Fig. 3: Differential abundance analyses indicate specific taxa are related to urban/rural living.

a Volcano plot visualizing genera enriched in rural or urban living individuals. Statistical significance between groups (rural/urban living) was assessed using linear models with genus-level abundance as outcome, adjusting for vaccination status, age and sex. Genera with p_adj < 0.05 and log₂-fold change (FC) <-1.5 or >1.5 are colored and genera with a p_adj < 1 × 10^-5 and log₂FC <-1.5 or >1.5 were annotated. The shape of the data points indicates whether these genera were previously considered to belong to VANISH (volatile and/or associated negatively with industrialized societies of humans) or BloSSUM (bloom or selected in societies of urbanization/modernization) taxa. 2 × 2 tables showing the number of BLoSSUM (b and d) or VANISH taxa (c and e) across urban- and rural-associated taxa. The number between brackets indicates the percentage of VANISH/BloSSUM/other taxa out of the total number of (non-)-rural-/urban-associated taxa. Statistical significance was assessed using Fisher’s Exact tests. f Stacked bar chart showing the genus-level taxonomic composition of each sample as relative abundances. Bar colors are based on a hierarchical color palette with hues specified by Phylum and shades specified by Genus. Samples are arranged based on Bray-Curtis dissimilarities and the plot is divided by living location. Right of the per-sample bar chart, a bar chart showing mean relative abundance for each taxon per group is shown. g Density plots showing the relative abundance distribution of Bacteroides, Succinivibrio and Treponema within rural or urban living individuals. Modes are indicated by dashed lines.