Table 3.
Summary of the potential of the tested primer pairs in-silico and in application.
| Primer set | Specificity [%] | Alpha diversity | Beta diversity | |||
|---|---|---|---|---|---|---|
| Experimental | Database coverage observed [%] | Observed α-Diversity in the dataset | Dissimilarity to metagenome | |||
| OTU 97% | OTU 99% | |||||
| ArchaeaV34 | 10.9 | 74.0 | 2.4 | 5.7 | 0.145 | |
| ArchaeaV46 | 16.4 | 79.0 | 4.1 | 7.2 | 0.290 | |
| ArchaeaV56 | 64.5 | 76.5 | 2.7 | 7.6 | 0.197 | |
| PrkV4 | Archaea | 3.2 | 88.6 | 4.9 | 8.8 | 0.213 |
| Bacteria | 96.8 | 88.2 | 41.2 | 40.5 | 0.489 | |
| BacteriaV12 | 100.0 | 60.2 | 23.9 | 21.8 | 0.453 | |
| BacteriaV35 | 99.9 | 85.6 | 32.5 | 34.7 | 0.462 | |
Specificity refers to the percentage of sequences belonging to the targeted domain in the final dataset used for the analysis. Alpha diversity includes the potential coverage as calculated by the use of the SILVA-database version 123 and the observed alpha diversity calculated for the experimental datasets. Beta diversity summarizes the mean Bray-Curtis dissimilarity between the primer pairs and the 16S rRNA gene sequence composition extracted from the shotgun metagenome.