Please add notes for methods/analysis regarding the VDP. Add contact name for potential questions)
### METHODS FOR SAMPLES COLLECTION/ HANDELING/ BLOOD ANALYSES
A home sampling kit was provided to all participants which included detailed picture illustrated instructions for
sampling, 3 barcoded tubes for stool samples, a flushable sheet, spoons and an opaque zip-lock bag. Participants
were instructed to lay the sheet in a tray to collect their fresh fecal sample, enabling sampling without contact with
urine or toilet water. After that, participants were told to transfer feces from the tray into the tubes using the
spoons provided, right after completing toileting. Closed tubes were stored in the opaque bags and
immediately stored in home freezers (-18°C).
together with accurate medical information, extensive lifestyle and early life events data and blood values were
combined in a geographically confined region.
In short, people in Flanders (+/- 6.5 million inhabitants, +/- 13500 km2) could subscribe online to participate in
this project from January 2013 onwards. Sampling rounds were organized between June 2013 and January 2014. At
their subscription, they got information about the study and could consent for receiving a sampling kit.
They also filled in a first questionnaire about early life events and general information. When a sampling round was
performed, participants received a sampling kit about one month before. They were instructed to make an
appointment with their general practitioner, to go there fasted for blood sampling, medical check-up and filling in an
extended medical questionnaire including medication usage in the past 6 months and antibiotic usage in the past 12
months.
After the GP visit, they used the sampling kit we had provided to collect and store their feces and saliva at home.
Samples were fresh frozen in household freezers and transported frozen within a week to one of the collection
points. Twice a week, the frozen samples were picked up at the collection points and transported on dry ice to the
lab.
Blood samples were analyses were performed at
### STOOL SAMPLE EXTRACTION PROTOCOL
### SAMPLE SELECTION
Freeze1: N=1198
1205 samples had no inconsistencies between medical (GP) and blood
(CMA) data (gender, birthdate), and with quality checks on BMI
extremes and random selection of samples. Under-age (<18) individuals
were excluded.
5 samples were subsequently excluded due to low sequencing depth.
2 samples were subsequently excluded due to incongruence between
medical/CMA and database gender and birthdate.
### 16S DATA FILES (Jun)
localization (zeus): /raeslab/group/data/MiSeq_data_V4/FINAL1200
### METADATA FILES
# VDPMAIN_METADATA
contains:
1) ids (sample,database,CMA), Age, Gender, BMI, blood pressure (BP.sys,BP.dia)
(GP origin) and smoking + basic (study level, marital status, ethnicity, geoloc)
info (self reported) #QC done (Sara)
2) All clinical (blood) variables (CMA) #QC done (Sara)
3) Health scores (Sara)
4) enterotyping (original JSD (3ETs), JSD (2ETs) and DMM (4ETs)) (Doris)
Note: Smoker (1=defined has having smoked during the past 3 months)
Summary of main fields of interest:
Gender
F
M
Count
652.00 546.00
Percent 54.42 45.58
Smoker
0
1 <NA>
Count
1032.00 106.00 60.00
Percent
86.14
8.85 5.01
Age
BMI
height
weight
Sedimentation.1h.mm
Hemoglobine.g.dL
Hematocriet..perc
RBC.milj.mm3
MCV.fl
MCH.pg
MCHC.g.dL
WBC..mm3
Lymfocyten..perc
Lymfocyten..mm3
Neutrofiele.segmenten..perc
Eosinofielen.perc
Monocyten.perc
Monocyten..mm3
Basofielen..perc
Basofielen..mm3
Neutrofielen..mm3
Eosinofielen..mm3
Trombocyten.1000.mm3
Vit..B12.ng.L
CRP.mg.L
HbA1c.mmol.mol
HbA1c..perc
Gluc.nuchter.mg.dL
Insuline.nuchter.mU.L
Ureum.mg.dL
Creatinine.mg.dL
e.GFR..CKD.EFI..mL.min.1.73m2
Urinezuur.mg.dL
Ferritine.microg.L
Totaal.Eiwit.g.L
Albumine..perc
Albumine.g.L
Alfa1Globulines..perc
Alfa1Globulines.g.L
Alfa2Globulines..perc
Alfa2Globulines.g.L
BetaGlobulines..perc
BetaGlobulines.g.L
GammaGlobulines..perc
GammaGlobulines.g.L
mean
sd median
min
max valid.n
50.88
13.78
53.00
18.00
85.00
1198
24.91
4.35
24.14
16.18
51.89
1198
171.12
8.64 170.00 149.00
198.00
1198
73.17
15.07
71.00
43.00
143.00
1198
6.26
7.02
5.00
1.00
116.00
1195
14.29
1.20
14.30
10.10
18.10
1197
42.45
3.27
42.40
29.00
52.90
1197
4.68
0.39
4.67
3.17
6.21
1197
90.87
4.64
91.00
61.00
109.00
1197
30.61
1.61
31.00
19.00
37.00
1197
33.74
1.21
34.00
28.00
38.00
1197
5974.98 1619.81 5750.00 2250.00 17260.00
1197
33.31
7.95
33.30
8.50
65.00
1197
1943.50 566.34 1881.00 540.00 6149.00
1197
54.44
8.69
54.40
30.50
82.80
1197
2.90
1.96
2.40
0.00
13.80
1197
8.80
2.21
8.60
0.00
20.80
1197
518.08 170.45 492.00
0.00 1774.00
1197
0.55
0.35
0.50
0.00
3.20
1197
31.23
19.15
29.00
0.00
169.00
1197
3313.67 1270.10 3063.00 1131.00 11564.00
1197
168.54 121.03 139.00
0.00 1318.00
1197
247.71
57.45 244.00
82.00
753.00
1197
510.65 279.17 458.00
30.00 2000.00
1198
2.01
4.01
0.90
0.30
64.10
1198
37.31
5.23
37.00
15.00
89.00
1198
5.56
0.48
5.50
3.50
10.30
1198
87.98
16.92
85.00
28.00
309.00
1198
9.03
8.88
7.10
0.40
164.90
1198
30.35
8.06
29.60
9.10
63.50
1198
0.84
0.17
0.83
0.44
1.91
1198
84.72
8.78
90.00
35.00
90.00
1095
4.88
1.25
4.80
2.20
10.50
1198
145.20 124.01 118.00
5.00 1088.00
1198
69.92
3.94
70.00
55.00
86.00
1198
61.98
3.08
62.20
49.60
74.70
1198
43.31
2.91
43.30
29.20
56.00
1198
3.75
0.61
3.70
2.10
8.80
1198
2.61
0.41
2.60
1.60
4.80
1198
9.13
1.34
9.00
4.90
17.60
1198
6.38
0.93
6.30
3.40
11.10
1198
10.89
1.35
10.80
6.30
18.30
1198
7.62
1.06
7.50
3.80
13.40
1198
14.25
2.36
14.20
1.20
24.00
1198
10.00
1.96
9.90
0.70
18.50
1198
Chol..Totaal.mg.dL
Triglyceriden.mg.dL
HDL.chol..mg.dL
Ratio.chol..tot..HDL.chol.mg.mg
LDL.chol..gem..mg.dL
Bilirubine.tot..mg.dL
Bilirubine.dir..mg.dL
Bilirubine.indir..mg.dL
GOT.U.L
GPT.U.L
Gamma.GT.U.L
CK.U.L
Cortisol.ochtend.mcg.dL
BP.sys
BP.dia
SCORE
GFR_CDK.EPI
PhysioHealthScore
Cardiov_penalty
Nefrol_penalty
197.87
101.55
64.44
3.37
118.13
0.61
0.22
0.39
21.81
22.66
25.06
109.85
16.03
122.98
76.43
2.09
91.88
97.10
0.04
0.06
37.78
62.70
17.24
4.10
33.44
0.31
0.09
0.23
8.97
13.28
25.17
68.91
7.44
14.08
8.32
2.81
16.03
3.23
0.06
0.10
196.00
86.00
62.00
3.09
116.00
0.54
0.20
0.34
20.00
19.00
17.00
92.00
15.20
120.00
80.00
1.00
92.08
98.31
0.02
0.00
83.00
20.00
23.00
1.36
32.00
0.11
0.10
0.10
7.00
6.00
3.00
15.00
0.50
80.00
40.00
0.00
35.46
77.64
0.00
0.00
472.00
683.00
165.00
141.00
376.00
2.68
0.76
1.99
135.00
122.00
232.00
711.00
49.30
190.00
108.00
18.00
141.70
100.00
0.38
0.61
1198
1198
1198
1198
1198
1197
1197
1197
1198
1198
1198
1198
1198
1109
1104
1053
1198
1051
1053
1198
# VDP metadata numeric
contains:
1) vdpmetadata_countscontinuous.txt: continuous metadata in VDPMAIN_METADATA
with dates converted into numeric values (Karoline)
2) vdpmetadata_binary.txt: binary and binarized categorical metadata in
VDPMAIN_METADATA (Karoline)
3) README_continuous.txt: Details on 1) (Karoline)
4) README_binary.txt Details on 2) (Karoline)
localization (owncloud): VDP feeze 1/VDP metadata numeric