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Background  Data on the lung microbiome in HIV-infected children is limited. The current study sought to determine the lung microbiome in HIV-associated bronchiectasis and to assess its association with pulmonary exacerbations.    Methods  A cross-sectional pilot study of 22 children (68% male; mean age 10.8 years) with HIV-associated bronchiectasis and a control group of 5 children with cystic fibrosis (CF). Thirty-one samples were collected, with 11 during exacerbations. Sputum samples were processed with 16S rRNA pyrosequencing.    Results  The average number of operational taxonomy units (OTUs) was 298 ± 67 vs. 434 ± 90, for HIV-bronchiectasis and CF, respectively. The relative abundance of  Proteobacteria  was higher in HIV-bronchiectasis (72.3%), with only 22.2%  Firmicutes . There was no correlation between lung functions (FEV 1 % and FEF 25/75 %) and bacterial community ( r  = 0.154;  p  = 0.470 and  r  = 0.178;  p  = 0.403), respectively. Bacterial assemblage of exacerbation and non-exacerbation samples in HIV-bronchiectasis was not significantly different (ANOSIM, R HIV-bronchiectasis  = 0.08;  p  = 0.14 and R CF  = 0.08,  p  = 0.50). Higher within-community heterogeneity and lower evenness was associated with CF (Shannon-Weiner (H′) = 5.39 ± 0.38 and Pielou’s evenness (J) 0.79 ± 0.10 vs. HIV-bronchiectasis (Shannon-Weiner (H′) = 4.45 ± 0.49 and Pielou’s (J) 0.89 ± 0.03.    Conclusion  The microbiome in children with HIV-associated bronchiectasis seems to be less rich, diverse and heterogeneous with predominance of  Proteobacteria  when compared to cystic fibrosis.

The lung microbiome in children with HIV-bronchiectasis: a cross-sectional pilot study