amplicon sequencing or metagenomics?

Question

[linnet.roque6]

amplicon sequencing or metagenomics?

What is the difference between the two main methods for studying the microbiome: amplicon sequencing and metagenomic sequencing. What kind of information does each of them provide? What are its advantages, disadvantages and biases?

[microfuge]

One way I approach this is the way NCBI SRA characterizes these terms. Amplicon is classified as strategy in SRA and metagenomic is described as source.

• Strategy in SRA or as described here https://www.ebi.ac.uk/ena/submit/reads-library-strategy "Amplicon sequencing: An assay in which a DNA or RNA input molecule amplified by PCR is sequenced."

• metagenomic is classified as a source i.ie pertaining to the type of sample.

Overall amplicon sequencing is a type of method/assay which not_only but can_also be applied to a sample of type metagenomic.

Answer 1

[h.mon]

I believe what you want to ask is what are the differences and similarities between amplicon sequencing metagenomics vs shotgun metagenomics. There is a good number of papers and posts attempting to answer this question, you can start reading the posts (shorter and simpler):

16S Sequencing vs Shotgun Metagenomic Sequencing

16s vs shotgun

16S sequencing vs. Shotgun metagenomics: Which one to use when it comes to microbiome studies

Metagenomic Shotgun Sequencing

Then move on to some papers, which will provide a more complete view of both techniques, at the expense of being longer, more complex, and harder to read:

Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms