Fig. 1: B. longum subsp. infantis eventually dominates the breastfed infant’s gut due to efficient utilization of human milk oligosaccharides.

a–k Longitudinal relative abundance (bars) and absolute abundance (dots connected by dashed lines) of the major bacterial taxa detected in faeces of eleven full term, vaginally delivered, antibiotics naïve, breastfed infants from the Copenhagen Infant Gut cohort, as measured by 16 S rRNA gene amplicon sequencing (bars) and qPCR (dots), respectively. Only the abundant Bifidobacterium species, B. longum subsp. longum, B. longum subsp. infantis, B. breve and B. bifidum were quantified by qPCR. Dashed line illustrate the limit of detection (LOD) of the qPCR assay. *time points where solid foods have been consumed. #time points where breastfeeding was supplemented with formula milk. $Inconsistency between qPCR and 16 S rRNA gene amplicon sequence data regarding the dominant Bifidobacterium species. l, m, n Longitudinal absolute abundance of B. longum subsp. infantis and residual HMOs in faeces across all eleven infants displayed in panel (a–k) (the last sample from CIG01 was excluded due to cessation of breastfeeding). Statistical significance of the associations between B. longum subsp. infantis and (l) Fucosyllactoses, (m) Sialyllactoses and (n) Lacto-N-(neo)tetraoses were evaluated by linear mixed models, with β denoting the subject adjusted association coefficient. Locally weighted scatterplot smoothing (LOWESS) curves were fitted to the data points.