Fig. 1

Longitudinal shotgun metagenomics of the nasal microbiome and Staphylococcus aureus carriage in 36 mother-infant pairs. Nasal swabs were taken from 36 mother-infant pairs at birth and monthly for the first year after birth. Culture testing for S. aureus was performed on all samples to assess carriage. Culture results, red for S. aureus positive and blue for S. aureus negative, are shown as the icon fill color. A subset of 208 samples was profiled with shotgun metagenomic sequencing and retained after quality control (the “Methods” section) for further analyses. Sequencing is shown as performed only for samples that passed QC procedures. Square icons indicate samples where sequencing was performed, and the outline color, red for S. aureus positive and blue for S. aureus negative, indicates whether S. aureus was identified by sequencing. Infants displayed three unique patterns of S. aureus carriage highlighted here and used for sequenced sample prioritization: “Early” (acquisition by month one), “Late” (acquisition after month one, also typically transient), and “Never” (no acquisition during the study period)