Briefly describe the differences between the amplicon (16S rRNA gene) and shotgun metagenomics approaches for characterising microbial communities (2 marks).
Discuss the benefits and drawbacks of both amplicon and shotgun metagenomic approaches for studying microbial communities (4 marks).
Compare and contrast an OTU (Operational Taxonomic Unit) from an ASV (Amplicon Sequence Variant) and describe the benefits of using ASVs over OTUs (2 marks).
In the context of 16S amplicon analysis, what is a ‘feature’ (1 mark)?
What is rarefaction? Why might it be important in microbial community analysis (2 marks)?
How should one choose a rarefaction depth (1 mark)?
What is alpha- and beta-diversity? What are some commonly used metrics used for both (2 marks)?
What is a statistical test that can be used to identify significant differences in beta-diversity between groups? What is ‘dispersion’ in the context of this test, and why might it be important to control for it (2 marks)?