Lung microbiota compositions differ between influenza, COVID-19 and bacteria-related acute respiratory distress syndrome

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Background: ARDS is responsible for 400,000 deaths per year worldwide. Lung microbiota is involved in chronic inflammatory pulmonary diseases and could play a role in ARDS. Failure in the development of new therapeutics in ARDS is partly due to its high heterogeneity, including various types of aetiologies. The aim of this study is to compare lung microbiota compositions between ARDS aetiologies. Patients and Methods: 24 COVID-19-, 18 consecutive influenza-, and 11 bacteria-related ARDS patients had endotracheal aspirate collected at admission. After DNA extraction, V3-V4 and ITS2 regions were amplified by PCR, sequencing performed on MiSeq sequencer (Illumina®) and data analysed using DADA2 pipeline. Results: Bacteria-related ARDS patients had lower lung bacteriobiota α-diversity compared with COVID-19-related ARDS patients (p=0.042 and p=0.029 for Shannon and Simpson indices, respectively). Influenza-related ARDS patients had higher lung mycobiota α-diversity compared with COVID-19-related ARDS ones (p=0.01 and 0.05 for Shannon and Simpson indices, respectively). Lung bacteriobiota composition was dissimilar between COVID-19-related and both influenza- and bacteria-related ARDS patients (β-diversity, Permanova p=0.05). Lung mycobiota composition was dissimilar between influenza-related and both COVID-19- and bacteria-related ARDS patients (p=0.01 and p=0.04, respectively). Conclusions: Compositions of both lung bacteriobiota and lung mycobiota are different between influenza-, COVID-19- and bacteria-related ARDS. Future studies investigating the role of lung microbiota in ARDS pathophysiology should take aetiology into account.

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