Fig. 3
Transmission of functions by distinct microbial strains. a Taxa which were detected in gut microbiomes of mothers (diagonal line) and neonates (on postnatal day 3 (below the line) and/or day 5 (above the line), indicated by shading) in vaginal delivery (VD), caesarean section delivery (CSD) and CSD with small for gestational age (SGA) status (CSD + SGA) groups. The level of evidence of transmission is indicated by the shading colour, with darker shading for stronger evidence. A taxon without link describes a taxon that was found in the maternal samples, but not shared between mother and neonate. P based on PhyloPhlAn; S based on StrainPhlAn. Neonates C115 and C116 are twins. b Inter-population fixation indices (FST) comparing maternal (M) and neonatal (days 1, 3, 5) faecal samples. Phylum-level colour key is given in a. Encircled symbols highlight strains that are shared with the respective mother. c Intra-population diversity index (π). Circles and triangles represent maternal and neonatal faecal samples, respectively. d, e Relative abundance of the metagenomic operational taxonomic units (mOTU) belonging to Bacteroides dorei/vulgatus (d) and Staphylococcus epidermidis (e) in maternal faecal (M), maternal vaginal (MV) and neonatal faecal (days 1, 3, 5) samples from VD, CSD and CSD + SGA groups; *false discovery rate (FDR)-adjusted P < 0.05 in Wilcoxon rank-sum test for two-group comparisons; boxplots: centre line – median, bounds – first and third quartile, whiskers <= 1.5 x interquartile range. f, g Strain-level phylogenetic trees of B. vulgatus (f) and S. epidermidis (g); black bordered and borderless symbols represent genome reconstructions and read-based strain-level identity, respectively; genome reconstructions marked with a red asterisk are represented in h and i. h, i Genome reconstructions of B. vulgatus from neonatal faeces (C117; VD; day 3; bin P2.2.1) (h) and S. epidermidis from neonatal faeces (C112; CSD; day 5; bin P2.2) (i). Circular tracks represent: assembled contigs (1), single-nucleotide variants (black), shared between mother and neonate (red) (2), positions of strain markers (3), abundance fold-changes between VD and CSD (±SGA) neonates for functionally annotated genes in forward (4) and reverse directions (5); long spokes highlight genes affiliated with enriched pathways as depicted and colour-coded in Fig. 2a
