The gut microbiome

Question 1

Why does the gut microbiome thrive?

Answer 1

Large surface area of the intestinal lining for colonisation
A bioreactor and nutrient-rich environment supplying microbes with essential energy
Specialised niches with varying oxygen levels create distinct microenvironments for a diverse range of microbial species
Bacteria form structured communities and communicate to enhance survival

Question 2

What is the composition of the microbiome?

Answer 2

Community includes bacteria, archaea, viruses and fungi
Bacteria are most prominent
Dominant gut phyla are firmicutes, Bacteroidetes, actinobacteria and proteobacteria
In a healthy mammalian microbiome there’s a near equal proportion of firmicutes and Bacteroidetes

Question 3

How is the flora made?

Answer 3

First encounter with microbes during birth
Vaginal birth exposes infants to the maternal birth canal microbes
C-section deliveries introduce skin-associated microbes
Mother’s microbiota, antibiotic use and feeding choices shape the microbiome
Microbes from family, pets and the environment
Solid food shifts the microbiome from milk-specialists like Bifidobacterium to more diverse species like Bacteroides

Question 4

How does the flora evolve?

Answer 4

Microbial selection
The process is dynamic and the microbiome evolves dramatically within the first 2 years
Factors causing growth change include diet, antibiotics and environmental shifts
By adulthood a stable core microbiome dominated by Firmicutes and Bacteroidetes form

Question 5

Main functions of the microbiome

Answer 5

Act as bioreactors breaking down otherwise indigestible compounds to extract energy and nutrients
Influences drug metabolism, bile acid recycling and fibre digestion
Limits pathogen growth through inhibitory compounds, physical barriers and immune signalling
Stimulates immune maturation
Modifies bile acids and other host-related compounds
Contributes to genetic diversity
Millions of genes available for vitamin production (in particular B and K)
Microbial metabolites affect mood, sleep and overall systemic function
Supports GI physiology

Question 6

Maintenance of a healthy microbiome (eubiosis)

Answer 6

Prebiotics include specific carbohydrates
Probiotics may support gut health (microbes that feed other microbes)
Dominated by firmicutes and bacteroidetes
Balanced diet rich in fibre, fruit and veg promotes diversity and nourish beneficial bacteria

Question 7

Dybiosis- microbiome imbalance causes

Answer 7

Causes include antibiotic use, dietary changes, disease states such as IBD, ageing increases pro-inflammatory species, external factors like pregnancy and menstruation

Question 8

Health impacts of dysbiosis

Answer 8

IBD and T2D linked to inflammation and metabolic changes
Neurological disorders like Alzheimer’s and anorexia
Asthma
C difficile infections
Hepatic diseases
Systemic consequences including the gut-brain axis, gut-skin axis and the gut-lung axis

Question 9

Inflammatory bowel disease

Answer 9

Chronic inflammatory condition of the GI marked by gut microbiome dysbiosis and reduced microbial diversity
Includes Chron’s disease and ulcerative colitis
UC = superficial inflammation restricted to the mucous layer
CD = transmural inflammation affecting the full intestinal wall
Highest prevalence in western countries
Microbial changes include a proliferation of facultative anaerobes and loss of diversity
Metabolic changes include reduced SCFAs and metabolite diversity