L12. Benefits and Mischiefs of Normal Microbiota

Question 1

What is the human microbiome?

Answer 1

Humans live with a whole range of COMMENSAL organisms in and on their body. This CO-EVOLUTION of species has led to collaboration and genetic sources to enable PHYSIOLOGICAL DIVERSITY.
= Mutualist relationship

Question 2

What is dysbiosis? What is the consequence of this?

Answer 2

Dysbiosis is the disruption of the mutualistic relationship between host and bacterium.
Leads to disease. Eg. malnutrition, infection, inflammation, autoimmune disease, obesity and metabolic syndrome, allergy

Question 3

What is the general profile and distribution of bacteria along the gut?

Answer 3

It is highly diverse and variable: between people.
There is both a site specific and a individual specific distribution of bacteria.

The gut is generally colonised with gram negative, anaerobic bacteria. And the area of highest concentration is distally along the tube.

Question 4

What four bacterial phyla make up the majority of commensal species in humans?

Answer 4

1. Firmicutes
2. Bacteriodetes
3. Actinobacteria
4. Proteobacteria

Question 5

How does the composition of bacteria vary within a host?

Answer 5

It is generally stable in the host unless dysbiosis or major impacts occur

Question 6

The microbiota are able to function in favour of and influence the host. What are some major ways it does this? [4]

Answer 6

1. Metabolism
2. Development
3. Immune System development and regulation
4. Protection against enteropathogens (competition)

Question 7

What factors influence the gut microbiota? [6]

Answer 7

1. Mode of delivery (eg. vaginal or ingestion)
2. Age of the individual
3. Diet
4. Genes and Environment
5. Antibiotic usage
6. Chronic Inflammatory states

Question 8

What is the effect of age on the gut microbiota?

Answer 8

The diversity of the gut microbiota increases with age especially as diet and environmental factors change.

Infants have very volatile profiles and change dramatically with major changes in diet.

Question 9

What is the effect of diet on the gut microbiota?

Answer 9

Fat and fibre content affects microbiota profile (available of nutrients for bacteria to consume)
Animal based or plant based diets alter composition

Question 10

How does antibiotic use affect the gut microbiota?

Answer 10

Kills some microflora and allows some others to thrive. Thus the whole environment is changed.
Different antibiotics cause different changes.
Often takes a very long period of time for the gut to recover the baseline (pre-antibiotic) profile.

Question 11

What role do microbiota have in nutrition?

Answer 11

Microbiota is very important to nutrition in 2 ways:

1. Direct supply of nutrients (eg. Vitamin B2, K, folate, CHO) = metabolic pathways
2. Altering the metabolic machinery of the host celld by inducing gene changes or by maintaining differentiation and functions

Question 12

How does colonic fermentation of dietary fibres affect the gut?

Answer 12

Microbiota in the colon ferment complex carbs (digested into oligosaccharides and monosaccharides) that can’t be broken down further or absorbed yet.

Bacteria FERMENT these into short chain fatty acids (acetate, proprionate, butyrate).

• These are absorbed in the colon and provide energy for colonic epithelial cells.
• They also move to the liver and peripheral organs and acts as substrates for gluconeogenesis and lipogenesis.
• Short Chain fatty acids also control colonic gene expression

Question 13

What is important about how the immune system works in the gut?

Answer 13

The immune system needs to be able to differentiate between the host’s microbiome and the pathogenic and dangerous organisms.

Thus there needs to be a highly regulated system to maintain HOMEOSTASIS between microbiome and immune activity.

Question 14

The mucosa-associated lymphoid tissue (MALT) is the largest collection of lymphoid tissue in the body. Why is this so?

Answer 14

Because the gut is exposed to large amounts of antigenic challenge.

• requires protection from pathogens
• requires tolerance to normal microbiota

Question 15

There are three major sites of lymphocyte COLLECTIONS in the gut. Where and what are these?

Answer 15

1. Isolated Lymphoid Follicles (ILFs) in the large and small intestines in the lamina propria
2. Payer’s Patches are patches in the small intestine immediately beneath the the enterocytes (especially under M cells) that are the sites for induction of T and B cell activation
3. Mesenteric Lymph Nodes along the GIT

Question 16

What are some innate defences of the gut?

Answer 16

Peristalsis and flushing action
Acidity and presence of many digestive enzymes and bile
Commensal microorganisms
Mucous layer
Paneth Cells located in the base of the crypts that secrete antimicrobials
Innate leukocytes: NK cells and specialised immune cells (IELs)
M cells and dendritic cells

Question 17

There are several specialised T cell populations in the gut. What are some examples of these?

Answer 17

1. Innate Lymphoid Cells (ILCs)
2. Lymphoid Tissue Inducer Cells (LTi)
3. Intraepithelial lymphocytes (IELs)
4. NK22 cells
5. Mucosal associated invariant T cells (MAIT)
6. Invariant NKT cells
7. Macrophages

Question 18

What are the innate lymphoid cells?

Answer 18

They act like Th cells by secreting multiple cytokines like IFN-y, IL-17, IL-22, IL-5 and IL-13

Question 19

What are the lymphoid tissue inducer cells?

Answer 19

They stimulate the recruitment of DC, T and B cells to the peyer’s patches and isolated lymphoid follicles

Question 20

What are the intraepithelial lymphocytes?

Answer 20

Lymphocytes of CD8 T cell subsets that are scattered in between the intestinal epithelia.
These CD8 cells have LIMITED DIVERSITY - innate cells

They are associated with protection, epithelial repair, promotion of tolerogenic DCs, and produce IL-22.

Question 21

What is the role of the NK-22 cells?

Answer 21

They act like Th17 cells and have a regulatory role. They secrete cytokines like IL-22, which enhances antimicrobial defences and others like epithelial repair.

Question 22

What are the mucosal associated invariant T cells?

Answer 22

These respond very rapidly to bacterial antigens and secrete IL-12 and IL-18. Their function as a whole is still unknown.

Question 23

What is the role of the Invariant NK T cells?

Answer 23

They secrete pro-inflammatory cytokines

Question 24

How do the Microfold (M) cells control antigenic access?

Answer 24

M cells are located interspersed between epithelial cells; they don’t have microvilli nor do they secrete mucous hence antigens are more readily accessing to these cells.

They allow transcytosis of antigens or they are a target for bacterial killing allowing antigens to pass into the mucosa and interact with the lymphoid tissues.

M cells do not express MHC II and so cannot act as antigen presenting cells.

Question 25

What is underneath the M cells?

Answer 25

Dendritic cells and Peyer’s Patches

Question 26

Dendritic cells in the mucosa are specialised. Describe what is meant by this.

Answer 26

STEADY STATE/NORMAL:
DC cells induce Treg (TGFb) and the Th2 response. The Th2 switches isotype to IgA. These ultimately lead to DEREGULATION OF INFLAMMATION

INFLAMMATORY CONDITIONS:
They instead induce Th1 and Th17 to bias the isotype switch to secretory IgA and PROMOTE INFLAMMATION.

Question 27

What is an important function of the specialised dendritic cell in the gut?

Answer 27

Induces mucosal HOMING RECEPTORS called ADRESSIN a4b7 on the presented to and activated T and B cells such that they express this receptor whose ligand is ONLY on gut epithelia (gut endothelial cells selectively express integrin MAdCAM1).

Hence activated T and B cells will leave the patches and follicles and drain into the lymph nodes before eventually entering the circulation and home to the gut and bind and act in the gut.

Question 28

What additional receptor will T and B cells activated in the gut mucosa express?

Answer 28

CCR9 which is a receptor for CDL25, a ligand expressed only by small intestinal epithelium.

Question 29

The activated B cells in the gut produce large amounts of IgA every day. Why is this so?

Answer 29

The majority of these secretions are directed against commensal organisms