Human samples

Studies:

Body Sites

vagina

 839

nose

 374

rectum

 186

eye

 106

lung

 73

colon

 22

location

100%
USA (country)
 13733
China (country)
 3848
Israel (country)
 3790
Canada (country)
 3169
other values
79469

resolution of location info

100%
country
 43875
city
 42697
site
 9440
region
 6731
other values
 1266

source material

100%
fecal material [ENVO:00002003]
88105
saliva material [ENVO:02000036]
 3485
supragingival dental plaque [UBERON:0016485]
 1164
fossa cubitalis ventralis [UBERON:3000786]
 631
other values
 10624

source material environment

100%
intestine environment [ENVO:2100002]
89130
mouth environment [ENVO:08000002]
 6528
skin environment [ENVO:2100003]
 4838
vagina [UBERON:0000996]
 839
other values
 2674

days since first sample

94%
0
62365
1
 1405
2
 823
3-42
 14641
43-3639
 19423

sex

61%
female
 32796
male
 30707

age (years)

60%
0.00-0.50
 12504
0.50-21.00
 12678
21.80-35.00
 12408
35.08-57.00
 12722
57.10-113.00
 12084

age range (years)

 31%
adult
 12287
50 to 64
 2177
18 to 70
 1259
baby
 1041
other values
 15779

age category

91%
adult
67505
baby
 20571
child
 3622
adolescent
 1461
other values
 1780

weight (kg)

 14%
0.4-9.7
 3047
9.7-57.0
 3187
57.1-66.3
 2887
66.4-79.4
 3117
79.5-210.5
 2963

body mass index

 25%
10.0-20.3
 5332
20.3-22.8
 5334
22.8-25.0
 5470
25.0-28.2
 5201
28.2-76.7
 5314

height (cm)

 13%
29.0-149.9
 2843
149.9-160.0
 2742
160.0-168.0
 3053
168.2-176.0
 2650
176.2-255.7
 2600

diet

 8%
omnivore
 4961
breastfed
 1790
formula- and breastfed
 916
formula-fed
 705
other values
 866

smoking status

 7%
non-smoker
 6688
smoker
 682
ex-smoker
 367

disease status

88%
COHORT
 47347
CTR
 13283
type 2 diabetes
 2326
critically ill patient
 1893
other values
 27212

artificial or special treatment

 0%
cultivation
 481
virome enrichment
 156
paleosample
 112
enrichment
 96
other values
 63

kind of intervention

 21%
antibiotics
 9498
diet intervention
 2905
probiotic
 2216
drug treatment
 1977
other values
 5587

medication

 16%
ATC J01
 2911
Ciprofloxacin
 802
Ciprofloxacin; Metronidazole
 421
Ibuprofen
 418
other values
 12966

type of birth

 9%
Vaginal birth
 5606
Caesarean section
 4454

time series data available?

100%
no
55845
yes
 48164

time series: count of timepoints

100%
0-1
55845
2
 11485
3
 9608
4-5
 8258
6-193
 18813

time series: length in days

95%
0
 50034
1
 1905
2-27
 7537
28-180
 21117
181-3639
 18373

Blood_group

 0%
A+
 36
B+
 34
O+
 19
AB+
 5
other values
 4

Comorbidities

 0%
Hypertension, renal impairment, hyperlipidemia
 7
Diabetes mellitus, hypertension, hyperlipidemia
 4
Hypertension, Chronic hepatitis B carrier
 4
Obesity, hypertension
 4
other values
 11

Drug_antibiotic_last3y

 0%
No
 206
2 months
 5

Other_meds

 0%
N
 38
Y
 23

age_days

 7%
7
 620
21
 475
4
 357
266
 302
other values
 5602

age_months

 0%
10
 28
11
 27
8
 27
9
 27
other values
 322

amy1cn

 0%
10.82439393
 6
12.7950299
 6
3.655166954
 6
3.689326826
 6
other values
 116

antibiotic

 0%
oral ciprofloxacin 500 mg bi-daily and oral metronidazole 500 mg tri-daily for a period of 7 days
 421
Broad spectrum antibiotics
 25
Narrow spectrum antibiotics
 7
Cefazolin 3/22/2017
 1
other values
 12

antibiotic_dosage

 0%
100 mg twice daily for 56 days
 30
20 mg twice daily for 56 days
 24
TMP/SMX; 160/800 mg twice daily for 14 days
 9
500mg three times daily for 14 days
 9

birth_country

 0%
SWE
 130
DEU
 4
DNK
 2
YUG
 2
other values
 7

birth_gestational_age_weeks

 4%
26
 343
25
 340
28
 330
30
 286
other values
 3079

birth_mode

 2%
Vaginal Delivery
 2419
Caesarean Section
 292

birth_term_status

 7%
preterm
 3273
extremely preterm
 1569
very preterm
 1215
full term
 722
other values
 872

birth_weight_kg

 0%
0.734
 24
2.847
 21

bmi_range

 1%
over 30
 431
over 23
 259
20 to 25
 174
over 35
 146
other values
 568

bristol_stool_scale

 1%
4
 479
3
 192
5
 177
6
 172
other values
 535

cause_of_death

 0%
Sudden cardiac death
 4
multiple organ failure
 2
enteric volvulus, hemorrhagic infarct
 1
hemorrhagic shock after cholecystectomy
 1
other values
 3

cohort

 0%
exercise cohort
 39
sedentary cohort
 38
validation cohort
 30

common_timepoint

 0%
0
 166
7M
 55
5M
 51
4M
 49
other values
 475

comorbidities

 0%
Liver steatosis
 5
Acute respiratory disease
 2
COPD
 2
Chronic gastritis
 2
other values
 45

couple_id

 1%
10009
 11
10049
 11
10007
 10
10031
 10
other values
 1843

couple_timepoint

 1%
7
 551
21
 325
4
 310
266
 302
other values
 493

cultivation_condition

 0%
maximum enrichment broth anaerobic culture (MEB-ANA)
 48
maximum enrichment broth aerobic culture (air enriched with 5% CO2) (MEB-CO2)
 48
aerobic (with 5% CO2) culture in the presence of 32 μg/ml cefoxitin (FOX-CO2)
 48
anaerobic culture in the presence of 32 ug/ml cefoxitin (FOX-ANA)
 47

cultivation_duration

 0%
7 days
 191

days_since_antibiotics

 2%
0
 678
83
 410
4
 114
7
 82
other values
 1532

days_since_fmt

 0%
-1
 6
-2
 5
11
 5
19
 5
other values
 96

diet_full

 2%
expressed breast milk
 811
formula-fed
 244
expressed breast milk and formula-fed
 170
others
 139
other values
 1159

donor_d0

 0%
Smillie_2018_FMT_CDI.FMT2
 43
PT-18-0008
 42
PT-18-0002
 40
DB
 36
other values
 683

donor_d28

 0%
SAMN03955540
 3
SAMN03955542
 3
SAMN03955544
 3
SAMN03955545
 3
other values
 6

ethnicity

 11%
White
 3895
Caucasian/Hispanic
 1578
Caucasian
 1098
White/Caucasian
 621
other values
 4510

family

 5%
Dubois_2024_HELMi_infant.NA
 79
MyMicrobes.FAM02
 75
MyMicrobes.FAM01
 64
MyMicrobes.FAM06
 45
other values
 4904

fmt_donor

 0%
D0097
 56
D0044
 45
D0485
 16

full_description

 1%
stool sample (during watchful waiting) of participant 802
 12
stool sample (during watchful waiting) of participant 803
 12
stool sample (during watchful waiting) of participant 804
 12
stool sample (during watchful waiting) of participant 805
 12
other values
 1565

gestational_age_weeks

 0%
33.85714286
 13
32.85714286
 9
34.42857143
 9
34.85714286
 8
other values
 253

gestational_state

 0%
pregnant
 292

group

 0%
14
 85
7
 52

hip_cm

 0%
103
 7
99
 7
100
 6
106
 6
other values
 90

host

 0%
Homo sapiens
 39

intervention_full

 2%
probiotic (4 g per 2 strips of powder, once daily at bedtime) and berberine (0.6 g per 6 pills, twice daily before meal)
 311
placebo
 301
probiotic (4 g per 2 strips of powder, once daily at bedtime)
 301
berberine (0.6 g per 6 pills, twice daily before meal)
 279
other values
 1546

lifestyle

 0%
rural agriculturalist
 114
Peri-urban industralist
 77
Hunter-gatherer
 28
traditional hunter-gatherers
 24
other values
 87

linked_to

 1%
M0018_mother
 5
M0038_mother
 5
M0059_mother
 5
M0072_mother
 5
other values
 1298

medical_history_notduringstudy

 0%
AV block; ADHD
 1
Afib, hyperlipidemia
 1
At least two recurrences of CDI; obesity; RA
 1
CAD, CHF, CKD, HTN
 1
other values
 22

medical_operation

 0%
vertical sleeve gastrectomy
 18
Roux-en-Y gastric bypass
 18
metbaolic gastric bypass
 2
gastric band
 1

medication_full

 16%
antibiotic
 1719
antibiotics
 986
ciprofloxacin
 730
ciprofloxacin; metronidazole
 421
other values
 13210

medicinal_plant

 0%
Tripterygium wilfordii
 67

menopausal_status

 0%
Post-Menopausal
 162
Pre-Menopausal
 31
Going Through Menopause
 22

note

 6%
dataset contains multiple samples per subject, but these cannot be linked with the available metadata
 2934
additional metadata available upon request (see paper)
 924
The stated sample location differs between the paper and the uploaded metadata. Coordinates follow the paper.
 400
no antibiotic treatment 2 months before sampling
 368
other values
 2215

original_timepoint

 0%
7
 256
8
 254
5
 212
6
 207

pregnancy_week

 0%
37
 34
30
 34

pregnant

 0%
0
 200
1
 162

probiotic

 1%
Labinic
 640
Supherb Bio-25 bi-daily
 454
InfloranUK
 251
Bifidobacterium infantis
 68

range_days_since_ABXs

 0%
0
 7
4
 4
13
 2
18
 1
other values
 3

range_days_since_antibiotics

 2%
unclear data
 1439
0-7
 368
0-90
 176
0-180
 59
other values
 179

recipient_donor

 0%
recipient
 226
Recipient
 117
donor
 48
Donor
 42

sample_description

 41%
Keywords: GSC:MIxS;MIMS:5.0
 7398
Keywords: GSC:MIxS;MIMS:6.0
 2589
saliva_metagenome_from_USA
 1929
Metagenomic data of Microbial Community from patient stool
 624
other values
 31003

sample_title

75%
Metagenome or environmental sample from human gut metagenome
 4734
MIMS Environmental/Metagenome sample from human gut metagenome
 3068
Metagenome or environmental sample from metagenome
 2348
Preterm stool metagenome
 2288
other values
66091

skin_site_type

 1%
sebaceous
 564
moist
 548
rarely_intermittently_moist
 136
dry
 106
other values
 105

stool_consistency

 0%
Normal
 277
Hard
 63
Mushy
 58
Diarrheic
 17

study_accession

 1%
PRJNA912122
 850
PRJEB48269
 272
PRJEB60773
 248
PRJNA834762
 83
other values
 137

subject_disease_status_full

 6%
CTR
 1421
prediabetes
 803
obesity
 770
PD
 374
other values
 3809

synbiotic

 0%
Bifidobacterium infantis, human milk oligosaccharides
 68

time_period

 0%
1770-1855
 44
1200-1400 BP
 3
5300 BP
 2
21 BC-127 AD
 1
other values
 7

timepoint_note

 0%
second clinic visit 4 to 19 weeks (on average 60 days)
 24
precision of date: day
 22
colostrum (milk at birth)
 16
fecal infant 1 month
 16
other values
 74

tissue_type

 1%
Stool
 751
Transverse colon mucosa
 83
Descending colon mucosa
 82
Rectum mucosa
 82
other values
 615

vaccine_name

 0%
BioNTech
 287
SinoVac
 95

vaginal_pH

 0%
4
 62
4.4
 27
4.7
 26
5.3
 25
other values
 52

village

 0%
FijiCOMP.village.1
 168
FijiCOMP.village.3
 101
FijiCOMP.village.2
 69
FijiCOMP.village.4
 64
other values
 469

waist_cm

 0%
80
 25
79
 24
82
 24
89
 22
other values
 585