The Human Microbiome (Healthy)

Question 1

ILO’s

Answer 1

1. Have knowledge of the human microbiome project
2. Have knowledge of the normal healthy human microbiota.
3. Discuss the potential role of the human microbiota in health and impact of disappearance of some microbiota in health and disease.

Question 2

Human Gut Microbiome

Answer 2

‘super organisms’ of human and microbial cells

co evolution hypothesis

Protects against disease by crowding out pathogenic organisms

Question 3

What do gut microbes do?

Answer 3

Immune system regulation
Removal of toxins
Crowd out pathogens 
Improve intestine function
Gut-brain links in communication
Important as liver- metabolites in gut
Considered a vital organ

Question 4

HMP

Answer 4

Highly parallel DNA sequencers combined with high throughput mass spectrometers enable characterisation of whole microbial communities : genomes, proteins, metabolic products

Question 5

HMP analysis

Answer 5

16S rRNA - component of the 30S subunit (prokaryotic ribosomes)

This is a highly conserved region with variable regions - it can be used to identify and distinguish between bacteria (taxonomic groups)

Allows design of a primer for PCR for these hyper variable regions

Metagenome sequencing - identifying functions and pathways in the microbiome, defines the microbiome

Question 6

HMP: culture independent sequencing techniques

Answer 6

for less common types of organisms

Question 7

HMP: technology and tool development

VBNC

Answer 7

VBNC: viable non culturable - vast majority

Advances made in culture methods and genome sequencing in the absence of culture allowed analyzation of the microbiome

Scale of data necessitated informatics

Question 8

The normal healthy human microbiota

Answer 8

The core human microbiome is the set of genes present in the human gut

The variable human microbiome is the set of genes present in a smaller subset of humans

It is genes because they can move between microbes (e.g. plasmid vectors, HGT or transformation)

Variables:

• host genotype
• physiological status (including: innate and adaptive immune systems)
• host pathobiology (disease)
• host lifestyle (inc, diet)
• host environment

Presence of transient populations of microorganisms and microevolution

Question 9

The gut microbiome

Answer 9

The most heavily colonised organ is the GI tract

Contains approx 70% of all microbes in the body

Strict anaerobes predominate over facultative aerobes and anaerobes

Dominated by 2 phyla: Bacteriodetes (bacteriodes) and Firmicutes (clostridium)

The human gut contains 500-1000 species

Bacterial abundance increases as we move from the stomach to the colon

Colonization begins at birth

Diversity of the microbiome is heavily influenced by microbial habitat