Metagenomics

Question 1

What is a metaorganism?

Answer 1

• community of interacting biological entities
  
  • microbiomes (community of microorganisms) with thousand of species
  • tens of million genes

Question 2

16S DNA sequencing (amplicon based)

Answer 2

• DNA extraction from microbial community

- multiple copies of fragments from target gene

Question 3

Metagenomic sequencing

Answer 3

• DNA extraction from microbial community
  
  • short sequence fragments from all DNA
  • assembly
  • gene finding & annotation (classify using coverage and k-mer profiles)
  • phylogenetic binning
  • metabolic reconstruction

Question 4

16S RNA sequencing (amplicon based)

Answer 4

• ribomosal RNA
  
  • 16s gene, codes small subunit of the ribosome [prokaryotes]
• Advantages:
  
  • cheap and efficient, limited sequences necessary
  • software simple and easy to use
  • host contaminant DNA is not an issue
  • sequences are taxonomic informative
• Limits
  
  • functional processes can be determined indirectly
  • PCR primers can limit comparison
  • universal primers can miss some species

Question 5

What is a metagenome?

Answer 5

• a collective genome representative of the many organisms existing in a community

Question 6

Metagenome taxonomy?

Answer 6

• Taxonomy based on Relative Evolutionary Divergence (RED)
• Standardized bacterial taxonomy
  
  • revised phylogeny

Question 7

What is Metabolic flux balance analysis?

Answer 7

• prediction of metabolic exchanges and interactions between microbe
  
  • competition (- -)
  • parasitism (+ -)
  • amensalism (- =)
  • neutralism (= =)
  • commensalism (+ =)
  • mutualism (++)