What is microbiota?
Qualitative and quantitative information about the different microbes present in a system – so who is there and how abundant.
What is the microbiome?
Functions that these microbiota have, e.g. bile metabolism – their gene catalogue
What is metagenomics?
Either “gain-of-function” or DNA based approach to create gene catalogues, used to define the microbiome.
What is metataxonomics?
Creation of 16S rRNA gene inventories, used to define the microbiota
What is metabonomics?
Catalogue of the metabolites in a sample (metabolomics in a tissue or isolate)
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
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
How much of the stool is microbial biomass?
50-55% of stool sample - 50-250g
How much of the microbial biomass is contained in the large intestine?
What are the different concentrations of microbial biomass in each part of the GIT (stomach, duodenum, small intestine, colon)?
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
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
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)
What should humans be thought of as?
Superorganisms, with it's own genome contributing to the familiar and extended genome - predominantly bacterial
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
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
How does absence of a microbiome impact the host?
Inestinal, exocrine, vascular, endocrine, infection, immunity, epithelia, morphology, metabolism, nutritional, hepatic
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
How can bacterial colonisation be influenced in first year of life?
What are the ecological interactions between members of different species?
What does amensalism involve?
One organism growing and in doing so inadvertently damages another, but it is not evolved to do so – collateral damage.
What is the problem with inflammatory bowel disease?
It is a multi-factorial disease and involves environmental factors but no pathogen has been identified
Which diseases don't occur in sterile rodent models?
Colocrectal cancer, breast cancer, metabolic syndrome and diabetes
Is there a connection between the gut microbiota and the host?
The microbiota aren't isolated, they are interconnected
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]
What is a positive point of metataxonomics?
There is no need to cultivate any bacteria, it is just analysing DNA
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
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
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
What is mutualism?
Good for the host and the microbiome
What is commensalism?
Probiotic microbes which don't reproduce in the host
What is metataxonomics?
Checking what microbes are there and their abundance
What is metagenomics?
What are the microbes are doing
What is metabonomics and metabolonics?
Metabonomics - metabolites from many sources Metabolonics - metabolites from one source
What are the main 2 phyli in the gut biome?
Firmicutes, Bacteroidetes and actinobacteria
How is metabonomics/ metabolomics investigated?
Sample (faeces, urine, blood), tested with H1 NMR and LC-MS which is analysed
What can be the result of a metabonomics/ metabolomics?
Metabolic profiles, biomarkers, metabotypes
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
What happens if you are at either end of the microbiome spectrum?