Animal samples

Studies:

Host Species

85677

 34

location

100%
Australia: NSW (region)
 892
China: Guangxi (region)
 471
China (country)
 375
United Kingdom (country)
 365
other values
9115

resolution of location info

100%
region
 5092
country
 2253
city
 1860
exact_location
 1378
other values
 635

collection date

100%
1861–2011
 367
2012–2014
 2068
2015–2016
 3045
2017–2018
 2033
2019–2024
 2025
spans several years
 1680

source material

100%
fecal material [ENVO:00002003]
6755
ruminal fluid [UBERON:0010228]
 588
lumen of digestive tract [UBERON:0006909]
 526
digestive tract [UBERON:0001555]
 495
other values
 2854

source material environment

100%
intestine environment [ENVO:2100002]
8317
rectum [UBERON:0001052]
 696
rumen [UBERON:0007365]
 695
caecum [UBERON:0001153]
 132
other values
 1378

days since first sample

99%
0
9412
1
 10
2
 3
3
 52
0-930
 1676

sex

 43%
female
 2337
male
 2329
castrated male
 184

age (years)

 24%
0.00-0.19
 555
0.20-1.00
 744
1.01-1.97
 262
2.00-4.99
 560
5.00-48.00
 656

weight (kg)

 4%
0.4-3.0
 109
3.0-4.4
 111
4.4-5.4
 108
5.5-7.0
 115
7.2-210.0
 104

diet

 24%
herbivore
 914
omnivore
 405
complete primate diet
 159
carnivore
 128
other values
 1155

disease status

 37%
COHORT
 2923
CTR
 806
diarrhea
 279
chronic enteropathy
 53
other values
 106

artificial or special treatment

 1%
cultivation
 155
paleosample
 19
post-mortem
 2

host species

100%
Sus scrofa
 1908
Bos taurus
 1089
Gallus gallus
 1039
Bubalus bubalis
 745
other values
6437

kind of intervention

 12%
ABX
 502
antibiotics
 428
diet
 280
diet intervention
 118
other values
 118

breed or strain

 12%
Guang Xi swamp buffalo
 252
Labrador Retriever
 113
hybrid buffalo
 112
Beagle
 82
other values
 827

provider of animal

 14%
Guangdong Medical Labora- tory Animal Center
 245
Beef and Sheep Research Centre of Scotland's Rural College
 240
Mauritian or South-East Asian
 159
China Agricultural University
 145
other values
 848

housing lab

 16%
Jiangxi Agricultural University
 500
Beef and Sheep Research Centre of Scotland's Rural College
 283
UK Health Security Agency (UKHSA), Porton Down
 159
Nestle Purina Pet Care
 129
other values
 752

number of pooled individuals

 42%
1
 3831
25
 425
5
 210
30
 169
other values
 149

medication

 1%
ATC QI09AE03
 40
Amoxicillin
 40
Colistin
 40
Gentamicin
 40
other values
 45

lower size cutoff (collection filter pore size, µm)

 0%
0.45
 32
0
 23
2
 19

upper size cutoff (pre-filter pore size, µm)

 1%
900-483000
 67
Infinity
 55
12
 19

time series data available?

100%
no
8968
yes
 2250

time series: count of timepoints

100%
0
 59
1
8909
2
 370
3
 166
4-24
 1714

time series: length in days

99%
0
8869
2
 5
3
 11
6-11
 42
12-933
 2232

added_matter

 0%
penicillin, streptomycin
 11
chloramphenicol
 3

age range (years)

 7%
adult
 745
<1
 48
calf
 36
senior adult
 7
other values
 9

age_days

 5%
28
 49
35
 49
42
 49
49
 49
other values
 394

antibiotic

 0%
40mg oxytetracycline hydrochloride
 7

captivity status

98%
domestic
6721
wild
 2167
captive
 1976
pet
 130
unknown
 19

captivity_status_full

 1%
5 Months
 35
1 Month
 34
Long
 25
Wild
 23
2 Months
 6

depth (meters)

 1%
1.5
 21
1870
 21
1164
 16
1860
 10
other values
 110

diet_full

 0%
dried ants: 10g, dried termites: 10g, and water: 80g
 4

elevation (meters)

 3%
1046.5
 30
204.7
 30
1193.7
 20
45.2
 20
other values
 251

host

 1%
Ifremeria nautilei
 60
Alviniconcha strummeri
 26
Alviniconcha boucheti
 24
Alviniconcha kojimai
 16
other values
 43

host_common_name

 0%
Pere David's deer
 30
Giant panda
 16
North Atlantic Right Whale
 6
Red panda
 6
other values
 10

host_scientific_name

 2%
Pan troglodytes verus
 69
Apis mellifera carnica
 54
Pan troglodytes
 36
Elaphurus davidianus
 30
other values
 97

intervention_full

 0%
no immunosuppressive therapy
 8
glucocorticoids (either prednisone or dexamethasone) and chemotherapy (cytarabine)
 4

medication_full

 1%
Escherichia live bacterial vaccines
 40
amoxicillin
 40
colistin
 40
gentamicin
 40
other values
 45

note

 0%
HiSeq2500
 17
Early stage worker
 13
New stage worker
 10
Late stage worker
 8
other values
 26

phenotypic_information

 1%
Lean to normal
 65
Overweight to obese
 64

sample_collection_timepoint

 0%
35 days
 36
14 days
 25
0 days
 7

sample_description

 40%
not applicable
 575
F corresponds to Farm number; S corresponds to sample number
 363
Keywords: GSC:MIxS;MIMS:5.0
 361
NA NA
 285
other values
 2991

sample_title

88%
Metagenome or environmental sample from pig gut metagenome
 877
Metagenome or environmental sample from gut metagenome
 755
Metagenome or environmental sample from chicken gut metagenome
 545
luminal digesta samples
 370
other values
7320

study_accession

 4%
PRJNA556790
 103
PRJNA563508
 34
PRJNA574146
 24
PRJNA565265
 18
other values
 313

time_period

 0%
600-1050 AD
 9