Microbiology of the gut

Question 1

How many episodes of diarrhea and vomiting do Bangladeshi children experience by age 2?

Answer 1

On average 15 episodes by the age of 2.

Question 2

How many deaths under age 5 are caused by gastroenteritis annually according to WHO?

Answer 2

525,000 deaths per year.

Question 3

What are the three main GI infection syndromes?

Answer 3

Non-inflammatory, Invasive, Penetrating.

Question 4

Can pathogens exhibit more than one mechanism in GI infection?

Answer 4

Yes, some pathogens may manifest more than one mechanism.

Question 5

Name a virus that uses the GI tract as a portal of entry but causes little/no GI symptoms.

Answer 5

Poliovirus.

Question 6

Which pandemic virus can also involve the GI tract?

Answer 6

COVID.

Question 7

Do antibiotics usually help in gastroenteritis?

Answer 7

No, they rarely help and can make E. coli O157 worse.

Question 8

What infection control measures are needed for gastroenteritis patients?

Answer 8

Barrier nursing; avoid cohorting.

Question 9

Why is travel and contact history important in gastroenteritis?

Answer 9

It helps identify the source.

Question 10

What host defences help protect against GI infection? (Name 5)

Answer 10

Gastric pH, bile salts/acids, peristalsis, mucus, physical barrier.

Question 11

Name two immune defences against GI infection.

Answer 11

Secretory IgA, cellular immunity.

Question 12

What is “colonization resistance”?

Answer 12

Normal flora occupying space and resources, preventing pathogen growth.

Question 13

How does normal GI flora inhibit pathogens? (List 3 mechanisms)

Answer 13

Produces bacteriocins, toxic metabolites, stimulates local immunity.

Question 14

Where in the GI tract are bacterial numbers highest?

Answer 14

Colon (10¹² organisms/gram faeces).

Question 15

How many known species are in the colon?

Answer 15

Over 400 known; possibly up to 1500.

Question 16

What is the ratio of anaerobes to other bacteria in the colon?

Answer 16

1000:1.

Question 17

How much does the human gut microbiome weigh?

Answer 17

2–5 kg.

Question 18

What percentage of stool is bacteria?

Answer 18

40–60%.

Question 19

What vitamins are synthesized by the gut microbiome?

Answer 19

Folate, biotin.

Question 20

Name three benefits of the microbiome.

Answer 20

Releases nutrients (iron, calcium, amino acids), removes toxins, competes out pathogens.

Question 21

What are heterocyclic amines?

Answer 21

Carcinogens from cooking that gut flora can help detoxify.

Question 22

What diseases result from gut flora being in the wrong place? (Name 2)

Answer 22

Peritonitis, urinary tract infection.

Question 23

What organism causes Clostridium difficile infection?

Answer 23

Clostridium difficile.

Question 24

What triggers C. difficile infection?

Answer 24

Antibiotic therapy.

Question 25

Name the “four Cs” antibiotics associated with C. difficile infection.

Answer 25

Clindamycin, cephalosporins, ciprofloxacin, co-amoxiclav.

Question 26

Who is most at risk of C. difficile infection?

Answer 26

Elderly or infirm patients, especially in hospitals/nursing homes.

Question 27

What is the pathogenesis of C. difficile infection?

Answer 27

Antibiotics disrupt flora → C. difficile overgrowth → toxins A & B → mucosal damage.

Question 28

How is C. difficile infection diagnosed?

Answer 28

Toxin detection or PCR.

Question 29

Why is stool culture alone not diagnostic for C. difficile?

Answer 29

Because asymptomatic carriage is common in the elderly.

Question 30

What are the first steps in managing C. difficile infection?

Answer 30

Stop antibiotics if possible; isolate patient.

Question 31

Name two antimicrobials specific for C. difficile.

Answer 31

Oral vancomycin, oral fidaxomicin.

Question 32

What probiotic is sometimes used for C. difficile?

Answer 32

Saccharomyces cerevisiae.

Question 33

What is a faecal flora transplant?

Answer 33

Transfer of stool flora from a healthy donor to treat relapsing C. difficile.

Question 34

Where in the GI tract should bacterial numbers normally be low?

Answer 34

Stomach, duodenum, jejunum.

Question 35

What bacteria normally colonize the upper GI tract?

Answer 35

Gram-positive organisms (lactobacilli, enterococci).

Question 36

Name 4 mechanisms keeping bacterial numbers low in the upper GI tract.

Answer 36

Peristalsis, gastric acid/enzymes, bile, mucosal IgA.

Question 37

What symptoms are caused by bacterial overgrowth?

Answer 37

Diarrhoea, bloating, abdominal pain, flatulence, steatorrhoea, weight loss.

Question 38

What test diagnoses bacterial overgrowth?

Answer 38

Hydrogen breath test.

Question 39

What bacterial count is diagnostic of bacterial overgrowth?

Answer 39

10¹⁰ organisms/ml.

Question 40

What is the treatment for bacterial overgrowth syndrome?

Answer 40

Treat underlying condition; antibiotics like rifaximin.

Question 41

What nutrient deficiencies can result from bacterial overgrowth?

Answer 41

Fat-soluble vitamin deficiency, macrocytic anaemia.

Question 42

What are prebiotics?

Answer 42

Chemicals that alter the microbiome.

Question 43

Name an example of a prebiotic.

Answer 43

Mannan.

Question 44

What are probiotics?

Answer 44

“Friendly bacteria” used to prevent or treat infection.

Question 45

How do probiotics work? (2 mechanisms)

Answer 45

Direct inhibition of pathogens; indirect stimulation of immunity (e.g., sIgA).

Question 46

In what non-infective disease might probiotics be used?

Answer 46

Chronic inflammatory bowel disease.

Question 47

What challenges affect probiotic research? (List 3)

Answer 47

Small study sizes, different strains/doses, uncertain colonization evidence.

Question 48

Is gastroenteritis usually managed with antibiotics?

Answer 48

No, antibiotics rarely help.

Question 49

Should diarrhoea patients be barrier nursed?

Answer 49

Yes, until proven non-infectious.

Question 50

What are the four key host defences against GI infection?

Answer 50

Behavioural, innate, immune, protective flora.

Question 51

What happens when the normal GI flora is disturbed?

Answer 51

It can cause disease.

Question 52

How can antibiotics damage the microbiome?

Answer 52

By disrupting normal flora, leading to infections like C. difficile.

Question 53

What protective immune molecule is secreted into the GI tract?

Answer 53

Secretory IgA.

Question 54

What organisms cause non-inflammatory GI infections? 3

Answer 54

- Vibrio cholerae - Bacillus cerus - E.coli - Sometimes COVID

Question 55

What organisms cause inflammatory GI infections? 4

Answer 55

- Shigella - Salmonella - Campylobacter jejuni - Enterohaemorrhagic/E.coli

Question 56

What organisms cause penetrating GI infections? 2

Answer 56

- Salmonella typhi - Listeria monocytogenes