Lung microbiota assessment in dogs with bronchomalacia
Evaluation du microbiote pulmonaire chez des chiens atteints de bronchomalacie

The lungs are now recognized to harbor a low biomass and a diversemicrobial community which is altered in lung diseases. However,whether lung microbiota (LM) alteration is a cause or a consequenceof lung pathologies is still a subject for debate. Bronchomalacia (BM),that is defined as a regional to diffuse dynamic airway collapse ofbronchi causing airflow limitation, has been inconsistently associatedwith bacterial infection and it is unclear whether bacteria contributeto the disease pathogenesis and progression or not.In this study, we assessed the LM in dogs with reported bronchomala-cia at bronchoscopy (BM-dogs; n = 25) in comparison with healthydogs (H-dogs; n = 37). Dogs with primary or secondary bacterial andparasitic infection were excluded based on Baerman test and bronch-oalveolar lavage fluid (BALF) cytology, culture and Bordetella bronchi-septica, Mycoplasma cynos, Angiostrongylus vasorum and Crenosomavulpis qPCRs; as were dogs receiving antimicrobial drug in the weekbefore sampling. LM was characterized using DNA extracted fromnaïve BALF subjected to 16S rRNA amplicon sequencing. Bacterialload was measured in duplicate using qPCR targeting the V2-V3 region of the 16S rRNA gene. Bacterial composition, load and ecologi-cal parameters were calculated and compared between BM-dogs andH-dogs using MOTHUR v3, STAMP v2.1.3, XLSTAT v4.1 and R veganpackage v 3.6.2.Among the 25 BM-dogs, based on BALF analysis, 3 had concomitanteosinophilic and 15 neutrophilic infiltrations, while others had a nor-mal analysis. No significant differences between bacterial loads(P = 0.075) were found between groups. In BM-dogs, the LM wasdominated by Conchiformibius, Streptococcus, Staphylococcus, Chryseo-bacterium and Serratia genera and some genera of the Pasteurellaceaefamily. Linear discriminant analysis effect size revealed that the LM inBM-dogs was enriched in 19 genera present in lower proportion inH-dogs and commonly found in upper airways or digestive microbiota.Permutational multivariate analysis of variance detected a significantdifference in LM between BM-dogs and H-dogs (P = 0.001). Finally,decreased bacterial alpha-diversity (median and interquartile range of8.03 (2.81 – 10.72) vs. 9.14 (5.51 – 15.08); P = 0.037) and evenness(0.06 (0.03 – 0.10) versus 0.09 (0.06 – 0.18); P = 0.011) were observedin BM-dogs compared with H-dogs.This comparative study provides evidence for alteration of the LM inBM-dogs. Because of the increase in genera from upper airways anddigestive microbiota, altered LM might be secondary to an increase inthe micro-aspiration rate which is suggested in that disease. Furtherstudies are warranted to determine if such bacteria have a role in dis-ease onset or progression.