Poyet_2019_BIOML

Study: A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

Publication: Poyet et al., A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research (2019, Nature Medicine)

External link: SPIRE database (MAGs, genes and proteins including annotations)

Study accession: PRJNA544527

Last annotation change: 2025-10-09

Human Metadata

ADD_ADHD

99%
No
559

Abnormal_Pap_Smear_TestResult

 11%
No
 65

Alcohol(drink/week)

98%
7
 210
0
 95
1-2
 79
15
 59
other values
 114

Alopecia

 11%
No
 65

Alzheimer_Dementia

99%
No
561

Anonymous_Sexual_Contact

99%
No
559

Antibiotics_Last3months

99%
No
558
Yes, 2 months ago
 1

Anxiety

99%
No
559
Anxiety disorder
 2

Asthma

99%
No
559
Yes
 2

Atopic_dermatitis

 11%
No
 65

Autism_Asperger

99%
No
561

Avoid_Food

99%
No
380
Spicy foods
 76
Citrus
 59
Meat
 4
other values
 40

BP_(mmHg)

 14%
101/81
 3
105/76
 3
121/71
 3
101/76
 2
other values
 70

Babesiosis

99%
No
559

Bipolar_disorder

99%
No
561

Blood_In_Stool

 11%
No
 65

Blood_Transfusion

99%
No
559

Body_Temperature

 14%
98.3
 16
98.4
 15
98.5
 13
98.6
 6
other values
 29

BowelMovement_Day

99%
2-3
 281
1-2
 123
1
 115
2
 20
other values
 20

Breast_Feeding

 11%
No
 65

Celiac_disease

99%
No
561

Central_obesity

 11%
No
 65

Chagas

99%
No
559

Chronic_Fatigue_syndrome

99%
No
559

Chronic_constipation

99%
No
561

Chronic_diarrhea

99%
No
561

Clotting_Factor_Concentrates

99%
No
559

Colon_Cancer

99%
No
559

Colonoscopy_endoscopy

99%
No
555
Yes
 2
Endoscopy at 15yo
 2

Connective_tissue_disease

99%
No
561

Constipation

99%
No
559

Contact_Hospital

 11%
No
 65

Contact_LongTermCareSetting

 11%
No
 65

Contact_OutpatientSetting

 11%
No
 63
Yes
 2

Contact_withBlood

99%
No
559

Country_Birth

 43%
USA
 239
Canada
 2
Bosnia
 1

Country_Birth_Outside_USA_Europe_Japan_Canada_Australia_NZ

100%
No
562
Yes
 1

Cycling_LastWeek(h)

 11%
0
 43
1-3
 11
3
 9
-1
 2

Depression

99%
No
561

Diabetes(TypeI/II)

99%
No
559

Diarrhea

99%
No
557
Frequently
 2

Diet

65%
Vegetarian
 220
omnivorevore
 148

Difficulty_Flushing_Stool

 11%
No
 65

Eating_disorder

99%
No
561

Eczema

 11%
No
 65

Experimental_medication

99%
No
559

Exposed_to_Diagnosed_CJD

99%
No
559

Fever_LastTwoWeeks

99%
No
555
Yes
 2
Cold
 2

Fibromyalgia

99%
No
559

Food_Allergy

99%
No
559

Food_Intolerance

 11%
No
 65

Former_Current_Usmilitary

100%
No
563

GI_infection

99%
No
558
3-4 years ago, stomach bug
 1

GI_malignancy_polyposis

99%
No
559

GI_surgery

99%
No
559
Appendectomy
 2

Growth_Hormone

99%
No
559

HIV

99%
No
559

HPV

 11%
No
 65

Handling_HumanAnimal_Tissue

 11%
No
 61
Rats
 2
Human and mice
 2

Heart_disease

99%
No
559

Heart_rate_(Bpm)

 14%
63
 12
64
 10
76
 6
67
 5
other values
 48

Helicobacter_pylori

 11%
No
 65

Hepatitis

99%
No
559

High_Fasting_Glucose

 11%
No
 65

High_blood_pressure

99%
No
559

High_cholesterol

 11%
No
 65

History_blood_stool

99%
No
560
Yes, because of large stool
 1

Hospitalization_Last12months_OutsideUS

99%
No
561

Hospitalization_Last12months_US

99%
No
561

Hospitalization_LongTermCare

99%
No
561

Housework_Childcare_LastWeek(h)

 11%
1-3
 23
3
 21
-1
 11
0
 8
No
 2

IBD...185

99%
No
559

IBD...35

99%
No
561

IBS

99%
No
561

In_UK_1980-1996

100%
No
563

Incarceration_PrisonJail_More72h

99%
No
559

Infection_CRE

 11%
No
 65

Infection_ESBLs

 11%
No
 65

Infection_MRSA

 11%
No
 65

Infection_Other

 11%
No
 65

Infection_VRE

 11%
No
 65

Inflammatory_arthritis

99%
No
561

Insulin_FromCows

99%
No
559

Intranasal_Intravenous_Drug

99%
No
559

Liver_disease

99%
No
561

Lumpy

 11%
No
 65

Lyme_disease

99%
No
559

Malaria

99%
No
559

Manual_Evacuation

 11%
No
 65

Marijuana_Use

 11%
No
 57
Yes
 4
Yes occasionally
 2
1 per month
 2

Men_With_Men_Intercourse

99%
No
559

Movement_disorder

99%
No
561

Mucus_In_Stool

 11%
No
 65

Multiple_Sexual_Partners_Last6months

99%
No
559

Multiple_sclerosis

99%
No
561

New_Sexual_Partner_Last6months

99%
No
556
Yes
 3

Other...112

99%
No
345
Deviated septum
 206
Deviated septum, rhabdomyolysis
 2
Lazy eye (6yo)
 2
other values
 6

Other...177

99%
No
559

Other...186

99%
No
514
BreastCancer(Mom)
 4
Parkinson(GrandPa) Meniere's disease(GrandMa)
 3
Alzheimer
 2
other values
 36

Other...44

99%
No
561

Other...72

99%
No
559

Other...78

99%
No
559
Migraine Once per year
 2

Other...86

99%
No
561

Other...88

99%
No
559

OtherSymptoms_PastTwoWeeks

99%
No
557
Constipated_LastWeek
 2

Other_Allergy

99%
No
541
Amoxycillin
 2
Amoxycillin and ceclor
 2
Apple, grass, dirt, mold
 2
other values
 12

Other_auto_immune

99%
No
561

Other_chronic_pain

99%
No
559

Other_skin_condition

 11%
No
 65

Others

99%
No
556
Urinal Tract Infection
 3

Parkinson_disease

99%
No
561

Particular_Diet

99%
No
546
Vegetarian
 5
Lacto/ovovegetarian
 3
Eat a lot of meat
 2
other values
 3

Pectic_ulcer_disease

 11%
No
 65

Personality_disorder

99%
No
561

Pet_allergy

99%
No
551
Cat, dog
 4
cat
 2
Cat
 2

Phantom_Pain

99%
No
559

PhysicalExercise_LastWeek(h)

 11%
3
 31
1-3
 22
0
 6
-1
 6

Pregnant

99%
No
559

Probiotics

99%
No
544
Kombucha
 3
Accutane
 2
Acidophilus tablets
 2
other values
 8

Profession

99%
PhysicalTherapist
 206
Student
 99
Homecare
 74
Music
 65
other values
 116

Psoriasis

99%
No
561

Rash

 11%
No
 65

Reaction_medication

99%
No
545
Amoxycillin and ceclor
 2
Benzoyl peroxyde
 2
Ceclor
 2
other values
 8

Recent_tick_bite

 11%
No
 65

Receptive_Anal_Intercourse

 11%
No
 65

Recurrent_Abdominal_Pain

99%
No
559

Recurrent_Bloating

99%
No
559

Rejected_BloodDonation

99%
No
551
Yes (Low Iron)
 4
Yes (low heart rate)
 2
Yes (Cold)
 2

Relationship_status

 15%
Relationship
 48
Married
 30
Single
 7
Dating
 2

Resp_rate_(breadth/min)

 11%
16
 39
14
 22
18
 2
15
 2

Schizophrenia

99%
No
561

Seasonal_Pollen_allergy

99%
No
529
Yes
 17
Pollen
 3
Dust
 2
other values
 8

Sensation_Incomplete_Evacuation

 11%
No
 65

Sensation_Obstruction_Blockage

 11%
No
 65

Sex_Trade_Worker

99%
No
559

Sexual_Contact_withHIVinfected_Person

99%
No
559

Sexual_Contact_withHemophiliaInfected_Person

99%
No
559

Sexual_Contact_withHepatitisInfected_Person

99%
No
559

Sexual_Contact_withSTD

99%
No
559

Sexual_Contact_with_Men_whoHad_MWM_Intercourse

99%
No
559

Sexually_transmitted_infection

99%
No
559

Short_Term_Diet_LastYear

 11%
No
 65

Straining

 11%
No
 65

Supplements

98%
No
498
Multivitamin
 10
Vitamin C
 7
Protein shakes
 5
other values
 36

Tattoo_Piercing_Last6months

99%
No
559

Thyroid_disease

99%
No
561

Tobacco_Use

99%
No
553
Yes
 4
Cigar
 2
1-2 per week
 2

Transplantation

99%
No
561

Travel_Abroad_LastYear

99%
No
308
Canada
 212
China
 4
Costa Rica
 4
other values
 33

Travel_Abroad_NextYear

 11%
No
 51
Europe
 4
Bahamas
 2
Canada
 2
other values
 6

Tuberculosis

99%
No
559

Usual_BristolStool_scale

 17%
4
 37
3-4
 35
3
 8
4-5
 6
other values
 10

Vaccination_Last3weeks

99%
No
542
Flu
 17

Waist_circ_(cm)

85%
88.9
 222
85.9
 74
76.2
 71
83.8
 12
other values
 100

Walking_LastWeek(h)

 11%
3
 38
1-3
 25
-1
 2

sample_description

100%
Keywords: GSC:MIxS;MIMARKS:5.0
359
Keywords: GSC:MIxS;MIMS:5.0
 204

sample_title

100%
MIMARKS Specimen sample from human gut metagenome
359
MIMS Environmental/Metagenome sample from human gut metagenome
 204

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Sample alias Spire sample name Longitude Latitude Geographic location Location resolution Collection date Collection date end Last change Tax id Environment material Environment biome Environmental package Environment feature Artificial Pmid Doi