v. Dysbiosis and Disease + Microbes and The Biofilm Concept

Question 1

What is Dysbiosis?

Answer 1

Dysbiosis: Change in the microbiota, no longer the normal balance between the different types of organisms and different proportions of each species.

Question 2

What are the effects of dysbiosis? (3)

Answer 2

• Loss of overall diversity
• Change in the ratios of the major phyla
• Bloom of a specific bacterium, especially one with the potential to cause damage

Question 3

NOTE: Do not know whether the change in the microbiota that is associated with a disease is either the CAUSE of the disease or an EFFECT of the disease being present. THERE IS ASSOCIATION OF CHANGES IN THE MICROBIOTA WITH SPECIFIC DISEASES. So far it cannot be said conclusively that if you change the _____, you will stop the disease.

Answer 3

microbiota

Question 4

Some of the associations between gut dysbiosis and disease: MAJOR CHANGE IN THE MICROBIOTA IS ASSOCIATED WITH THESE DISEASES OF VARIOUS ORGANS.

• Brain disorders:

Answer 4

Autism, Depression, Stress, Stroke (atherosclerosis)

Question 5

Some of the associations between gut dysbiosis and disease: MAJOR CHANGE IN THE MICROBIOTA IS ASSOCIATED WITH THESE DISEASES OF VARIOUS ORGANS.

• Lung:

Answer 5

SCFAs produced by the microbiota supress the immune response in allergic Asma.

Question 6

Some of the associations between gut dysbiosis and disease: MAJOR CHANGE IN THE MICROBIOTA IS ASSOCIATED WITH THESE DISEASES OF VARIOUS ORGANS.

• Liver:

Answer 6

Non-alcoholic fatty liver disease(NAFLD) and Non-alcoholic steatohepatitis (NASH)

Question 7

Some of the associations between gut dysbiosis and disease: MAJOR CHANGE IN THE MICROBIOTA IS ASSOCIATED WITH THESE DISEASES OF VARIOUS ORGANS.

• Skin:

Answer 7

Atopic dermatitis, Psoriasis

Question 8

Some of the associations between gut dysbiosis and disease: MAJOR CHANGE IN THE MICROBIOTA IS ASSOCIATED WITH THESE DISEASES OF VARIOUS ORGANS.

• GIT:

Answer 8

Inflammatory bowel disease (Ulcerative colitis, Crohn’s disease)

Question 9

Some of the associations between gut dysbiosis and disease: MAJOR CHANGE IN THE MICROBIOTA IS ASSOCIATED WITH THESE DISEASES OF VARIOUS ORGANS.

• Whole body:

Answer 9

Metabolic syndrome (Diabetes T2, atherosclerosis – increased blood pressure)

Systemic lupus erythematosus: Autoimmune disease (Upregulation/Lack of inhibition of IS is contributing to the increased incidence of these diseases)

Undernourishment: Children chronically malnourished even with correct feeding for extended periods (incorrect gut flora).

Question 10

Antibiotics are one of the cornerstones of modern medicine but WE ARE USING THEM TOO MUCH AND INCORRECTLY!
Effects on the individual: (4)

Answer 10

Question 11

Maintaining our Gut Microbial ‘Lawn’:

How is this maintained? (3)

Answer 11

• Probiotics
• Prebiotics
• Bacteriotherapy

Question 12

Maintaining our Gut Microbial ‘Lawn’:
- Probiotics:

Answer 12

• Probiotics: SEEDS. Live microorganisms that, when administered in adequate amounts,
  confer a health benefit for the host.
  Organisms known to be a part of the healthy gut microbiota. Only contain about 15 different organisms YET we need about 500-1000 different organisms in our gut. Cannot just buy probiotics to completely re-establish you microbiota.

Question 13

Maintaining our Gut Microbial ‘Lawn’:
- Prebiotics:

Answer 13

• Prebiotics: FOOD/FERTILIZER. Non-digestible food ingredients that, when consumed in sufficient amounts selectively stimulate the growth/activity of a limited number of microbial genera or species in the gut that confer(s) health benefits to the host
  Intense forms of fibre – Need diversity of fibres (eat as much variety in our diets as possible to feed the greatest amount of different bacterial species as possible).

Question 14

Maintaining our Gut Microbial ‘Lawn’:
- Bacteriotherapy:

Answer 14

Transplantation of the entire ecosystem (Faecal transplants) Encapsulated versions are being developed. Take note of the different areas within the GIT and how not all the species of bacteria are represented in faceal matter due to the distribution in mucosal folds. Thus, even if you use a faecal transplant, you may not necessarily regenerate all the organisms that the original donor had.
Faecal transplants are very useful, especially for patients who have chronic gut infections (avoid further doses of antibiotics).

Question 15

Establishment of microbiota: (2)

Answer 15

1. FOOD IS MEDICINE – MICROBIOTA EFFECT
   The discovery of the microbiota and effects on the body is like the discovery of a whole new organ that requires treatment and care.
2. GOOD MICROBIOTA = GOOD HEALTH AND MENTAL STATE
   - Mom via vaginal organism
   - Correct feeding/nutrition via breast milk
   - Balanced diet high in variety of fibres.

Question 16

The Biofilm Concept:
- September 17, 1683: _____ ____ ______ gives us reason to brush & floss
- Scraped plaque from his own ____
- Observed _______ under his primitive microscope
- It’s the first known description of a ____

Answer 16

Antoine van Leeuwenhoek
teeth
“animalcules”
biofilm

Question 17

What is a biofilm? (4)

Answer 17

• Accumulations/aggregate of microorganisms of mono or poly microbial aggregates
• Enclosed within a self-produced matrix of extracellular polymeric substances (EPSs)
• The microorganisms produce the EPS (slime) for protection
• Irreversibly associated to each other and/or to a surface

Question 18

What is a biofilm:
- Common misconception :
- Reality:

Answer 18

Question 19

What is the morphology of biofilm? (2)

Answer 19

• Biofilms have varied morphologies (seen under SEM) which depend on the constituent
  bacteria and the conditions under which the biofilm was formed.
• A: Pseudomonas aeruginosa which is isolated attached to a glass surface.
  C: Staphylococcus aureus biofilm growing in vivo

Question 20

Biofilm structure:
- The structure of the extracellular polymeric substance (EPS) matrix of biofilms is composed: (3)

Answer 20

o One or more of extracellular polysaccharides (exopolysaccharide)
High molecular weight polymers that are composed of sugar residues and are
secreted by bacteria into the surrounding environment.
o DNA
o Proteins

Question 21

Biofilm structure:

• ______ in the biofilm allow for water, air and nutrients to get to all parts of the structure.
• Biofilms may form on ____ or _____ surfaces
• Present in natural, industrial, & hospital settings (living tissues, medical devices - catheter)

Answer 21

Channels
Biotic
Abiotic

Question 22

What is a pre-requisite of biofilm?

Answer 22

Pre-requisite of biofilm formation is that bacteria should get close enough to a surface. As bacteria approaches a surface, several forces will act (both attractive and repulsive forces). When the bacteria is 10/20 nm away from the surface, the negative charges on the bacteria is repelled by the negative charges on most environmental surfaces. This repulsion may be overcome by attractive Van Der Waal forces between the bacterial cell and environmental surface, with the use of fimbria and flagella – Providing mechanical attachment to surface.

Question 23

How is biofilm formed: 5 Major stages of biofilm development:

Answer 23

5. Dispersion:

Occurs because there is lack of nutrition due to growing population or due to intense competition among different bacterial species within the biofilm. May disperse as a whole or a specific part of the biofilm. When dispersed as a whole, they will form another biofilm

Question 24

What are the reasons for biofilm formation? (2)

Answer 24

• Enhance the tolerance of bacteria to harsh environmental conditions.
• Resistance to antibiotics & host immune system

Question 25

Reason for biofilm formation: - Enhance the tolerance of bacteria to harsh environmental conditions. How does this process occur? (2)

Answer 25

o Bacteria can avoid being washed away by water flow or blood stream by simply attaching to a surface or tissue. o Cells in biofilms are about 1000 times more resistant than their planktonic

Question 26

Reason for biofilm formation: - Resistance to antibiotics & host immune system What are the factors affecting this? (6)

Answer 26

Question 27

Communication/Signalling in biofilm formation: Quorum sensing - Quorum sensing:

Answer 27

- Quorum sensing: Cell-cell communication process that regulates gene expression at high cell density.

Question 28

What is the process of Quorum sensing? (7)

Answer 28

Question 29

Quorum sensing (QS): - Chemical signals produced by _______ cells are not concentrated enough to cause changes in genetic expression - The EPS in biofilms holds cells in close _______ & allows concentrations of signal molecules to build up in sufficient quantity to effect changes in cellular _______ - Microorganisms will only activate some genes when they are able to sense (via cell signalling) that their population is large enough to make it advantageous and/or "safe" to initiate that genetic activity. Do not just upregulate certain genes whenever, they will sense a need for something specific and will produce it when it is advantageous or safe to initiate specific _____ _______. - Example: Some bacterial pathogens will not produce ______ until they sense that an adequate population has been established to survive host defences.

Answer 29

planktonic proximity behaviour genetic activity toxins

Question 30

Biofilms in Infectious Diseases: - About 65% of all bacterial infections are associated with bacterial biofilms - Two types of medically important biofilms : (2)

Answer 30

Question 31

Biofilms & Hospital Acquired Infections: Main nosocomial infections associated with biofilms: (4)

Answer 31

Question 32

Biofilm-related disease example: Cystic fibrosis (CF) - CF in the lung causes the formation of thick and sticky mucus, which blocks _____ and makes it hard for patients to breath. - 80% of CF patients are chronically infected by _______

Answer 32

airway P. aeruginosa

Question 33

Biofilm-related disease example: Cystic fibrosis (CF): - Medical instruments, devices and tools can also be ______ with P. aeruginosa. - Several cases of hospital acquired P. aeruginosa infections have been reported, but unfortunately, there are not many good antibiotics that are available for treating ______ P. aeruginosa infection. Because bacterial infection is occurring in a biofilm it is difficult for antibiotics to penetrate into the infection AND transfer of ______ ______ genes.

Answer 33

contaminated refractory antibiotic resistant

Question 34

Biofilm-related disease example: Cystic fibrosis (CF): - For patients who are infected with P. aeruginosa , _______ treatment often relieves the symptom of the infection but not necessarily cures the infection. - The lack of complete cure is mainly due to P. aeruginosa biofilms that act as _____ for disease recurrence (persister cells).

Answer 34

antibiotic reservoir

Question 35

Biofilm-related disease example: Cystic fibrosis (CF): - Beyond acting as disease reservoirs, the components of biofilms, such as the major ______ of P. aeruginosa matrix (alginate), are virulence factors. For example, alginate can cause lung damage. - Mucoid variant (large colony) will overproduce the alginate (virulence factor in the matrix of the biofilm). Mucoid _____ are only found in patients with chronic biofilm infection. Thus, ______ is a biofilm-specific antigen. Nonmucoid variant (small colony)

Answer 35

polysaccharide colonies alginate

Question 36

Device-related Case Scenario: - Mr. Kevin Naidoo is a 37 y/o with a history of extensive small bowel resection for Crohn’s disease. - Presenting complaint: o 7-day history of low grade fever (mean: 37.8 C) & malaise o He is receiving long term parenteral nutrition (TPN) that he was taught to infuse overnight at home via a Hickman intravascular line - On examination (in casualty department): o Skin around the Hickman line insertion site is red & tender o Pus is oozing from the insertion site o Now spiking a temperature of 38.6 C & looking very ill - He is admitted to hospital - A pus swab and blood cultures are taken for microscopy, culture & sensitivity - He is started on IV antibiotics

Answer 36

READ

Question 37

Management of biofilm-related infections: - Current approaches: (7)

Answer 37

Question 38

Management of biofilm-related infections: - Novel and future approaches: (6)

Answer 38

Question 39

What is a biofilm?

Answer 39

- Biofilms are defined as aggregated microorganism communities attached to surfaces and embedded in a self-produced matrix which is composed of extracellular polysaccharide, DNA and proteins. Combination of sessile and planktonic cells gathered together.

Question 40

- There are 5 major steps in biofilm formation:

Answer 40

1. Initial reversible attachment 2. Irreversible attachment 3. Micro-colony (growth & cell division) 4. Maturation (production of EPS) 5. Dispersion.

Question 41

- The biofilm structure provides the bacteria with the ability to tolerate _____ environmental conditions, resistance to antibiotics and host immune systems, and provides an optimal environment for _______ DNA (plasmid) - Various human diseases are related to biofilm. Biofilms play an important role in _____ diseases.

Answer 41

harsh extracellular dental

Question 42

- Signalling in biofilm formation: (2)

Answer 42

o Bacteria synchronize their gene expression by producing and responding to autoinducers. o Quorum sensing regulates biofilm formation in several bacterial species.

Question 43

- Biofilms in vivo:

Answer 43

o The microenvironment in vivo is different from that in vitro. It is important to investigate biofilms inhibition in vivo in animal models.