Molecular Methods to Study Microbiomes

Question 1

What is amplicon sequencing?

Answer 1

sequencing of one gene amplified from the DNA extracted from an environmental sample, most commonly 16S rRNA or 18S rRNA
Well suited for PCR amplification and sequencing
PCR primers hybridise to conserved regions to allow amplification of variable regions

Question 2

What is metagenomics?

Answer 2

sequencing all of the DNA extracted from an environmental sample

Question 3

What is metatranscriptomics?

Answer 3

sequencing of the genomic RNA (rRNA/mRNA) extracted from an environmental sample

Question 4

What is nano pore?

Answer 4

Strand sequencing method
Major advantage is it produces long reads so
More overlap with other reads
Easier assembly back into the correct order

Question 5

What are the 4 steps of illumina ?

Answer 5

Library preparation
Cluster generation
Sequencing
Analysis

Question 6

What is an ion torrent?

Answer 6

Sequencing performed using a semiconductor chip
In these wells, chemical information from DNA sequences is translated into digital information (base calls)
DNA sample is fragmented; each fragment is attached to a bead; fragment is copied until it covers the bead; each bead goes into a well where complementary strands will be synthesised by a polymerase
* Chip is flooded with 1 of the 4 DNA nucleotides

Question 7

What are 2 advantages of nano pore?

Answer 7

More overlap with other reads
Much easier to assemble back
into the correct order
Produces longer reads