Fig. 2

Oligotyping of the bacterial core microbiota. Indicated are the bacterial families of the core microbiota and the corresponding oligotypes (OTs), single-nucleotide polymorphisms (SNPs), and the taxanomic assignment. The latter was derived by choosing a representative sequence of each OT, which was defined as the most abundant unique sequence belonging to an OT, and assigning the taxanomy by using BLAST (Basic Local Alignment Search Tool). A negative binomial regression (NBR) model was used for the relative abundance of the OTs and a linear mixed effect (LME) model for the binary-based analysis. The fixed effects of both models were age, season, season of birth, symptoms of lower respiratory tract infection (LRTI), and vaccine era. The random effects were intercepts for the infants and by-infant random slopes for the effect of the vaccine era. The PCV7 era (n = 355 samples) was compared to the PCV13 era (n = 408 samples), whereas the PCV7 era was used as baseline. Inputs were either the relative abundance of the OTs (abundance-based NBR model) or the binary matrix (binary-based LME model). Indicated are the Estimates and the Standard Errors. Abundance-based NBR: OT P2 (H. influenzae 2) and P3 (H. influenzae 2) significantly increased and OT C2 (C. accolens) decreased in the PCV13 era as compared to the PCV7 era (P = 0.03, P = 0.005, and P = 0.04, respectively). Binary-based LME: following OTs were significantly increased in the PCV13 era: P2 (H. influenzae 2), P3 (H. influenzae 3), P6 (H. influenzae 6), Sta1 (S. aureus 1), M2 (M. lincolnii 2), and Stre2 (S. dentisani/oralis/tigurinus/oligofermentans/infantis) (P = 0.001, P = 0.0001, P = 0.002, P = 0.04, P = 0.0004, and P = 0.003, respectively)