Fig. 3: Dynamics and stability of NGM community states and their driver species.

a,b, Stability of NGM community states (a) and levels of three species driving NGM community states (b) (week 1, based on the earlier sample of day 4 or 7) in neonates longitudinally sampled from weeks 1 to 3 (day 21, total N = 306; VD N = 140; CS N = 166). The proportion of community states that remained consistent from weeks 1 to 3 is depicted as a percentage of their initial sample size in week 1 (labelled in black). Participants starting with BB or BL on week 1 were significantly more likely to retain their community state in week 3 compared with those with EF (pairwise chi-square tests with FDR correction, P < 0.001). c–e, Persistence of the dominant abundance of driver species of NGM community states in week 1 (c,d) or week 3 (e) in the paired longitudinal samples obtained later at week 3 (c) and in infancy (d,e). f, Persistent carriage of week-1 driver species in paired longitudinal samples obtained later in infancy. Species carriage is defined using a threshold of 0.1% relative abundance. Sample sizes of participants longitudinally sampled for weeks 1 and 3 shown in a–c are: total N = 306; VD N = 26/39/75 among BB/EF/BL, respectively; CS N = 26/114/26 among BB/EF/BL, respectively; for week 1 and infancy (also referred to as the ‘infancy persistence’ group) shown in d and f: total N = 302; VD N = 27/43/90 among BB/EF/BL, respectively; CS N = 17/108/17 among BB/EF/BL, respectively; and for week 3 and infancy shown in e: total N = 146; VD N = 12/11/43 among BB/EF/BL, respectively; CS N = 17/37/26 among BB/EF/BL, respectively. Colour represents NGM community states or driver species: BB and B. breve in green; EF and E. faecalis in purple; BL and B. longum in orange. Boxplots as in Fig. 1. Statistical differences in abundance between time points (a), species (c–e) and carriage frequency (f) were determined using paired t-tests, Wilcoxon tests and chi-square tests (all two-sided) with FDR correction, respectively.