Fig. 3

Non-metric multidimensional scaling of Bray-Curtis distances based on genus abundance profiles derived from the different 16S rRNA gene amplicon methods (V1 V2/V3 V4, one-step/two-step) and shotgun-derived genus profiles highlighting a host differences and b differences between host environments (terrestrial/aquatic; see Table 2). Non-metric multidimensional scaling of Jaccard distances based on genus presence/absence profiles derived from the different 16S rRNA gene amplicon methods and shotgun-derived genus profiles highlighting c host taxon differences and d differences between host environments (terrestrial/aquatic; see Table 2). Both panels show a separation based on host organisms and environments and not by method. Large symbols indicate the centroid of the respective host groups and vertical lines help to determine their position in space. Sample sizes are equal to Fig. 2 (see also Additional file 2: Table S1)