Microbiology

Question 1

Define microbiome

Answer 1

complex mixture of microbes that live in gut

Question 2

What’s normal flora?

Answer 2

on all our surfaces + gut

Question 3

What’s resident flora?

Answer 3

for life, microbial melting pot

Question 4

What’s transient flora?

Answer 4

colonise us but can temporarily be reduced, carried or changed according to factors eg environment

Question 5

eg a change in transient flora?

Answer 5

-baby ->adult
-change from bifidobacter which likes breast milk
-other changes could be stress, hormones, age
-1st baby defacates (sterile meconium)
-change in stools as baby aquires microbial flora
-start with facultative anaerobes
(live anaerobically but can live in oxygen too)
-ends up being strictly anaerobic gut that live in colon
-bifidobacterium is strict anaerobe
-metabolise breast milk sugars that gives itself energy + produces nutrients
-as wean off breast milk
-get adult-like gut microbiota eg bacteroides, clostridia, eubacteria - gram -ve

Question 6

Features of bifidobacterium?

Answer 6

• Gram +ve
• Produce lactic acid
• Prevent growth of Gram -ve
• Metabolise breast milk sugars

Question 7

Are gut flora commensal?

Answer 7

No one species of gut flora is a commensal but together

flora are commensal (no harm to the host) due to extensive co-evolution.

Question 8

Percentage of colon gut bacteria?

Answer 8

51% Firmicutes
Gram +ve phyla:
Bacillus, Listeria, Staphylococcus, Streptococcus, Enterococcus, Clostridium
48% Bacteriodetes

Question 9

Why are there microbiome alterations + eg?

Answer 9

-Associated with disease states
-Generalised diversity changes + species differences
-Dysbiosis
Crohn’s disease
Inflammatory bowel disease – ulcerative colitis
Irritable bowel syndrome – IBS
Clostridium difficile
Colon Cancer
Allergy
Celiac disease (gluten)
Diabetes – type I and II
Obesity (↓Bacteroidetes/↑Firmicute ratios)
Mental health + depression

Question 10

Why are there microbiome alterations + eg?

Answer 10

-Associated with disease states
-Generalised diversity changes + species differences
-Dysbiosis
Crohn’s disease
Inflammatory bowel disease – ulcerative colitis
IBS
Clostridium difficile
Colon Cancer
Allergy
Celiac disease
Diabetes – type I + II
Obesity (↓Bacteroidetes/↑Firmicute ratios)
Mental health + depression

Question 11

eg of change in microbiome?

Answer 11

• Faecal transplants
• Gastric bands –> weight loss, microbiome changes, altered metabolism, bile acid profiles, ↑adipogenesis (heart disease)
• Duodenal infusion of donor faeces resolves C.difficile infections
• Weight loss due to ↑Bacteroidetes, ↓Firmicutes
• Microbiome - age related, sex differences, partner selection + attraction

Question 12

Defence mechanisms of gut?

Answer 12

• Structural : seamless epithelium, tight junctions, sloughing/turnover
• Mechanical : peristalsis, chewing, fluid movement
• Biochemical : gastric acid, bile, mucous
• Immunological : secretory IgA, intra-epithelial lymphocytes

Question 13

Problems with defence mechanisms of gut?

Answer 13

Problems - Spread of infections to the body

damage of barriers, pH change, overgrowth, AIDS

Question 14

Benefits of gut flora?

Answer 14

• Colonisation resistance : blocks pathogens
• Metabolites of benefit to host : Vit K2, B12, organic acids, enhanced utilisation of AA, butyrate for colonocytes – maintain anerobiasis
• Development of immunity tolerance : antigenic stimulation, Tregs, IL17
• Digestion : fermentation of sugars (10% of energy), gases H2 or methane, regulation of fat storage

Question 15

Use of probiotics in medicine?

Answer 15

• probiotic organisms produce lactic + organic acids
• 10% absorbable energy from dietry fibre
• ↑ diversity of polysaccharides for metabolism eg beans, Raffinose, Stachyose – non-absorbable

Question 16

Role of probiotics + eg?

Answer 16

organisms we think will contribute to a healthy
biome - produce lactic acid + organic acids
eg Lactobacillus acidophilus, Bifidobacteria - B.longum, Bacterioides thetaiotamicron, Some Streptococci

Question 17

Role of prebiotics + eg?

Answer 17

prebiotic nutrients alter gut ecosystem
eg breast milk - ‘bifidus factor’
certain oligosaccharides eg fructo-oligosacchs
fermented in colon by probiotic organisms promotes growth of probiotes

Question 18

Role of microbial antagonism?

Answer 18

• Maintains flora by complex interactions
• Competition between flora
• Limits growth of competitors + PATHOGENS

Question 19

Describe how microbial antagonism works

Answer 19

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 20

What happens if there’s loss of flora?

Answer 20

Bacterial or pathogen overgrowth

Question 21

Effect of certain antibiotics eg ciprofloxacin on gut?

Answer 21

• ciprofloxacin antibiotic disrupt microbiome
• antibiotic associated colitis (inflammation of colon caused by introduction of antibiotics)
• reduced gut flora + changed it (returns normal in 1 month)
• overgrowth of clostridium difficile
• pseudomembranous colitis

Question 22

Effect of clostridium difficile?

Answer 22

• Cytotoxins
• Ulcerations – inflammation to produce fibrinous coating
• Severe diarrhoea
• Serious hospital cross-infection risks (carriage rate up to 70%)
• Treatable with antibiotics

Question 23

Define diarrhoea

Answer 23

watery or liquid stools with an increase in stool weight above 200g daily, increase in daily stool freq, sense of urgency

Question 24

Clinical consequence of diarrhoea?

Answer 24

-Severe dehydration :
excessive fluid and electrolyte loss
hypovolaemia; hypokalaemia; 
organ failure
-Long-term morbidity + reduced growth

Question 25

What’s dysentery?

Answer 25

Inflammatory disorder of GI tract – large intestine, associated with blood, pus, pain, fever, abdominal cramps

Question 26

Impact of diarrhoeal diseases?

Answer 26

• 3 billion episodes / year
• 760,000 deaths / year - due to dehydration
• Under-5’s ; 6–8 episodes / year - global health burden
• Preventable

Question 27

How do diarrhoeal diseases occur?

Answer 27

Infectious : microorganisms, bacteria, viruses, parasites – protozoal + worms
Shed in faeces – transmission to new hosts
Faecal – oral route

Question 28

Pattern of dysentery?

Answer 28

Acute or chronic diarrhoea + blood + Pus

Question 29

Pattern of poor fat adsorption?

Answer 29

Chronic diarrhoea + or malabsorption

Question 30

Pattern of ano-rectal STIs?

Answer 30

Infective proctitis

Question 31

Pattern of ulcers Helicobacter pylori?

Answer 31

Dyspepsia (indigestion)

Question 32

Pattern of oesophagus and Candida?

Answer 32

dysphagia

Question 33

Damage resulting from GIT infection + eg?

Answer 33

• Pharmacological action of bacterial toxins which have local or distant effects to site of infection eg Cholera
• Local inflammation from superficial microbial invasion eg shigella dysentery or campylobacter food poisoning
• Deep invasion to blood, lymphatics, dissemination of organism to other body sites (enetric feevrs) eg typhoid fever, Hep A
• Perforation/Ulceration of mucosal epithelium, peritonitis, intra-abdominal abscess eg Entamoeba

Question 34

Mechanisms of diarrhoea?

Answer 34

-Bacterial toxins : enterotoxins are toxins that affect gut
Exotoxins effect fluid/electrolyte transport by ↑/↓ cAMP
Cytotoxins produce direct cell damage
-Adherence : damage to epithelium eg E.coli EPEC enteropathogenic
-Penetration + invasion : disruption of tissue architecture, function, inflammation

Question 35

Properties of intestinal physiology effected by microbiome?

Answer 35

• Energy balance regulation + pathophysiology of obesity
• Modulates digestion + absorption ↑ energy harvesting
• Microbiome influenced by diet, antibiotics, surgery, genes
• Microbiome contributes to host metabolism +energy homeostasis beyond nutritional processing eg endocrine function + inflammatory signals

Question 36

Features of gut viruses?

Answer 36

Astrovirus (star)
Calicivirus (Star of David)
Norwalk (SRSVs)/ Norovirus (ill-defined lacelike)
Poliovirus (featureless)
Rotavirus  (wheel)

Question 37

Effect of enteropathogenic E.coli?

Answer 37

Attaching + effacing lesion
Microvillus elongation
Effacement of apical membrane
Pedestal formation