The Role of the Microbiome in Health and Disease

Jakob Begun

Mater Hospital Brisbane

Mater Research Institute - University of Queensland

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Disclaimers• Advisory Boards and consulting:

• Gilead, Janssen, Celgene, Takeda, Pfzier, MSD, Abbvie

• Honorarium for educational activities• Abbvie, Janssen, Shire, Takeda, Ferring, Emerge Health, Pfizer

• Industry Research grants• Abbvie, Pfizer, Ferring

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But there are 100 million times as many bacteria on earth as there are

stars in the universe

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The microbiome is hot

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Pub Med References

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The taxonomic tree of life

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What is the human microbiome• Microbial community colonising humans

- over 10 trillion organisms • Majority of microbiome mass localised within

the gut ~ 2 kg

• By DNA content we are >90% microbe and <10% H. sapiens = human holobiont

• Complex interactions with the epithelium, metabolism, immune system, hormonal axes, and nervous system

• A dynamic relationship to human health

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Studying the human microbiome

• Historically – viewed through the lens of culture dependent methods and microscopic observation

• Primarily in context of disease and identification of pathogens

• Successful approach for diagnosis and treatment

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Culture independent investigation• Advent of next generation sequencing and bioinformatics has

revolutionised the field• 16S rRNA – allows selective identification of bacterial species

• Metagenomic approaches provide detailed views of microbial genomes

• New sequence based approaches for studying the virome and mycobiome

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Coupling sequence with big data

DNA Library preparation

and sequencing

16S rRNA sequencing

Match OTU reads

against database

Bacterial taxonomy

Relative abundance

Gene annotationMetagenomic

sequencing

Genome assembly

Map onto database

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A dynamic microbiome

• The microbiome is a dynamic community

• Significant impact of environmental exposures

• Significant changes with age

Ottman, N., et al., Front Cell Infect Microbiol, 2012. 2: p. 104

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Microbiome associations with disease• Alterations in microbiome composition have been associated with

many human diseases and states of health• Metabolic disease – diabetes, heart disease

• Cancer – bowel cancer, melanoma, hepatocellular carcinoma, lung cancer

• Neurologic/psychiatric – Parkinson’s, anxiety/depression, Autism

• Inflammatory diseases – rheumatological, pulmonary, genitourinary, neurologic, autoimmune disease

• Gastrointestinal disease – irritable bowel syndrome, Coeliac disease, inflammatory bowel disease

• Focus on the gut microbiome

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A word about the gut microbiome

• Oral cavity contains multiple distinct communities

• Upper GI tract characterized by limited diversity adapted to harsh environment (acidic, bile, digestive enzymes)

• The lower intestine is oxygen poor, nutrient rich, and neutral pH

Sartor, R.B. Gastroenterology, 2008. 134(2): p. 577-94.

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Metabolic outputs of the microbiome

• Gut microbiota utilise insoluble fibre, mucus, and non-absorbed carbohydrates, protein and fat as energy sources

• Metabolic outputs vary as a function of the microbial composition and diet

• Produce a variety of secondary metabolites

• Metabolise drugs

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Microbiome and obesity • Ob/Ob mice develop obesity due to a leptin mutation

• But phenotype is dependent on microbiome

• Compared to WT mice, Ob/Ob mice have lower diversity and a higher Firmicutes : Bacteroidetes ratio• Corresponds to more efficient energy utilisation

Turnbaugh, P.J., Nature, 2006. 444(7122): p. 1027-31.

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Is human obesity transmissible?• Twins discordant for obesity

• Obese twin microbiome characterized by reduced diversity and increased firmicutes

• Effect of microbiome on germ-free mice

Turnbaugh, P.J., et al. Nature, 2009. 457(7228): p. 480-4.

Ridaura, V.K., et al. Science, 2013. 341(6150): p. 1241214.

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Weight loss surgery and the microbiomeDoes weight loss surgery shift the microbiome?

Liou, A.P., et al. Sci Transl Med, 2013. 5(178): p. 178ra41.

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Weight loss surgery and the microbiomeIs the post-RYGB surgery microbiome therapeutic?

Liou, A.P., et al. Sci Transl Med, 2013. 5(178): p. 178ra41.

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Gut-Brain Axis

• Bi-directional signalling between the CNS and the gut micorbiome

• CNS → Gut• Motility, secretion, intestinal permeability

• Gut → CNS• Modulation of neurotransmitter release by

the gut and direct microbial production

• Modulation of endocrine and immune signalling

Clarke, G., et al. Mol Endocrinol, 2014. 28(8): p. 1221-38.

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Microbiome in rodents

• Natural behaviours of mice (e.g BALB/c – impaired sociality and exaggerated caution)• Altered in the germ free state

• Can be manipulated through microbiome transfer from different strains

• Antibiotic treatment can cause behavioural changes and changes in stress hormone levels

• Probiotic studies in animals can reduce anxiety/depression• Lactobacillus rhamnosus directly stimulates vagus nerve

• Gut derived serotinin production influenced by the microbiome composition

Bruce-Keller, A.JBiol Psychiatry, 2018. 83(3): p. 214-223.

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Microbiome - Autism Spectrum Disorder• ASD is increasing in incidence (as high as 1 in 45)

• Higher incidence in developed world

• GI symptoms are prominent in ASD individuals

• In animal models manipulation of the microbiome can result in Autism like behaviours

• In human studies the microbiome signature of ASD is distinct• Decreased Bacteroidetes/Firmicutes ratio

• Decreased SCFA production, and carbohydrate fermentation

• Confounded by diet

• Small trial with oral vancomycin and minocyclineshowed some efficacy signal

Vuong, H.E. and E.Y. Hsiao, Biol Psychiatry, 2017. 81(5): p. 411-423.

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Microbiome - Autism Spectrum Disorder

Vuong, H.E. and E.Y. Hsiao, Biol Psychiatry, 2017. 81(5): p. 411-423.

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Bowel cancer and the microbiome

• Colon cancer is the second most common cancer in men and women

• Lifetime risk is ~1 in 11 for men and 1 in 15 for women

• Multiple epidemiologic links including increased red meat, decreased fibre, smoking, obesity, family history etc.

• Bowel cancer location mirrors microbial density

• Patients with colorectal cancer have decreased bacterial diversity globally and within the cancers

• Multiple studies show increase in Fusobacterium and a decrease in Faecalibacterium, associated with decreased SCFA

• Streptococcus Bovis translocation is a marker of CRC

• Links between gut inflammation and tumour development• Bacterial induced inflammation increase mutation rates

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An integrated model of carcinogenesis

Tlaskalova-Hogenova H et al. Cancer J 2014;20:217-24.

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Dietary manipulation of microbiome to decrease CRC risk• African Americans have high incidence of CRC, while CRC

rates are low in Africa• Microbiome of African American’s is “high risk” compared to rural

South Africans

• American diet has 2-3 times more fat and animal protein than African diet, which was higher in fibre

• 2-week food exchange in subjects from each population

• 20 subjects in each group• Sigmoidoscopy at baseline and after two weeks

• Times series – microbiome, metabolomics, ImmunophenotypingO'Keefe, S.J., et al., Nat Commun, 2015. 6: p. 6342.

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Dietary manipulation of microbiome to decrease CRC risk

O'Keefe, S.J., et al., Nat Commun, 2015. 6: p. 6342. AA on NA diet NA on AA diet

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Microbiome and response to cancer therapy• Checkpoint inhibitors targeting CTLA-4 and PD-1/PD-1L have

emerged as an effective therapy for melanoma and other cancers

• In mice engrafted with melanoma the presence of Bifidobacterium was associated with decreased tumour growth and response to anti PD-1L treatment

Sivan, A., et al. Science, 2015. 350(6264): p. 1084-9.

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Role of microbiome in clinical response to anti-PD-1 therapy

• Examined the microbiome of a cohort of melanoma patients receiving anti-PD-1 therapy

• Responders had higher diversity and increased relative abundance Faecalibacterium• Signal for Ruminococcaceae bacteria

Gopalakrishnan, V., et al. Science, 2018. 359(6371): p. 97-103.

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Introduction to Inflammatory bowel diseaseIBD is a chronic relapsing, or progressive inflammatory condition of the GI tract

Ulcerative colitis

• Limited to the colon

• Continuous ulcerating inflammation from rectum proximal

Crohn’s disease

• Can occur anywhere throughout the GI tract

• Discontinuous, transmural inflammation +/- granuloma

Normal colon Ulcerative colitis Crohn’s disease

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Worldwide burden of IBD

• Worldwide prevalence ~400/100,000 (~30M patients)• Incidence in Australia 29.3/100,000 → Approximately 85,000 patients diagnosed

with IBD• Current treatment paradigms consist primarily of immunosuppressive therapy

including potent biologic therapyNg, S.C., et al. The Lancet, 2017. 390(10114): p. 2769-2778.

Crohn’s disease incidence Ulcerative colitis incidence

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Increasing incidence of IBD over time

Crohn’s

Disease

Ulcerative

Colitis

Talley et al. AJG 2011; 106: S2-S25

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The current model of IBD pathogenesisMultiple hits:

• Genetics

• Dietary factors

• Environmental factors

• Microbial changes

Immune dysregulation

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Microbial “dysbiosis” associated with IBD

Gevers et al Cell Host Micro 2014. 15: 382-392

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Manipulation of microbiome in IBD• Antibiotics are effective in luminal and perianal Crohn’s disease

• Faecal microbiota transplantation(FMT) is effective at inducing remission in ulcerative colitis

Paramsothy S, Kamm MA, et al. The Lancet 2017

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Role of individual bacteria in IBD

• Protective effect of bacteria - F. prausnitzii

• Produces the MAM peptide – which is NF-kB supressive

F. prau abundance post-operatively Protective effect in a mouse model

Sokol, H., et al., Proc Natl Acad Sci U S A, 2008. 105(43): p. 16731-6.

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Microbiome as a pharma target• Historically the market has been dominated by nutraceuticals

with a paucity of clinical trials• Despite the lack of evidence, sales expected top $50B in 2020

• Evidence of FMT in C. difficile colitis is established, and IBD is growing with significant interest• Openbiome – Finch, currently conducting Phase 2 trials in C. difficile

• Janssen Microbiome Institute – targetting IBD, T2D

• Seres Therapeutics – Spore based formulation in Ph 2 trials for UC and CDI

• Rebiotix acquired by Ferring Pharmaceuticals – CDI

• Nextbiotix – Bacterial treatment for IBD (F. prau)

• FDA/EMA regulatory pathways

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Summary

• New techniques in microbiome research have led to unprecedented detail of human microbiome composition

• Multiple associations between microbiome alterations and disease states

• Functional aspects of these changes remain relatively unexplored and are somewhat limited by existing datbases

• Microbiome state influences drug metabolism and response

• Evidence in gastrointestinal disease that targeting the microbiome can treat disease such as IBD

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