Table 1.

Summary of studies illustrating changes in the respiratory microbiome that occur during chronic lung disease

Disease		Taxonomic changes at the genus level 1	Sample type	Cohort size	[Ref.]
Asthma	Increased abundance of Haemophilus		Bronchoscopy	11	16
	Increased abundance of Haemophilus, Neisseria, Fusobacterium and Porphyromonas		Bronchoscopy	42	29
	Increased abundance of Streptococcus		Nasopharyngeal	234	30
COPD	Increased abundance of Lactobacillus		Lung tissue	24	17
	Increased abundance of Fusobacteria, Leptotrichia and Fusobacterium		BAL	32	31
CF	Increased abundance of Burkholderia, Streptococcus and Staphylococcus		Sputum	23	25
	Increased abundance of Pseudomonas, Staphylococcus, Stenotrophomonas and Achromobacter		Sputum	17	32
	Increased abundance of Staphylococcus, Streptococcus and Pseudomonas		BAL	95	33
IPF	Increased abundance of Haemophilus, Streptococcus, Neisseria and Veillonella		BAL	65	19
	Increased abundance of Staphylococcus and Streptococcus		BAL	55	20
	Increased abundance of Streptococcus, Prevotella, Veillonella, Haemophilus and Pseudomonas		BAL	35	26

BAL, bronchoalveolar lavage; CF, cystic fibrosis; COPD, chronic obstructive pulmonary disease; IPF, idiopathic pulmonary fibrosis.

¹Changes in the microbiota in cases compared with controls.