Microbiota Flashcards
What is culturing?
This is where ‘live’ microbes are grown to be tested in a lab. they are required in development of therapies.
What is 16 rRNA gene profiling? (bacteria and archaea)
This is where a sample bacteria and archaea sequence is amplified, then it is clustered to work out the species. To work out the species it is compared to existing data in database references.
What is metagenomics? (DNA - shotgun approach)
all the DNA is sequenced and it is matched with a known genome. This gives you an idea of what genes are encoded by a species, for example, you can tell if it has a specific toxin or enzyme.
What is metatranscriptomics?
This is metagenomics but performed with RNA instead of DNA. This allows you to see genes present AND the level at which they are being expressed.
What is metabolomics?
This looks at what the product levels are - not what is carrying out the functions. Products could include bile salts, sugars or SCFA.
What is proteomics?
provides a similar read out to transcriptomics as it looks at the proteins made as a result of transcription - tells you exactly what is happening within the microbiota.
What is culturomics and its importance?
This cultures ‘unknown’ microbes which is done through inspection of spores. It helps to rebirth culture techniques and helps improve reference databases for further NGS approaches.
What are the four main types of bacterial phyla in the gut microbiota?
Proteobacteria
Actinobacteria
Firmicutes
Bacteroidetes
There are 2500+ species capable of colonising the gut.
Where do anaerobes and aerobes lie in the gut?
Anaerobes - closer to the colon
Aerobes - such as general E.coli are higher in the gut.
Examples of bacteria in the duodenum, ileum, colon:
Duodenum - streptococcus and yeast species
Ileum - clostridium and Enterobacteriaceae
Colon - fusobacteria and proteobacteria
What is the function of the gut microbiota?
Degradation osfcomplex carbs: human genome has 97 genes for carb lysing, only 17 linked with carb digestion. B.thetaiotaomicron has 300 genes encoded for carb degradation.
What are human milk oligosaccharides and their importance?
They encourage growth of healthy bacterua and colonise the gut, they help prime the immune system. The sugars in human milk look like that of eukaryotic cells, viruses get confused and invade them instead of the body.
How does pregnancy, birth, and post natal affect the microbiota?
pregnancy - if you get an infection it may pass into amniotic fluid and get to the baby.
birth - vaginal birth leads to child inheriting colonisation the same as mothers. they have contact with their mothers and healthcare staff.
Post-natal - breast milk vs formula, family structure and environment e.g. pets, pollution. Antibiotics before the age of 1 wipe out any bacteria the baby has colonised.
What is viral colonisation?
Once bacteria start to colonise, this means that phage will want to enter and thrive in the gut, therefore leading to pathogenic viruses potentially.
What is colonisation resistance?
Inhibit overgrowth of resident bacteria that is normally present at low levels.
