The Gut Microbiome in Metabolic Disorders

Question 1

What is the microbiome?

Answer 1

Collection of microorganisms and their genes and proteins living within our mucosae, skin, and secretions

Question 2

What is the exposome?

Answer 2

Environment

Question 3

What are the two most dominant phyla in the colons of healthy adults?

Answer 3

Firmicutes

Bacteroidetes

Question 4

What are the Firmicutes mainly made of?

Answer 4

Gram positive Clostridia

Question 5

What are the Bacteroidetes mainly made of?

Answer 5

Gram negative Bacteroides

Question 6

Are the less important phyla functionally important?

Answer 6

Yes

Question 7

What are the two approaches to sequencing the microbiome?

Answer 7

16S ribosomal sequencing

Metagenomic shotgun sequencing

Question 8

How does 16S ribosomal sequencing work?

Answer 8

Takes areas common to most bacteria in 16S ribosomal subunit gene and amplifies it
Those areas that are different are also amplified
On this basis, bacteria can be separated

Question 9

What is the speed and ease of 16S ribosomal sequencing?

Answer 9

Simple
Fast
Straightforward to analyse

Question 10

What does 16S ribosomal sequencing report?

Answer 10

Operational taxonomic units, not sequences of species

Question 11

Does 16S ribosomal sequencing resolve well at the species level?

Answer 11

No

Question 12

What are the shortcomings of 16S ribosomal sequencing?

Answer 12

May fail to resolve substantial fraction of diversity
Not ID novel/highly diverged microbes
Can’t resolve biological functions associated with taxa

Question 13

How does metagenomic shotgun sequencing work?

Answer 13

Microbial and human DNA separated

Microbial DNA randomly sheared into short segments > sequenced > re-assembled

Question 14

Does metagenomic shotgun sequencing reveal microbial genes that are active?

Answer 14

No, only those that are present

Question 15

What is alpha diversity?

Answer 15

Measure of species diversity within sample

Question 16

What is beta diversity?

Answer 16

Measure of diversity between samples

Question 17

What is dysbiosis?

Answer 17

Disturbance/imbalance in biological system

Question 18

How is a newborn baby seeded with microbiota?

Answer 18

Vagina
Gut
Skin
Breast milk

Question 19

What are the dominant species in the vagina with which the baby is seeded?

Answer 19

Lactobacillus

Prevotella

Question 20

What does a healthy microbiome do in a baby?

Answer 20

Induces maturation and maintains integrity of
- Gut
- Immune system
- Neurological system
- Others
Protects against infection
Produces nutrients and vitamins
Utilises energy > regulates metabolism and weight

Question 21

What happens to the breast milk microbiome after elective C-section?

Answer 21

Altered

Question 22

What childhood diseases is C-section associated with?

Answer 22

Allergic rhinitis
Asthma
Coeliac disease
Type 1 diabetes

Question 23

What evidence is there to show that the microbiome regulates development of type 1 diabetes?

Answer 23

Incidence of T1D in wild mice very low
More than half of mice reared in specific pathogen free environments developed T1D
All mice reared in germ-free environment, and had no microbiome, developed T1D

Question 24

What does diet protection against autoimmune diabetes need?

Answer 24

Microbiome

Question 25

What is the relationship between gut microbial diversity and seroconversion to clinical type 1 diabetes?

Answer 25

Decrease in diversity with seroconversion | Significant decrease in diversity with diagnosis T1D compared to controls

Question 26

How does the gut microbiome change in children with type 1 diabetes?

Answer 26

Diversity decreases Actinobacteria and Firmicutes decreased Bacteriodetes increased Butyrate-producing species within Clostridium decreased

Question 27

How are short-chain fatty acids, such as butyrate, produced?

Answer 27

Bacteria ferment undigested starch

Question 28

What do short-chain fatty acids do?

Answer 28

``` Maintain epithelial integrity Absorbed > go to - Liver - Muscle - Brain - Etc Anti-inflammatory - Bind and activate GTRs - Inhibit histone deacetylases ```

Question 29

How does a fast food diet change the gut microbiome?

Answer 29

Decreases diversity | Has many additives affecting microbiome

Question 30

What is the gut microbiome like in type 2 diabetes?

Answer 30

Fewer butyrate-producing bacteria | More opportunistic pathogens > can cause infections

Question 31

What is a better predictor of insulin resistance than BMI?

Answer 31

Metagenomic signature

Question 32

Is there evidence that a faecal microbiota transplant cures anything?

Answer 32

No clear evidence that it cures anything except recurrent C difficile infection

Question 33

How did things change in people with metabolic syndrome with the transfer of gut microbiota from lean donors?

Answer 33

Increased insulin sensitivity Increased diversity in faecal microbiome Butyrate-producing bacteria increased

Question 34

Is obesity transmissible by gut bacteria?

Answer 34

Yes

Question 35

What are the issues with probiotics?

Answer 35

Contain only few bacteria Evidence for passage to large bowel Varying resistance to acid and bile across species and strains Lack of randomised clinical trials

Question 36

What are prebiotics?

Answer 36

Food parts that promote specific changes in growth/activity of gut bacteria to confer health benefit to host Examples - Non-digestible carbohydrates - Phytochemicals = chemicals in plants