Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age

Abstract

The upper respiratory tract (URT) is a crucial site for host defense, as it is home to bacterial communities that both modulate host immune defense and serve as a reservoir of potential pathogens. Young children are at high risk of respiratory illness, yet the composition of their URT microbiota is not well understood. Microbial profiling of the respiratory tract has traditionally focused on culturing common respiratory pathogens, whereas recent culture-independent microbiome profiling can only report the relative abundance of bacterial populations. In the current study, we used both molecular profiling of the bacterial 16S rRNA gene and laboratory culture to examine the bacterial diversity from the oropharynx and nasopharynx of 51 healthy children with a median age of 1.1 years (range 1-4.5 years) along with 19 accompanying parents. The resulting profiles suggest that in young children the nasopharyngeal microbiota, much like the gastrointestinal tract microbiome, changes from an immature state, where it is colonized by a few dominant taxa, to a more diverse state as it matures to resemble the adult microbiota. Importantly, this difference in bacterial diversity between adults and children accompanies a change in bacterial load of three orders of magnitude. This indicates that the bacterial communities in the nasopharynx of young children have a fundamentally different structure from those in adults and suggests that maturation of this community occurs sometime during the first few years of life, a period that includes ages at which children are at the highest risk for respiratory disease.

The Microbiome

“…10 Similar results were observed in a recent study of healthy children from a Canadian city, except that a Haemophilus-dominant group was not observed. 110 The microbiota of young children (<2 years) was distinct from that of adults, while that of older children in this study (up to 4 years) was similar to adults, although too few individuals were sampled in this age group to make strong conclusions. The nasopharynx of adults was colonized with larger proportions of Firmicutes and Actinobacteria, whereas younger children had similar groups, but less diversity of their microbiome, and larger proportions of Proteobacteria, Firmicutes, and Enterococcus.…”

“…66,95 Quantitative culture also suggests that the total bacterial burden is much higher in young children and decreases after the first few years of life. 110 Interestingly, the oropharyngeal microbiota in this study was more similar between children than adults. Seasonal variations in microbiota in young children may also contribute to susceptibility to pediatric tonsillitis and ear infections.…”

Upper Respiratory Dysbiosis in Children

“…Сравнительные исследования метагенома носоглотки здоровых детей выявили некоторые отличия от взрослых индивидуумов по распре-делению удельных весов основных бактери-альных типов: Proteobacteria (64%), Firmicutes (21%), Bacteroidetes (11%), Actinobacteria (3%) и Fusobacteria (1,4%) [23]. Авторы считают, что микробиом верхних дыхательных путей изме-няется с возрастом, в том числе и за счет увели-чения гетерогенности родов [23].…”

“…Авторы считают, что микробиом верхних дыхательных путей изме-няется с возрастом, в том числе и за счет увели-чения гетерогенности родов [23].…”

Statistical models and computational algorithms for discovering relationships in microbiome data

“…Detailed information on processing is available from the original publication (Stearns et al, 2015). Briefly, the v3 region of the 16S rRNA was amplified and sequenced using the Illumina MiSeq instrument and aligned with PANDASeq.…”