Microbiota and What the Clinical Gastroenterologist Needs

Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”1

Microbiota and What the Clinical Gastroenterologist Needs to Know

Co-Speakers: Premysl Bercik and Michael Surette, Farncombe Family Digestive Health Research InstituteMcMaster University

Small Group Session: Sunday, February 11, 11h00-11h40Room: Saskatchewan

http://rcpsc.medical.org/canmeds

Conflict of Interest Disclosure(over the past 24 months)

Commercial or Non-Profit Interest Relationship

Takeda Pharmaceuticals consultant

Weston Foundation research support

Gilead research support

BioK sponsored research

Name: Dr. Michael Surette

Conflict of Interest Disclosure(over the past 24 months)

Commercial or Non-Profit Interest Relationship

Nestle Switzerland Consultant, research support

Allergan Canada advisory board, consultant

LUPIN Pharma Canada advisory board

IM HealthScience advisory board

Innovate Biopharma advisory board

Name: Dr. Premysl Bercik


PB Medical Expert (as Medical Experts, physicians integrate all of the CanMEDS Roles, applying medical knowledge, clinical skills, and professional values in their provision of high-quality and safe patient-centered care. Medical Expert is the central physician Role in the CanMEDS Framework and defines the physician’s clinical scope of practice.)

Communicator (as Communicators, physicians form relationships with patients and their families that facilitate the gathering and sharing of essential information for effective health care.)

Collaborator (as Collaborators, physicians work effectively with other health care professionals to provide safe, high-quality, patient-centred care.)

PB Leader (as Leaders, physicians engage with others to contribute to a vision of a high-quality health care system and take responsibility for the delivery of excellent patient care through their activities as clinicians, administrators, scholars, or teachers.)

Health Advocate (as Health Advocates, physicians contribute their expertise and influence as they work with communities or patient populations to improve health. They work with those they serve to determine and understand needs, speak on behalf of others when required, and support the mobilization of resources to effect change.)

PBMS

Scholar (as Scholars, physicians demonstrate a lifelong commitment to excellence in practice through continuous learning and by teaching others, evaluating evidence, and contributing to scholarship.)

Professional (as Professionals, physicians are committed to the health and well-being of individual patients and society through ethical practice, high personal standards of behaviour, accountability to the profession and society, physician-led regulation, and maintenance of personal health.)

CanMEDS Roles Covered



Learning Objectives:At the end of this session participants will be able to:

1. Understand the basic analysis of microbiota profiling analysis and metagenomics, and reported measures (such alpha and beta diversity);

2. Understand the differences in methodological approaches and how they may influence outcome;

3. Review our current understanding of the role of microbiota in GI diseases, focusing on clinical studies in IBD and IBS.



MicrobiomePubMed publications with key word “Microbiome”

1,300 papers published

11,000 paper by end of 2018













The organisms, their genomes and environments on or in us is the human microbiome.

The Human Microbiome

Nature Rev. Microbiol. 9,279-290 (2011)

Every surface on the human body has a distinct microbiome.

Every individual has their own unique microbiome.



Stomach101 – 103 cfu/ml

Jejunum/ileum104 – 107 cfu/ml

Duodenum101 – 103 cfu/ml

Colon1011 – 1012 cfu/ml

• Varies in composition and increase in bacterial density along its length.

• GI tract is 10m in length• Stool is representative of the colon

The Human Microbiome


http://upload.wikimedia.org/wikipedia/commons/4/4f/Complete_GI_tract_-_transparent_-_wider.png


• produce vitamins that we need (e.g. K, B12).

• break down our food to extract energy and nutrients (SCFAs).

• train and maintain our immune systems.

• first-line defense against pathogens –colonization resistance.

What does your gut microbiome do for you?



Human Microbiome1,000,000+ genes

Human Genome23,000 genes

The Complexity of the Human Gut Microbiota

Comprised of 500-1000+ species of bacteria.



The Microbiome Across the Life Course

• We are born essentially sterile• Colonized at birth• Stabilizes by 1-3 years• Co-evolves with immune

system uniquely in each individual

In the absence of disease, the microbiome is stable throughout most of life

• Later in life the immune and microbiome disentangle and lose stability



The Microbiome Across the Life Course

Perturbations to the microbiome can havelong term consequences, particularly early in life.

e.g. Antibiotics, Infection, Diet



Changes in the gut microbiome have been correlated with a wide range of chronic diseases.

Inflammatory Bowel Disease

Obesity

CardiovascularDisease

Allergy& Asthma

Psychological Disorders e.g. Anxiety and Depression

DiabetesIrritable Bowel Syndrome



Early Life Adulthood Late Life

Immature Host(Immune)

Immature Microbiome

Birth



Immature Host(Immune)

Immature Microbiome

Birth Chronic Disease

Dysbiosis: an imbalance of the microbiome with respect to the host (immune system).

Not define by the composition of the microbiome but by its interaction with the host.



Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Haiser HJ et al , Science. 2013

• Digoxin is a medication used to treat various heart conditions• Known that there are responders and non-responders • Some patients excrete the inactive digoxin metabolite

dihydrodigoxin• Co-administration of broad spectrum antibiotics increases serum

digoxin

• Eggerthella lenta in vivo

• cgr1 cgr2 dependent

• Non-responders had cgr1 cgr2

Dihydrodigoxin

This reaction is inhibited by arginine and dietary protein in monocolonizedmice.

Only 1 of 3 isolates of E. lentahad cgr1 cgr2 and were capable of inactivating digoxin

ie. Strain not Species dependent



EggerthellaMean abundance <0.001

MetaQuery

Some processes, like bulk metabolism (eg SCFA production) are carried out by prominent members of the gut community and are usually redundant functions (in many different bacteria).

Some processes, like drug metabolism can be carried out by low abundant members of the gut community and are usually specialized functions.

Does relative abundance matter?



• ‘Good’ vs ‘bad’ bacteria are often context dependent, their functionality is influenced by environment (e.g diet)

• Low abundant organisms are not necessarily unimportant

• Often specific functions are strain not species specific



Three approaches to the microbiome

1) Microbial Profiling who is there?

2) Metagenomics what genes are there?

3) Metatransciptomics what genes are expressed



Alpha Diversity

• The species diversity within a population and is independent of taxonomy (i.e. Two populations can have the same alpha diversity but not share species in common)

• Richness = the number of species present

• Evenness = includes the proportion of a species within a population

Observed_species (OTUs) ; Chao1; Shannon Diversity; Simpson Diversity; Phylogenetic Diversity



Beta Diversity• Is a measure or comparison between different populations

and is therefore sensitive to species composition

• Weighted vs unweighted – takes into account the relative abundance of each species (weighted) or simply the presence or absence of a species (unweighted)

• Phylogenetic beta diversity also include taxonomic distance when calculating distance between two populations (e.g. unifrac)

Bray-Curtis Dissimilarity, Weighted Unifrac and Unweighted Unifrac



Bacterial Community

Sample Collection

Sample Processing

DNA (RNA)

Extraction

Amplification and

Sequencing

Bioinformatics

Inferred Community/

Genomics

?

StudyDesign



• Each of these steps can influence the outcome

• Differences between similar studies may arise because of differences in protocols (i.e. technical not biological)

• Even the samples data run through two different bioinformatics pipelines can give different results



• Variability in methodology study to study.

• Relationship of data is in relative not absolute abundances.

• Large compositional variation between individuals results in sparse (zero inflated >70%) datasets.

• Large datasets >> multiple test correction.

Statistical Challenges with Microbiome Data



Walters & Knight. FEBS Lett 2014

Microbiota composition in obesity studies




Microbiota composition in obesity studies




Microbiota composition in UC vs Healthy

Unweighted Unifrac



Microbiota composition in Crohn’s vs Healthy


Unweighted Unifrac



Temporal variation in the microbiota

Halfvarson et al, Nat Microbiology 2017


https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=5319707_nihms841832f4.jpg


Inconsistent microbiota signature in UC

Courtesy of F. Tse, G. Leontiadis and P. Moayyedi, unpublished



Microbiota transplantation in germ-free mice(examples)

• Mice with UC microbiota have increased sensitivity to experimental colitis (Natividad et al, Inflamm Bowel Dis 2015)

• Microbiota from IBS-D patients induces immune activation and gut dysfunction (De Palma et al, Science Transl Med 2017)

• Microbiota from patients with UC display temporal changes in proteolytic activity (Bermudez et al, poster #....).



Pan-Canadian study:2000 patients with Crohn’s disease2000 patients with Ulcerative colitis2000 patients with IBS2000 healthy controls

Followed for 5 years


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Documents

Microbiota and What the Clinical Gastroenterologist Needs