The Metagenome

Question 1

What is genomics?

Answer 1

study of the whole human genome

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

The study of whole cell metabolite content

Question 5

What is metagenomics?

Answer 5

study of genetic material recovered directly from environmental or biological systems/ compartments

Question 6

What is the Microbiome?

Answer 6

a microbial community occupying a well defined habitat

Question 7

What is a microbiota?

Answer 7

ecological community of commensal and pathogenic microorganisms

Question 8

How many variable regions is the 16S ribosome divided into?

Answer 8

9

Question 9

What is the method for 16s targeted PCR amplification

Answer 9

Sample collection, DNA extraction, 16s PCR amplification, sequencing and analysis

Question 10

What do you choose the variable region based on?

Answer 10

the phylogenetic signal and Amplicon length

Question 11

What does your choice of region determine?

Answer 11

Resolution

Question 12

How do you mitigate contamination?

Answer 12

Randomising samples, Note batch numbers of reagents and sequencing negative controls

Question 13

Why is targeted 16S PCR amplification biased?

Answer 13

Because it only affects bacteria

Question 14

What is targeted 16S PCR amplification used for?

Answer 14

To assess taxonomic diversity in the sample

Question 15

Is whole genome shotgun sequencing biased?

Answer 15

No

Question 16

How do you analyse samples in whole genome shotgun sequencing?

Answer 16

Either build an assembly of the sequences or bin them (sort them into groups based on similarity)

Question 17

What is whole genome shotgun sequencing used to do?

Answer 17

Assess composite gene functions in the sample

Question 18

What are some issues with whole genome shotgun sequencing?

Answer 18

Host cells often in excess in the sample, no amplification step to enrich for bacterial DNA and Sample dependant

Question 19

How can you enrich without amplification?

Answer 19

Pre or post extraction

Question 20

How do you enrich the sample before whole genome shotgun sequencing?

Answer 20

differential lysis of Mammalian Cells, Enrich for intact microbial cells

Question 21

What does pre-extraction enriching DNA in whole genome shotgun workflow cause?

Answer 21

potential bias towards gram-positive bacteria

Question 22

How do you enrich the sample after whole genome shotgun sequencing?

Answer 22

Enzymatic degredation of methylated nucleotides that targets mammalian DNA

Question 23

What does pre-extraction enriching DNA in whole genome shotgun workflow cause?

Answer 23

Bias against AT rich bacterial genomes

Question 24

What are the four metagenomic applications?

Answer 24

Environmental, animal, clinical diagnostics and public health

Question 25

What is metagenomics used to find out in the environment?

Answer 25

The diversity and relative abundance of organisms

Question 26

What does MALDI stand for?

Answer 26

Matrix assisted laser desorption/ionisation

Question 27

Why can’t we always use MALDI?

Answer 27

Lots of things cant be cultured

Question 28

What is MALDI used to do?

Answer 28

Identifying hard to culture organisms in patient samples and antibiotic resistant repertoires from clinical samples

Question 29

How are metagenomics used in public health?

Answer 29

Infection control and outbreak management and surveillance of antimicrobial resistance in the food supply