Microbiology Flashcards
Define microbiome
complex mixture of microbes that live in gut
What’s normal flora?
on all our surfaces + gut
What’s resident flora?
for life, microbial melting pot
What’s transient flora?
colonise us but can temporarily be reduced, carried or changed according to factors eg environment
eg a change in transient flora?
-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
Features of bifidobacterium?
- Gram +ve
- Produce lactic acid
- Prevent growth of Gram -ve
- Metabolise breast milk sugars
Are gut flora commensal?
No one species of gut flora is a commensal but together
flora are commensal (no harm to the host) due to extensive co-evolution.
Percentage of colon gut bacteria?
51% Firmicutes
Gram +ve phyla:
Bacillus, Listeria, Staphylococcus, Streptococcus, Enterococcus, Clostridium
48% Bacteriodetes
Why are there microbiome alterations + eg?
-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
Why are there microbiome alterations + eg?
-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
eg of change in microbiome?
- 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
Defence mechanisms of gut?
- Structural : seamless epithelium, tight junctions, sloughing/turnover
- Mechanical : peristalsis, chewing, fluid movement
- Biochemical : gastric acid, bile, mucous
- Immunological : secretory IgA, intra-epithelial lymphocytes
Problems with defence mechanisms of gut?
Problems - Spread of infections to the body
damage of barriers, pH change, overgrowth, AIDS
Benefits of gut flora?
- 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
Use of probiotics in medicine?
- probiotic organisms produce lactic + organic acids
- 10% absorbable energy from dietry fibre
- ↑ diversity of polysaccharides for metabolism eg beans, Raffinose, Stachyose – non-absorbable
Role of probiotics + eg?
organisms we think will contribute to a healthy
biome - produce lactic acid + organic acids
eg Lactobacillus acidophilus, Bifidobacteria - B.longum, Bacterioides thetaiotamicron, Some Streptococci
Role of prebiotics + eg?
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
Role of microbial antagonism?
- Maintains flora by complex interactions
- Competition between flora
- Limits growth of competitors + PATHOGENS
Describe how microbial antagonism works
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
What happens if there’s loss of flora?
Bacterial or pathogen overgrowth
Effect of certain antibiotics eg ciprofloxacin on gut?
- 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
Effect of clostridium difficile?
- Cytotoxins
- Ulcerations – inflammation to produce fibrinous coating
- Severe diarrhoea
- Serious hospital cross-infection risks (carriage rate up to 70%)
- Treatable with antibiotics
Define diarrhoea
watery or liquid stools with an increase in stool weight above 200g daily, increase in daily stool freq, sense of urgency
Clinical consequence of diarrhoea?
-Severe dehydration : excessive fluid and electrolyte loss hypovolaemia; hypokalaemia; organ failure -Long-term morbidity + reduced growth
What’s dysentery?
Inflammatory disorder of GI tract – large intestine, associated with blood, pus, pain, fever, abdominal cramps
Impact of diarrhoeal diseases?
- 3 billion episodes / year
- 760,000 deaths / year - due to dehydration
- Under-5’s ; 6–8 episodes / year - global health burden
- Preventable
How do diarrhoeal diseases occur?
Infectious : microorganisms, bacteria, viruses, parasites – protozoal + worms
Shed in faeces – transmission to new hosts
Faecal – oral route
Pattern of dysentery?
Acute or chronic diarrhoea + blood + Pus
Pattern of poor fat adsorption?
Chronic diarrhoea + or malabsorption
Pattern of ano-rectal STIs?
Infective proctitis
Pattern of ulcers Helicobacter pylori?
Dyspepsia (indigestion)
Pattern of oesophagus and Candida?
dysphagia
Damage resulting from GIT infection + eg?
- 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
Mechanisms of diarrhoea?
-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
Properties of intestinal physiology effected by microbiome?
- 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
Features of gut viruses?
Astrovirus (star) Calicivirus (Star of David) Norwalk (SRSVs)/ Norovirus (ill-defined lacelike) Poliovirus (featureless) Rotavirus (wheel)
Effect of enteropathogenic E.coli?
Attaching + effacing lesion
Microvillus elongation
Effacement of apical membrane
Pedestal formation
