April 3

Question 1

What is amplicon sequencing vs metagenomics?

Answer 1

Amplicon seq is diversity based on genetic info of specific loci. Metagenomics is function of genes

Question 2

What is used to classify bacteria?

Answer 2

16S rRNA, it is highly conserved. Look at conserved regions to specifiy species of bactera

Question 3

What are operational taxonomic units (OTU)

Answer 3

It is using small rRNA and % similarity threshold to determine if microbes are in the same group or not. Thresholds are not often reliable

Question 4

How is amplicon sequencing done?

Answer 4

It is when have primers target conserved regions, then add sequence adaptors and index to barcode DNA.

Question 5

What are issues with taking sample and finding out what composition of bacteria make up sample?

Answer 5

Could contaminate sample, then storage conditions before sequencing can alter levels. Then extraction bias, some DNA preferred over others. Then also have primer bias, so some primers bind better, so get more PCR product of them

Question 6

What is a PCR jackpot?

Answer 6

It is error that happens with polymerase, if earlier, then error propogated and is worse

Question 7

What is the metagenome?

Answer 7

It is all genetic info in the sample, not just the organism. So if did human, would get our genes, but also gut microbiota and other genes

Question 8

Wha is binning in metagenomics

Answer 8

It is grouping contigs, and assigning them to genome of origin as in metagenomics we look at all specie(s) genetic info in sample