Supplementary Material for: Airway microbiome composition and co-occurrence network are associated with inflammatory phenotypes of asthma

Introduction
The composition and co-occurrence network of the airway microbiome might influence the asthma inflammatory phenotype. Airway microbiota change with asthma phenotypes, and the structure of the bacterial community in the airway might differ between different asthma inflammatory phenotypes and may also influence therapy results. Identifying airway microbiota can help investigate the role that microbiota plays in the asthma inflammatory process.
Methods
Induced sputum from 55 subjects and 12 healthy subjects from Beijing, China, was collected and analyzed for the bacterial microbiota. Microbiome diversity, composition, co-occurrence networks, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were predicted and compared between the study groups.
Results
Significant differences in the sputum microbiome composition, co-occurrence network, and predicted functional pathways were observed between the two inflammatory phenotypes. Asthmatics in the low FeNO group exhibited lower α-diversity in the sputum microbiota and had higher abundance of the phylum Proteobacteria compared with that of the high FeNO group. Compared with the low FeNO group, the network in the high FeNO group was more “closed” and “connected”, and an alteration in the abundance of keystone species T. socranskii was found. Significantly different predicted metabolic subfunctions including nucleotide metabolism, lipid metabolism, energy metabolism, replication and repair, drug resistance antimicrobial and carbohydrate metabolism between the two studied phenotypes were also observed.
Conclusion
Our findings confirm that the airway microbiota is associated with the asthma inflammation process. The differences in the airway microbiome composition and co-occurrence network may affect distinct asthma inflammatory phenotypes. Our findings suggest the possibility that more targeted therapies could be applied based on the airway bacterial genera.