A cohort of people with asthma – both children and adults – from two geographical areas with distinct climatic characteristics – Greece and Poland – was established and followed up closely. Healthy volunteers were also followed in parallel, as controls. Disease activity was documented at regular visits, as well as with a prospective electronic monitoring system, while upper respiratory and other samples were obtained at different time points, spanning from hours, up to a whole year. Next generation sequencing (NGS) and an in-house developed analytical pipeline were used to describe and understand the differences of respiratory metagenomes between the healthy and asthmatic individuals, as well as fluctuations in time. The metagenomes included the complete bacterial, viral, archeal and eukaryote microbiome; human sequences were removed. We have identified location, age and gender as major sources of respiratory microbiome compositional variability. Furthermore, it was confirmed that the respiratory microbiomes are ‘personal’ i.e. differences are larger between individuals than between different time points within an individual, similarly to what has been described in the gut and other body sites and expanding this concept for the complete metagenome. Highly interesting findings resulted from the study of metagenome variability in time. Microbiomes of people with asthma were more diverse, but also less stable in time, in comparison to healthy controls. Within different microbiome clusters, defined mostly by location and age, asthma microbiomes were always more different between themselves in contrast to healthy metagenomes that were more alike, following the “Anna Karenina” principle of dysbiotic microbiomes. To further support the biological relevance of this finding, within the asthmatic population, dysbiosis was associated with disease severity and activity. Phages were affected in only some subpopulations. In a theoretical model, we discovered that the balance between lytic and lysogenic phages may be able to affect the stability of the microbiome. In parallel to the NGS analyses, innate immune and epithelial responses to phages were studied both in-vitro and ex-vivo. It was thus established that phages have no direct effect on human epithelium, however they are capable of protecting from bacterially induced epithelial inflammation. In addition, they are capable of differentially activating subclasses of innate lymphoid cells.
Finally, the CURE centres in Georgia, in collaboration with the other partners, focused on isolating and characterising an expanded collection of phages against bacteria potentially relevant in asthma, establishing a biobank of more than 70 phages.
