S2: Introduction to Microbiology of the Gut

Question 1

What is the microbiome?

Answer 1

The complex mixture of microbes that live in a particular enviroment e.g. gut

Question 2

What is normal flora?

Answer 2

Normal flora describes the flora of microorganisms that normally live within our intestines.
We have microorganisms on all our surfaces including the gut.

Question 3

What is resident flora and transient flora?

Answer 3

Resident flora is flora that is there for life

Transient flora are organisms that colonise us but can temporarily reduced, carried or changed according to various factors including enviroment, age, stress, hormones

Question 4

Describe baby faecal transitions (transient flora)

Answer 4

• First time baby defacates (sterile meconium) it is sterile
• There is a change in stool as baby acquires microbial flora
• In the beginning there is facultative anaerobes
• Then they end up being strictly anaerobic in the gut (survive in O2 free enviroments) that live in the colon e.g. bifidobacter
• They metabolise breast milk sugars that gives itself energy and produces nutrients for the baby.
• As we wean off the breast milk, the microorganisms change, we quite adult-like gut microbiota.

Question 5

What are facultative anaerobes?

Answer 5

Organisms that live anaerobically but can live in presence of oxygen also

Question 6

Is gut flora commensal?

Answer 6

Not one species of gut flora is a commensal, but together the flora may be regarded as commensal (no harm to the host). This is a product of extensive co-evolution.

Question 7

What 3 compenents does symbiosis include?

Answer 7

Commensalism
Parasitism
Mutualism

Question 8

Breifly describe how bacteria is distributed throughout the GI tract

Answer 8

There are very few in the stomach due to the high acidity.

As we move through the duodenum and ileum and get to the terminal ileum we see much more bacteria here and a more complex mixture.

The colon, which is an anaerobic environment, contains facultative and obligate anaerobes. There are a very large amount of bacteria here and a very complex mixture.
e.g. bacterioides, clostridia, E.coli

Question 9

What are microbiome alterations associated with?

Answer 9

Microbiome alterations are associated with disease states ( generalised diversity changes and species difference )
e.g. Crohn’s disease, Inflammatory bowel disease, IBS, C.difficle etc. In someone with inflammatory bowel disease the distribution of bacteria in the gut is very different.

Changing the microbiome of the gut will substantially change the physiology of the gut e.g. the hormones it releases.
Exposure to antibiotics can affect the microbiome leading to a change in gut physiology.

Question 10

How are we not overwhelmed by microbe in our gut?

Answer 10

There must be a balance in place whereby we can control our gut flora. Our gut therefore has defence mechanisms.

Question 11

List defence mechanisms of our gut

Answer 11

Structural:
- A seamless epithelium surface with tight junctions there is rapid turnover/sloughing

Mechanical:
-Peristalsis moves things from one end to the other, fluid movement

Biochemical:
- Secretion of gastric acid, bile, mucus

Immunological:
- Secretory IgA (main Ig protector at mucosal surfaces), intra-epithelial lymphocytes

Question 12

What are the benefits of gut flora?

Answer 12

Colonisation resistance: Ecological niches have been taken up by commensals so it is hard for pathogens to get in and start to divide

Metabolites of benefit to the host: Some bacteria produce metabolites that are useful and we cannot synthesise them ourselves e.g. vitamin K, B12, organic acid

Normal development of immunity: Important in normal immunological development, in tolerating certain organisms and antigens at birth. We don’t want immune attack all the time for everything that enters the gut, so normal flora is important in this tolerance balance allowing us to live with these organisms.

Germ free: Being germ free could be bad, problems with flora lead to things like asthma and eczema

Aids digestion:About 10% of our energy is released from our colon, a lot of sugars we cannot digest until the microbial flora ferment the sugars into a form we can.

Question 13

What are probiotics and what do they release?

Answer 13

Probiotics are organisms we think will contribute to a healthy biome

The best probiotic organisms produce lactic acid and organic acids e.g. Lactobacillus, Bifidobacteria, B.longum, Bacterioides thetaiotamicron, some streptococci

Question 14

What are prebiotics?

Answer 14

Pre-biotics encourage good microbes to grow e.g. breast milk

Question 15

List use of probiotics in medicine

Answer 15

1. Control diarrhoea in infants
2. Relieve constipation
3. Improve digestion of lactose

Question 16

What is microbial antagonism?

Answer 16

Microbial antagonism is the idea that some organisms inhibit the growth of other organisms.

Question 17

Function of microbial antagonism

Answer 17

It limits the growth of competitors and pathogens

• Bacteriocins
• Reduced numbers of available epithelial receptors
• Keeps pH low
• Controls oxidative potential (anaerobic growth)
• Limits pathogen growth
• Occupy all niches
• High numbers
• Waste products

Question 18

What is antibiotic associated colitits?

Answer 18

Certain antibiotics (e.g. ciprofloxacin) disrupt our microbiome more than others.

This leads to antibiotic associated colitis (inflammation of colon caused by introduction of antibiotics).
The antibiotics have reduced the no. of gut flora and changed it, this may lead to overgrowth of clostridium difficile = pseudomembranous colitis.

Question 19

What does loss of flora lead to?

Answer 19

Bacterial or pathogen overgrowth

Question 20

What is Gastroenteritis?

Answer 20

An acute syndrome characterised by generalised gastrointestinal symptoms in any combination including: nausea, vomiting, diarrhoea and abdominal discomfort

Question 21

What is Diarrhoea?

Answer 21

Watery or liquid stools, usually with an increase in stool weight and an increase in daily stool frequency and a sense of urgency.

Question 22

Clinical consequences of diarrhoea

Answer 22

• Severe dehydration due to excessive fluid and electrolyte loss, hypovolemia, hypokalemia, organ failure
• Long term morbidity and reduced growth

Question 23

What is Dysentry?

Answer 23

Inflammatory disorder of the GI tract usually in the large intestine. it is often associated with blood and pus (as penertrated natural barriers) as well as pain, fever and abdominal cramps.

Question 24

What is Enterocolitis?

Answer 24

Inflammation involving mucosa of small and large intestine e.g. crohns disease

Question 25

Common reasons for intestinal disease and diarrhoea

Answer 25

• Bacteria
• Virus
• Parasites (protozoal and worms)

These are shed in faeces and spread to new host (faecal-oral route)

Question 26

What bacteria usually causes travellers diarrhoea?

What causes antibiotic related diarrhoea?

Answer 26

Normally e.coli

Altered normal flora

Question 27

What is food poisoning?

Answer 27

Diarrhoea from eating food, either due to eating food containing toxins that make us ill or food that contain bacteria that then grow inside us and produce toxins

Question 28

List some immunocompromised hosts

Answer 28

• AIDs
• Immunosupressed
• Elderly
• Very young

Question 29

What is the damage resulting from infection of gastrointestinal tract?

Answer 29

1. Pharmacological action of bacterial toxins that have local or distant effects to the site of infection e.g. Cholera
2. Local inflammation in response to superficial microbial invasion e.g. shigella dysentry or campylobacter food poisoning
3. Deep invasion to blood and lymphatics and dissemination of organisms to other body sites e.g. typhoid fever
4. Preforation/ulceration of mucosal epithelium, peritonitis

Question 30

What is the mechanism of diarrhoea?

Answer 30

1. Bacterial toxins
   Exotoxins affect fluid/electrolyte transport by increasing/decreasing cAMP. Cytotoxins produce direct cell damage.
2. Bacteria can adhere to the cells below, and damage the epithelium e.g. e.coli - enteropathogenic
3. Penertration and invasion into epithelium - enteroinvasive

Question 31

What are enterotoxins?

Answer 31

Toxins that affect the intestines

Question 32

What does enteropathogenic mean?

Answer 32

Tending to produce disease in the intestinal tract.

Question 33

Main function of villus and crypt in intestine

Answer 33

Function of villus is for absorption, function of crypts mainly is secretion

Question 34

Explain how bacterial toxins (heat stable and heat labile toxins) work to cause diarrhoea

Answer 34

There are heat stable toxins which are not destroyed by heat so if consumed, food poisoning could occur..
Heat labile toxins can be inactivated by cooking.

The toxins work by affecting electrolyte channels in the cell:

• Heat labile toxin stimulates AC causing cAMP to disregulate protein kinase (increases). This results in the changing chloride channel resulting in electrolyte imbalance and thus fluid imbalance
• Heat stable toxin does this same thing but with GC (guanylate cyclase)

Question 35

Explain how bacteria or viruses penetrate the villi and cause diarrhoea

Answer 35

Virus or bacteria can penetrate into the villi resulting in villus atrophy.
Crypt hyperplasia occurs to try and replace the villus and secretion occurs at the same time.

There is no absorptive capacity + secretion + atrophy = anti-absorptive diarrhoea

Question 36

How can E.coli be a friend of foe?

Answer 36

E.coli can act as a commensal gut organism

It can also act as a pathogen producing:

• Diarrhoea
• Dysentry
• Haemolytic uraemic syndrome (HUS)
• Septicaemia
• Pneumonia and meningitis

Virulence factors:
- Toxins, adhesins, invasins

Question 37

Difference between food associated infections vs food poisoning

Answer 37

A food-associated infection is live organisms that grow in the gut and causes symptoms i.e. you get infected by microorganism (by eating food with it on) and then they grow in your gut

Food poisoning is food that has been contaminated by a food-spoilage organism that has produced toxins on the food, often heat labile, that when we eat the food we get an immediate effect of the toxin.

• Food associated infection is longer as bacteria needs time to grow
• Food poisoning is rapid
• We tell the difference by incubation period and duration of symptoms - this depends on dosage of bacteria

Question 38

How is food associated infection and food poisoning diagnosed?

Answer 38

Confirmation by culture, microscopy and identification