Gut microbiota in health and disease

Gut Microbiota in Health and Disease

Arjumand [email protected]

Presentation Overview• Overview of Gut Microbiota• Microbiota in Health

• Symbiosis• Role in innate immunity• Role in adaptive immunity

• Microbiota in Disease-dysbiosis• Diseases of the GUT• Non-mucosal diseases

• Symptoms of dysbiosis• Treatment

A human body: the traditional view • A human body is a collection

of ~10 trillion cells• Most cells have 23 pairs of

chromosomes • Approximately 23,000-25,000

genes are located on the different chromosomes

• Different genes are expressed in different tissues and organs each with its own function.

A human body: The revolutionaries' view

”Microbes maketh man”• In every human being, and especially in his or her guts, dwells the microbiome: 100 trillion bacteria of several hundred species bearing 3m non-human genes

• Total weight=~1-1.5Kg)• The revolutionaries believe that in the human

body, these too should count. • As the microbiome is composed of members of

a community, playing important role, of which the human “host” is a single member

• Hence, humans are not single organisms, but superorganisms made up of lots of smaller organisms working together.

Microbiota in the Human Body- >90% of cells in the human body are microbes• In the gastro-intestinal tract

• The intestine is a preferred site and >70% of all bacteria are found in the colon

• large organ• rich in nutrients

• In the genitourinary tract• On the skin• On the mucosal membranes

• All mucosal surfaces are colonized with bacteria

Gut Microbiota in Health• Microbes colonize in the human body-

Ecosystem• Colonization occurs early in life and

stabilizes by the age of 1-3 years• The GIT is colonized by a large number

of commensal (relationships between two organisms where one organism benefits from the other without affecting it) bacteria.

• Resident bacteria form complex ecosystemsCommensal microflora (normal microflora, indigenous microbiota) consists of those micro-organisms, which are present on body surfaces covered by epithelial cells and are exposed to the external environment (gastrointestinal and respiratory tract, vagina, skin, etc.)

A short story• One day the body parts were fighting with each other as to who

is the most important• The brain said: I am the most important as I control everything• The heart said: I am the most important as my beating keeps

the body going• The liver said: I am the most important as help in metabolism,

excretion, detoxication, etc• ----------• Finally the GUT said: I am the most important, I digest, absorb,

protect, excrete, produce hormones, reabsorb etc EVERYONE LAUGHED---HA HA HA

• The GUT got angry and shut down• Within a few days all the other body systems agreed, it was the

most important!

• The intestinal microbiota have coevolved with the human host to perform a number of functions that affect the host’s physiology and metabolism.

• The host and its microbiota have mutually beneficial and

cooperative interactions

• The metabolic activity of the human gut microbes has been suggested to function as an auxiliary, virtual organ in the human body.

Valm et al, PNAS 2011

• Microbial composition is heavily influenced by environment (diet, stress)

• Under specific conditions are able to overcome protective host responses and exert pathologic effects.

Role of microbiota in Health

• Symbiotic relationship: (Interaction between two different organisms living in close physical association, typically to the advantage of both).

• Shaping and maintaining immunity:• Innate immunity• Adaptive immunity

Gut Microbiota in Health- symbiosis

Human (host) Microbiome

Provides:• Nutrients• Shelter

• Increases the metabolic capacity of the host -digest plant carbohydrates, milk products (glycans) - ~10% of the calories from diet

• Provide vitamins (e.g. B2, B12, K and folic acid)• Protect from colonization with pathogenic bacteria

(Colonization resistance)

• Produce pathogen-associated molecular patterns (PAMPs) and metabolic by-products and regulate intestinal immune responses

• PAMPs are recognized by pattern recognition receptor (PRR)-bearing cells of the innate immune system and many epithelial cells

Gut Microbiota in Health- innate immunity

Gut Microbiota in Health: Adaptive immune system

• Microbiota stimulation leads to B cell switch to IgA, regulatory T cell induction, T cell differentiation to Th17

Bacterial-derived Metabolites are key components of cross-talk

Dysbiosis and disease• Dysbiosis: microbial imbalance or maladaptation on or inside the body

(impaired microbiota)• Microbial dysbiosis is found in many different diseases• Proposed causes of dysbiosis of the microbiota:

↑ Fungus/yeast (Candida), parasites, viruses and pathogenic bacteria.

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Host genetics and the microbiome

A few genes exert strong control over a few microbes.

Many genes exert strong distal control over many microbes

due to founder effects.

Many genes exert indirect control over many microbes due to polygenic immunity

and disease phenotypes.

Environment exerts strong proximal control over many microbes.

A few microbes and many functions are

strong proximal indicators or

controllers of disease.

Monogenic effect Multifactorial effectNOD2, IL23R, IL17R, ATG16L, IGRM

Dysbiosis: Proposed mechanism/s leading to disease

• Genetic and environmental factors induce impaired barrier function

• Overgrowth of pathogenic bacteria; inhibition of protective bacteria

• Translocation of bacteria and bacterial products

• Immune activation and proinflammatory cytokine production

• Chronic inflammation leads to tissue destruction and complications

The Root of several Diseases- Dysbiosis

The Root of Health- Symbiosis

Dysbiosis and diseases• Diseases of the GUT

• Malabsorption syndrome• Malignancies: Colorectal cancer• Inflammatory Bowl disease (IBD)• Irritable Bowl syndrome• Diarrheal diseases

• Non-mucosal diseases• Obesity and metabolic syndrome• Malignancies: liver cancer, breast cancer• Complications of liver cirrhosis• Allergic conditions• Autoimmune disorders (T1DM, arthritis etc)• Abnormalities of the gut-brain axis- Autism and other

neurological disorders• Obesity and other metabolic disorders• Chronic fatigue syndrome• Periodontal diseases

Malabsorption syndrome• In health: The bacterial growth is restricted in the upper small bowel under the influence of acid and motility.• Factors predisposing to bacterial overgrowth:

Surgical, anatomical, motor (scleroderma & DM), hypochlohydra (atrophic gastritis, post gastrectomy)

• Consequences of bacterial overgrowth:- Fat malabsorption due to:

Bacteria deconjugation of bile acids which allows free bile acids to be reabsorped decrease luminal bile acid concentration ---limit micelle formation.Patchy mucosal damage by bacteria or toxic effects of FFA

- CHO and protein malabsorption due to mucosal damage or bacterial metabolism of these nutrients.

- B12 malabsorption: B12 is utilized by the bacteria, in contrast bacteria produces folic acid.

GIT malignancies: Colorectal cancerColonic bacteria may initiate cancer through:1- Production of carcinogens from diets rich in meat and fat

(nitroso compounds).2- Elevation in damage to DNA of colonic cells by dietary

carcinogens (heterocyclic aromatic amines found in cooked meat).

3- Disproportionate pro-inflammatory signaling at the GIT mucosa, leads to increased sloughing and repair of epithelium, which can ultimately lead to neoplasia and malignancy.

4-Certain microbial species can have direct or indirect (through host cell activation) cytotoxic effects on cells

5- Microbial metabolism can produce by-products toxic to epithelium;

6- Abnormalities in repair can lead to neoplastic transformations

• High risk of colon cancer was associated with presence of Bacteroides vulgatus and Bacteroides stercoris while, low risk was associated with presence of Lactobacillus acidiphilus, Eubacterium aerofaciens.

• Although the evidence is not conclusive, colonic flora seem to be a major environmental factor that modulates risk of colonic cancer in human beings.

Inflammatory Bowl Disease (IBD)A group of inflammatory and autoimmune conditions that affect the colon and small intestine, typically resulting in severe abdominal pain, weight loss, vomiting and diarrhea.  • Affects all layers of the bowel wall

• Granuloma formation in up to 60% of patients

• Affects superficial mucosal layers

IBD is driven by T cellsmucosal homeostasis

cytokine production by regulatory (TReg) T cells supresses pro-inflammatory responses

mucosal inflammation increased production of pro-inflammatory cytokines by T helper (TH) cells

TH1, TH2, TH17 TReg

TNF, IFNγ, IL-17

TReg transfer can prevent the induction of experimental colitis

adapted from Bouma and Strober, Nat rev Immunol., 2003 and Vignali et al., Nat rev Immunol., 2008

Involvement of the microbiota in regulating the balance between TH and TReg cell subsets in the gut

• germ-free animals show defective TH17 cell development in the small intestine

• ATP generated by intestinal bacteria increases the production of IL-17 in the colon

• germ-free mice have reduced numbers of TReg cells in the mesenteric lymph nodes

• increased numbers of Treg cells in the small intestine of germ-free mice

Intestinal bacteria direct the differentiation of both pro- and anti-inflammatory T cell populations and may therefore play a crucial role in IBD

TRegTH

Crohn's disease • Intestinal T-lymphocytes become hyper-reactive against

bacterial antigens (local tolerance mechanisms are abrogated)

• Increased intestinal mucosal secretion of IgG against a broad spectrum of commensal bacteria (normally IgA is produced). IgG activates the complement and the cascade of inflammatory mediators

• Higher amounts of bacteria attached to epithelial surfaces compared to healthy people. This causes unrestrained activation of the intestinal immune system

• Incidence is the highest in developed countries

Mutation in NOD2 gene (16q12.1)

• Normally:LPS interact with NOD2----activation of NF-β------- production of cytokines and resistance to apoptosis• Mutation in NOD2 gene:Diminished macrophage activation in presence of bacterial LPS chronic intracellular infection or failure to develop tolerating immune response in presence of commensal flora.Mutations: Some patients with Crohn's disease (17–25%) have mutations in the NOD2 (Nucleotide-binding oligomerization domain-containing protein 2) gene expressed in macrophages which encodes intracytoplamic receptor for bacterial Lipopolysaccharide (LPS)[LPS are recognized as pathogen associated molecular pattern (PAMPs) by the pattern recognition receptors (PRRs), among them toll like receptors (TLRs)]

Deranged GUT microbiota and non-mucosal diseases

Obesity and metabolic syndromeOver the past 25 years, the prevalence of obesity has risen dramatically in several developed and developing countries. Recent evidence suggests that the gut microbiota plays a role in energy harvest, storage, and expenditure. - Germ-free mice are protected against obesity and that the transfer of gut microbes from conventionally raised animals results in dramatic increases in body fat content and insulin resistance. - The composition of the gut microbiota is shown to differ in lean and obese humans and animals and to change rapidly in response to dietary factors. - The gut microbiota may also influence the development of conditions characterized by low-level inflammation, such as obesity and type 2 diabetes, through systemic exposure to bacterial lipopolysaccharide derived from the intestinal microbiota.- Gut microbiota (and diet- induced changes in microbiota composition) may contribute to low- grade inflammation- Chronic low-grade inflammation is associated with obesity and metabolic dysfunction (insulin resistance)

Hence, recent research has implicated the gut microbiota as a critical determinant of nutrient uptake, energy regulation, and ultimately, weight and metabolic disorders

Study: Different gut microbial community structure in obese mice

Firmicutes

Bacteroidetes

% S

eque

nces

Ley et al., PNAS 102: 11070-5 (2006)

Study: Effects of dieting

Ley et al. Nature 444: 1022 (2006)

Study: Microbiota fecal transplantation

• The transfer experiment tested this hypothesis:

• microbiotas were taken from the fat mice, transferred to gf recipients, and those that received the microbiotas from the obese donor gained more weight, even though they didn’t eat more.

• Shifting the relative abundances of the microbiota is changing the function of the community in a way that has an impact on the host.

Conventionalized mice (CONV-D) are formerly germ-free (GF) recipients of a gut microbiota transplant from

conventionally-raised (CONV-R) donors

Mice that receive a fecal transplant from obese donors not only become obese, but do so while eating less food…

Study: Effect of transplant of microbiota from 1st and 3rd trimester pregnant female

Altered Microbiota and obesity: possible

mechanismsAltered Microbiota:• ↑SCFA → ↑ lipogenesis; ↑ Fat storage• ↑ Fasting-Induced Adipose Factor (FIAF) expression → ↑lipoprotein lipase

(Lpl) activity; ↑ fat storage• ↑Gut permeability → ↑LPS → ↑eCB1 receptors → activates the

endocannabinoid → ↑adipogenesis• ↑LPS → ↑Proinflammitory cytokines• ↓AMPK → ↑adipogenesis(AMPK is a master nutrient and energy sensor that maintains energy homeostasis)

Study: Microbiota and Diabetes mellitus

Mucosal-associated invariant T cell alterations in obese

and type 2 diabetic patients

MAIT: Mucosal Associated Invariant T-cellsMagallas et al.(2015) I Clin Invest.Lehen et al. (2015) ICAN

Microbiota and diabetes mellitus

Insulin Resistance

Microbiota and gut-brain axis

Clinical assessments for dysbiosis• Swab and culture • DNA probe / PCR • Antigen tests (e.g., stool H. pylori antigen) • Breath hydrogen/methane for SIBO • Jejunal aspiration – fungus and SIBO • Response to treatment: objective markers (e.g., ESR, CRP,

disease activity indexes)

Treatment of dysbiosis• See your doctor• Diet• Pre and probiotics

How do we suspect dysbiosis?

• Frequent gas or bloating • Cramping, urgency, and/or mucus in faeces• Brain fog, anxiety, or depression• Food sensitivities• Missing micronutrients• Chronic bad breath• Loose stool, diarrhea, constipation, or a combination• Irritable Bowel Syndrome (IBS)• History of “stomach bugs,” gastroenteritis, and/or food poisoning• History of prolonged antibiotics• Carbohydrate intolerance, particularly after eating fiber and/or beans• Fatigue or low energy• Use of anti-acids for heartburn, reflux, or hiatal hernia?• Autoimmunity, or an autoimmune condition such as Hashimoto’s thyroiditis, psoriasis, or multiple

sclerosis• Sinus congestion

If five or more of these symptoms are present, then we may be suffering from dysbiosis