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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
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
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”4
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
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”5
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.
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”6
MicrobiomePubMed publications with key word “Microbiome”
1,300 papers published
11,000 paper by end of 2018
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”7
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”8
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”9
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”10
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”11
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”12
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.
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”13
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
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”14
• 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?
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”15
Human Microbiome1,000,000+ genes
Human Genome23,000 genes
The Complexity of the Human Gut Microbiota
Comprised of 500-1000+ species of bacteria.
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”16
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
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”17
The Microbiome Across the Life Course
Perturbations to the microbiome can havelong term consequences, particularly early in life.
e.g. Antibiotics, Infection, Diet
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”18
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
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”19
Early Life Adulthood Late Life
Immature Host(Immune)
Immature Microbiome
Birth
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”20
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.
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”21
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
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”22
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?
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”23
• ‘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
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”24
Three approaches to the microbiome
1) Microbial Profiling who is there?
2) Metagenomics what genes are there?
3) Metatransciptomics what genes are expressed
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”25
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
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”26
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
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”27
Bacterial Community
Sample Collection
Sample Processing
DNA (RNA)
Extraction
Amplification and
Sequencing
Bioinformatics
Inferred Community/
Genomics
?
StudyDesign
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”28
• 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
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”29
• 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
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”30
Walters & Knight. FEBS Lett 2014
Microbiota composition in obesity studies
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”31
Walters & Knight. FEBS Lett 2014
Microbiota composition in obesity studies
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”32
Walters & Knight. FEBS Lett 2014
Microbiota composition in UC vs Healthy
Unweighted Unifrac
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”33
Microbiota composition in Crohn’s vs Healthy
Walters & Knight. FEBS Lett 2014
Unweighted Unifrac
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”34
Temporal variation in the microbiota
Halfvarson et al, Nat Microbiology 2017
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”35
Inconsistent microbiota signature in UC
Courtesy of F. Tse, G. Leontiadis and P. Moayyedi, unpublished
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”36
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 #....).
Copyright © 2015 The Royal College of Physicians and Surgeons of Canada. http://rcpsc.medical.org/canmeds. Reproduced with permission.”37
Pan-Canadian study:2000 patients with Crohn’s disease2000 patients with Ulcerative colitis2000 patients with IBS2000 healthy controls
Followed for 5 years