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Table 2 Taxonomic distance-based PERMANOVA results for differences in community composition (genus level) between host species and host environments based on shared abundance (Bray-Curtis) and shared presence (Jaccard), based on whole genome shotgun and different amplicon strategies (P values are adjusted via Hommel’s procedure)

From: Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

Distance Factor Data Classifier DF F P P Hommel R 2 adj. R2
Bray-Curtis Organism Shotgun MEGAN 10,49 6.3517 0.0001 0.0001 0.5645 0.4756
Amplicon V1 V2 one-step 10,43 7.1026 0.0001 0.0001 0.6229 0.5352
V1 V2 two-step 10,42 4.2297 0.0001 0.0001 0.5018 0.3831
V3 V4 one-step 10,43 7.8964 0.0001 0.0001 0.6474 0.5654
V3 V4 two-step 10,41 3.7917 0.0001 0.0001 0.4805 0.3538
Environment Shotgun MEGAN 1,58 5.8958 0.0001 0.0004 0.0923 0.0766
Amplicon V1 V2 one-step 1,52 6.1588 0.0001 0.0001 0.1059 0.0887
V1 V2 two-step 1,51 4.6185 0.0001 0.0001 0.0830 0.0651
V3 V4 one-step 1,52 5.4975 0.0001 0.0001 0.0956 0.0782
V3 V4 two-step 1,50 3.3349 0.0001 0.0001 0.0625 0.0438
Jaccard Organism Shotgun MEGAN 10,49 4.7458 0.0001 0.0001 0.4920 0.3883
Amplicon V1 V2 one-step 10,43 3.6867 0.0001 0.0001 0.4616 0.3364
V1 V2 two-step 10,42 2.9760 0.0001 0.0001 0.4147 0.2754
V3 V4 one-step 10,43 4.0248 0.0001 0.0001 0.4835 0.3633
V3 V4 two-step 10,41 2.9343 0.0001 0.0001 0.4171 0.2750
Environment Shotgun MEGAN 1,58 4.3872 0.0001 0.0004 0.0703 0.0543
Amplicon V1 V2 one-step 1,52 3.8714 0.0001 0.0001 0.0693 0.0514
V1 V2 two-step 1,51 3.6541 0.0001 0.0001 0.0669 0.0486
V3 V4 one-step 1,52 4.3213 0.0001 0.0001 0.0767 0.0590
V3 V4 two-step 1,50 3.6646 0.0001 0.0001 0.0683 0.0497