Fig. 4

Transmission of donor strains to the patient and maternal transmission to the infant. A The proportion of donor and pre-FMT patient strains from four different species detected in the infant at birth and 3 and 6 months after birth, based on discriminative positions. B The phylogenetic tree for HG4D.0018—Eubacterium rectale containing 246 strains identified from publicly available adult and infant samples from healthy Danes. Donor and patient samples are highlighted in blue and red, respectively. The phylogenetic tree highlighted in the box is the zoom of the bigger tree. C Detection of donor strain in patient and infant samples across 120 different species based on the percentage of identical alleles between strains identified in the donor and in the patient or infant samples. Fecal samples were collected from the FMT donor and an independent (not-used) feces donor as well as from the patient during active CDI before the FMT (P-pre-FMT) and at 1 week (P1w), 8 weeks (P8w), 15 weeks (P15w), 22 weeks (P22w), 26 weeks (P26w, at term), and 50 weeks (P50w, 6 months after giving birth) after the FMT. Fecal samples were collected from the infant at birth (I0m, meconium), 3 months old (I3m), and 6 months old (I6m)