Fig. 1

Core microbiome identified through species occupancy abundance diagrams. A stringent occupancy criteria A, B, C is incorporated where we clump all the samples in a single site (no site specific occupancy), and then calculate the ranking of ASVs based on their occupancy and replicate consistency within a single category. Alternatively, we calculate the occupancy and replicate consistency of these ASVs separately (site specific occupancy) for each site where for D, site represents province of residence for males; for E, site represents province of residence for female; and for F, site represents the gender. Once we have obtained the rankings depending on which criteria used, Bray–Curtis similarity is calculated for the whole dataset, and then also for only the top-ranked taxa. The contribution of the top-ranked taxa is divided by the total Bray–Curtis similarity to calculate a percent contribution of the prospective core set to beta diversity. The next-ranked taxon is added consecutively to find the point in the ranking at which adding one more taxon offers diminishing returns on explanatory value for beta diversity (G, H, I). The red line represents the stringent “Elbow approach” where the change is maximal between the left and right side of dotted red threshold in terms of first-order differences, and “Last 2% decrease” criteria where ASVs are incorporated in the core subset until there is no more than 2% decrease in beta diversity. In this study, we are only identifying core microbiome (red, green and blue points) using “Last 2% decrease” criteria. Independently, a neutral model is fitted with those ASVs that fall within the 95% confidence interval (shown in green), and those that fall outside the 95% model confidence to be inferred as deterministically assembled, i.e., non-neutral ASVs. Points above the model are selected by the (host) environment (shown in red), and points below the model are dispersal limited (shown in blue). The proportion of core ASVs belonging to different phyla are then shown with a pie chart whilst the count of neutral/non-neutral ASVs are shown with the bar plots