Gut Microbiota

Question 1

What is the make up of a normal microbiota?

Answer 1

It is mostly composed of anaerobic bacteria (100-1000 fold more than aerobic/facultative anaerobes)
10-fold more unique genes than their host
The most abundant phyla are the firmicutes and bacteroidetes
The collective metabolic activity of these microorganisms is approximately the same as that of the liver which is what has led to suggestions that it is now considered its own organ

Question 2

What have been the paradigm shifts in immunology as a result of studying the microbiota?

Answer 2

Instead of the immune system recognizing self and non-self there is now the super-organism theory where the microbiota is considered part of self
Host mucosal immune system is tolerant rather than responsive to these microorganisms
There may be an immune system-microbiota alliance

Question 3

What are the costs of having a complex immune system which is dependent on the microbiota?

Answer 3

Allergic, autoimmune and inflammatory disorders may occur from a failure to control misdirected immune responses against self microbiota derived or environmental antigens
Changes in microbiota composition or function may occur in response to antibiotics, dietary changes and recent elimination of key constituent’s namely helminthes may have transformed our microbial allies into potential liabilities

Question 4

What are the tools commonly used to study the microbiota?

Answer 4

Next-generation sequencing where there can be comparisons made between the microbiota in patients with disease vs healthy individuals
Germ-free mice where there can be manipulation by antibiotic treatment or microbiota reconstitution

Question 5

How is the microbiota obtained and maintained?

Answer 5

Our first contact with microorganisms is thought to be during passage through the birth canal with this initial exposure establishing the context for subsequent mucosal and systemic immune function
It is maintained through the actions of tolerance, early exposure to colostrum/breast milk, diet and the environment to which we are exposed

Question 6

How is there tolerance to the microbiota?

Answer 6

There is a reduced production of inflammatory cytokines with the B and T cell responses skewed towards regulation

Question 7

How does early exposure to colostrum/breast milk regulate the microbiota composition?

Answer 7

This contains live microbes, metabolites, maternal IgA, immune cells and cytokines and drives the infants microbiota to form with the correct composition

Question 8

How does diet impact the microbiota?

Answer 8

Dietary changes are capable of rapidly and reproducibly altering the human gut microbiome with evidence suggesting that there are alterations within one day of diet change

Question 9

What are the possible factors which lead to microbiota symbiosis?

Answer 9

High fibre diet
Natural birth
Breast feeding
Environmental exposure to microbes
Prevalence/consumptions of probiotics
Favourable genetics

Question 10

What are the possible effects of symbiosis?

Answer 10

Resolution of inflammation
Epithelial barrier integrity
Regulation of neutrophil activity
Regulation of dendritic cell function
A decrease in  the proportion of Th17 and increase in the proportion of Treg

Question 11

What are the possible factors for dysbiosis?

Answer 11

Antibiotic use in children
Antibiotics entering the food chain through livestock
Western diet
Obesity
Hygiene
Stress
Infection with pathogenic bacteria

Question 12

What are the consequence of dysbiosis?

Answer 12

Unresolved inflammatory responses
Cancer
Autoimmunity
An increase in Th17 to Treg ratio

Question 13

What is the role of the microbiota in health?

Answer 13

Stimulation and maintenance of the mucosal firewall (through low levels of stimulation of the immune system)
Development of mucosal associated lymphoid tissue (as without a microbiota there is a reduction in mucus production and submucosa development)
Inhibition of pathogen growth (through colonization resistance)
Dampening of immune responses
Priming of mucosal immune responses

Question 14

What is colonization resistance?

Answer 14

This is one of the key was in which our microbiota protects us from pathogens this is done by occupying the same niche, affecting nutrient availability, stimulating the release of antibacterial products, targeting of related species

Question 15

How do commensal bacteria interact with CD4 T cells?

Answer 15

They induce their differentiation with species such as clostridium stimulating Treg development and B. fragilis stimulating Th1 development

Question 16

What is the role of PAMPs and gut homeostasis?

Answer 16

Ongoing exposure to PAMPs stimulates gut immune development
RegIIIgamma is produced in response to MyD88 mediated signalling
Exposure to TLR ligands alone can induce maturation of the germ free gut mucosa

Question 17

How does TLR-5 mediated signalling provide a link between the microbiota and patient response to vaccination?

Answer 17

WhenTLR5 knockout mice were given a vaccine they develop a response slower than that of those that functional TLR5
As the vaccine does not stimulate TLR5 it is likely that this was a result of microbiota stimulation
Germ free mouse studies have supported this where germ free mice did not generate an effective response to a flu vaccine compared to normal mice

Question 18

What is the relationship between the microbiota and short chain fatty acids?

Answer 18

The microbiota is capable of digesting many plant compounds which we cannot to produce short chain fatty acids
These can signal the colonic epithelium where they act as the main energy source, result in less oxidative DNA damage, regulate proliferation, maintenance of barrier function, tumour suppression and cytokine production
They can also signal the immune system to allow an enhanced ROS burst, cause more phagocytosis, induction of apopotosis, modulate recruitment and cause cytokine production

Question 19

What is the effect of omega-3 fatty acids on immune cells?

Answer 19

There is less recruitment
Lower proinflammatory cytokine production
And this is associated with an anti-diabetic phenotype

Question 20

What is the connection between the microbiota provided by GPR43 signalling and immune cell functions?

Answer 20

This is a chemoattractant receptor which can be triggered by microbiota produced SCFA

Question 21

What are the protective and pathogenic roles of the gut microbiota in IBD?

Answer 21

As a symbiont it can inhibit pathobionts leading to increased growth of beneficial bacteria which upregulate Treg cell production, IL-10 and REGIIIgamma this occurs at the same time as unclassified bacteria lead to GALT development, increased TH17 and TH1 populations as well as increasing the barrier function
This promotes gut homeostasis
In dysbiosis the benefical bacteria are los allowing pathobiont growth which stimulates chronic inflammation through decreasing Treg, IL-10 and REGIIgamma while greatly increasing TH17 and TH1 populations