Upper airways microbiota profiling in a case/control study between wheezing and healthy children from the tropics of Ecuador

Background: The relationship between living in rural areas and the acquisition of protective environmental factors against the development of asthma and atopy gave rise to the hygiene hypothesis. Between the environmental factors attributed to asthma, particular airways microbiota patterns have been encountered in adult asthmatics using molecular independent techniques (Hilty et al., 2010) and in children using conventional culture methods (Bisgaard et al., 2007). Here a retrospective time series study has been performed using samples from infants at different ages to study the microbiome variations in a population with very low antibiotic use history and no corticosteroid usage. Methods: Pyrosequencing of amplicons of the bacterial 16S rRNA gene was performed from oropharyngeal samples from 134 infants with episodic wheezing versus 200 healthy infants (total of 334 infants examined) sampled at different ages (7, 12 and 24 months). Bioinformatic analyses were conducted using QIIME 1.7 software and Phyloseq package on R. Additionally a new culture-independent pyrosequencing approach using the map gene was successfully developed to enable discrimination of streptococci at species level. Results: Significant abundance differences between infants with wheezing history and healthy controls were found for the Fusobacteria, Proteobacteria and Actinobacteria phyla. At genera level a significant increase in potential pathogenic bacteria (Neisseriacea, Haemophilus, Staphylococcus) was found in wheezers whilst a higher prevalence of Veillonella spp. was seen in controls. In addition, using map gene pyrosequencing, Streptococcus salivarious was found to be statistically significantly related with wheezing syndrome whilst Streptococcus mitis was more prevalent in controls. When age was considered differences were found in the microbiota displayed as species numbers increased (alpha diversity). Conclusions: The respiratory microbiota is different at phyla, genera and Operational Taxonomic Unit levels when comparing between wheezing and healthy children. A progressive more complex respiratory microbial community develops with age.Open Acces