The Microbiome: The Ultimate Social Network

Question 1

What is the Microbiome?

Answer 1

The Microbiome is the combined genetic material of microorganisms of an individual. Joshua Lederberg argues the microbiome must be recognised as a collective entity inclusive of the individual’s own genetic material.

Question 2

What is the Holobiont?

Answer 2

The holobiont is the interaction between the host and the microbiome, which collectively can be recognised as an individual under evolutionary selective presssures - 10 trillion bacteria in/on us, 100 times more bacterial genes

Question 3

What is Symbiosis?

Answer 3

Close and Long-term beneficial interaction between two species

Question 4

What is a Symbiont?

Answer 4

A species involved in a symbiotic relationship

Question 5

What is Mutualism?

Answer 5

A symbiotic relationship which is of benefit to of either both or just one of the two species

Question 6

What is Commensalism?

Answer 6

In which one species obtains a benefit from its relationship with the other, with no detrimental or beneficial effects being imparted to the other species

Question 7

What is the Hologenome Theory of Evolution by Zilber-Rosenburg et al. 2008?

Answer 7

Proposes that evolutionary forces acting at the level of an individual organism are instead acting on the “holobiont” - the inherent community of a host plus all of its symbiotic microbes.Consequently, the collective genomes of the holobiont form a “hologenome”. Variation in the hologenome encodes variation in phenotypes upon which evolutionary forces such as selection or neutrality can operate.

Question 8

How do microbes communicate with one and other?

Answer 8

Via Quorum Sensing via a chemical language

Question 9

What is QS?

Answer 9

QS enables gene regulation of a microbial population in response to cell-density and other environmental determinants - it has been recently recognised as a ‘rule’ rather than an ‘exception’

Question 10

What are autoinducers?

Answer 10

Autoinducers are signaling molecules that are produced in response to changes in cell-population density. As the density of quorum sensing bacterial cells increases so does the concentration of the autoinducer. The detection of a minimal threshold stimulatory concentration incites an alteration in gene expression

Question 11

What is an example of QS?

Answer 11

B.Bassler recognised V.fischeri released light on the Hawain bobtail squid. It only releases light under high density.

Question 12

How does QS work in V.fisheri

Answer 12

Autoinducer, acyl-homoserine lacton is secreted by transcription of LuxI gene, these are absorbed by the neighbouring cells and binds to cytoplasmic LuxR proteins, forming autoinducer complex which bind DNA and activate transcription of luxICDABE.

Question 13

Where are the microbes found?

Answer 13

Skin, crevaces, GI tract. Collectively making up 1-2Kg of the body’s weight - to every 1 eukaryotic cell there are 10 prokaryotic cells.

Question 14

What contributes to the species composition of the microbiome?

Answer 14

Dispersal, Biotic, Abiotic and Genetic factors.
J Li et al. 2014 - different fish hosted different composition of microbiomes dependent on feeding environment.
Kohl et al. 2014 - greater genetic diversity during periods of fasting in toads - ability to digest all accounts of nutrition - anything available.
Goodrich et al. 2014 - monozygotic twins demonstrated a higher degree of similarity than dizygotic twins, additionally those related had a higher similarity than those who are not.

Question 15

What are the roles of the microbiome?

Answer 15

Immunomodulation (Fassano 2000), gut development, energy homeostasis, nutrient aquisition, behaviour.

Question 16

How do microbes contribute to immunomodulation?

Answer 16

Secretion of polysaccharides during gut development, enables the host to recognise the microbes as commensals.
Additionally, presence of microbes and activation of the immune system, prevents over-stimulation post-developmental stages, decreasing chances of developing autoimmune diseases (Fassano 2000)

Question 17

How does the microbiota aid fighting pathogens?

Answer 17

Microbiota secrete/produce free radicals that can attack pathogenic species, additionally they fight for nutrients against the pathogens.

Question 18

How do microbes aid gut development?

Answer 18

Functional maturation and intestinal function.

Question 19

How do microbes aid Energy homeostasis

Answer 19

via provision of metabolites such as folate, short chain fatty acids and dietry lipids

Question 20

How do microbes provide nutrients?

Answer 20

Metabolic breakdown of fibres

Question 21

How do microbes effect behaviour?

Answer 21

The brain-gut axis stimulated by the vagus nerve.

1. Microbiome releases serotonin, which is a neurotransmitor which stimulates the brain via vagus nerve.
2. Some bacterial molecules, such as butyrate, have an effect on the blood-brain barrier.
3. Cytokines released in response to microbes hold an effect on neurophysiology.

Question 22

What are the four stages of microbiome colonisation?

Answer 22

1. Sterile Gut
2. Initial Aquisition
3. Breast or Bottle fed
4. Start on solid foods

Question 23

How can we study the microbiome?

Answer 23

1. Microscopy - stains/morphological characteristics

2. Culturing - growth/phylotyping/metabolomics

Question 24

How has C.elegans been used as a model organism?

Answer 24

70% of C.elegans proteins have a human orthologue. It holds associated pathologies, used as a model organism to understand pathogenesis and antibiotic resistance

Question 25

What are gnotobiotic mice?

Answer 25

Mice with no microbiome - used to insert microbiome and then manipulate using diet

Question 26

How are D.melongaster used as a model organism?

Answer 26

Easy to generate germ-free flies. Powerful genetics, which can be easily manipulated. Additionally have a functionally segmented gut.

Question 27

What is VitB12?

Answer 27

VitB12 requires folate for synthesis and is essential for microbial biosynthesis, most proteins contain it and is used in riboswitches. B12 additionally regulates hosts metabolism, can activate beta-oxidation through upregulation of acetyl-CoA. B12 additionally increases developmental rates.

Question 28

How does folate regulate development?

Answer 28

Lack of folate leads to Megalobstic anemia and fetal neural tube defects (spina bifida). Extends C.elegans lifespan.

Question 29

Is there a universal CORE mirobiome?

Answer 29

The Core Measurable Microbiome (CMM) are a conserved selection of microbiota species which are conserved within a host species. CMM make up a significant amount of the total abundance of the gut microbiota (anywhere between 20-70%).

Question 30

What contributes to genetic diversity of gut?

Answer 30

1. Age
2. Diet
3. Host genetics

Question 31

What constitutes the CMM?

Answer 31

Similarity: 50% of an individuals genes are shared by at least 50% of the cohort.
Individuality: Genes shared by less than 20% of individuals = 2.4 million genes.
Qin et al.

Question 32

How does diet effect microbiome?

Answer 32

The specific diet alters microbial activity and gene expression. Certain microbes which are otherwise unable to metabolise certain nutrients will deplete in numbers, whilst others flourish - altering the diversity of the microbiome.
Demonstrated that those on a Veg. diet will hold a greater diversity, and biomass of microbes (Lawrence et al. 2014)

Question 33

How do xenobiotics shape the microbiome?

Answer 33

Ab, but not host-targeted, alter microbial physiology. Abs can target the cell wall biosynthesis, changing structure of active microbiota –> damage. Short-term exposure to Ab results in altered community-wide gene expression.

Question 34

What is dysbiosis?

Answer 34

State of microbial imbalance in the gut leading to host dyshomeostasis.

Question 35

What is the pathobiont?

Answer 35

Member species of the microbiota that under altered physiological conditions, specifically altered microbiota diversity, can result in pathology, such as C.difficile.

Question 36

What is the relationship between dysbiosis and obesity?

Answer 36

Cox et al. 2014 showed that mice subject to penicilin treatment in early stages of treatment went on to develop obesity, holding a causal-role in inducing metabolic changes, changes which can be replicated in a gnobiotic mice –> obese.

Question 37

How do pathobionts effect the gut wall?

Answer 37

Leads to inflammation as their increased numbers, and decreased numbers in ‘peace-keeping’ bacteria leads to damaged epithelial and increased bacterial adherence and penetration –> leading to pathological inflammation.

Question 38

What is the relationship between dysbiosis and cancer?

Answer 38

Shown that decrease in diversity of the microbiome can increase the risk of cancer in gnobiotic mice versus controlled mice with differing genetic diversity in the microbiome. Increased dysbiosis –> increased MAMPs, these cause activation of bacterial genotoxins, alters expression of genes such as dietry nitrosamine, oestrogen and testosterone, increased energy harvest –> prevents the maintenance of healthy cell growth –> cancer (Schwabe et al. 2013)

Question 39

What is the relationship between the microbiome and artherosclerosis?

Answer 39

Red meat increase the concentration of Clostriiaceae in the cut –> release TMA which is metabolised in the liver by FMO to produce TMAO, this decreases RCT and bile acid synthesis –> artherosclerosis.

Question 40

What is bacteriotherapy?

Answer 40

Replenishing the gut microbiota in order to warrant positive effects on the individual, following C.diff induced dysbiosis, or simply unhealthy microbiome.
Roos et al. 2001 - commensal alpha hemolytic streptococci reduced reccurrent ottis media and recurrent tonsilitis
Hakatta et al. 2001 - milk containing lactobacilius GG give to children reduced the rate and severity of respiratory infections

Question 41

Described C.diff.

Answer 41

Anaerobic, spore-forming bacillus, symptoms resultant from dysbiosis are diarrhoea, high T count, painful abdominal cramps, toxic megacolon. Risk increased following prolongued Ab exposure.
Treated with fecal transplant to replenish microbiota.

Question 42

What is metformin?

Answer 42

It is the world’s most widely prescribed anti-diabetic drug. The drug is poorly absorbed by the GI hence 300X higher concentration in the gut lumen, this leads to folate and B12 deficiency.

Question 43

How does metformin alter microbiota?

Answer 43

Alters metabolic pathways, improves glucose homeostasis, alters bacterial structure - an increase in Akkermansia spp population, specifically the number of mucin producing cells, which improves glucose tolerance.

Question 44

What does metformin do?

Answer 44

Shown to positively effect ageing in C.elegans by altering microbial folate (impairs) and methionine metabolism. However increase in age is dose specific and requires presence of E.coli in gut.