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Introducing the Microbiome
Dr Ailsa Hart
Director IBD Unit, Consultant Gastroenterologist, St Mark’s
Honorary Senior Clinical Lecturer, Imperial College
Introduction
What is the gut microbiome?
How does the gut microbiome play a role in disease?
- role in inflammatory bowel disease
How can we modulate the gut microbiota as a therapy
- faecal transplant
The gut microbiota
1014 gut bacteria and 1013 cells in body
Most densely populated ecosystem on Earth
4 major phyla (Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria)
Provide traits we have not had to evolve on our own
“Virtual” organ
Genes in gut flora 100 times our own genome
Function of gut microbiota
Germ-free animals
Exist and survive
But abnormalities of:
 Immune function (oral tolerance)
 Metabolic function (altered enzymes)
 Physiological function (altered motility)
 Trophic function (altered cell turnover)
Function of gut microbiota
Host – microbiota interactions
Hooper et al. Science 2001
A single commensal bacteria switches on genes involving
Mucosal barrier function
Nutrient absorption/ dietary energy extraction
Enteric nervous system
Intestinal maturation
Immune system development
The Meta HIT project
The Human Microbiome Project
The human microbiome project
• 5 year project
• 242 healthy men/women - samples from different body sites
• 10,000 different types of organism found
• Is there a core set of microbes that all humans share?
• Diversity of microbes across human beings
• Diet, host genetics, early microbial exposure
• Unique communities of microbes at different body sites
• At specific body sites, many microbes had similar genes/functions
Challenges thinking of one-microbe model of disease
More likely “function” of group of microbes changes
Gut microbiota “pathology”
e.g. inflammatory bowel diseases
functional bowel disease
gastrointestinal infections
non-GI diseases
- obesity, metabolic syndrome, atopy/allergy
2011
2008
2007
2001
1980’s
>160 independent
IBD susceptibility loci
2012
Genetics of IBD
What has genetics taught us about IBD?
> 75,000 cases &
controls
-
Information about pathways involved in disease process
Over 2/3 of genes are shared between UC &CD
30 CD-specific and 23 UC-specific
Particular overlap between ankylosing spondylitis and psoriasis
1Jostins
et al Nature 491 (7422):119-124; 2Lees et al Gut 2011;60:1739-53 (diagram)
Experimental models of colitis
Germ-Free
No Colitis
Animal models
of colitis
Experimental models of colitis
Germ-Free
No Colitis
Animal models
of colitis
Bacterial
Colonisation
Colitis
In humans…

Faecal stream diversion alleviates Crohn’s

Reanastomosis triggers recurrence

Infusion of luminal contents into excluded normal
bowel induces inflammation
What part of the gut microbiota
drives inflammation?
Single organism?
Expansion or relative contraction?
“Functional” changes?
Reduced diversity of faecal microbiota In CD
Reduced Firmicutes in Crohn’s disease
- Reduction of a major member of Firmicutes,
F. prausnitzii, associated with higher risk of
postoperative recurrence of ileal CD.
Experimental replacement of F. prausnitzii had anti-inflammatory effects
But changes in “function” of microbiota….
Mucosa/stool samples from 231 IBD patients & controls
16S gene pyrosequencing/shotgun metagenomics



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Major shifts in oxidative
stress pathways
Decreased carbohydrate
metabolism
Decreased amino acid
synthesis
In ileal Crohn’s, increases
in virulence and secretion
pathways
Microbial function more consistently altered than microbial composition
Morgan et al. Genome Biology Sept 2012
Challenges
Clinical
• phenotype
• confounders
• age, gender, smoking
• ethnicity, diet, surgery
• medications
Sampling
• faeces v mucosa
• axial and longitudinal variation
•
replication
• multiple samples from same region
• longitudinal sampling
• “healthy” controls
Communication
• clinicians
• microbial ecologists
• bioinformatics
• statisticians
Technical
• 16S sequence
• metagenomics
• metatranscriptomics
• metabonomics
• … economics
Can the gut microbiota be modified?
If so, how?
Faecal transplantation - history

1600s – “transfaunation” – gastric contents transplanted into animals
unable to ruminate

Bedouin of northern Africa – “coprphagia” – ingestion of camel dung as
treatment for dysentery

WWII – same practice in soldiers – led to Bacillus subtilis as probiotic

Faecal transplant (FT ) - treatment in humans for pseudomembranous
colitis in1958
Landy et al. Aliment Pharmacol Ther 2011; 34: 409-15
Publications on faecal transplantation
Faecal transplantation in C. difficile

Over 376 cases of faecal transplant (FT) for C. diff infection

17/22 studies of FT are in refractory/fulminant C. diff

Enemas; via duodenal tubes; via colonoscopes

Overall success rates of >90%
Landy et al. Aliment Pharmacol Ther 2011; 34: 409-15
Faecal transplantation in C. difficile

First randomised controlled trial

Aimed to recruit 120 patients – stopped early

13/16 (81%) in FT group – resolution of diarrhoea

4/13 (31%) in vancomycin group

3/13 (23%) in vancomycin + bowel lavage

After FT, ↑diversity (similar to healthy donors)
Van Nood et al. NEJM January 2013
Faecal transplantation in IBD
41 patients with IBD (27 UC; 12 CD; 2 indeterminate)
Majority (19/25) had reduction in symptoms/ 15/24 remission
Resolution of C. diff infection in 15/15
Damman et al. Am J Gastro. 2012; 107: 1451-9; Anderson et al. APT Sept 2012
Faecal transplantation in pouchitis
Hypothesis – increasing diversity and altering selection of resistant bacteria
with faecal transplantation may be effective in refractory pouchitis
• Pilot study of faecal transplantation in patients with chronic pouchitis
• Microbiological; immunological; histological & clinical assessment
pre and post transplant
Faecal transplantation in pouchitis
PDAI
CGQoL score
pouch frequency
No major adverse events; 3 patients reported adverse effects nausea (n=3); bloating (n=2)
Landy et al. ECCO 2013
Unresolved issues…

Can microbiota be altered in IBD with FT?

If so, does genetic pressure / indigenous bacteria affect ability to change?

Donor - mixture of phylogenetically diverse bacteria – which?

Frequency and route of administration?

Use of concomitant treatment?

Fresh versus frozen (banks)?

Safety?
Altering microbiota - beyond IBD …..
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Other gastrointestinal disorders
•
Functional bowel disorders

Gastrointestinal infections e.g. Clostridium difficile, rotavirus
Non-intestinal disorders

Atopic diseases

Type I diabetes/ metabolic syndrome

Obesity ……
Obesity
Obesity

Calorie extraction from food varies
depending on gut flora

“Obese flora” more effective at
extracting energy from food
Could manipulation of gut microbiota influence obesity?
Malnutrition

Calorie extraction from food varies
depending on gut flora

“Obese flora” more effective at
extracting energy from food
Could manipulation of gut microbiota influence malnutrition?
Summary

Gut microbiota – virtual organ; microbiome; metobonome

Role of microbiota in IBD

Modulation of gut flora as a therapeutic intervention

Mechanistic approach

Far reaching potential in GI (and non-GI) disease