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Childhood is a critical time for respiratory health, with environmental and infectious exposures being linked to future respiratory disease and susceptibility.1 2 Respiratory microbiome research has introduced a new context for these exposures due to the presence of a pre-existing microbial community in both the upper and lower respiratory tract in healthy children.3–5 Variation in community composition has been observed in chronic lung diseases,6 7 and particular micro-organisms or combinations of organisms in infants have been associated with future disease development. Thus deviation from a healthy microbiota in early life appears to play an important role in disease development, with changes evident by 1 week of age.8 The dynamics of the infant airway microbiota and its relationship to disease development has therefore been the focus of increasing attention.
Acute respiratory infections (ARIs) are common in children under 5 years of age,9 and indications suggest that susceptibility might be, at least partly, determined by the microbiota.5 8 Toivonen and colleagues10 have conducted the largest study of the respiratory microbiome in infants to date, obtaining a nasal swab at 2 months of age from 839 infants and parent-recorded data on respiratory infections until 24 months of age to look at the incidence of ARI.
The study was conducted, described and controlled, taking into account many of the methodological issues that can arise when using the 16S …
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