GIS13 The Gut Microbiome In Complex Chronic Disease

Question 1

Microbiome vs Microbiota vs Dysbiosis

Answer 1

Microbiome:

• total collection of microbe
• aggregate of All microbial species, their Genomes, and the Ecosystem in which they interact

Microbiota:

• individual microbial species that constitute the microbiome
• formerly known as “the normal flora”

Dysbiosis:

• Imbalances in the **Composition and **Function of Microbiota
• associated with wide range of chronic diseases

Question 2

Metagenomics

Answer 2

Culture-independent molecular assays
—> analysis of microbial **genomes to identify species and function
—> allow detection of microbes otherwise **cannot be cultured by conventional methods

Question 3

Human microbiome studies

Answer 3

Understand the role of human microbiome in
- Maintenence of health
- Causation of disease
—> prevent and treat diseases

Question 4

US human microbiome project (HMP)

European metagenomics of the human intestinal tract (MetaHIT)

Answer 4

HMP: describe composition and diversity of the microbial communities, create integrated dataset of biological properties

MetaHIT: establish association of human gut microbiome with health and disease, esp IBD and obesity

Question 5

Core microbiome

Answer 5

Common set of microbial species / genes shared by most individuals

HMP: generated a catalogue of ~800 reference genomes from multiple body sites

MetaHIT: 40% of genes were shared by majority of individuals , 99% of genes were of bacterial origin

Question 6

Variation in composition of microbiome

Answer 6

Considerable inter-individual variation (時地人)

• Anatomical site
• Person: host genetics
• Time: maximum diversity in adolescence, less diverse and less stable in old age
• Environment: diet, antibiotics

Question 7

Adult gut microbiome

Answer 7

Main phyla:

• ***Firmicutes (gram +ve)
• ***Bacteroidetes (gram -ve)
• mainly ***anaerobes

Question 8

Where do we get gut microbiota

Answer 8

1. Transfer via placenta (almost sterile before birth)
2. Vagina, faeces and skin during birth
   —> differ by mode of delivery
3. Early feeding
   —> ***breastfed: Bifidobacteria; formula-fed: more Bacteroides / Clostridium spp.
4. Solid food introduction
   —> more like adult microbiome by 2-3 years, can digest wide range of food
5. Early life exposures
   —> antibiotics

Question 9

Barriers for microbes living in the gut

Answer 9

1. Acidic environment
2. Saliva and bile
3. Immune system
4. Attaching to intestinal wall
5. Surviving the diet

Upper GI:

• ***highly acidic in stomach
• most gastric microbiota also found in oropharynx
• H pylori negative individuals: diversity of gastric microbiota higher

Small intestine:

• **higher bile concentration and **short transit time
• more challenging environment for microbial colonisers
• mostly ***Facultative Anaerobes

Large intestine:

• neutral to mildly acidic, **low oxygen, **slow flow rate
• largest microbial community in body
• mostly ***Obligate Anaerobes

Question 10

Metabolic potential of gut microbes

Answer 10

1. Metabolism of complex carbohydrates
   - digest dietary fibre and ferment into ***short-chain fatty acid
2. Biotransformation of Bile acids
   - Bile acids produced in liver degraded by intestinal bacteria and reabsorbed, completing ***enterohepatic cycle
3. Metabolism of ***Choline in liver

Question 11

Impacts on host health

Answer 11

Rats raised in sterile environment have to eat 30% more calories to maintain same weight as rats with normal microbiome

Question 12

***Gut microbiome function

Answer 12

1. ***Digest carbohydrates, protein and fats
2. Produce ***nutrients
   - Biotin (vit B7), vitamin K
3. Trains immune system
   - short-chain fatty acids (fermented by gut microbe) increase growth of gut epithelial cells and increase growth of ***lymphoid tissue
   - immune system fights harmful bacteria but leaves helpful bacteria alone
4. Stops growth of pathogenic bacteria
   - competition
   - fermentation make colon ***more acidic: less attractive for bad bacteria
5. Modifies production of ***neurotransmitter
6. Modifies ***drugs during metabolism

Question 13

Factors influencing gut microbiome

Answer 13

1. Antibiotics
2. Prebiotics (益生元) / probiotics (益生菌)
3. Dietary composition: microbiome respond changes in diet rapidly
4. Losing weight
5. Possibly other environmental exposures e.g. arsenic

Question 14

How to identify gut microbiota

Answer 14

1. Collect stool sample
2. Extract genetic material
3. Analyse genetic material
   - recognise genetic sequences —> identify types of bacteria, viruses, fungi
   - techniques:
   —> **Biomarker sequencing (16S rRNA)
   —> **Metagenomics (study of microbial genomes)
   —> ***Metatranscriptomics (study of gene expression / RNA sequences)

Question 15

Manipulation of gut microbiota

Answer 15

1. Antibiotics
2. Prebiotics: food ingredients that confer specific changes in gut microbiome and lead to beneficial effects in the host
3. Probiotics: selection of microbes thought to confer benefit to host
4. Faecal transplant
5. Create germ-free animals then add back specific pathogens

Question 16

Chronic disease relevance to microbiome

***Correlation is not causation

Answer 16

1. Malnutrition
   - mice receiving faecal transplant from twin with kwashiorkor lost more weight
2. Obesity:
   - high BMI: higher ratio of Firmicutes to Bacteroides, more bacteria to digest carbohydrates, mice receiving faecal sample from obese human gained more fat mass —> common ground hypothesis: reproduction of distinct disease phenotype through transplantation of the dysbiotic disease-associated gut microbiota to a genetically susceptible rodent host
3. Diabetes
   - Chinese with diabetes: decrease in butyrate-producing bacteria and increase in some opportunistic pathogen (Clostridium spp. and E. coli)
   - Caucasians with insulin resistance: increased Lactobacillus and Clostridium spp.
   - women received probiotics early in pregnancy show reduced gestational diabetes
4. Infections
   - C. difficile infection: old age, hospitalisation, antibiotic exposure, IBD, chemotherapy —> less diversity of microbiota
   - infusion of stool from healthy donor via colonoscopy / mouth —> C. difficile-associated diarrhoea stopped
5. Auto-immunity / allergy
   - IBD: associated with diminished gut microbial diversity and early life antibiotic exposure —> faecal transplantation look promising
   - Atopic diseases: childhood acquisition of gastric H. pylori may be associated with lower risk of asthma, child born by C-section may have higher risk of asthma, airway microbiota may be involved in asthma
6. Cardiovascular disease
   - Gut microbiota may be involved in process of atherosclerosis
7. Cancer
   - Fusobacterium numbers may be associated with increased risk of colorectal cancer, possibly through inflammatory mechanism
   - Bacteroides may induce colitis and tumourigenesis by stimulating exaggerated immune response through T-helper 17 cells
   - Colonic microbiota may affect expression of host genes involved in cell cycle regulation, thus inducing epithelial proliferation
8. Psychiatric disease
   - Microbiota-gut-brain axis: microbiota may have effect on hypothalamic-pituitary-axis, regulating response to stress, digestive function, immune system, mood and emotions
   - Higher Firmicutes : Bacteroides ratio in gut associated with irritable bowel syndrome and autism spectrum disorders
   - Reduced diversity in gut microbiota associated with depression

Question 17

Challenges of microbiota study

Answer 17

1. Extracting clinical relevance from large amount of microbiome data
2. Limited longitudinal and interventional studies so far (most studies under-powered and prone to ***reverse causation)
3. Most studied focused primarily on bacterial rather than other species
4. Bacterial genome databases remain incomplete (majority of genes have unknown functions)

Question 18

Future directions

Answer 18

1. Confirm causality for chronic disease
2. Assess potential unintended consequences
3. Find acceptable modes of treatment in human
4. Resolved ethical, legal and regulatory issues
5. Personalize treatment for humans