The metagenome

Question 1

What is genomics?

Answer 1

Whole cell gene content

Question 2

What is transcriptomics?

Answer 2

Whole cell gene expression

Question 3

What is proteomics?

Answer 3

Whole cell protein content

Question 4

What is metabolomics?

Answer 4

Whole cell metabolite content

Question 5

What is metagenomics?

Answer 5

It’s the study of genetic material recovered directly from environmental or biological systems

Question 6

What is microbiota?

Answer 6

It is the ecological community of commensal and pathogenic microorganisms
Includes: bacteria, archare, protists and fungi

Question 7

What is microbiome?

Answer 7

It is the collective genomes of the microorganisms in these communities

Question 8

How is microbiomes to each individual and so what can we deduce?

Answer 8

Microbiome are unique to each individual, so more to do with environmental factors

Question 9

What can gut microbiome in individuals classify?

Answer 9

Gut microbiome can classify individuals as lean or obese with >90% accuracy

Question 10

What are early life gut microbiomes linked to?

Answer 10

Early life gut microbiomes linked to development of allergic conditions

Question 11

What is the effect on stool microbiome during CDI?

Answer 11

Stool microbiome during clostridium infection is quite different from healthy stool microbiome

Question 12

What does CDI have a greater effect on?

Answer 12

CDI has a greater effect on stool microbiome than host genetic factors

Question 13

What can cure CDI?

Answer 13

Faecal microbiota transplant is able to cure CDI

Question 14

What technological approaches to metagenomics can we use?

Answer 14

Targeted PCR amplification and we use 16S rRNA

Question 15

What is 16s rRNA?

Answer 15

16s rRNA is a component of 30s small subunit of prokaryotic ribosome

Question 16

What do we use to diversify between species?

Answer 16

We use the variable regions to diversify between species

Question 17

What are the steps involved in targeted PCR amplification?

Answer 17

• We collect a mixed sample collection
• Then carry out DNA extraction of all bacteria
• Afterwards we do 16s PCR amplification
• We then put the PCR products in the sequencing machine and carry out analysis

Question 18

What factors do we take into account when choosing the variable regions to choose in 16s PCR amplification?

Answer 18

• Phylogenetic signal

- Amplicon signal

Question 19

What controls do we use in 16s PCR amplification?

Answer 19

We mitigate contaminations by:

• Randomise samples
• Note batch numbers of reagents
• Use sequence negative controls

Question 20

What is whole genome shotgun technique?

Answer 20

Has the same steps as 16s PCR amplification but the whole genome is sequenced instead of only 16s rRNA

Question 21

What do we to do the data we obtain from whole genome shotgun technique and how can we use this data?

Answer 21

The sequence from the sequencing machine is reassembled to make sense

• Can use the data to do a taxonomic diversity assessment
• Can also use the data for gene prediction

Question 22

How do we enrich without amplification?(Pre extraction)

Answer 22

• Different lysis of mammalian cells
• Enrichs for intact microbial cells
• However potential bias towards gram positive bacteria

Question 23

How do we enrich without amplification?(Post extraction)

Answer 23

• Enzymatic degradation of methylated nucleotides targets mammalian DNA
• Bias against AT rich bacterial genome