Table 1.

Comparison of amplicon sequencing and shotgun metagenomics approaches.

Amplicon sequencing – Advantages	Metagenomics – Advantages
•Easy to use & cost-effective •Standardised approaches & mature bioinformatics •Clearly defined taxonomy •Good software for reference-free “species” delineation	•PCR free approach •Genomes of actual strains in sample can be assembled •MAGs can be the basis of or associated to GSMs •Very diverse analyses possible
Amplicon sequencing – Disadvantages	Metagenomics – Disadvantages
•Taxonomic biases in amplification •Resolution limited to genus or species level •Abundance estimates unreliable due to 16S/18S copy number variations and PCR biases •Actual gene content of species unknown •Taxonomic representation dependent on primer choice (e.g. Archaea require specific primers [13])	•Limitations imposed by sequencing depth, coverage requirements for successful assembly usually only met for dominant microbes •Complex bioinformatics & analysis •Still costly