapid variation in niche size due to daily fluctuation in diet

ABRUPT CHANGES IN GM CONFIGURATION

disruptive windows resulting in broad community disturbance: travel to developing nation (A) Salmonella infection (B):nation (A), Salmonella infection (B):

A) reversible environmental disturbanceB) non-reversible community disturbance

gut microbiome variation involves changes in relative abundance of already present bacteria (allocative efficiency), colonization of new species (dynamic efficiency) is

relatively rare

TEMPORAL VARIABILITY IS A PERSONALIZED MICROBIOME FEATURE 85 adults, weekly sampling, 3 months, recording of lifestyle and dietary habits

Flores et al., Genome Biol. 2014

INDIVIDUAL VARIATION IN THE DEGREE OF GM TEMPORAL

VARIABILITYVARIABILITY

INDIVIDUALS WITH MOREINDIVIDUALS WITH MORE STABLE GM COMPOSITION

ARE INDIVIDUALS WITH MORE DIVERSE COMMUNITY

BACTEROIDACEAE WERE THE OS SMOST ABUNDANT IN STABLE

INDIVIDUALS, CLOSTRIDIACEAE AND LACTOBACILLACEAE INLACTOBACILLACEAE IN VARIABLE INDIVIDUALS

The gut microbiota describes an adaptive trajectory along human aging 

Candela M., Biagi E., Turroni S., Maccaferri S., Figini P., Brigidi P. Dynamic efficiency of the human intestinal i bi t C iti l R i i Mi bi l 2013 S t O li bli h dmicrobiota. Critical Reviews in Microbiology, 2013. Sept, Online published.

GUT MICROBIOTA CHANGES ITS PHYLOGENETIC AND FUNCTIONAL PROFILE FROM INFANCY TO ELDERLY PROVIDING THE HOST WITH ECOLOGICAL SERVICES CALIBRATED FOR EACH STAGE OF LIFE

CONVENTIONALIZATION OF GERM-FREE MICE

CONVENTIONALIZATION OF GERM-FREE MICE ALLOWS THE RECOVERY OF THE LOST MICROBIOTA-DEPENDENT ECOLOGICAL

SERVICESSERVICES

SPECIFIC TIME WINDOW ENTIRE LIFE SPAN

• IMMUNE FUNCTION (INFANCY)• REGULATION OF CENTRAL NERVOUS

S S O ( C )

• NUTRITION• PROTECTIONSYSTEM AND BEHAVIOR (INFANCY)

• REGULATION OF SEX HORMONES(PUBERTY)

PROTECTION• GIT STRUCTURE

Infant‐type microbiota: Bifidobacterium‐dominated, simple and readily changeablesimple and readily changeable 

INFANT‐TYPE MICROBIOTA IS STRUCTURED TOCOPE WITH INFLAMMATION, BEING CO‐EVOLVEDTO PRIME THE EARLY IMMUNE SYSTEM IN THETO PRIME THE EARLY IMMUNE SYSTEM IN THECONTEXT OF TRANSIENT INFLAMMATORYRESPONSES

Centanni M., Turroni S., Consolandi C., Rampelli S., Peano C., Severgnini M., Biagi E., Caredda G., De Bellis G., Brigidi P., Candela M. The enterocyte‐associated intestinal microbiota of breast‐fed infants and adults responds differently to a TNF‐α‐mediated pro‐

inflammatory stimulus. PLoS ONE. 2013 Nov; 8(11): e81762. 

Adult‐type microbiota: complex and adaptable ecosystem dominated by Firmicutes and Bacteroidetesdominated by Firmicutes and Bacteroidetes

HIGHLY DIVERSE, THE ADULT-TYPE GM IS AN ADAPTIVE COMMUNITY FUNCTIONALLY STRUCTURED TO DEGRADE A VAST RANGE OF

INDIGESTIBLE DIETARY AND HOST SUBSTRATESINDIGESTIBLE DIETARY AND HOST SUBSTRATES

RANGE OF METABOLIC ENDPOINTS WITH THE POTENTIAL TO MODULATE AND REGULATE SEVERAL ASPECTS OF OUR PHYSIOLOGY

ENERGETIC HOMEOSTASIS IMMUNE HOMEOSTASIS

HOST POLYSACCHARIDES STARCH AMINO ACIDSPLANT CELL WALL

cellulose

RuminococciSOLUBLE CELL WALLPOLYSACCHARIDES

hemicellulose, xylan, pectin, mannans,inulin, fructans ACETATE

Bacteroidetes Clostridium clustersIV and XIVa

proteolyticclostridia and

low CO2 IV and XIVaFaecalibacterium prausnitzii,

Butyrrivibrio, Roseburia, Eubacterium rectale

Bacteroidetes(Alistipes) ACETATE

SUCCINATE

low CO2

PROPIONATE BUTYRATE

SUCCINATE

SCFA

acetogensmethanogens

PROPIONATE

H2BCFA

PHENOLIC AND INDOLICacetogens

Blautia hydrogenotrophicamethanogens

Methanobrevibacter smithii

sulfate-reducing bacteriaCH4

METHYLAMINES

INDOLIC METABOLITES

ACETATEbacteria Bilophila wadsworthia

H2S

CH4 ACETATE

IMPACT OF DIETARY FAT ON THE GUT MICROBIAL COMMUNITIESCOMMUNITIES

DIETARY FATS BILE SECRETION

BILE ACIDSIN THE GUT

MICROBIOTA

EnterobacteriaceaeFirmicutesClostridia, Erysipelotrichi

MAKE-UP

sulfate-reducing Bacteroidetes

H2SSECONDARY BILE ACIDS

bacteria Bilophila wadsworthia

SCFA POSSESS A KEY MULTIFACTORIAL ROLE IN HUMAN BIOLOGY, METABOLIC HOMEOSTASIS,

Tilg et al., Gut 2014

peptide Pyy expression (2): inhibition of gut motility; increase ofpeptide Pyy expression (2): inhibition of gut motility; increase of intestinal transit rate; reduction of energy harvest from diet

glucagon-like peptide 1 expression (3): increase of insulin sensitivity

ENERGY SOURCE FOR

COLONOCYTESintestinal gluconeogenesis activation (5): favors glucose control

expression of fasting-induced adipose factor (6): favors fat storageexpression of fasting-induced adipose factor (6): favors fat storage

suppression of insulin signaling in adipose tissue (4)

SCFA POSSESS A KEY MULTIFACTORIAL ROLE IN HUMAN BIOLOGY, REGULATION OF THE HOST IMMUNE FUNCTION,

Tilg et al., Gut 2014

development of colonic and extrathymic Treg

regulation of bone marrow hematopoiesisregulation of bone marrow hematopoiesis

regulation of dendritic cell function

Immune homeostasis

GM PLASTIC RESPONSE TO DIET

DIFFERENT GM COMPONENTS SHOW A DIFFERENT PERFORMANCE IN THE DEGRADATION OF DIETARY SUBSTRATES

substrate selection for the better metabolizers

GM-HOST CO-METABOLIC LAYOUTS

diets regulates microbiota composition and metabolic output with a final g p pimpact on host physiology

amino acids animal fatcomplexSACCHAROLYTIC

METABOLISMPROTEOLYTIC METABOLISM

FATADAPTATION

amino acids animal fatcomplex polysaccharides

highly diverse community of low diverse community selection of a low diverse polysaccharide-degrading

Bacteroidetes andClostridia establishing

yenriched in specialized

proteolytic Alistipes and Clostridia

community made of bile resistantErysipelotrichi,

Bilophila wadsworthia, syntrophy in the gut Enterobacteriaceae

SCFA PHENOLIC AND

H2SSECONDARY BILE ACIDS

SCFA PHENOLIC AND INDOLIC

METABOLITESSCFACH4SUCCINATE

BCFAMETHYLAMINESHealth

promotingDisease

associatedp g associated

THE GM-HOST MUTUALISTIC AGREEMENT

THE GM-HOST MUTUALISTIC AGREEMENT INVOLVES THE CONSTANT CONSUMPTION OF PLANT FOODS WITH AN

OCC S O CO S O O OO SOCCASIONAL CONSUMPTION OF ANIMAL FOODS

PALEOLITHIC AND NEOLITHIC DIETSPALEOLITHIC AND NEOLITHIC DIETS(99% of our evolutionary history)

Providing the host with SCFA from indigestible plant polysaccharides GM allows the host to improve energy extraction

from diet and regulates energy homeostasisfrom diet and regulates energy homeostasis

THE GM OF HADZA HUNTER-GATHERERSA mirable example of GM-host adaptive co-evolution in p p

response to diet

FORAGING SUBSISTENCE

- direct interface with the natural environmentdirect interface with the natural environment, deriving their wild food

- no cultivation or domestication of plants and animals minimal agricultural products fromanimals, minimal agricultural products from external sources, < 5% calories

HEAVY PLANT BASED DIETHEAVY PLANT BASED DIET

- 70% of kcal from plant foods; 30% from bird and animal meat (dry season);

- diet rich in polysaccharides, starch and protein while lean in fat;

Schnorr SL.†, Candela M.†, Rampelli S., CentanniM., Consolandi C., Basaglia G., Turroni S., Biagi E.,Peano C., Severgnini M., Fiori J., Gotti R., De BellisG., Luiselli D., Brigidi P., Mabulla A., Marlowe F.,protein while lean in fat;

- wild foods: tubers, leafy green foliage, baobab fruit, berry, honey and meat

Crittenden A.N., Henry A.G. Gut microbiome fromthe Hadza hunter-gatherers. Nature Communication.2014 Apr; 5: 3654.

HADZA POSSESS A UNIQUE CONFIGURATION OF THEIR GM THAT CAN BE LINKED TO THEIR FORAGING LIFESTYLEGM THAT CAN BE LINKED TO THEIR FORAGING LIFESTYLE

HADZA GM IS ADAPTED TO THEIR FORAGING LIFESTYLELIFESTYLE

GM FEATURE HOST NEEDS IN HADZA LAND

ENRICHMENT IN FIBROLYTIC BACTERIA

HIGH BACTERIAL DIVERSITY HARD DIGESTIBLE FOOD

HEAVY PLANT BASED DIETENRICHMENT IN FIBROLYTIC BACTERIA high abundance in xylan-degrading Prevotella, Treponema, unclassified Bacteroidetes and Clostridiales

SEX-RELATED DIVERGENCE IN GM STRUCTURE hi h T i H d

SEX DIFFERENCES IN DIET COMPOSITION (higher consumption

f l t f d i )higher Treponema in Hadza women

ABSENCE OF BIFIDOBACTERIUM

of plant foods in women)

ABSENCE OF AGRO-PASTORAL-DERIVED FOODS

ENRICHMENT OF OPPORTUNISTIC BACTERIA

IMMUNE EDUCATION TO THE DIRECT INTERFACE WITH NATURAL ENVIRONMENTProteobacteria and Spirochaetes NATURAL ENVIRONMENT

MUTUALISM INTERRUPTION

MUTUALISM

Switch-like behavior, making sudden jumps from different steady states

ABNORMAL IMMUNE

DEREGULATIONDIETARY INTAKE

INFLAMMATIONINFECTIONANTIBIOTIC

INTAKE

RUPTURE OF THE GM-HOST MUTUALISTIC AGREEMENT AND COMPROMISED HOST ENERGY BALANCE AND IMMUNE

HOMEOSTASISHOMEOSTASIS

AN INCREASE IN CALORIC INTAKE (HIGH FAT – HIGH SUGAR DIET) SELECTS FOR OBESOGENIC GMDIET) SELECTS FOR OBESOGENIC GM

HIGH FERMENTATIVE INCREASE OF ENERGY HIGH FERMENTATIVE CAPACITY

HIGH BILE ACID

HARVEST FROM FOOD

MODULATION OF DIETARY METABOLISM

OVERALL INFLAMMATORY POTENTIAL

FAT ABSORPTION

METABOLIC ENDOTOXEMIAPOTENTIAL ENDOTOXEMIA

GUT MICROBIOTA DYSBIOSES IN T2D Biagi E., Candela M., Soverini M., Quercia S., Consolandi C., Severgnini M., Fallucca F., Pianesi M., Pozzilli P.,

S S f 2Rampelli S., Turroni S., Brigidi P. Modulation of gut microbiota dysbioses in type 2 diabetic patients by macrobioticMa-Pi 2 diet. IHMC. Luxembourg 2015

Depletion in health-promoting SCFA producers

Reduced production of arginine (insulinogenic) and higher alanine (associated with BMI and cholesterol level)

Higher load of pro-inflammatory Enterobacteriaceae and Collinsella

level)

Higher load of functions involved in immuno-escaping processesEnterobacteriaceae and Collinsella immuno escaping processes

GUT MICROBIOTA IN INFLAMMATORY DISEASES

VERY RECENT NATURE COMMENT

Microbial Ecology of Health UNITDept Pharmacy and Biotechnology University of Bologna ItalyDept. Pharmacy and Biotechnology, University of Bologna, Italy

Marco Candela

Silvia Turroni

Sara Quercia

Prof. Patrizia

Matteo Simone

QuerciaBrigidi

Matteo Soverini

Simone Rampelli

Elena Biagi