10/4/2014

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The Microbiome vs.

the Gastroenterologist

John K. Marshall MD MSc FRCPC AGAF

Division of Gastroenterology

McMaster UniversityJKM 2014

Human Microbiome

Finlay BB. Scientific American 2010;302:56-63JKM 2014

Mouth

Microbiome and Host Physiology:

A Delicate Balance

Brandt LJ. Am J Gastroenterol 2013;108:177-85JKM 2014

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Effects of an Altered Microbiome

Smits LP. Gastroenterology 2013;145:946-53JKM 2014

Smits LP. Gastroenterology 2013;145:946-53

How An Altered Microbiome

Contributes to Disease

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A

B

C

Characterizing the Microbiome

JKM 2014 Owyang C, Wu GD. Gastroenterology 2014;146:1433-6

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Irritable Bowel Syndrome

• Chronically altered bowel habit

and abdominal discomfort

• Common in general population

(10%-20%)

• Diagnosis of exclusion (no

biomarkers)

• No cure

• Treatment unsatisfactory

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JKM 2011

% w

ith R

om

e I IB

S

10.1%

36.2%

27.5%

N=701 N=904 N=464

OR 4.8 (95% CI 3.4,6.8); p<0.001

p<0.001

Acute Gastroenteritis During Outbreak

p<0.001

Incidence of IBS 2 Years After Acute

Gastroenteritis in Walkerton Ontario

Marshall JK. Gastroenterology 2006;131:445-50JKM 2014

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Post-Infectious

Irritable Bowel Syndrome• Altered bowel habit and abdominal discomfort that persist

after acute enteric infection despite clearance of the inciting

pathogen and recovery from the acute illness

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?

Global and Deep Molecular Analysis

of Microbiota in IBS

Rajilic-Stojanovic M. Gastroenterology 2011;1792-801JKM 2014

Species-Specific Changes in

Micobiota

Define IBS Subtypes

Jeffery IB. Gut 2012;61:997-1006JKM 2014

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RCT of Bifidobacterium infantis

35624 for Treatment of IBS (AlignTM)• 362 primary care patients with IBS (any subtype)

Whorwell PJ. Am J Gastroenterol 2006;101:1581-90JKM 2014

Definitions• Probiotics are live microorganisms which, when

administered in adequate amounts, confer a health benefit to the host.

• Prebiotics are non-digestible food ingredients that stimulate the growth and/or activity of bacteria in the digestive system that are beneficial to the host

• Synbiotics are nutritional supplements combining probiotics and prebiotics in a form of synergism

http://www.hc-sc.gc.ca/fn-an/label-etiquet/claims-reclam/probiotics_qa-qr_probiotiques-eng.php

JKM 2013

Pseudomembranous Colitis

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Pseudomembranous Colitis

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Clostridium Difficile

• Gram-positive spore-forming bacterium

• Non-invasive, toxin-producing (A and B)

• Fecal oral transmission– Environmental surface contamination in healthcare facilities

• Asymptomatic carriage in 5-15% of healthy adults– Up to 84% of infants

– Up to 57% of long-term care residents

• Risk factors for acquisition:– Exposure to antibiotics

– Comorbid conditions

– Gastrointestinal surgery

– Proton pump inhibitors

Surawicz CM. Am J Gastroenterol 2013;108:478-98JKM 2014

C. Difficile Pathogenesis

Peniche AG. Current Opinion Infect Dis 2013;26:447-53JKM 2014

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Reduced Microbial Diversity in CDI

Antharam VC. J Clin Microbiol 2013;51:2884-92

• N=39 CDI, N=36 CD-negative nosocomial diarrhea, N=40 HC

• Culture-independent high-density Roche 454 pyrosequencing

• 526,071 partial 16S rRNA sequence reads of V1-V3 regions aligned with 16S databases to identify 3,531 bacterial phylotypes

JKM 2014

Probiotics for Prevention of

C. Difficile-Associated Diarrhea

Johnston BC. Ann Intern Med 2012;157:878-88JKM 2013

Lactobacillus acidophilus Lbc80r and

Lactobacillus casei CI 1285 (Bio-K+TM)

• Randomized double-blind placebo-controlled dose-

response trial in 255 adult inpatients starting antibiotic

therapy at a single centre in Shanghai

Gao XW. Am J Gastroenterol 2010;105:1636-41JKM 2014

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JKM 2011

Probiotics: Who What Where When?

• Reasonable clinical evidence:

– VSL#3 or Mutaflor for ulcerative colitis

– VSL#3 for pouchitis

– BioGaia for H. pylori

– Align or TuZen for IBS

– Bio-K+ or Florastor for AAD or CDAD

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Genetically Modified Probiotics

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Clinical Guide to Probiotics

Available in Canada

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Fecal Transplantation

• First reported use for

C. difficile in 1958

Eiseman B. Surgery 1958;44:854-9JKM 2014

Why I Donated My Stool

Lee MMO. New York Times. July 7 2013

“This spring I saved a friend from a terrible illness, maybe even death.

No, I didn’t donate a kidney or a piece of my lung. I did it with my stool…”

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Early FMT

• Dong-jin dynasty (4th century):

– Ge Hong resports using an oral human fecal suspension for

food poisoning or severe diarrhea.

– Medical miracle returned patients from brink of death

• Ming dynasty (16th century):

– Li Shizhen reports using fermented fecal solution, fresh fecal

suspension, dry feces, or infant feces for abdominal diseases

with severe diarrhea, fever, pain, vomiting, or constipation

Zhang F. Am J Gastroenterol 2012;107:1755JKM 2014

Home Fecal Transplantation

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Duodenal Infusion of Donor Feces

for Recurrent C. difficile

Van Nood E. N Engl J Med 2013;368:407-15JKM 2014

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Pathogenesis of IBD

Luminal Antigens

Environmental Triggers

Genetic Susceptibility

IBD

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Treatment of UC by Implantation

of Normal Colonic Flora

• 1st author (Bennet) had endoscopically and

histologically confirmed UC for 7 years,

refractory to sulfasalazine and steroids

• Received FMT using large-volume retention

enemas from healthy volunteer donor

• Histologic remission at 3 months

• Clinical remission at 6 months

Bennet JD. Lancet 1989;333:164JKM 2014

Fecal Transplantation for UC in

Children and Young Adults (N=10)

Kunde S. J Ped Gastroenterol Nutr 2013;56:597-601JKM 2014

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RCT of FMT for UC

• Moayyedi (PI), Marshall, Armstrong, Surette, Lee

• Funding: CCFC

• Subjects: active ulcerative colitis (N=130)– Mayo >3 with endoscopy sub-score ≥1

• Intervention: weekly FMT vs. placebo for 6 weeks– Unrelated healthy donor

– 6 additional weeks “open label” available to non-responders

• Primary outcome: remission (Mayo<3) with endoscopic subscore 0– Endoscopy at weeks 3 and 6

– Roche 454 pyrosequencing and Illumina sequencing to characterize microbiome

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• Healthy unrelated donors– No medications for 3d prior to collection

– Detailed health questionnaire

– Negative tests for: HIV, HAV, HBV, HCV, syphilis, HTLV I/II, VRE, MRSA,

• Stool specimen analyzed– No visible blood, mucus, urine

– Negative tests for: O&P, C. difficile, Salmonella, Shigella, E. coli 0157:H7, Yersinia, Campylobacter, norovirus, adenovirus, rotavirus

RCT of FMT for UC

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RCT of FMT for UC

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• Stool processed within 5h of collection

– 50g of stool mixed with 300ml water

– Emulsified with spatula and allowed to settle

– Supernatant (150ml) decanted and filtered

– Refrigerated at 2-8oC for up to 24 hours

• Delivered as retention enema

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RCT of FMT for UC

JKM 2014

• Interim analysis: 63 randomized, 53 completed– 45% pancolitis– 42% on steroids, 19% on IMM, 9% on biologics

– Partial responders on HBT offered additional 6 weeks of “open-label” therapy with overall remission rate of 9/27 (33%)

• Conclusion: no evidence from this RCT that FMT effective

• DSMB advised that recruitment be halted!

Moayyedi P et al. DDW 2014

23.68

5.4

0

5

10

15

20

25

FMT Control

RCT of FMT for UC

Primary Endpoint:Week 7 Remission (Mayo ≤2 with Endoscopic Subscore 0)

JKM 2014 Moayyedi P et al. [submitted]

P=0.025

TOP SECRET

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Schwartz M. Am J Gastroenterology 2013;108:1367JKM 2014

Effects of an Altered Microbiome

Smits LP. Gastroenterology 2013;145:946-53JKM 2014

Chronic Gut Inflammation Induces

Anxiety and Alters CNS Biochemistry

in Mice

Bercik P. Gastroenterology 2010;139:2102-12JKM 2013

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• Germ-free mice colonized with fecal microbiota from twins discordant for obesity

• Changes in body composition monitored by MRI

Gut Microbiota from Twins Discordant

for Obesity Affect Metabolism in Mice

JKM 2014Ridaura VK. Science 2013;341:1241214

Effects of Intestinal Microbiota

on Human Metabolism

Nieuwdorp M. Gastroenterology 2014;146:1525-33JKM 2014

Ideal Fecal Donors?

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Summary

• We are vastly outnumbered

• Technology to profile structure and function of the microbiome is advancing

• Bioinformatic challenges remain

• Manipulation of the microbiome can utilize diet, antibiotics, probiotics, and fecal transplantation

• Potential efficacy across spectrum of human disease

• Your colon is the next frontier

JKM 2014

Thank You

JKM 2014