Objective To explore the characteristics of respiratory tract microbiota and its clinical significance in children with protracted bacterial bronchitis (PBB).Methods Twelve children aged from 5 months to 2 years old with PBB (PBB group) and 12 age-matched tracheomalacia(TM) children (TM group) were included in this study,who were admitted into the Respiratory Department of Shenzhen Children's Hospital.Their bronchoalveolar lavage fluid (BALF) samples were collected.Bacterial DNA was extracted from their BALF samples and the 16S rRNA V3-V4 region was sequenced by using Illumina MiSeq TMII system,and the findings were analyzed by bioinformatics methods.Results Principal component analysis revealed the difference in microbiota composition between 2 groups.Compared with TM group,PBB group exhibited lower microbial diversity:the Shannon indices were also 1.683 ± 0.703 and 2.324 ± 0.142 for PBB group and TM group respectively,and the differences were also significant(all P ＜ 0.05),and the Simpson indices were 0.416 ± 0.216 and 0.191 ± 0.025 for PBB group and TM group,respectively,and the differences were also significant (all P ＜ 0.05).The relative abundance of Actinobacteria was significantly lower in PBB group [(0.215 ± 0.228) ％] than that in TM group [(3.028 ± 0.592) ％] (P ＜ 0.01).The proportions of beneficial genera obviously decreased in PBB group,including Lactococcus [(13.464±7.319)％ in PBB group,and (44.784 ± 5.020)％ in TM group,P ＜0.01],Lactobacillus [(0.153 ±0.076)％ in PBB group,and (0.313 ±0.060)％ in TM group,P＜0.01],andArthrobacter [(0.024 ±0.018)％ in PBB group,and (2.970 ±0.584)％ in TM group,P＜0.01].On the other hand,the relative abundances of opportunistic pathogenic genera increased in PBB group significantly,including Haemophilus [(14.319 ± 29.532) ％ in PBB group,and (0.047 ± 0.127) ％ in TM group,P ＜ 0.Ol],Pseudomonas [(10.406 ± 25.439) ％ in PBB group,and (7.228 ± 0.948) ％ in TM group,P ＜ 0.01],and Escherichia [(0.432 ±0.441)％ in PBB group,and (0.055 ±0.035)％ in TM group,P ＜0.01].Conclusion These findings confirmed the existence of respiratory tract microbiotia dysbiosis in PBB,which probably was one of the pathogenetic mechanisms for PBB.