Table S1. List of reported dominant microbes in sputum samples for individual patients from available literature using culture independent
approaches.
Number of Patients With Most Abundant Bacterium
Study
Blainey et al.
n=
16
Pseudomonas
3
Stenotrophomonas
0
Achromobacter
0
Rothia
0
Staphylococcus
1
Streptococcus
11
Other
0
Method
16S pyrosequencing
Cuthbertson et al. *
8
3
0
2
0
0
1
2
16S pyrosequencing
Delhaes et al.
4
3
0
0
0
0
0
25
16S pyrosequencing
Filkins et al.
35
22
1
0
0
0
7
5
16S pyrosequencing
Goddard et al.
9
8
0
1
0
0
0
0
16S pyrosequencing
Guss et al.
3
2
0
0
0
0
0
1
16S pyrosequencing
Lim et al. 2013
3
2
0
0
1
0
0
0
Metagenomics
Lim et al. 2014
3
0
1
0
1
0
0
1
Metagenomics
Maughan et al. **
24
15
1
0
0
0
5
3
16S pyrosequencing
Price et al. ***
13
9
0
1
0
0
0
3
16S pyrosequencing
Quinn et al.
5
1
1
0
3
0
0
0
Metagenomics
Rogers et al.
71
43
2
0
0
4
0
22
16S TRFLP
Salipante et al.
66
23
1
1
0
8
6
27
Smith et al.
18
17
0
0
0
0
0
1
16S Ion Torrent
sequencing
16S pyrosequencing
Twomey et al. **
75
68
0
0
0
0
0
7
16S pyrosequencing
Willger et al.
6
3
0
0
0
0
1
1
16S Illumina sequencing
Zemanick et al.
21
9
0
0
0
1
0
11
16S pyrosequencing
Zhao et al. ****
6
4
0
0
0
0
0
2
16S pyrosequencing
This study
7
2
0
0
0
0
4
1
16S Illumina sequencing
Average for All
Patients
393
60.3%
1.8%
1.3%
1.3%
3.6%
8.9%
28.7
%
*Samples only at time=0h considered, **Order level phylogeny reported, ***Only baseline/stable samples considered, ****Most recent sample of
longitudinal data set
Footnote: If possible, the most abundant bacterium was determined for each patient from their sputum microbiome profiles either by visual
interpretation of graphs or mining supplemental information. Only studies on adult patients were considered, and if longitudinal data sets were
reported, only stable samples were analyzed.
Table S2. Richness and Shannon-Weiner indices of microbiome and metabolomes for each CF sample. The Pearson’s Rho correlation
coefficient of the trend of the CF microbiome and metabolome diversity is also included.
Microbiome
Richness
Metabolome
Richness
Microbiome
Diversity
Metabolome
Diversity
Pearson’s r
of Diversity
37
Microbiome
Evenness
0.54
1148
1.97
4.35
-0.12
31
0.28
1441
0.96
4.14
CF9
47
0.32
1359
1.25
4.31
CF10
39
0.37
1685
1.37
4.63
60
0.55
854
2.23
4.50
22
0.45
781
1.37
5.25
26
0.33
982
1.08
4.96
H1
137
0.66
765
3.26
3.96
H2
85
0.59
589
2.63
3.67
H3
116
0.56
889
2.68
3.99
66
127
142
0.63
738
669
827
2.65
3.47
3.12
3.79
3.87
4.03
CF1
CF6
CF11
CF12
CF13
H4
H5
H6
0.55
0.63
0.43
Table S3. Clinical culture, disease status and treatment information for CF patients in this study. Patient disease severity is an overall
assessment based on clinical parameters by the attending physicians at the UCSD clinic.
Patient
1
Sputum Volume
(mL)
29.5
Cultures
Disease State
Antibiotic Therapy
6
12.0
P. aeruginosa,
S. maltophilia
E. coli (ESBL*)
Stable
Unknown
Stable
Amphotericin B
9
8.4
P. aeruginosa
Stable
Azithromicin, recently inhaled aztreonam
10
14.0
Achromobacter
xylosoxidans
Post treatment
Chronically inhaled tobramycin, alternating
aztreonam, inhaled aztreonam at time of
sampling
11
7
Stable
12
3.5
P. aeruginosa,
S. maltophilia
MRSA, P.
aeruginosa
13
1
MRSA
On treatment
*Extended beta-lactam resistant strain.
On treatment
Alternates inhaled toby/aztreonam, Just
completed 4 weeks of intravenous
tobramycin and aztreonam
Azithromycin
Table S4. Chemical characteristics of molecules identified using the VIP from supervised random forest of CF vs. non-CF. Molecular
features are listed according to their variable importance values. Annotations are listed where possible and correspond to fragmentation
patterns in figure S4.
Retention
Time (s)
MS1
Detected In
Most
Abundant
Putative Annotation
525
701.55
CF
CF
Sphingomyelin (d18:1/16:1)
585
184.07
CF, non-CF
CF
Phosphocholine
585
765
264.26
760.20
CF
non-CF
CF
non-CF
585
703.58
CF, non-CF
CF
585
685.65
CF
CF
375
339.28
CF, non-CF
CF
525
366.13
CF
CF
525
645
525
675.54
724.52
1107.75
CF, non-CF
CF
CF
CF
CF
CF
405
595.38
CF, non-CF
CF
765
758.21
non-CF
non-CF
555
705
884.60
612.18
CF
CF, non-CF
CF
non-CF
585
725.55
CF, non-CF
CF
375
480.30
CF, non-CF
CF
525
1195.65
CF
CF
555
585
689.55
502.49
CF
CF
CF
CF
315
288.28
CF
CF
765
150.12
CF, non-CF
non-CF
345
315.32
CF
CF
465
304.26
CF
CF
Fragment of Ceramide
M=2H+ of 758
Sphingomyelin (d18:1/16:0)
Sphingomyelin (d16:1/16:0)
M=2H+ of 610.18
Na+ adduct of 703.5
Sphingomyelin (d18:1/15:0)
Fragment of ceramide
Na+ adduct of 282.2
645
746.51
CF
CF
Na+ adduct of 724.5
645
369.3505
CF
CF
Fatty Acid
375
475.21
CF
CF
525
1227.76
CF
CF
345
478.29
CF
CF
555
862.62
CF, non-CF
CF
tetra-glyco-ceramide - d18:1/16:0
lactosylceramide (d18:-16:0)