The present invention relates to methods for predicting the risk of developing pulmonary colonization/infection by P. aeruginosa. The inventors analyzed the respiratory tract microbiota from 65 patients sputum samples and compared microbiota data. The inventors found that patients that will remain uninfected from P. aeruginosa exhibited 3-fold higher abundance of Porphyromonas compared to the other groups. In particular, the present invention relates to a method for predicting the risk of developing pulmonary colonization/infection by P. aeruginosa in a subject suffering from cystic fibrosis (CF) comprising measuring the abundance of Porphyromonas genus bacteria in a biological sample obtained from said subject.