Metagenomics sequencing enables the study of genome diversity of an entire microbial flora (including non-cultivable bacteria) or micro-organisms present in a given sample.

Prokaryotic metabarcoding studies are mostly based on the prokaryotic 16S ribosomal RNA gene sequencing, which is a universal region of the prokaryotic ribosomal 30S subunit. The region is 1,500 bp long and contains 9 hypervariable regions interspersed between conserved regions. Sequencing this variable regions using universal primers allows the microbial taxonomic diversity identification, the structure of prokaryotic communities and their phylogenetic classifications within a sample.

Metagenomics sequencing enables the study of genome diversity of an entire microbial flora (including non-cultivable bacteria) or organisms present in a given sample.

The eukaryotic 18S ribosomal RNA gene is an universal region of the eukaryotic ribosomal 40S subunit. The region is 1,869 bp long and contains both hypervariable regions interspersed between conserved regions. Sequencing this variable regions using universal primers allows the eukaryotic taxonomic diversity identification, the structure of eukaryotic communities and their phylogenetic classifications within a sample.

Their associated internal transcribed spacer region ITS has a higher degree of sequence variation. ITS 1 is located between 18S and 5.8S rDNA and ITS 2 between 5.8S and 28S rDNA. They are used as a universal fungi barcode marker.

While the 18S rRNA is mainly used for high resolution taxonomic studies of eukaryotes, the ITS region is used to classify fungal diversity in environmental samples. ITS1 and ITS2 have been found to be the most suitable markers for fungal phylogenetic analysis due to their variable sequences, conserved primers and multicopy nature.

Metagenomics sequencing enables the study of genome diversity of an entire microbial flora (including non-cultivable bacteria) or organisms present in a given sample.

Even if the 16S ribosomal RNA gene sequencing is mostly used in prokaryotic metabarcoding studies, it is also possible to analyze other markers or functional genes (like rpoB, groEL, gyrB, recA, hsp, nirK, nosZ genes…) to identify specific bacterial genus from a specific pathway.

Depending on your sample type, it is also possible to identify others types of organisms with others markers: COI (mitochondrial cytochrome C oxidase subunit I gene) for arthropods, fish, birds and mammals, rcbl or matK plastid markers (in chloroplast genome) for plant or seaweed studies, etc.