TABLE 2.

Genera detected in bronchial tree (S), oropharynx (OP) and nose (N) (median [IQR]).

		Friedman test				Wilcoxon test
Phylum	Genus	Sputum (S)	Oropharyngeal swab (OP)	Nasal lavage (N)	p	S vs. OP	S vs. N
Acidobacteria	Ellin6075_g	0 (0–0)	0 (0–0)	0.21 (0–2.65)	0.002	0.32	0.03
Actinobacteria	Actinomyces	1.31 (0.43–1.91)	2.23 (0.06–3.3)	4.17 (0.21–6.38)	0.263	0.12	0.09
Actinobacteria	Rothia	11.71 (5.85–23.34)	2.11 (0.8–12.35)	0.53 (0–1.99)	0.001	0.31	0.03
Actinobacteria	0319-7L14_f_g	0 (0–0)	0 (0–0)	1.05 (0–2.46)	0.001	1	0.03
Actinobacteria	Corynebacterium	0.04 (0.01–0.11)	0.12 (0–0.64)	0.58 (0–1.57)	0.382	0.25	0.06
Actinobacteria	Nocardioidaceae_g	0 (0–0)	0 (0–0.2)	0.28 (0–1.32)	0.002	0.13	0.03
Actinobacteria	Propionibacterium	0 (0–0)	0 (0–0.2)	0.93 (0.17–1.99)	0.002	0.09	0.03
Actinobacteria	Atopobium	0.34 (0.05–0.61)	0.23 (0–0.64)	0.93 (0–4.26)	0.789	0.98	0.29
Bacteroidetes	[Prevotella]	2.2 (1.72–4.29)	1.66 (0.92–3.51)	0 (0–0)	0.002	0.98	0.03
Bacteroidetes	Porphyromonas	5.79 (1.19–7.77)	0.7 (0.06–1.78)	0 (0–2.26)	0.002	0.03	0.03
Bacteroidetes	Prevotella	12.88 (5.96–16.13)	8.28 (2.49–14.76)	6.38 (0.26–14.35)	0.024	0.07	0.16
Bacteroidetes	Capnocytophaga	1.52 (0.68–2.78)	0.15 (0–0.67)	0 (0–0.01)	0.004	0.03	0.04
Chloroflexi	Gitt-GS-136_o_f_g	0 (0–0)	0 (0–0)	0.53 (0–3.13)	0.002	1	0.03
Firmicutes	Gemellaceae_g	11.32 (6.77–14.34)	2.56 (0.5–3.84)	0.01 (0–1.39)	0.001	0.08	0.03
Firmicutes	Granulicatella	4.14 (2.46–5.81)	0.81 (0.32–2.48)	0 (0–1.57)	0.001	0.08	0.03
Firmicutes	Streptococcus	0.78 (0.47–1.38)	2.3 (1.37–4.43)	1.06 (0.02–3.83)	0.021	0.03	0.19
Firmicutes	Clostridiales_f_g	0.14 (0.02–0.25)	1.88 (0–3.18)	0 (0–0.35)	0.02	0.03	0.88
Firmicutes	Veillonella	8.81 (3.73–12.3)	5.72 (3.76–7.71)	6.53 (0.03–11.5)	0.296	0.09	0.36
Firmicutes	Staphylococcus	0.11 (0–0.66)	0 (0–0.03)	0.21 (0–1.58)	0.046	0.04	0.65
Firmicutes	[Mogibacteriaceae]_g	0.25 (0–0.58)	0.82 (0–1.99)	0 (0–1.06)	0.144	0.05	0.96
Firmicutes	Parvimonas	0.15 (0–0.17)	0 (0–0.01)	0 (0–0)	0.002	0.03	0.03
Firmicutes	Lachnospiraceae_g	0.68 (0.32–1.07)	0.7 (0.12–1.94)	0.01 (0–3.28)	0.391	0.67	1
Firmicutes	Catonella	0.36 (0.03–0.64)	0.1 (0–0.23)	0 (0–0)	0.002	0.09	0.03
Firmicutes	Moryella	0.26 (0.03–0.76)	0.2 (0–0.35)	0 (0–0)	0.034	0.32	0.38
Firmicutes	Oribacterium	0.86 (0.25–2.54)	0.35 (0–0.75)	0 (0–2.24)	0.077	0.04	0.22
Firmicutes	Peptostreptococcus	0.29 (0.1–0.55)	0 (0–0.35)	0 (0–0)	0.002	0.2	0.18
Firmicutes	Megasphaera	0.25 (0–1)	0.44 (0–3.31)	0 (0–0)	0.015	0.09	0.12
Firmicutes	Selenomonas	0.14 (0.05–0.3)	0.4 (0.1–1.33)	0 (0–0.85)	0.014	0.07	1
Firmicutes	Bulleidia	0.22 (0.09–0.71)	0.49 (0.1–2.71)	0 (0–0.7)	0.118	0.2	0.41
Firmicutes	Aerococcaceae_other	0.12 (0–0.43)	0 (0–0)	0 (0–0)	0.012	0.05	0.09
Fusobacteria	Fusobacterium	6.81 (2.82–9.76)	2.35 (1.29–7.44)	0 (0–1.28)	0.001	0.25	0.03
Fusobacteria	Leptotrichia	3.61 (2.05–8.6)	0.99 (0.15–1.99)	0 (0–1.05)	0.001	0.03	0.03
Planctomycetes	WD2101_f_g	0 (0–0)	0 (0–0)	0.87 (0–1.99)	0.002	1	0.03
Proteobacteria	Campylobacter	1.29 (0.35–2.12)	1.38 (0–3.97)	0 (0–0)	0.002	0.46	0.03
Proteobacteria	Haemophilus	1.73 (0.58–4.19)	0 (0–0.26)	0 (0–0)	0.001	0.03	0.03
Proteobacteria	Lautropia	0.18 (0–0.87)	0 (0–0.03)	0 (0–0)	0.004	0.03	0.04
Proteobacteria	Pseudomonadaceae_g	0 (0–0)	0 (0–0)	0.18 (0–1.99)	0.002	1	0.03
Spirochaetes	Treponema	0.11 (0–0.37)	0 (0–0.12)	0 (0–0)	0.015	0.03	0.62
TM7	TM7-1_o_f_g	0 (0–0.05)	0 (0–0.12)	1.05 (0.01–4.63)	0.024	0.42	0.03
TM7	TM7-3_o_f_g	0.59 (0.07–1.25)	4.49 (0.89–30.09)	0.11 (0–1.48)	0.016	0.03	0.86

Taxa with relative abundances median > 0.1% in at least one type of sample included.