Lloyd-Price_2019_HMP2IBD

Study: Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Publication: Lloyd-Price et al., Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases (2019, Nature)

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

Study accession: PRJNA398089

Last annotation change: 2025-09-29

Human Metadata

Abdominal_pain

 22%
Mild
 227
Moderate
 61
Severe
 9

Abscess

100%
No
1304
Yes
 12

Age_at_diagnosis

72%
16
 119
15
 90
29
 61
13
 58
other values
 620

Alcohol_beer_brandy_spirits_hard_liquor_wine_aperitif_etc

98%
No, I did not consume these products in the last 7 days
820
Yesterday, 1 to 2 times
 182
Within the past 2 to 3 days
 162
Within the past 4 to 7 days
 92
Yesterday, 3 or more times
 39

Alopecia_areata

100%
No
1316

Anal_fissure

100%
No
1296
Yes
 20

Ankylosing_spondylitis

100%
No
1316

Aphthous_ulcers

100%
No
1311
Yes
 5

Arthralgia

100%
No
1286
Yes
 30

Arthralgias

100%
No
1297
Yes
 19

Arthritis_uncertain_diagnosis

100%
No
1316

Asthma

100%
No
1316

Autoimmune_hemolytic_anemia

100%
No
1316

Autoimmune_hepatitis

100%
No
1316

Beans_tofu_soy_soy_burgers_lentils_Mexican_beans_lima_beans_etc

97%
No, I did not consume these products in the last 7 days
672
Within the past 4 to 7 days
 225
Yesterday, 1 to 2 times
 194
Within the past 2 to 3 days
 185
Yesterday, 3 or more times
 11

Bechet_s_syndrome

100%
No
1316

Blood_in_the_stool

 12%
Trace (a little blood)
 125
Occasionally frank (ocassionally a lot of blood)
 31
Usually frank (usually a lot of blood)
 7

Bowel_frequency_during_the_day

 27%
0 - 3
 303
6-Apr
 44
9-Jul
 12

Bowel_frequency_during_the_night

 5%
3-Jan
 66
6-Apr
 2

Cancer_Hodgkin_s_lymphoma

100%
No
1316

Cancer_Non_Hodkin_s_lymphoma

100%
No
1316

Cancer_breast

100%
No
1316

Cancer_cholangiocarcinoma

100%
No
1316

Cancer_colon_or_rectum

100%
No
1316

Cancer_liver

100%
No
1316

Cancer_lung

100%
No
1316

Cancer_lymphoma_not_otherwise_specified

100%
No
1316

Cancer_ovarian

100%
No
1316

Cancer_prostate

100%
No
1316

Celiac_sprue

100%
No
1316

Chronic_bronchitis

100%
No
1316

Dairy_milk_cream_ice_cream_cheese_cream_cheese

98%
Yesterday, 1 to 2 times
752
Within the past 2 to 3 days
 213
Within the past 4 to 7 days
 125
Yesterday, 3 or more times
 117
No, I did not consume these products in the last 7 days
 87

Dermatitis_herpetiformis

100%
No
1316

Did_the_patient_sign_informed_consent

100%
Yes
1316

Did_the_subject_withdraw_from_the_study

100%
No
1316

Diet_soft_drinks_tea_or_coffee_with_sugar_Stevia_Equal_Splenda_etc

98%
No, I did not consume these products in the last 7 days
965
Yesterday, 1 to 2 times
 117
Within the past 4 to 7 days
 89
Within the past 2 to 3 days
 83
Yesterday, 3 or more times
 41

Education_Level

97%
Some high school
 357
7th grade or less
 275
Bachelor's degree
 167
Unknown/Not Reported
 160
other values
 321

Eggs

97%
Yesterday, 1 to 2 times
 393
No, I did not consume these products in the last 7 days
 342
Within the past 2 to 3 days
 307
Within the past 4 to 7 days
 224
Yesterday, 3 or more times
 20

Erythema_nodosum

100%
No
1316

Erythema_nodosum_1

100%
No
1316

Familial_Mediterranean_fever

100%
No
1316

Fish_fish_nuggets_breaded_fish_fish_cakes_salmon_tuna_etc

98%
No, I did not consume these products in the last 7 days
755
Within the past 4 to 7 days
 236
Within the past 2 to 3 days
 169
Yesterday, 1 to 2 times
 123
Yesterday, 3 or more times
 11

Fruit_juice_orange_apple_cranberry_prune_etc

98%
No, I did not consume these products in the last 7 days
 419
Yesterday, 1 to 2 times
 377
Within the past 2 to 3 days
 232
Within the past 4 to 7 days
 221
Yesterday, 3 or more times
 48

Fruits_no_juice_Apples_raisins_bananas_oranges_strawberries_blueberries

98%
Yesterday, 1 to 2 times
 563
Within the past 2 to 3 days
 308
No, I did not consume these products in the last 7 days
 163
Within the past 4 to 7 days
 146
Yesterday, 3 or more times
 110

General_well_being_over_the_past_24_hours

 27%
Very well
 194
Slightly below par
 146
Poor
 14
Very poor
 4

General_wellbeing

 43%
Very Well
 332
Slightly below par
 157
Poor
 48
Very Poor
 27
Terrible
 6

Grave_s_disease

100%
No
1316

Guillian_Barre_Syndrome

100%
No
1316

Hashimoto_s_autoimmune_thyroiditis

100%
No
1316

Hispanic_or_Latino_Origin

100%
Not Hispanic or Latino
1296
Hispanic or Latino
 20

Idiopathic_pulmonary_fibrosis

100%
No
1316

Idiopathic_thrombocytopenia_purpura

100%
No
1316

If_other_explain

 0%
serving as HC but pt has fistula
 9

Irritable_bowel_syndrome

100%
No
1316

Multiple_sclerosis

100%
No
1316

Myasthenia_gravis

100%
No
1316

Myocarditis

100%
No
1316

Neuropathy

100%
No
1316

New_fistula

100%
No
1314
Yes
 2

Number_of_liquid_or_very_soft_stools_in_the_past_24_hours

 42%
0
 265
1
 148
2
 59
3
 27
other values
 62

Occupation

100%
Student
738
Paid
 452
Unknown/Not Reported
 78
Retired
 25
Unpaid/volunteer
 23

Partial_Endoscopy

100%
No
1316

Partial_Endoscopy_1

100%
No
1316

Pemphigus_vulgaris

100%
No
1316

Pericarditis

100%
No
1316

Pernicious_anemia

100%
No
1316

Polymyositis_or_dermatomyositis

100%
No
1316

Primary_biliary_cirrhosis

100%
No
1316

Primary_sclerosing_cholangitis

100%
No
1316

Probiotic

98%
No, I did not consume these products in the last 7 days
1018
Yesterday, 1 to 2 times
 186
Within the past 2 to 3 days
 43
Within the past 4 to 7 days
 36
Yesterday, 3 or more times
 9

Processed_meat_other_red_or_white_meat_such_as_lunch_meat_ham_salami_bologna

98%
No, I did not consume these products in the last 7 days
 399
Yesterday, 1 to 2 times
 313
Within the past 2 to 3 days
 304
Within the past 4 to 7 days
 269
Yesterday, 3 or more times
 8

Psoriasis

100%
No
1316

Pyoderma_gangrenosum

100%
No
1316

Pyoderma_gangrenosum_1

100%
No
1316

Reason_for_withdrawal_or_termination

 2%
Lost to follow-up
 23
Patient lost interest
 15

Red_meat_beef_hamburger_pork_lamb

98%
Yesterday, 1 to 2 times
 393
Within the past 2 to 3 days
 338
No, I did not consume these products in the last 7 days
 280
Within the past 4 to 7 days
 260
Yesterday, 3 or more times
 23

Rheumatoid_arthritis

100%
No
1316

Sarcoidosis

100%
No
1316

Scleroderma_systemic_sclerosis

100%
No
1316

Shellfish_shrimp_lobster_scallops_etc

98%
No, I did not consume these products in the last 7 days
995
Within the past 4 to 7 days
 125
Within the past 2 to 3 days
 101
Yesterday, 1 to 2 times
 68
Yesterday, 3 or more times
 5

Sjogren_s_syndrome

100%
No
1316

Soft_drinks_tea_or_coffee_with_sugar_corn_syrup_maple_syrup_cane_sugar_etc

98%
Yesterday, 1 to 2 times
 463
No, I did not consume these products in the last 7 days
 427
Within the past 2 to 3 days
 164
Within the past 4 to 7 days
 160
Yesterday, 3 or more times
 78

Specify_race

 4%
Portugese and Cape Verdean
 20
Hispanic/Latino & African American
 12
White and African American
 9
1/2 Cauc, 1/2 Hisp, Jewish and Non-Jewish mixed
 8
other values
 14

Starch_white_rice_bread_pizza_potatoes_yams_cereals_pancakes_etc

98%
Yesterday, 1 to 2 times
658
Within the past 2 to 3 days
 259
Yesterday, 3 or more times
 149
Within the past 4 to 7 days
 145
No, I did not consume these products in the last 7 days
 82

Sweets_pies_jam_chocolate_cake_cookies_etc

98%
Yesterday, 1 to 2 times
 645
Within the past 2 to 3 days
 240
Yesterday, 3 or more times
 149
Within the past 4 to 7 days
 131
No, I did not consume these products in the last 7 days
 130

Systemic_lupus_erythematosis

100%
No
1316

Tea_or_coffee_no_sugar_and_no_sugar_replacement

98%
No, I did not consume these products in the last 7 days
882
Yesterday, 1 to 2 times
 208
Within the past 4 to 7 days
 81
Within the past 2 to 3 days
 72
Yesterday, 3 or more times
 49

Temporal_arteritis

100%
No
1316

Thyroid_disease_uncertain_diagnosis_not_cancer

100%
No
1316

Type_I_Diabetes_Juvenile_Diabetes

100%
No
1316

Urgency_of_defecation

 14%
Hurry
 156
Immediately
 27
Incontinence
 8

Uveitis

100%
No
1315
Yes
 1

Uveitis_1

100%
No
1316

Vegetables_salad_tomatoes_onions_greens_carrots_peppers_green_beans_etc

98%
Yesterday, 1 to 2 times
661
Within the past 2 to 3 days
 228
Yesterday, 3 or more times
 200
Within the past 4 to 7 days
 114
No, I did not consume these products in the last 7 days
 89

Vitiligo

100%
No
1316

Was_HBI_completed

 44%
Yes
 570
No
 15

Was_SCCAI_completed

 28%
Yes
 359
No
 13

Was_subject_terminated_by_investigator

100%
No
1278
Yes
 38

Water

98%
Yesterday, 3 or more times
933
Yesterday, 1 to 2 times
 285
Within the past 4 to 7 days
 42
Within the past 2 to 3 days
 34
No, I did not consume these products in the last 7 days
 2

Wegener_s_granulomatosis

100%
No
1316

White_meat_chicken_turkey_etc

98%
Yesterday, 1 to 2 times
 488
Within the past 2 to 3 days
 378
Within the past 4 to 7 days
 237
No, I did not consume these products in the last 7 days
 158
Yesterday, 3 or more times
 30

Whole_grains_wheat_oats_brown_rice_rye_quinoa_wheat_bread_wheat_pasta

98%
Yesterday, 1 to 2 times
 409
No, I did not consume these products in the last 7 days
 345
Within the past 2 to 3 days
 283
Within the past 4 to 7 days
 222
Yesterday, 3 or more times
 36

X1_In_the_past_2_weeks_have_you_received_any_of_the_following_medications

96%
No
917
Yes
 347

X2_In_the_past_2_weeks_have_you_undergone_a_colonoscopy_or_other_procedure

96%
No
1233
Yes
 36

X3_In_the_past_2_weeks_have_you_used_an_oral_contrast

96%
No
1240
Yes
 29

X4_In_the_past_2_weeks_have_you_had_diarrhea

96%
No
750
Yes
 520

X5_In_the_past_2_weeks_have_you_been_hospitalized

96%
No
1246
Yes
 24

X6_Have_you_ever_had_bowel_surgery

96%
No
1141
Yes
 123

Yogurt_or_other_foods_containing_active_bacterial_cultures_kefir_sauerkraut

98%
No, I did not consume these products in the last 7 days
674
Yesterday, 1 to 2 times
 259
Within the past 2 to 3 days
 193
Within the past 4 to 7 days
 163
Yesterday, 3 or more times
 4

baseline_montreal_location

 39%
L3
 148
L3+L4
 139
L1
 101
L1+L4
 64
other values
 65

data_type

100%
metagenomics
1316

hbi

 41%
0
 115
1
 113
2
 106
3
 74
other values
 137

sample_description

100%
Keywords: GSC:MIxS;MIMS:5.0
1316

sccai

 27%
1
 89
0
 76
2
 75
3
 47
other values
 71

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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