AS Lecture 11 - Microbiome of the gut

Question 1

What is microbiota?

Answer 1

Qualitative and quantitative information about the different microbes present in a system – so who is there and how abundant.

Question 2

What is the microbiome?

Answer 2

Functions that these microbiota have, e.g. bile metabolism – their gene catalogue

Question 3

What is metagenomics?

Answer 3

Either “gain-of-function” or DNA based approach to create gene catalogues, used to define the microbiome.

Question 4

What is metataxonomics?

Answer 4

Creation of 16S rRNA gene inventories, used to define the microbiota

Question 5

What is metabonomics?

Answer 5

Catalogue of the metabolites in a sample (metabolomics in a tissue or isolate)

Question 6

How does metataxonomics work?

Answer 6

Take a sample (faecal) > DNA/RNA extracted from all microbes in sample > PCR SSU rRNA or any house keeping gene detected by illumina MiSeq and analysed

Question 7

What can be found out in a metataxonomics analysis?

Answer 7

Popn/Community dynamics, diversity indices, microbial biomarkers, DNA=diversity, RNA=metabolic activity, robust/strong bioinformatic support, 20-50£ per sample

Question 8

How much of the stool is microbial biomass?

Answer 8

50-55% of stool sample - 50-250g

Question 9

How much of the microbial biomass is contained in the large intestine?

Answer 9

1-2kg

Question 10

What are the different concentrations of microbial biomass in each part of the GIT (stomach, duodenum, small intestine, colon)?

Answer 10

Question 11

What do the microbes do as an asset to the host?

Answer 11

Defence - bacterial antagonism Priming of mucosal immunity - IBD is thought to be autoimmune to the gut flora Peristalsis Metabolism of dietary carcinogens Synthesis of B and K vitamins Epithelial nutrients (e.g. SCFAs - butyrate) Conversion of prodrugs Utilisation of indigestible (CH2O)n

Question 12

What do the microbes do as a liability to the host?

Answer 12

Procarcinogens -> carcinogens (hydrogen sulphide) Overgrowth syndromes (C. Difficile infections) Opportunism - Translocation Essential ingredient for IBD **Utilisation of indigestible (CH2O)n – obesity Role in insulin resistance and non-alcoholic fatty liver disease.** ** controversial topics

Question 13

How many different types of microorganisms colonise the gut?

Answer 13

Viruses (1200), eukaryotes (very few in humans, but murine systems show large fungal diversity), bacteria (>1000 species in total but 160 species per person)

Question 14

What should humans be thought of as?

Answer 14

Superorganisms, with it’s own genome contributing to the familiar and extended genome - predominantly bacterial

Question 15

What is the specificity of the microbiome?

Answer 15

It is host specific and can be changed by diet, drugs, pregnancy and surgery Family and pets share a common bacterial popn, more similar than with some random person

Question 16

Which diseases have very strong association for microbiota’s role? I.e. Which diseases are thought to have microbes as a cause?

Answer 16

Asthma, eczema, diabetes, obesity, Non-alcoholic fatty liver disease, depression, heart disease, colon cancer, inflammatory bowel disease

Question 17

How does absence of a microbiome impact the host?

Answer 17

Inestinal, exocrine, vascular, endocrine, infection, immunity, epithelia, morphology, metabolism, nutritional, hepatic

Question 18

How is bacterial colonisation predicted?

Answer 18

It is inevitable, not pre-ordained or the same for every individual - predictable at phylum level but contains degree of randomness

Question 19

How can bacterial colonisation be influenced in first year of life?

Answer 19

By antibiotics

Question 20

What are the ecological interactions between members of different species?

Answer 20

Question 21

What does amensalism involve?

Answer 21

One organism growing and in doing so inadvertently damages another, but it is not evolved to do so – collateral damage.

Question 22

What is the problem with inflammatory bowel disease?

Answer 22

It is a multi-factorial disease and involves environmental factors but no pathogen has been identified

Question 23

Which diseases don’t occur in sterile rodent models?

Answer 23

Colocrectal cancer, breast cancer, metabolic syndrome and diabetes

Question 24

Is there a connection between the gut microbiota and the host?

Answer 24

The microbiota aren’t isolated, they are interconnected

Question 25

What are the 2 types of omic approaches to microbiome investigation?

Answer 25

Bottom up - start from DNA -> metabolite [metataxonomics and metagenomics] Top down - metabolite -> DNA [metabolomics, metabonomics]

Question 26

What is a positive point of metataxonomics?

Answer 26

There is no need to cultivate any bacteria, it is just analysing DNA

Question 27

Are people born sterile?

Answer 27

12-18 months is when you are colonised and a community is established - if born vaginally you have Lactobacilli, if born from C section then staph aureus will be present Some people are born sterile but bacteria have been found in the placenta and in the mucus plug in the baby’s rectum

Question 28

How is the gut biome resilient?

Answer 28

It stays the same over a long time, with not much change occurring, unless antibiotics or surgery or diet change Even if antibiotics given, then when they are stopped, after a couple of weeks it will return to ‘normal’ colony type

Question 29

What is another problem of microbes in the gut?

Answer 29

They can break down some drugs, so can respond differently to the drug which could cause big issues when treating different patients

Question 30

What is mutualism?

Answer 30

Good for the host and the microbiome

Question 31

What is commensalism?

Answer 31

Probiotic microbes which don’t reproduce in the host

Question 32

What is metataxonomics?

Answer 32

Checking what microbes are there and their abundance

Question 33

What is metagenomics?

Answer 33

What are the microbes are doing

Question 34

What is metabonomics and metabolonics?

Answer 34

Metabonomics - metabolites from many sources Metabolonics - metabolites from one source

Question 35

What are the main 2 phyli in the gut biome?

Answer 35

Firmicutes, Bacteroidetes and actinobacteria

Question 36

How is metabonomics/ metabolomics investigated?

Answer 36

Sample (faeces, urine, blood), tested with H1 NMR and LC-MS which is analysed

Question 37

What can be the result of a metabonomics/ metabolomics?

Answer 37

Metabolic profiles, biomarkers, metabotypes

Question 38

What are bacterial proteases important for?

Answer 38

They are known to be the communicators between host genes, env and microbiome (so are affected by each as well) They are also a potential virulence factor in colorectal cancer and IBD - so can compromise tight junction integrity

Question 39

What happens if you are at either end of the microbiome spectrum?

Answer 39