Gut metagenome in autoimmune disease, case-control, Beijing
133 fecal metagenome samples from Beijing, China, comparing patients with autoimmune/inflammatory disease (108 samples) to healthy controls (21 samples), in a case-control study examining gut microbial associations with ankylosing spondylitis and related autoimmune conditions. machine-written summary
134 samples · 134 runs · CN · Age unknown · 2018 · 7.01 Gbp / sample · cohort Alterations in the gut virome in patients with ank
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 921 sample values (collection date, country, health condition, health condition detail, location locality, location region, subject id) |
| ✓ Abstract / description | 2 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10098016 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 511 sample values (age, antibiotic exposure, bmi, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
21 of 107 people sampled more than once (43 samples; median 2, up to 3 per person) · follow-up median 10.0 y (max 27.0 y) · median interval between samples 10.0 y (time from age at collection).
Each row is one person (4 shown of 21); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 118 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 122 | 91% | ||||
| country | 134 | 100% | 134 | |||
| health_condition | 132 | 99% | 129 | 3 | ||
| subject_id | 129 | 96% | 129 | |||
| collection_date | 134 | 100% | 134 | |||
| health_condition_detail | 134 | 100% | 129 | 3 | 2 | |
| detailed_location | 133 | 99% | ||||
| location_locality | 133 | 99% | 133 | |||
| location_region | 133 | 99% | 133 | |||
| antibiotic_exposure | 129 | 96% | 129 | |||
| sex | 129 | 96% | 129 | |||
| bmi | 125 | 93% | 125 | |||
| age_at_collection_days | 122 | 91% | 122 |
- Alterations in the gut virome in patients with ankylosing spondylitis. 2023 PMID 37063855 PMC10098016 unsure
Archive description
Public description： Ankylosing spondylitis (AS) is a common autoimmune disease. Due to the early pathogenesis and long duration, patients suffer from morning stiffness, low back pain, chest pain, alternating hip pain and other symptoms. And the disability rate is high, which seriously affects the quality of life. According to statistics, the prevalence of ankylosing spondylitis in China is about 0.3%, mostly young men. On average, patients need to stop working after fifteen or six years of illness. After 20 years of illness, more than 85% of patients lose the ability to live independently and become so-called "puppet people." In response to key scientific issues, these datas is devoted to the use a metagenomic wide association studies to explore new key biomarkers and therapeutic targets of AS from intestinal micro-organisms, so as to improve early diagnosis, accurate prediction and classification, and improve prognosis.And combine with other datas which already published of autoimmune disease,we identified conflicts and contradicts points of RA ,AS ,behcet disease and T1D.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host study.description · “prevalence of ankylosing spondylitis in China”
- body site run.scientific_name · “feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5054094 | age_at_collection_days | 19723.5 | R2 | 0.75 | external.cmd source | age: 54; age_unit: (empty); age_group: Adult |
| SAMEA5054094 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA5054094 | bmi | 21.22 | R2 | 0.75 | external.cmd source | bmi: 21.224 |
| SAMEA5054094 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMEA5054094 | country | CN | R1 | 0.90 | sample.attr.geographic_location | China:Beijing |
| SAMEA5054094 | health_condition | autoimmune_inflammatory | R1 | 0.70 | sample.name_rule:sample_name | AS0104A |
| SAMEA5054139 | health_condition | autoimmune_inflammatory | R2 | 0.75 | external.cmd source | disease: Ankylosing Spondylitis |
| SAMEA5054094 | health_condition_detail | AS | R1 | 0.70 | sample.name_rule:sample_name | AS0104A |
| SAMEA5054139 | health_condition_detail | Ankylosing Spondylitis | R2 | 0.75 | external.cmd source | disease: Ankylosing Spondylitis |
| SAMEA5054181 | health_condition_detail | mixed_case_control: ankylosing spondylitis patients vs healthy controls | R4 | 0.50 | paper.abstract | 193 AS patients and 59 healthy subjects |
| SAMEA5054094 | location_locality | Beijing | R1 | 0.85 | biosample.attribute:geographic_location | China:Beijing |
| SAMEA5054094 | location_region | Beijing | R1 | 0.85 | biosample.attribute:geographic_location | China:Beijing |
| SAMEA5054094 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
| SAMEA5054094 | subject_id | 0104 | R1 | 0.70 | sample.name_rule:sample_name | AS0104A |
Sequencing
134 runs over 134 samples · mean 7.39 Gbp per run (median 7.01 Gbp, total 989.91 Gbp; 134 runs with a base count) · layout PAIRED 134 · platform ILLUMINA 134 · models Illumina HiSeq 2000 (134) · 89% of runs with a Sandpiper profile · first public 2018-11-06
Authors (11)
Li C first · Zhang Y · Yan Q · Guo R · Chen C · Li S · Meng J · Ma J · You W · Wu Z · Sun W last
Downloads
PRJEB29373.csv.gz (5.4 KB) · parquet (77.8 KB) — all 134 samples, every field with route and confidence · PRJEB29373_determinations.csv.gz (16.4 KB) — 1,434 evidence rows