Normal gut flora

Question 1

DEfine normal flora

Answer 1

• 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.
• 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)

Question 2

Describe bacteria in terms of their o2 requriemenss

Answer 2

• 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

Question 3

categorise according to pH and temperateure requirements

Answer 3

• 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

Question 4

provide an overview of bacterial density throught he GIT

Answer 4

• 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

Question 5

What aer parameters that dictates growth

Answer 5

• 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)

Question 6

Describe H pylori

Answer 6

• 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

Question 7

DESCRIBE TEH small intestine and colonisaiton

Answer 7

• 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)

Question 8

Describe the large intestine and colonisatin

Answer 8

• 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

Question 9

Describe colonisation in the infant gut

Answer 9

• 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.

Question 10

describe nterindividual variation

Answer 10

• 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

Question 11

What are the dominant phylae?

Answer 11

• 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

Question 12

Discuss interplay between bacteriome and virome

Answer 12

• 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

Question 13

Discuss link between flora nad health

Answer 13

• 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

Question 14

how does flroa regulate digetion?

Answer 14

• 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

Question 15

how does flora regulate immunity?

Answer 15

• 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

Question 16

Discuss dysbiosis

Answer 16

• Altered or imbalanced normal gut flora can result in dysbiosis, which is associated with several human diseases.
• This imbalance can mean 3 things:
  
  1. Loss of beneficial microbial organisms in our gut.
  2. Expansion of potentially harmful microorganisms.
  3. Loss of microbial diversity.

These are not mutually exclusive and can
occur at the same time.

Question 17

what are some causes of dysbiosis and linked diseases

Answer 17

• 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

Question 18

Dysbiosis and chronic intestinal disease

Answer 18

• 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

Question 19

discuss opportunistic infections of gut flora

Answer 19

• 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).

Question 20

Discuss C difficile

Answer 20

• 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.

Question 21

Discuss B fragilis

Answer 21

• 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

Question 22

What can be done to alter flroa

Answer 22

§ 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.