Residential Airborne Microbiota and Childhood LRTI (16S-v5v6 + ITS1)

CHILDHOOD LOWER RESPIRATORY TRACT INFECTIONS LINKED TO RESIDENTIAL AIRBORNE BACTERIAL AND FUNGAL MICROBIOTAResidential microbiome composition contributes to the development of lower respiratory tract infections (LRTI) among children, but the association is poorly understood. We aimed to study the relationship between the indoor bacterial and fungal microbiome and childhood LRTI in Ibadan, Nigeria.Ninety-eight children under the age of five years hospitalized with LRTI were recruited and matched by age (+/-3 months), sex, and geographical location to 99 community-based controls without LRTI. Participants homes were visited and sampled over a 14-day period for airborne house dust using electrostatic dustfall collectors (EDC). In airborne dust samples, the composition of bacterial and fungal communities was characterized by a simultaneous meta-barcoding approach using amplicons targeting the bacterial 16S rRNA gene and the internal-transcribed-spacer (ITS) region-1 of fungi using the UNITE database.House dust bacterial, but not fungal, richness (OR 1.03; 95%CI 1.01-1.05) and Shannon diversity (OR 1.92; 95%CI 1.28-3.01) were both independently associated with childhood LRTI after adjusting for other indoor environmental risk factors. Beta-diversity analysis showed that bacterial (PERMANOVA p<0.001, R2=0.036), and fungal (PERMANOVA p<0.001, R2=0.028) community composition differed significantly between homes of cases and controls. Pair-wise differential abundance analysis using both DESEq2 and MaAsLin2 consistently identified the bacterial phyla Deinococcota (Benjamini-Hochberg (BH) adjusted p-value <0.001) and Bacteriodota (BH-adjusted p-value = 0.004) to be negatively associated with LRTI. Within the fungal microbiota, phylum Ascomycota abundance (BH adjusted p-value <0.001) was observed to be directly associated with LRTI, while Basidiomycota abundance (BH adjusted p-value <0.001)) was negatively associated with LRTI.Our study suggests that early-life exposure to certain airborne bacterial and fungal communities is associated with LRTI among children under the age of five years.