Gut Microbiology (Caroline)

Question 1

Describe the normal microbiota

Answer 1

• Prevents colonisation by pathogens.
• Produces compounds that are beneficial to the host.
• Opportunistic pathogens are members of the normal microbiota that produce disease under certain circumstances e.g. a compromised host.
• Microbial colonisation of the gut begins at birth. Vaginal birth results in a gut microbiota more similar to vaginal microbiota of mum. Cesarean section results in a gut microbiota more similar to skin microbiota of mum.
• Initial colonisation shapes composition of the adult’s gut microbiota.
• Infants born by C-section can be swabbed with a gauze incubated in the maternal vagina prior to the C-section. This enriches the newborn vaginal bacteria.

Question 2

Describe the gut microbiome (gastrointestinal tract)

Answer 2

Mouth
- Contains microbes that survive mechanical removal by adhering to gums and teeth.

Stomach

• Most microbes killed by acidic conditions.
• Some survive if they pass through the stomach quickly.
• Some can survive if they are ingested in food particles.

Small intestine

• The duodenum contains relatively few organisms.
• The pH in the ileum is more alkaline and gut flora becomes more similar to that in the colon.

Large intestine
- Contains largest microbial population of the body.

Question 3

Describe the factors that shape the gut microbiome

Answer 3

• Birth by vaginal delivery provides Lactobacillus whereas C-section provides staphylococcus.
• At infancy, milk consumption provides lactobacillus whereas introduction to solid food provides Clostridiales.
• Use of antibiotics depletes microbiota.
• Breast-feeding increases microbiota.
• Environmental exposure will impact the microbiota.

Question 4

Describe the interaction between the gut microbiome and immune system

Answer 4

• Mesenteric lymph nodes and Payer’s patches are present prenatally in the small intestine.
• Microbial colonisation of the gut occurs postnatally.
• The Payer’s patches sample luminal antigens and bacteria.
• Dendritic cells present these antigens to induce development of the immune system.
• Exposure to a homeostatic environment during early life will result in development of a healthy immune system.
• Exposure to a dysbiotic environment during early life will result in development of an unhealthy immune system.

Question 5

Name and describe the good and bad bacterial flora found in the gut microbiota

Answer 5

Good flora

• Bifidobacteria - help to regulate levels of other bacteria in the gut, modulate immune responses to invading pathogens, prevent tumour formation, and produce vitamins.
• Escherichia coli - involved in vitamin K2 production (essential for blood clotting) and help keep bad bacteria in check. Some strains can lead to illness.
• Lactobacilli - beneficial varieties produce vitamins, boost immunity, and protect against carcinogens.

Bad flora

• Campylobacter - infection usually occurs via the ingestion of contaminated food.
• Enterococcus faecalis - common cause of post-surgical infections.
• Clostridium difficile - most harmful following a course of antibiotics when it is able to proliferate.

Question 6

Describe the treatments for chronic gastrointestinal disease and gut dysbiosis

Answer 6

Prebiotics and probiotics

• Prebiotics are substances that can only be metabolised by gut bacteria and not the human host (food for bacteria). Food high in prebiotics includes berries, bananas, and legumes.
• Probiotics are active bacterial cultures. Food high in probiotics include yoghurt, pickles, and kimchi.
• Synbiotics are a combination of pro and prebiotics.

Faecal transplants

• This is the introduction of gut bacteria from a healthy donor into a patient, through transfer of an infusion of a faecal sample via a nasogastric tube.
• Used in treatment of patients with recurrent Clostridium difficile infection. It induces re-establishment of microbiota diversity and leads to the suppression of termination of C. difficile colonisation.
• Transplants from lean donors to individuals with metabolic syndromes. This increases faecal butyrate concentrations which increases microbial diversity and the relative abundance of bacteria related to the butyrate-producing Roseburia intestinalis.