Table 1.

Overview of studies investigating LRT mycobiota.

Study author, year of publication	Patients (pts)/study subjects (controls)	Sampling method	Material analyzed
Delhaes et al., 2012	four CF pts	sputum expectoration	sputum
Willger et al., 2014	six CF pts	sputum expectoration	sputum
Kramer et al., 2015a	56 CF pts	sputum expectoration	sputum
van Woerden et al., 2013 van Woerden et al., 2011	30 asthma bronchiale pts 13 controls	induced sputum expectoration	two pooled sputum samples (one from patients and one from controls)
Charlson et al., 2012	21 lung transplant pts one patient with suspected sarcoidosis one patient with adenocarcinoma	bronchoscopy (including 2-bronchoscope sampling in healthy controls) oral washes with saline bronchoscope saline flush	BAL Oral washes saline and bronchoscope flush
	six controls
Bittinger et al., 2014	42 lung transplant pts 19 HIV pts 13 pts with various pulmonary diseases 12 controls	bronchoscopy (including 2-bronchoscope sampling in healthy controls) oral washes with saline bronchoscope saline flush swabs	BAL oral washes laboratory water bronchoscope flushes saline sterile swabs lab tabletop surface
Cui et al., 2015	32 HIV pts [10 with chronic obstructive pulmonary disease (COPD)] 24 HIV negative pts	oral washes with saline induced sputum bronchoscopy	oral washes sputum BAL
Bousbia et al., 2012	160 ICU pts with pneumonia 25 ICU pts without pneumonia	bronchoscopy	BAL
Krause et al., 2016	39 ICU pts seven non-ICU patients with antibiotic therapy five ICU pts for sampling comparison eight controls	bronchoscopy through endotracheal tubes suction of endobronchial secretion through endotracheal tubes bronchoscope saline flush	BAL endobronchial secretion bronchoscope flushes saline