Imperial College London


Faculty of MedicineNational Heart & Lung Institute

Research Associate



+44 (0)20 7594 7974michael.cox1 Website




413Guy Scadding BuildingRoyal Brompton Campus






BibTex format

author = {Ahmed, B and Cox, MJ and Cuthbertson, L and James, PL and Cookson, WOC and Davies, JC and Moffatt, MF and Bush, A},
doi = {10.1371/journal.pone.0201156},
journal = {PLoS ONE},
title = {Comparison of the upper and lower airway microbiota in children with chronic lung diseases},
url = {},
volume = {13},
year = {2018}

RIS format (EndNote, RefMan)

AB - RationaleThe lower airway microbiota is important in normal immunological development and chronic lung diseases (CLDs). Young children cannot expectorate and because of the uncertainty whether upper airway samples reflect the lower airway microbiota, there have been few longitudinal paediatric studies to date.ObjectivesTo assess whether throat swabs (TS) and cough swabs (CS) are representative of the lower airway microbiota.MethodsTS, CS, bronchoalveolar lavage and bronchial brushings were prospectively collected from 49 children undergoing fibreoptic bronchoscopy for CLDs. Bacterial DNA was extracted and the 16S rRNA gene V4 region sequenced using the Illumina MiSeq.Results5.97 million high quality reads were obtained from 168 samples (47 TS, 37 CS, 42 BALF and 42 bronchial brushings). CS sequenced poorly. At a community level, no difference in alpha diversity (richness, evenness or Shannon Diversity Index) was seen between lower airway samples and TS (P > 0.05). Less than 6.31% of beta diversity variation related to sampling method for TS (P = 0.001). Variation between pathologies and individual patients was greater (20%, 54% respectively P ≤ 0.001) than between TS and lower airway samples. There was strong correlation in the relative abundance of genera between samples (r = 0.78, P < 0.001). Similarity between upper and lower airway samples was observed to be less for individuals where one sample type was dominated by a single organism.ConclusionsAt the community structure level, TS correlate with lower airway samples and distinguish between different CLDs. TS may be a useful sample for the study of the differences in longitudinal changes in the respiratory microbiota between different CLDs. Differences are too great however for TS to be used for clinical decision making.
AU - Ahmed,B
AU - Cox,MJ
AU - Cuthbertson,L
AU - James,PL
AU - Cookson,WOC
AU - Davies,JC
AU - Moffatt,MF
AU - Bush,A
DO - 10.1371/journal.pone.0201156
PY - 2018///
SN - 1932-6203
TI - Comparison of the upper and lower airway microbiota in children with chronic lung diseases
UR -
UR -
UR -
VL - 13
ER -