Nasopharyngeal microbiota profiles in rural Venezuelan children are associated with respiratory and gastrointestinal infections

BACKGROUND: Recent research suggests that the microbiota affects susceptibility to both respiratory (RTI) and gastrointestinal (GII) infections. Past work has mainly focused on westernised populations and the gut microbiota. In order to optimise global treatment options, it is important to characterise microbiota profiles across different niches and geographic/socioeconomic areas where RTI and GII prevalences are high. METHODS: We performed 16S sequencing of nasopharyngeal swabs from 209 Venezuelan Amerindian children aged 6 weeks - 59 months participating in a pneumococcal conjugate vaccine (PCV13) study. Using random forest models, differential abundance testing and regression analysis, we tested whether specific bacteria were associated with RTI or GII and variation in PCV13 response. RESULTS: Microbiota compositions differed between children with or without RTI (p=0.018) or GII (p=0.001). Several species were associated with absence of infections. Some of these health associated bacteria are also observed in developed regions, such as Corynebacterium (log2(FC)=3.30 for RTIs and log2(FC)=1.71 for GIIs), while others are not commonly observed in developed regions, such as Acinetobacter (log2(FC)=2.82 and log2(FC)=5.06, respectively). Klebsiella spp. presence was associated with both RTIs (log2(FC)=5.48) and GIIs (log2(FC)=7.20). The association between the respiratory microbiota and PCV13 antibody levels was limited. CONCLUSION: The nasopharyngeal microbiota of rural Venezuelan children included several bacteria thriving in tropical humid climates. Interestingly, nasopharyngeal microbiota composition not only differed in children with a RTI but also in those with a GII, which suggests a reciprocal interplay between the two environments. Knowledge of region-specific microbiota patterns enables tailoring of preventive and therapeutic approaches.