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Background  Bacterial colonization of the upper airways is a prerequisite for subsequent invasive disease. With the introduction of the 7- and 13-valent pneumococcal conjugate vaccines (PCV7 and PCV13), changes in pneumococcal upper airway colonization have been described. It is, however, less evident whether the vaccines lead to compositional changes of the upper airway microbiota. Here, we performed a case–control study using samples from a longitudinal infant cohort from Switzerland. We compared pneumococcal carriage and the nasal microbiota within the first year of life of healthy infants vaccinated with either PCV7 ( n  = 20, born in 2010) or PCV13 ( n  = 21, born between 2011 and 2013). Nasal swabs were collected every second week ( n  = 763 in total). Pneumococcal carriage was analyzed by quantitative PCR of the pneumococcal-specific  lytA  gene. Analysis of the bacterial core microbiota was performed based on  16S rRNA  sequencing and subsequent oligotyping. We exclusively performed oligotyping of the core microbiota members, which were defined as the five most abundant bacterial families ( Moraxellaceae ,  Streptococcaceae ,  Staphylococcaceae ,  Corynebacteriaceae , and  Pasteurellaceae ). Linear mixed effect (LME) and negative binomial regression models were used for statistical analyses.    Results  We found a higher number of samples positive for pneumococcal carriage in PCV7- compared to PCV13-vaccinated infants (LME model;  P  = 0.01). In contrast, infants vaccinated in the PCV13 era had an increased alpha diversity as measured by the richness and the Shannon Diversity Index (LME model;  P  = 0.003 and  P  = 0.01, respectively). Accordingly, the PCV13 era was associated with clusters of a higher diversity than PCV7-associated clusters. Furthermore, infants vaccinated with PCV13 had a higher binary-based within-subject microbiota similarity, as well as a decreased Jensen–Shannon distance over time as compared to PCV7-vaccinated infants, indicating a higher microbiota stability in the PCV13 era (LME model and  t  test;  P  = 0.06 and  P  = 0.03, respectively).    Conclusions  We hypothesize that the higher diversity and stability of the upper airway microbiota in the PCV13 era is the result of the lower pneumococcal carriage rate. This seems to indicate that the nasal bacterial microbiota of infants has changed in recent years as compared to the beginning of this study.    Electronic supplementary material  The online version of this article (doi:10.1186/s40168-017-0302-6) contains supplementary material, which is available to authorized users.

microbiome

Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case–control study