Supplementary materials for Beneficial Microbes: Beneficial effects of Lactiplantibacillus plantarum BGPKM22 manifest only in interaction with healthy, but not with diseased human bronchial epithelial cells

It has already been recognised that lung microbiota differs in healthy and diseased lungs. In chronic obstructive pulmonary disease (COPD), a change in the structure, abundance and diversity of lung microbiota correlates with the severity of disease. But how the members of lung microbiota influence healthy and diseased lungs, as well as how they are affected by the lung health status is still largely unknown. In this study, we applied a dual RNA sequencing in order to scrutinise an early interspecies interaction between healthy and diseased human primary bronchial epithelial cells exposed to the beneficial bacteria Lactiplantibacillus plantarum BGPKM22. In healthy and diseased cells interaction with BGPKM22 led to a change in expression of 52 and 45 genes, respectively. The genes IQCN, LINC01554, KCNB1, and CDK7 indicated a specific response of human bronchial epithelial cells exposed to the BGPKM22 strain, regardless of the health status. Markedly more genes showed a change in expression in the BGPKM22 strain in interaction with healthy than with diseased cells, 486 and 101, respectively. Interaction with human bronchial epithelial cells caused a stress to bacteria, but the response of bacteria depended on the health status of the cells. The adhesion of the BGPKM22 strain was better to healthy, than to diseased cells. The fitness of the BGPKM22 strain increased only in interaction with healthy, but not with diseased cells. Remarkably, interaction with healthy, but not with diseased cells, stimulated the synthesis of exopolysaccharide layer of the strain BGPKM22. So, beneficial effects of bacteria can be diminished in interaction with diseased cells. Also, a lowered affinity of bacteria towards diseased environment can explain microbiota dysbiosis in the diseased lungs, such as lung in patients with COPD.