Figure 1. Data and workflow overview.

(A) Oral-fecal transmission scores were calculated from salivary and fecal microbial SNV profiles. (B) Cohort and dataset overview. For longitudinal cohorts (DE-CTR, CN-RA and LU-T1D), both the total number of samples and the number of individuals are shown, as well as the number of individuals considered in time-series analyses. (C) Salivary and fecal microbial loads allow the calculation of physiologically expected levels of ‘passive’ microbial transmission (i.e., by ingestion, without growth). (D) The longitudinal coupling of microbial SNVs between salivary and fecal samples was used to infer transmission directionality and oral-fecal transmission rates (see Materials and methods).

Figure 1—figure supplement 1. Enrichment of oral species in the gut.

Relative to physiologically expected levels of ‘passive’ transmission (see Figure 1C), all tested species with paired observations (in saliva and stool of the same individual) showed a fecal enrichment by several orders of magnitude. The fecal enrichment (x axis) is shown on a log2 scale, so values approximate the effective number of cell divisions (without cell deaths) necessary to account for observed fecal levels based on matched oral samples. The left plot shows enrichment purely based on relative salivary and fecal abundance. On the right, the average oral and fecal depths of uniquely mapping reads is used as a reference, normalised by genome size.