Whole genome metagenomic sequencing or amplicon-based sequencing (16S, 18S or ITS)

Metagenomics is the study of genetic material recovered directly from environmental samples. Accurate species identification is a major challenge and can be achieved through two complementary approaches: whole genome sequencing (WG-Seq) and sequencing of 16S, 18S or ITS amplicons.

The latter is a cost-effective approach to study a large number of samples although it is limited to a specific gene, while the WG-Seq strategy can be applied to a smaller number of samples but works well for all organisms found in the same sample, prokaryotes and eukaryotes.