Fig. 2: Species-specific operational definition of a transmitted strain.

Strain boundaries should be identified on a species-by-species basis and based on a comparison of (phylo-) genetic distance distributions of strains detected in longitudinal samples from the same individual (same strain; green distribution) to those between unrelated individuals who have never been in contact (different strain; orange distribution). While some strain replacement events might occur within an individual’s microbiome even without any intervention (e.g., antibiotic treatment, diet changes), these are a limited minority in samples taken less than six months apart³⁶. Once such thresholds are established, the origin of a strain in the infant can be inferred (maternal: pink distribution; from an unknown source: gray distribution). Sampling of more environments, individuals, and body sites thus adds to the “from where/who” and “to where/who” dimensions, while the collection of samples from multiple time points allows to establish “when” the transmission event took place.