Background: Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease characterized by frequent exacerbation phenotypes independent of disease stage. Increasing evidence shows that the microbiota plays a role in disease progression and severity, but long-term and international multicenter assessment of the variations in viral and bacterial communities as drivers of exacerbations are lacking. Methods: Two-hundred severe COPD patients from Europe and North America were followed longitudinally for 3 years. We performed nucleic acid detection for 20 respiratory viruses and 16S ribosomal RNA gene sequencing to evaluate the bacterial microbiota in 1179 sputum samples collected at stable, acute exacerbation and follow-up visits. Results: Similar viral and bacterial taxa were found in patients from the USA compared to Bulgaria and Czech Republic but their microbiome diversity was significantly different (P < 0.001) and did not impact exacerbation rates. Virus infection was strongly associated with exacerbation events (P < 5E-20). Human rhinovirus (13.1%), coronavirus (5.1%) and influenza virus (3.6%) constitute the top viral pathogens in triggering exacerbation. Moraxella and Haemophilus were 5-fold and 1.6-fold more likely to be the dominating microbiota during an exacerbation event. Presence of Proteobacteria such as Pseudomonas or Staphylococcus amongst others, were associated with exacerbation events (OR > 0.17; P < 0.02) but more strongly associated with exacerbation frequency (OR > 0.39; P < 4E-10), as confirmed by longitudinal variations and biotyping of the bacterial microbiota, and suggesting a role of the microbiota in sensitizing the lung. Conclusions: This study highlights bacterial taxa in lung sensitization and viral triggers in COPD exacerbations. It provides a global overview of the diverse targets for drug development and explores new microbiome analysis methods to guide future patient management applications. Background Chronic obstructive pulmonary disease (COPD) is defined by airflow limitation but encompasses several lung diseases. This heterogeneity includes differences in clinical characteristics, source of inflammation, response to therapies and causes of exacerbation [1]. As COPD progresses, exacerbations become more frequent and more severe. Exacerbation rates reflect an independent susceptibility phenotype [2], which could be mediated by host factors [3], environmental factors [4], viral infections and/or the bacterial microbiome [5, 6]. Infections are predominant causes of COPD exacerbations, with approximately half reported to be caused by bacterial infections including non typeable Haemophilus influenzae (NTHi), Moraxella catarrhalis, Streptococcus pneumoniae, or Pseudomonas aeruginosa, and the other half by viral infections, primarily human Rhinovirus (HRV), but also Influenza virus, Coronavirus and