Summary of the respiratory microbiome in health and disease
| Respiratory microbiome | Micobiome | Virome | Mycobiome |
| In health | Bacteroidetes Proteobacteria Firmicutes Genus: Streptococcus, Prevotella, Veillonella | Anelloviridae Human herpes viruses Human papillomavirus | Ceriporia lacerate Saccharomyces cerevisiae Penicillium brevicompactum |
| Asthma | Proteobacteria Streptococcus Reduction in Prevotella and Veillonella | Cytomegalovirus Epstein–Barr virus | Psathyrella candolleana Termitomyces clypeatus Grifola sordulenta Malassezia pachydermatis |
| COPD | Proteobacteria Haemophilus Streptococcus | Picornaviruses Influenza Parainfluenza Respiratory syncytial viruses Adenoviruses | Alternaria Aspergillus Cladosporium Cryptococcus Mycosphaerella Penicillium Trametes Wickerhamomyces |
| Bronchiectasis | Pseudomonas Haemophilus Veillonella Prevotella | Siphoviridae Caudovirales Myoviridae Phycodnaviridae | Aspergillus Cryptococcus Clavispora |
| CF | Pseudomonas Staphylococcus Stenotrophomonas Burkholderia | Influenza Respiratory syncytial virus | Aspergillus Candida |
| IPF | Haemophilus Neisseria Streptococcus | Influenza A Human herpesvirus | Not yet established |
| Lung cancer | Veillonella Streptococcus Prevotella | Not yet established | Not yet established |