Metagenome

Question 1

Genomics

Answer 1

Whole cell gene content

Question 2

Transcriptomics

Answer 2

Whole-cell gene expression

Question 3

Proteomics

Answer 3

Whole cell protein content

Question 4

Metabolomics

Answer 4

Whole-cell metabolite content

Question 5

Metagenomics

Answer 5

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

Question 6

Microbiome

Answer 6

“a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity”

Question 7

Microbiota

Answer 7

• ecological community of commensal and pathogenic microorganisms. Includes bacteria, archaea, protists, fungi and viruses

Question 8

Human microbiome

Answer 8

Gut 
Skin
Oral
Vaginal
unique to each individual

Question 9

Prokaryotic ribosome

Answer 9

50S subunit - 5s and 23S

30S subunit - 16s

Question 10

Eukaryotic ribosome

Answer 10

60s subunit - 5s and 28s

40s subunit - 18s

Question 11

Workflow

Answer 11

Sample collection, DNA extraction, 16S PCR amplification, sequencing, analysis

Question 12

WGS shotgun

Answer 12

The assembly then either taxonomic diversity,
or
Gene prediction, pathways

Question 13

Pre extraction

Answer 13

• Differential lysis of mammalian cells
• Enrichs for intact microbial cells
• Potential bias towards gram-positive bacteria

Question 14

Post extraction

Answer 14

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

Question 15

How to enrich without amplification?

Answer 15

Pre-extraction and Post -extraction

Question 16

Metagenomics applications

Answer 16

• Environmental
• Animal
• Clinical diagnostics

Question 17

Environmental microbiomes

Answer 17

• 1.045 billion base pairs sequenced
• elucidate the gene content, diversity, and relative abundance of the organisms
• estimated to derive from at least 1800 genomic species
• identified 148 previously unknown bacterial phylotypes
• identified over 1.2 million previously unknown genes

Question 18

Animal microbiome

Answer 18

• First of four chambers of cow’s stomach
• Contains a mix of bacteria and other organisms which ferment complex carbohydrates to produce short chain fatty acids
• Generated 6.5 terabases short and long read sequence from 283 ruminant cattle
• Assembled 4,941 genomes including 3 whole-chromosome assemblies of rumen bacteria

Question 19

Diagnostic microbiology

Answer 19

• Gold standard is to culture isolate and then identify using matrix assisted laser desorption/ionization (MALDI)
• Many organisms cannot be cultured
• Can identify hard to culture organisms in patient samples e.g. neuroleptospirosis in a 14-year-old critically ill boy with meningoencephalitis
• Identify antibiotic resistance repertoires directly from clinical samples
• Potential to develop diagnostics based on differences in microbiomes

Question 20

Public

Answer 20

• Infection control and outbreak management

* Surveillance of antimicrobial resistance in the food supply

Question 21

Technological approaches

Answer 21

Targeted 16S PCR amplification
•	Assess taxanomic diversity in sample
•	Biased, only bacteria
Whole genome shotgun sequencing
•	Assess taxanomic diversity in sample
•	Assess composite gene functions in sample
•	Unbiased, all micro-organisms