Lecture 9: Microbiome 1

Question 1

What are two strengths of using WGS of single colonies?

Answer 1

1) Ultra high resolution for tracking emergence and spread of virulence
2) gives info on phenotypic properties eg antibiotic resistance and virulence

Question 2

What are the weaknesses of WGS of single colonies?

Answer 2

1) Some genes/regions don’t map to a reference so are difficult to assemble.
2) Sequencing one genome at a time gives no info on diversity of the bacterial community eg mutations in a single host (intrahost evolution) and the target species may interact with other species

Question 3

What is metagenomics? What doesn’t this require?

Answer 3

The application of modern genomic techniques to the study of microbes in their natural environments which doesn’t require isolation and culture.

Question 4

What does metagenomics tell us?

Answer 4

How communities as a whole can impact health

Question 5

What is metagenomics important for?

Answer 5

1) Comparing species richness in different habitats
2) discovering new genes and proteins for antibiotics, bioremediation etc.
3) Agriculture and understanding how bacterial soil communities can protect plants against pathogens
4) role of bacterial communities in biogeochemical cycles eg N, C

Question 6

How is the nitrogen cycle an example of the power of communities?

Answer 6

the Haber Bosche process fixes nitrogen in the atmosphere for fertilisers and resulted in the growth of the population. No single bacteria is able to do all nitrification eg first stage is degredation of NH3 to NO2- by ammonia oxidising bacteria and the second stage is oxidation of nitrite to nitrate by nitrobacter bacteria.

Question 7

Where in the body do bacteria colonise?

Answer 7

gut, skin, urino-vaginal, oral cavity, intestines

Question 8

How many bacterial cells are on us?

Answer 8

The same as we have cells, roughly 3 x10^13

Question 9

What conditions have we discovered the role of bacteria in recently?

Answer 9

Inflammatory bowel disease, kidney stones, eczema, diabetes and there are links to cognitive diseases such as autism and depression

Question 10

What does the human microbiome have an important influence on?

Answer 10

physiology, cognition, development, immunity and nutrition

Question 11

When was the first study of the microbiome conducted, who on and what were a high proportion of bacterial genes discovered for?

Answer 11

2006, two healthy adults, breakdown of plant derived polysaccharides, detoxification of xenobiotics (something produced by a different organism) and the synthesis of essential AAs and vitamins

Question 12

What was the human microbiome project?

Answer 12

5 year effort starting in 2008. 250 individuals screened at 15 sites in males and 18 sites in females with $115m budget

Question 13

What is metaHIT?

Answer 13

Metagenomics of human intestinal tract. Analysed stool samples fro, 124 subjects with various health conditions

Question 14

Describe one method by which bacterial genomes are sequenced.

Answer 14

1. take out bacteria and extract DNA
2. 16S rRNA is a marker gene and amplify it by PCR and sequence it
3. put together similar sequences into OTUs
4. Compare OTUs to databases and OTU vs abundance

Question 15

How are bacterial genomes sequenced in a functional way?

Answer 15

1. Sequence in a shotgun approach and assemble

2. Compare to databases eg BLAST and compare the functions vs abundance

Question 16

What were the key findings of the human microbiome project?

Answer 16

1. Links between microbial diversity and certain diseases
2. Different body sites characterised by different taxa eg oral cavity dominated by streptococcus
3. Considerable variation between healthy individuals, twins share less than 50% of bacterial taxa at species level
4. Variation may be associated with disease susceptibility etc.

Question 17

what 4 phyla dominate the human microbiome?

Answer 17

actinobacteria, bacterioidetes, firmicutes, proteobacteria.

Question 18

Where is ruminococcus mostly found?

Answer 18

in the gut

Question 19

Where is lactobacillus found?

Answer 19

mostly in the vagina

Question 20

What do different skin types that have similar pH, lipid content and sweat have?

Answer 20

Similar bacteria

Question 21

What do Lactobacillus in the vagina do?

Answer 21

produce lactic acid resulting in a low pH (4-4.5) to restrict pathogen growth

Question 22

What is the composition of the vaginal bacterial community influenced by?

Answer 22

oestrogen levels, menstruation, ageing, pregnancy, maybe stress.

Question 23

A study used 16S rRNA to characterise bacterial communities from 396 healthy individuals of women from 4 ethnic groups. How many community types were found, what were they dominated by and why was the 5th type different?

Answer 23

5, lactic acid bacteria, wasn’t abundant in lactic acid bacteria

Question 24

What other species was prevalent? What do they do? What was odd?

Answer 24

Prevotella. Cause growth of bacteria linked to vaginosis by providing these bacteria with key nutrients. No evidence they were any less healthy

Question 25

What is bacteria abundance affected by in some women?

Answer 25

Menstruation

Question 26

What is a key factor for bacterial communities in the vagina?

Answer 26

Amount of oestrogen as this stimulates glycogen production which is degraded to alpha amylase and then to simple sugars which are consumed by vaginal lactobacilli and fermented to produce lactic acid.

Question 27

What is lower in obese people? How was this confirmed?

Answer 27

Bacteroidetes and increases with weight loss. In 2010 by mice studies as obese ones were found to have more firmicutes and fewer bacteriodetes than leaner siblings. Germ free mice colonised with microbiota from obese mice gained more weight than those with microbiota from lean mice.

Question 28

What do short chain fatty acids have to do with it?

Answer 28

Microbes in the gut convert polysaccharides into manosaccharides and short chain fatty acids which are able to bind and activate 2GPCRs on gut ECs. This induces peptide YY which decreases gut motility, slowing intestinal transit and increasing nutrient uptake.

Question 29

What does CDI stand for?

Answer 29

Clostridium difficile infection

Question 30

What is CDI? When does it occur?

Answer 30

Bacterial infectious disease caused by clostridium difficile in the gastrointestinal tract. Occurs when patients recieve antibiotics which eradicate normal gut bacteria and allow other bacteria to grow which are pathogenic. There is loss of micriobial diversity.

Question 31

How is CDI treated?

Answer 31

Faecal matter transplant with a 90% success rate

Question 32

What other conditions is faecal matter transplant being investigated in?

Answer 32

Crohn’s disease, autoimmune disorders

Question 33

What went wrong with a FMT?

Answer 33

One woman gained 16kg after one

Question 34

What is diabetes associated with?

Answer 34

Decreased microbial diversity and replacement of firmicutes with bacteroidete species

Question 35

What is irritable bowl disease associated with?

Answer 35

increased E.coli and decreased clostridia