Both amplicon and metagenome sequencing have their own advantages and disadvantages.

Your method of choice should be selected based on your research aim. Generally, the successful outcome of a project depends on several factors such as community composition, the abundance of other close species or strains and sequencing coverage depth.

Amplicon sequencing offers suitable assessment of taxonomic composition and diversity of a large number of samples. As you have more power to detect subtle differences between microbial communities, the method is beneficial for statistical comparisons, such as for case control studies or for sampling environments over time.

Metagenomic sequencing is free of taxon-specific PCR biases due to the primer sets used. This enables more accurate representations of the analysed microbiota and more dependable estimations of species abundance levels. Metagenomics analysis can also help elucidate both taxonomic as well as functional characteristics of a given sample.