Introduction to the Microbiology of the Gut

• What is the definition of microbiota?

  Microbiota refers to the community of microorganisms (including bacteria, viruses, fungi, and archaea) that live in a particular environment, such as the human gut. It describes the actual organisms present.
• What is the definition of microbiome?

  The microbiome refers to the full collection of genomes (genetic material) of the microorganisms in a particular environment. It includes the microbiota and their genes, proteins, and metabolic products.
•  How do the terms microbiota and microbiome differ?

  • Microbiota = the organisms themselves
  • Microbiome = the organisms + their genetic material + their interactions with the host and environment
• Where is the gut microbiota primarily located?

  Primarily in the colon (large intestine), although microbial populations exist throughout the gastrointestinal tract.
• What is the significance of the gut microbiota in human health?

  Gut microbiota aids in digestion, synthesizes vitamins (e.g., vitamin K, B12), trains the immune system, protects against pathogens, and influences metabolism and brain function.
• What are some major phyla of bacteria found in the human gut microbiota?

  • Firmicutes
  • Bacteroidetes
  • (Also present: Actinobacteria, Proteobacteria, Verrucomicrobia in smaller amounts)
•  How is the gut microbiome established?

  It begins at birth (influenced by mode of delivery—vaginal vs. C-section) and is shaped by factors like diet, environment, antibiotics, and genetics.
• What is dysbiosis in the context of the gut microbiome?

  Dysbiosis is an imbalance in the gut microbiota composition, associated with diseases like IBD, obesity, diabetes, and mental health disorders.
• Why is the gut microbiome often called a “forgotten organ”?

  Because it performs essential functions (digestion, immunity, metabolism regulation) similar to an organ, despite not being a traditional tissue-based structure.
• What is the intestinal microbiota?

  The intestinal microbiota is the community of microorganisms, primarily bacteria, that inhabit the gastrointestinal tract and contribute to digestion, immunity, and homeostasis.
• When does the colonisation of the gut microbiota begin?

  Colonisation begins at birth, influenced by mode of delivery, environment, and feeding.
• How does the mode of delivery influence initial gut microbiota?

  • Vaginal delivery: exposes newborn to maternal vaginal and intestinal flora (e.g. Lactobacillus, Bacteroides).
  • C-section: initial colonisation by skin and environmental microbes (e.g. Staphylococcus, Corynebacterium).
• How does feeding method affect microbiota development?

  • Breastfeeding promotes Bifidobacterium and Lactobacillus.
  • Formula feeding results in more diverse microbiota, including Enterobacteriaceae and Clostridium.
• What is the progression of gut microbiota development in infancy?

  • Sterile or nearly sterile at birth.
  • Rapid colonisation within hours to days.
  • Shifts with feeding, environmental exposure, and weaning.
  • Stabilises into adult-like composition by ~2–3 years old.
• What factors influence the development of gut microbiota in early life?

  • Mode of delivery
  • Feeding type
  • Antibiotic exposure
  • Environment (e.g. hospital vs home)
  • Introduction of solid foods
• What are the dominant bacterial phyla in the adult gut?

  • Firmicutes (e.g. Clostridium, Lactobacillus)
  • Bacteroidetes (e.g. Bacteroides)Others: Actinobacteria, Proteobacteria, Verrucomicrobia
• How is microbiota distributed along the GI tract?

  • Stomach: low density, mostly Lactobacillus, Streptococcus (acid-tolerant).
  • Small intestine: increasing density; mostly Enterococci, Lactobacilli.
  • Large intestine: highest density & diversity; mostly Bacteroides, Clostridium, Firmicutes.
• Why is the colon more densely populated with microbes than the small intestine?

  • Slower transit time
  • Anaerobic environment
  • Abundance of undigested nutrients
  • Less bile and digestive enzymes
• What are the primary roles of the normal gut microbiota?

  • Digestion and fermentation of complex carbohydrates
  • Vitamin synthesis (e.g. vitamin K, B12)
  • Protection against pathogens
  • Immune system development
•  What is meant by "microbial succession" in gut colonisation?

  The dynamic process where early colonisers create conditions that allow later microbes to establish, leading to a stable, diverse community.
• What is microbial homeostasis and when is it achieved in the gut?

  Microbial homeostasis is a stable, diverse microbiota that maintains host health, typically established by age 2–3 years.
• How does the gut microbiota contribute to immune system development?

  It helps train the immune system by promoting tolerance to harmless antigens and enhancing the body's defence against pathogens through interactions with gut-associated lymphoid tissue (GALT).
• What is dysbiosis?

  An imbalance in the composition or function of the gut microbiota, often associated with disease. It may involve loss of beneficial microbes, overgrowth of harmful ones, or reduced diversity.
• How is dysbiosis linked to inflammatory bowel disease (IBD)?

  Dysbiosis in IBD includes reduced diversity and lower levels of beneficial SCFA-producing bacteria, contributing to chronic inflammation and mucosal damage.
• What role does the gut microbiota play in obesity?

  Certain gut microbiota profiles enhance energy extraction from food, increase fat storage, and influence hormones related to hunger and metabolism, contributing to obesity.
• How is gut microbiota linked to type 2 diabetes?

  Dysbiosis can lead to systemic inflammation and insulin resistance via changes in gut permeability, LPS (lipopolysaccharide) translocation, and altered SCFA production.
• What is the gut-brain axis?

  A bidirectional communication system between the gut microbiota and the brain, involving neural, hormonal, and immune pathways. It can influence mood, cognition, and behaviour.
• Which neurological conditions are associated with gut microbiota imbalance?

  Depression, anxiety, autism spectrum disorders, and Parkinson’s disease have all been linked to gut microbiota changes via the gut-brain axis.
• How can antibiotics disrupt gut health?

  Antibiotics can cause dysbiosis by killing beneficial bacteria, reducing microbial diversity, and increasing susceptibility to infections like Clostridioides difficile.
• What are probiotics and how do they affect health?

  Probiotics are live beneficial bacteria that, when consumed in adequate amounts, help restore gut microbiota balance, support immune function, and may improve digestive health.
• What is the role of prebiotics in gut health?

  Prebiotics are non-digestible food ingredients (like inulin or FOS) that promote the growth and activity of beneficial gut bacteria, improving gut microbiota composition.
• How does diet shape the gut microbiota?

  A high-fibre, plant-based diet promotes microbial diversity and SCFA production, while a high-fat, high-sugar diet reduces diversity and increases harmful species.
• How is the gut microbiota involved in colorectal cancer risk?

  Certain bacteria can produce carcinogenic metabolites or promote inflammation, which contributes to DNA damage and tumor development in the colon.
• What are the main categories of interventions used to modulate the gut microbiota?

  1. Probiotics
  2. Prebiotics
  3. Synbiotics
  4. Faecal Microbiota Transplantation (FMT)
  5. Antibiotics
  6. Dietary changes
• What are probiotics and how do they modulate gut microbiota?

  Live microorganisms (e.g. Lactobacillus, Bifidobacterium) that, when administered in adequate amounts, confer health benefits by:

  • Enhancing beneficial bacteria
  • Competing with pathogens
  • Modulating immune response
• What are the limitations of using probiotics as an intervention?

  • Strain-specific effects
  • Transient colonisation (often don't persist long-term)
  • Variable efficacy between individuals
  • Regulatory concerns (not all products are well-tested)
• What are prebiotics and how do they work in the gut?

  Non-digestible food components (e.g. inulin, fructooligosaccharides) that selectively stimulate growth/activity of beneficial gut bacteria like Bifidobacteria and Lactobacilli.
• What are synbiotics?

  A combination of probiotics and prebiotics designed to synergistically improve the survival and implantation of live microbes and stimulate beneficial bacteria in the gut.
• What is Fecal Microbiota Transplantation (FMT) and when is it used?

  Transfer of stool from a healthy donor to the GI tract of a patient to restore microbial balance.Commonly used for recurrent Clostridioides difficile infection (CDI) with high success rates.
• What are the benefits and risks of FMT?

  ✅ Benefits:

  • High efficacy in treating recurrent CDI
  • Restores microbial diversity quickly❌ Risks:
  • Potential pathogen transmission
  • Limited regulation
  • Long-term effects unknown