1
Q
DEfine normal flora
A
- Synonymous with microbiota, indigenous microbial population, microflora, commensal flora.
- A collection of microbial species found on tissue surfaces of normal healthy individuals.
- Coexist with the host in a non-disease-inducing manner, and are beneficial to the host.
- Includes those that can become opportunistic pathogens .
- Normally harmless organisms that can cause infection/disease when host immune system is compromised or natural barrier defences are breached
- Microbial communities that colonise the human gastrointestinal tract (GIT):
- GIT is organ site of largest microbial biomass
- Comprising 1012 -1013 bacteria in colon.
- Of at least 500-1,000 bacterial species.
- Composition of community varies within different parts of the GIT and between individuals.
- Plays a pivotal role in health and disease.
- GIT is organ site of largest microbial biomass
- BUT ALSO INCLUDES:
- Fungi (mostly Candida yeast e.g. Candida albicans).
- Protozoa (controversial but include Blastocystis and Entamoeba).
- Eukaryotic viruses
- Prokaryotic viruses (including bacteriophages/phages)
2
Q
Describe bacteria in terms of their o2 requriemenss
A
- Obligate aerobes require oxygen to grow.
- Methods of energy production and respiration depends on transport of electrons to oxygen
- Obligate anaerobes are killed in the presence of oxygen.
- Are killed in the presence of oxygen
- Energy-generating metabolic process not coupled with oxygen consumption
- Enzymes that breakdown toxic oxygen biproducts absent
- Facultative anaerobes can change their metabolic processes depending on presence of oxygen.
- Can change their metabolic processes depending on presence of oxygen
- Use respiration in presence of oxygen and fermentation in its absence
3
Q
categorise according to pH and temperateure requirements
A
- Temperature Requirements For Bacterial Growth:
- A psychrophile that grows optimally at temperatures <15°C.
- A mesophile grows optimally at temperatures between 20-45 °C.
- A thermophile that grows optimally at temperatures >60°C.
- Considering the temperature of human body is 37°C, gut microbes are mesophiles
- pH Requirements For Bacterial Growth:
- A neutrophile can grow in a range of neutral pH values (pH 5-8).
- An alkalophile is adapted to life at more alkaline extremes (pH 9-11).
- An acidophile is adapted to life at more acidic extremes (pH 2-4).
- pH varies along the tract: mouth is relatively neutral, stomach is acidic, intestine becomes progressively alkaline
4
Q
provide an overview of bacterial density throught he GIT
A
- Normal flora of gut is organ specific (adapts to local environment)
- In general, as you go from mouth to anus:
- Numbers of organisms (i.e. density) increase.
- Compositions become more complex (i.e. number of different species increases)
- Colon has highest density and complexity (i.e. many different species present in large numbers) - though small intestine has a more nutrient rich environment
5
Q
What aer parameters that dictates growth
A
- Bacteria often washed from mouth to stomach (e.g. via food particles) usually killed due to acidic pH.
- Generally referred to as ‘transient’ bacteria because are unable to colonise and grow
- But, transient bacteria can survive passage through stomach if resistant to gastric pH
- In this same way, acid-tolerant bacteria can colonise the stomach
- Mainly Gram-positive bacilli and cocci, facultative anaerobes (e.g. Lactobacillus, Streptococcus species)
6
Q
Describe H pylori
A
- Helicobacter pylori. Considered a commensal, that becomes pathogenic.
- Estimated to be present in >50% of world’s population
- Causes chronic inflammation of stomach (gastritis) and GERD
- Major cause of peptic ulcers. Increases risk of gastric cancers
7
Q
DESCRIBE TEH small intestine and colonisaiton
A
- Duodenum (proximal): very few organisms because of its close proximity to stomach.
- Inhibitory action of stomach acid juices, bile, and pancreatic secretions
- Organisms present are therefore similar to those in stomach
- Jejunum and ileum (distal): normal flora starts to resemble that found in colon as pH becomes more alkaline.
- Mainly anaerobes, some facultative anaerobes (e.g. Bacteroides species, members of the family Enterobacteriaceae, e.g. E. coli)
8
Q
Describe the large intestine and colonisatin
A
- Largest bacterial community in the body.
- 1-5% of bacteria are facultative anaerobes.
- e.g. Lactobacillus and Streptococcus species, members of the family Enterobacteriaceae.
- Function to remove oxygen making colon a fermentation vat populated by masses of anaerobes.
- 95-99% of bacteria are obligate anaerobes
- e.g. Bacteroides species, Clostridium species
9
Q
Describe colonisation in the infant gut
A
- Infants thought to be born with sterile intestines.
- Infant gut rapidly colonised following delivery by flora that varies depending on:
- Mode of delivery
- Feeding type
- Antibiotic use
- Infant gut flora gradually changes to resemble that of the adult with whom child lives most closely.
- By age 2, infant gut flora displays a community similar to adult gut.
10
Q
describe nterindividual variation
A
- Normal gut flora varies significantly between individuals (even identical twins!)
- Referred to as interindividual microbial diversity, which differs with respect to an individuals:
- Age
- Health (comorbidities eg cancer, stress, hormones, immunity)
- Lifestyle & physical activity
- Geographical location
- Diet & nutrition
- Genetics
- Medication eg antibiotics, PPIs
- Mode of birth
- Infant feeding type
11
Q
What are the dominant phylae?
A
- Generally, the adult gut is dominated by two phyla (>90% of bacteria):
- Firmicutes
- Bacteroidetes
- ratio to each associated with disease
- Other dominant phyla:
- Actinobacteria
- Proteobacteria
- Fusobacteria
12
Q
Discuss interplay between bacteriome and virome
A
- The composition, richness, and diversity of the gut virome change as a function of age.
- The ratio of phage to bacteria abundance changes as a function of age.
- neonate relatively high phageome, child high bacteriome, adult has homeostatic equilibrium
13
Q
Discuss link between flora nad health
A
- In general, greater diversity = better health.
- The normal gut flora lies at the interface of host metabolism and immunity.
- This complex network of interactions is key to human health
- commensal bacteria
- digestion and metabolism
- immune system
14
Q
how does flroa regulate digetion?
A
- Begins in the mouth, continues as food/digestive intermediates transit > 6 meters to end of adult GIT.
- Along the way, digestive slurry mixed with normal gut flora that extract, synthesize, and absorb many nutrients and metabolites.
- Bile acids
- Lipids
- Amino acids
- Vitamins
- SCFAs
- Gut flora-derived nutrients and metabolites are directly linked to diet and digestion so considered diet-dependent microbial products
15
Q
how does flora regulate immunity?
A
- Normal gut flora play a critical role in regulating development, homeostasis, and function of innate and adaptive immune cells.
- e.g. Major source of natural antigens that continuously stimulate GALT and induce mucosal immune tolerance/unresponsiveness to their molecular components
- Normal gut flora teach mucosal immune system to tolerate harmless antigens and induce protective immunity to harmful antigens.
- Normal gut flora are indirectly protective against pathogenic bacteria by competition for space/attachment sites and nutrients, preventing pathogens from colonising the gut
- Normal gut flora can produce anti-microbial substances that can kill or inhibit growth of invading pathogens, preventing their colonisation, e.g. Bacteriocins (peptides), SCFAs
16
Q
Discuss dysbiosis
A
- Altered or imbalanced normal gut flora can result in dysbiosis, which is associated with several human diseases.
- This imbalance can mean 3 things:
- Loss of beneficial microbial organisms in our gut.
- Expansion of potentially harmful microorganisms.
- Loss of microbial diversity.
These are not mutually exclusive and can
occur at the same time.
17
Q
what are some causes of dysbiosis and linked diseases
A
- Dysbiosis can be caused by various factors including deterioration of health, old age, malnutrition, diet, stress, genetics, infection, and antibiotic usage.
- Antibiotic usage – kills large numbers of normal gut flora, offering an ecological niche to bacteria that would not otherwise be able to compete.
- multiple consequences: asthma, coeliac, RA, obesity, NASH, NAFLD, stress
18
Q
Dysbiosis and chronic intestinal disease
A
- While specific causality is unclear, there is a link between microbial dysbiosis and:
- Irritable bowel syndrome (IBS)
Ø Increased Firmicutes:Bacteroidetes ratio, decreased Bifidobacterium - Inflammatory bowel disease
Ø Increased bacterial numbers in mucosa, decreased bacterial diversity - Colorectal cancer
Ø Increased Fusobacterium spp., E. coli - Obesity
Ø Increased Firmicutes:Bacteroidetes ratio, decreased bacterial diversity
19
Q
discuss opportunistic infections of gut flora
A
- Normal gut flora can also cause disease by known means, such as antibiotic-induced dysbiosis leading to infection with opportunistic pathogens (C. difficile), or upon escaping their natural habitat into abdomen/bloodstream when intestinal mucosa is compromised (e.g. when intestinal integrity disrupted, Bacteroides fragilis).
20
Q
Discuss C difficile
A
- Gram-positive spore-forming, anaerobic bacillus considered a member of the normal gut flora (~5% of population).
- Loss of normal gut flora barrier effect following broad spectrum antibiotics allows C. difficile to colonize and overgrow in the colon.
- egs beta lactams (ceftriaxone, piperacillin-tazobactam), clindamycin, fluoroquinolones eg ciprofloxacin - spectrum of disease from diarrhoea and abdominal pain to pseudomembranous colitis, to toxic megacolon and death
- Interaction of C. difficile with intestine leads to toxin release causing various symptoms.
- Mild diarrhoea
- Pseudomembranous colitis (inflammation of the colon)
- Toxic megacolon (acute toxic colitis with colon dilation)
- Death
- C. difficile secretes toxins that are internalised by host cells through receptor-mediated endocytosis.
- Toxins cause disruption to cytoskeletal architecture, which leads to cell death.
- Toxin-mediated cell death results in the loss of intestinal barrier integrity and the translocation of bacteria into underlying/deeper tissues including bloodstream.
- Toxin-mediated damage to the epithelium activates the host inflammatory immune response.
- An overly robust inflammatory response can be damaging to the host and contribute to disease pathology.
21
Q
Discuss B fragilis
A
- Gram-negative, anaerobic bacillus and prevalent member of the normal gut flora.
- Highly beneficial to the host (breaksdown complex carbohydrates, releases anri-inflammatory cytokines)
- Probiotic to treat a range of disorders characterised by up-regulation of pro-inflammatory cytokines (e.g. IBS, multiple sclerosis, autism, etc.)
- When intestinal integrity is disrupted, B. fragilis can escape into peritoneum, causing abscesses or peritonitis; or in blood causing bacteraemia and sepsis
- Treatment includes antibiotics targeted against B fragilis, reconstitution of gut flora, surgical procedures to drain pus and remove necrotic tissue if necessary
22
Q
What can be done to alter flroa
A
§ Prebiotics:
Ø Nutritional compounds used to promote growth of beneficial gut flora.
§ Probiotics:
Ø Bacterial cultures that restore the population of beneficial gut flora.
§ Faecal microbial transplantation (FMT):
Ø Isolation of beneficial bacteria from the faecal matter of healthy donor to
replace disrupted populations in diseased individuals.
Ø FMT is successful in treating C. difficile infection, with disease remission in
up to 92% of cases.
Ø FMT has promising results in the treatment of post-infectious IBS and and
various other gut microbiome imbalances (e.g. ulcerative colitis).
§ Antimicrobials (other than classical antibiotics):
Ø Eliminate pathogens or manipulate the normal gut flora to benefit the host.
GIT Mol Sci
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