Diet and Gut Microbiota

Leo Dieleman, MD PhD

Professor of Medicine

Div. of Gastroenterology, Univ. of Alberta, Edmonton

Financial Disclosure

Consultant for Abbvie, Janssen, Shire, Takeda

Grant support: CIHR, Alberta Innovates, Broad Foundation, Beneo-Orafti

Learning Objectives

Understand how gut microbiome affects health

Learn how diets affect microbiome composition and function

Understand the pathogenesis of IBD and role of diets

The Intestinal Microbiome – an “organ” of its own

Human gut contains more than 1000 species with 99% belonging

to about 40 species10-fold the number of human cells, and predicted to encode

100-fold more unique genes than our own genome

Beneficial role of microflora

Harvest of energy from food not digested by the host

Production of vitamin K

Production of short chain fatty acids

Trophic effects on the intestinal epithelium

Maturation of the host’s innate and adaptive immune

responses

Fragment length (bp)

50 100 150 200 250

Freq

uenc

y

0

50

100

150

200

250

300

0 week 9 week

Ent

erob

acte

riace

ae

Mor

axel

lace

aeB

acte

roid

acea

eBa

cter

oida

ceae

Leuc

onos

toca

ceae

(Leu

cono

stoc

)

Rum

inoc

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ceae

Lach

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ceae

Lach

nosp

irace

ae

Rik

enel

lace

ae

Leuc

onos

toca

ceae

(Wei

ssel

la)

Subject DMO

Dominant fecal microbiota remains stable at intra-individual level but is unique for each individual – data from β-fructans

(oligofructose enriched-inulin) interventional study in active UC

DGGE

0%

20%

40%

60%

80%

100%

sCLD

0wk

sCLD

9wk

sGTL

0wk

sGTL

9wk

sLAM

0wk

sLAM

9wk

sMEF

0wk

sMEF

9wk

sMPB

0wk

sMPB

9wk

sNM

R0w

ksN

MR

9wk

sPC

V0w

ksP

CV9

wk

16S rDNA sequencing

Fragment length (bp)

50 100 150 200 250

Freq

uenc

y

0

100

200

300

400

0 week 9 week

Met

hylo

bact

eria

ceae

Ent

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Stre

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orax

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Leuc

onos

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ceae M

icro

bact

eria

ceae

Stre

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ceae

(Lac

toco

ccus

)

Subject BJJ

In silico T-RFLP

Who is there – species/strains –16s rRNA gene sequencing 

What is their function?  Metagenomics

What are they doing?  Metabolomics

How to analyze the gut microbiome and use them in clinical medicine?

MicrobesHost

Luminalcontents

Role in Disease• Complex immune

disorders• IBD• Allergic disorders• RA• T1 diabetes

• Metabolism• T2 diabetes• Obesity

• Cancer• Development• Infectious diseases• Neurological/motor

disorders

Host-microbe interactions in the GI tract maintain health

Host immune systemHost immune system Host metabolism

HeartdiseaseHeartdisease

Type 2 DiabetesType 2 Diabetes

Colon CancerColon Cancer

Chronic inflammation

Chronic inflammation

Obesity

Allergies

Autoimmune Autoimmune diseases

Metabolic Metabolic syndrome

Dysbiosis

Inflammation

There is evidence for an involvement of intestinal dysbiosis in chronic diseases, with inflammation as one of the mechanistic links

Bacteria

>50 different phyla

Gut microbial dysbiosis associated with human disease

Spor et al. Nature Reviews Microbiology 9:279. 2011

Gut microbial dysbiosis associated with human disease

Obesity

Bacteroidetes ↓Firmicutes ↑

Abnormal gut barrier, pro-inflammatory immune response

Type 2 Diabetes

Faecalibacterium prausnitzii ↓Akkermansia municiphila ↓

Nonalcoholic Fatty Liver

Bacteroidetes ↓γ-Proteobacteria ↑

InflammatoryBowel Disease

Butyrate-producing ↓Enterobacteriaceae ↑

Intestinal microbiota dysbiosis and chronic inflammation

We can modulate composition of the human gut microbiota and induce changes that are predicted to be beneficial

Crohn’s disease

Crohn’s disease and ulcerative colitis have unique geographic features

IBD has been increasing over the past half century

Genetics• Nod2• TLR, TNF• Autophagy• IL23R

Environment• Microbes• Diet• Smoking

Immuneimbalance

DefectiveHost defense

IBD

Model of the Etiopathogenesis of IBD

http://longbottomline.com/tag/forks-over-knives/

Diets in the US have changed dramatically over the past century

Increase• Animal protein• Fat• Refined Carbohydrates

Decrease• Whole grains• Fruits and vegetables

Dietary Changes in Western Society

De Filippo C, et al. Proc Natl Acad Sci U S A. 2010; 107:14691-6

Impact of diet in shaping gut (fecal) microbiota – a study of modern versus rural diet

Bacteroides

RuminococcusPrevotella

Enterotypes are strongly

associated with long term diets:

- Bacteroides enterotype –

protein and animal fat

- Prevotella enterotype -

carbohydrates

Arumugam et al. Nat. 473: 174-180; Wu et al. Sci. 334: 105-8

Enterotypes of the human gut microbiome

Plant-based Animal-based

Fiberintake

Fatintake

Proteinintake

α-Diversity

β-Diversity

Animal-based diet showed greater impact on the gut microbiota than the plant-based

diet.

David LA et al. Nature 2013 doi: 10.1038/nature12820

Short-term effect of diet on the gut microbiota composition

WT mice:

Control chow‐ Day 0Control chow‐ Day 35Western Diet‐ Day 0Western Diet‐ Day 35

IL10 mice:

Control chow‐ Day 0Control chow‐ Day 35Western Diet‐ Day 0Western Diet‐ Day 35

PCA‐ Discriminant analysis: Stool Microbiom Day 0 and Day 35

Western Diet changed the composition of the gut microflora

Western Diet decreased microbial diversity

00.51

1.52

2.53

3.54

4.55

IL10 controlchow

IL10 westernchow

WT controlchow

WT westernchow

Shan

non‐wiene

r ind

ex

Mouse species and Treatment group

Day 0

Day 35

*

dietWT western 

diet

Western Diet decreased microbial diversity

C57Bl/6 mice fed different diets; Cecal samples harvested 21 days later

16S rRNA gene sequences were determined by Sanger-based clone library sequencing

Can diet affect the enteric microbiome?

Discovered in 1988 Often recovered from a 

variety of infections (pathobiont)

Bilophila = “bile‐loving”

Sulfite‐reducing bacteria (SRB‐ dsrA)

Production of H2S

LF + B.wad MF + B.wad

B. wadsworthia colonizes only when mice are on MF diet

Bilophila wadsworthia is a sulfite-reducing microbe that is uncommon in gut microbiota

Glycocholic acid

Taurocholic acid Diet-derived bile

MFLF PUFA

% T

auro

chol

ate

of to

tal b

ile

***

MF Bile

PUFA BileLF BileControl Media

Time (hrs)

Could differences in dietary fat-induced bile acid conjugation promote B. wadsworthia growth?

a

cbc bc

bc

b

a

bb

ccc

a

bbcbc

bcc

LF + Bw MF + Bw0% 0%

PUFA + Bw23%

MF + Bw

CD4

IFN

-γ

CD4Is

otyp

e

0% 0% 28%

MLN

B. wadsworthia induces TH1-mediated colitis(Bw monoassociation of GF mice)

CD4

IFN

-γ

CD4

Isot

ype

Therapeutic:Fecal transplantationAntimicrobials (Bacteriophages)Probiotics

Nutritional:ProbioticsPrebioticsFibers, resistant starches, and whole grain

•Bifidobacteria•Functional targets•SCFAs and Butyrate producers•Community diversity

Dietary strategies to modulate the gut microbiotaand redress disease associated dysbioses.

Dose-dependent clinical response in active UC by adjunct prebiotic inulin-enriched oligofructans

Fuso

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in fe

cal s

ampl

es

-1.0

-0.5

0.0

0.5

1.0

1.5

7.5 g dose 15 g dose

**

** * *

*

*

Actinobacteria Firmicutes Bacteroidetes Proteobacteria

Prebiotics inulin plus oligofructose alter fecal microbiota

Exhalation and

Flatulence

Excretion

GASES : CO2, H2, CH4

INULIN & OLIGOFRUCTOSE

BACTERIALBIOMASS

FERMENTED BY INTESTINAL BACTERIA

ACETIC ACIDPROPIONIC ACIDBUTYRIC ACIDLACTIC ACID

Criterium 2 : Prebiotics are FERMENTED BY the (endogenous) INTESTINAL MICROBIOTA

UCDAI

Acidovorax

-0.41

Faecalibacterium

Lactobacillus

Microvirgula

Sphingomonas

Enterobacter

Unclass. Moraxellacea

Roseburia

Dialister

Comamonas

Enterococcus0.53Fecal

calprotectin

Chryseobacterium

Enhydrobacter

Veillonella

Parabacteroides

Desulfovibrio

Sutterella

Correlations between colitis and mucosa-associated bacterial taxa

FOS – fructooligosaccharidesIMO – iso-maltooligosaccharides

Values in the same panel that do not share a common superscript differ significantly (P< 0.05, Bonferroni adjustment)

Cecum ColonH

isto

logy

sco

reIL

-1β

secr

eted

(ng/

g pr

otei

n)

Control ControlIMO IMOFOS FOS

Diet alters β-fructans protective effect in rodent colitis model

Acetate Propionate Butyrate

Isobutyrate Isovalerate Valerate

Diet rich in refined sugars and milk protein, but deficient in complex fiber and polyphenol, sources promotes protein fermentation versus carbohydrate (fiber) fermentation in cecum and colon of a rat colitis model

Diet rich in refined sugars changes the function of colonic bacteria

Dietary and bacterial-derived metabolites in serum and urine of UC patients predict future relapse

Take Home Points

• Diets as well the prevalence of certain “western GI disorders” have drastically changed in the last 50 years

• Diets affect the composition and function of the human microbiome

• Dietary therapy may be the solution to prevent and possibly cure these disorders