AS Lecture 11 - Microbiome of the gut Flashcards Preview

LSS 2 - Abdomen, Alimentary and Urinary systems > AS Lecture 11 - Microbiome of the gut > Flashcards

Flashcards in AS Lecture 11 - Microbiome of the gut Deck (39):
1

What is microbiota?

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

2

What is the microbiome?

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

3

What is metagenomics?

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

4

What is metataxonomics?

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

5

What is metabonomics?

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

6

How does metataxonomics work?

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

7

What can be found out in a metataxonomics analysis?

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

8

How much of the stool is microbial biomass?

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

9

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

1-2kg

10

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

11

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

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

12

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

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

13

How many different types of microorganisms colonise the gut?

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

14

What should humans be thought of as?

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

15

What is the specificity of the microbiome?

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

16

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

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

17

How does absence of a microbiome impact the host?

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

18

How is bacterial colonisation predicted?

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

19

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

By antibiotics

20

What are the ecological interactions between members of different species?

21

What does amensalism involve?

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

22

What is the problem with inflammatory bowel disease?

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

23

Which diseases don't occur in sterile rodent models?

Colocrectal cancer, breast cancer, metabolic syndrome and diabetes

24

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

The microbiota aren't isolated, they are interconnected

25

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

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

26

What is a positive point of metataxonomics?

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

27

Are people born sterile?

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

28

How is the gut biome resilient?

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

29

What is another problem of microbes in the gut?

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

30

What is mutualism?

Good for the host and the microbiome

31

What is commensalism?

Probiotic microbes which don't reproduce in the host

32

What is metataxonomics?

Checking what microbes are there and their abundance

33

What is metagenomics?

What are the microbes are doing

34

What is metabonomics and metabolonics?

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

35

What are the main 2 phyli in the gut biome?

Firmicutes, Bacteroidetes and actinobacteria

36

How is metabonomics/ metabolomics investigated?

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

37

What can be the result of a metabonomics/ metabolomics?

Metabolic profiles, biomarkers, metabotypes

38

What are bacterial proteases important for?

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

39

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