Nutrition and the Gut Microbiome – What is the impact in IBD?

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

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 species 10-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

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0 week 9 week

Ent

erob

acte

riace

ae

Mor

axel

lace

aeB

acte

roid

acea

eB

acte

roid

acea

e

Leuc

onos

toca

ceae

(Leu

cono

stoc

)

Rum

inoc

occa

ceae

Lach

nosp

irace

ae/R

umin

ococ

cace

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Ery

sipe

lotri

chac

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Stre

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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

sGT

L0w

k

sGT

L9w

k

sLA

M0w

k

sLA

M9w

k

sME

F0w

k

sME

F9w

k

sMP

B0w

k

sMP

B9w

k

sNM

R0w

k

sNM

R9w

k

sPC

V0w

k

sPC

V9w

k

16S rDNA sequencing

Fragment length (bp)

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0 week 9 week

Met

hylo

bact

eria

ceae

Ent

erob

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Stre

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(Stre

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orax

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Flav

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teria

ceae

Bra

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izob

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Leuc

onos

toca

ceae M

icro

bact

eria

ceae

Stre

ptoc

occa

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?

PresenterPresentation NotesFigure2Bacterial Phyla Identified in the Human Gut Microbiota�Distribution of predominant bacterial phylotypes in the human intestinal tract. The graphs depict relative abundance as a function of location along the cephalocaudal axis of the distal gut. DNA sequences were compiled from the studies of Eckburg etal., 2005 and Frank etal., 2007. Phylogenetic classifications were made by parsimony insertion of aligned sequences into a 16S rRNA tree provided by the Greengenes database (DeSantis etal., 2006), using ARB (Ludwig etal., 2004). Abbreviations: IBD, samples from patients with either Crohn's disease or ulcerative colitis (Frank etal., 2007); Normal, data from healthy young adults from Eckburg etal., 2005 plus the non-IBD controls reported in Frank etal., 2007; n.d., not done. A total of 18,405 16S rRNA sequences were analyzed (5405 IBD, 13,000 normal).

Microbes Host

Luminal contents

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 system Host metabolism

Heart disease

Type 2 Diabetes

Colon Cancer

Chronic inflammation

Obesity

Allergies

Autoimmune diseases

Metabolic syndrome

Dysbiosis

Inflammation

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

Obesity

Bacteroidetes ↓ Firmicutes ↑

Abnormal gut barrier, pro-inflammatory immune response

Type 2 Diabetes

Faecalibacterium prausnitzii ↓ Akkermansia municiphila ↓

Nonalcoholic Fatty Liver

Bacteroidetes ↓ γ-Proteobacteria ↑

Inflammatory Bowel Disease

Butyrate-producing ↓ Enterobacteriaceae ↑

Intestinal microbiota dysbiosis and chronic inflammation

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

Immune imbalance

Defective Host 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

Ruminococcus Prevotella

Enterotypes are strongly

associated with long term diets:

- Bacteroides enterotype –

protein and animal fat

- Prevotella enterotype –

fermentable 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

Fiber intake

Fat intake

Protein intake

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

Western Diet decreased microbial diversity

00.5

11.5

22.5

33.5

44.5

5

IL10 controlchow

IL10 westernchow

WT controlchow

WT westernchow

Shan

non-

wie

ner i

ndex

Mouse species and Treatment group

Day 0

Day 35

*

diet WT western

diet

Western Diet decreased microbial diversity

PresenterPresentation NotesMeasurement of microbial diversity: Shannon-wiener index

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 function of the gut 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 MF LF PUFA

% T

auro

chol

ate

of

tota

l bile

***

MF Bile

PUFA Bile LF Bile Control Media

Time (hrs)

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

PresenterPresentation NotesTaurocholic and Glycocholic represent 80% of all bile salts. B. wadsworthia needs sulfur as its terminal electron acceptor for anaerobic respiration.

http://en.wikipedia.org/wiki/File:Glycocholic_acid.pnghttp://en.wikipedia.org/wiki/File:Taurocholic_acid.png

a

c bc bc

bc

b

a

b b

c c c

a

b bc bc

bc c

LF + Bw MF + Bw 0% 0%

PUFA + Bw 23%

MF + Bw

CD4

IFN

-γ

CD4 Is

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 transplantation Antimicrobials (Bacteriophages) Probiotics

Nutritional: Probiotics Prebiotics Fibers, resistant starches, and whole grain

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

Dietary strategies to modulate the gut microbiota and redress disease associated dysbioses.

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

UCDAI

Acidovorax

-0.41

Faecalibacterium

Lactobacillus

Microvirgula

Sphingomonas

Enterobacter

Unclass. Moraxellacea

Roseburia

Dialister

Comamonas

Enterococcus 0.53 Fecal

calprotectin

Chryseobacterium

Enhydrobacter

Veillonella

Parabacteroides

Desulfovibrio

Sutterella

Correlations between colitis and mucosa-associated bacterial taxa

Exhalation and

Flatulence

Excretion

GASES : CO2, H2, CH4

INULIN & OLIGOFRUCTOSE

BACTERIAL BIOMASS

FERMENTED BY INTESTINAL BACTERIA

ACETIC ACID PROPIONIC ACID BUTYRIC ACID LACTIC ACID

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

Responders Non-responders

% B

utyr

ate

to to

tal

SCFA

% B

utyr

yl-C

oA-T

rans

fera

se

gene

cop

y nu

mbe

rs to

tota

l 16

S rD

NA

MCT

1 m

RNA

rela

tive

expr

essi

on

Intestinal butyrate metabolism is improved in UC patients responding to beta-fructans

High sucrose diet plus FOS worsens colitis and arthritis

Valcheva et al, poster CDDW 2015

Acetate Propionate Butyrate

Isobutyrate Isovalerate Valerate

Diet rich in refined sugars, but deficient in complex fiber and polyphenol sources promotes protein fermentation versus carbohydrate (fiber) fermentation in cecum and colon of a rat colitis model (Koleva, et al PlosOne 2014)

Diet rich in refined sugars changes the function of colonic bacteria

Urine metabolomics differ in UC versus non-IBD controls

PLS-DA, P

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

 Nutrition and the Gut Microbiome – What is the impact in IBD?Financial DisclosureLearning ObjectivesThe Intestinal Microbiome – an “organ” of its ownBeneficial role of microfloraDominant 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 UCSlide Number 7Slide Number 8Slide Number 9Slide Number 10Slide Number 11Slide Number 12 Slide Number 14Slide Number 15Slide Number 16Slide Number 17Slide Number 18Western Diet decreased microbial diversitySlide Number 20Slide Number 21Slide Number 22Slide Number 23Slide Number 24Slide Number 25Slide Number 26Slide Number 27Intestinal butyrate metabolism �is improved in UC patients responding to beta-fructansSlide Number 29Slide Number 30Slide Number 31Urine metabolomics differ in UC �versus non-IBD controlsSlide Number 33Take Home Points