Lecture A3 - Genomics of the Human Microbiota.

Question 1

What is the pangenome?

Answer 1

One species, with a collection of genomes.

Question 2

What is a microbial species typically made up of?

Answer 2

A mix of distinct clones which can vary dramatically in their genome sequences and phenotypic features.

Question 3

What is a metagenome?

Answer 3

Mix of microbial clones and species of a given habitat.

Question 4

What does metagenomics provide?

Answer 4

New and important opportunities to study human-microbes interactions at the molecular level.

Question 5

What is the difference between the microbiota and the microbiome?

Answer 5

The microbiota is the complete set of microbial lineages that live in a particular environment. Bacteria, archaea, eukarya, viruses.
The microbiome is the complete set of gene in the genomes of microbial lineages that live in a particular environment.

Question 6

What is whole genome sequencing?

Answer 6

Taking all the genomic DNA and sequence as many fragments of the DNA as possible.

Question 7

What can extracting the RNA do?

Answer 7

Can tell us what gene are transcribed.

Question 8

How many different species of human intestinal microbiota is there?

Answer 8

> 1000 with an aggregate biomass of 1.5kg per person.

Question 9

How many cells do bacteria outnumber somatic and germ cells?

Answer 9

1-2 fold (4x10 13 microbes).

Question 10

What do cross sectional studies do?

Answer 10

Observation of all members of a population or a representative subset, at one specific point in time.

Question 11

What do longitudinal studies do?

Answer 11

Research studies that involve repeated observations of the same variables over long periods of time - often many decades.

Question 12

What do case-control studies do?

Answer 12

Observational study in which two existing groups differing in some features are identified and compared on the basis of some supposed casual attribute.

Question 13

Describe archaea in the gut microbiota?

Answer 13

Less abundant and less diverse than bacteria.
Use hydrogen and CO2 to make methane that modulates the overall flow of metabolism.

Question 14

Describe the eukaryotes in the gut microbiota.

Answer 14

Less diverse and more patchily distributed than bacteria.

Question 15

What are CAZymes?

Answer 15

Carbohydrate active enzymes.
Encoded by the gut microbiota as a dramatic example illustrating the role and importance of the microbiota in human biology.

Question 16

What are the four major categories of CAZymes?

Answer 16

Glycoside hydrolase (GHs) - 130 families.
Polysaccharide lyase (PLs) - 22 families.
Carbohydrate estherases (facilitate activities of GH and PLs).
Glycosyl transferases (not degrading).

Question 17

Where are CAZymes found in bacteriodetes?

Answer 17

PULs - polysaccharide utilisation loci.

Question 18

What do PULs do?

Answer 18

Encode a suite of cell envelope associated glycan binding and important proteins that function in concert with surface an periplasmic enzymes to degrade a specific glycan.

Question 19

When does the microbiota change dramatically (diet)?

Answer 19

The moment the diet goes from fibre rich to fibre poor.
Fibre poor diet makes the mucus layer become thinner.

Question 20

What does fibre deprived gut microbiota contribute too?

Answer 20

Lethal colitis by Citrobacter rodentium.

Question 21

When does mucus collapse?

Answer 21

When fibre is poor and the microbiota and pathogens can enter the body causing disease and inflammation.