Microbiota in IBD arthropathy, RA, & controls, Rochester MN
180 stool samples from adults and elderly individuals in Rochester, MN, comparing IBD-associated arthropathy, IBD without arthropathy, rheumatoid arthritis, and non-IBD/non-arthritis controls, in a case-control study. machine-written summary
180 samples · 180 runs · US · Adult · 2018 · 0.51 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,040 sample values (age, antibiotic exposure, bmi, collection date, country, health condition, health condition detail, location locality) |
| ✓ Abstract / description | 180 sample values (subject id) |
| ○ Full text | read; no usable statement or table · PMC12268991, PMC6458525, PMC9741845 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 180 | 100% | ||||
| country | 180 | 100% | 180 | |||
| health_condition | 180 | 100% | 180 | |||
| subject_id | 180 | 100% | 180 | |||
| age_at_collection_days | 180 | 100% | 180 | |||
| antibiotic_exposure | 180 | 100% | 180 | |||
| bmi | 180 | 100% | 180 | |||
| collection_date | 180 | 100% | 180 | |||
| detailed_location | 180 | 100% | ||||
| health_condition_detail | 180 | 100% | 180 | |||
| location_locality | 180 | 100% | 180 | |||
| location_region | 180 | 100% | 180 | |||
| sex | 180 | 100% | 180 | |||
| smoking_status | 180 | 100% | 180 | |||
| medication | 35 | 19% | 35 | |||
| medication_detail | 25 | 14% | 25 |
- An Increased Abundance of Clostridiaceae Characterizes Arthritis in Inflammatory Bowel Disease and Rheumatoid Arthritis: A Cross-sectional Study. 2019 PMID 30321331 PMC6458525 own_data
- The systemic anti-microbiota IgG repertoire can identify gut bacteria that translocate across gut barrier surfaces. 2022 PMID 35976997 PMC9741845 unsure
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991 unsure
Archive description
The aim of the study was to investigate the compositional and functional features that characterize the gut microbiota of patients with inflammatory bowel disease (IBD)-associated arthropathy. We selected IBD patients without arthritis as controls for joint inflammation, RA patients without IBD as controls for inflammation in the gastrointestinal tract, and healthy individuals without IBD or RA as overall controls. We obtained extensive clinical metadata to allow us to make meaningful comparisons and account for potential clinical confounders. We found potential microbial features associated with IBD-associated arthropathy, as well as features common to both RA and IBD-associated arthropathy that are suggestive of a global role in joint inflammation.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “gut microbiota of patients”
- body site study.description · “gut microbiota of patients”
- life stage sample.attr.age · “60 (n=153/180)”
- life stage sample.attr.age · “68 (n=27/180)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09907206 | age_at_collection_days | 13149.0 | R1 | 0.85 | sample.attr.age | 36 |
| SAMN09907206 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | 0 |
| SAMN09907206 | bmi | 30.0 | R1 | 0.90 | sample.attr.bmi | 30 |
| SAMN09907206 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN09907206 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Rochester, MN |
| SAMN09907206 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:Diagnosis | C |
| SAMN09907270 | health_condition | crohns_disease | R1 | 0.90 | biosample_attr | CD |
| SAMN09907298 | health_condition | ibd_unspecified | R1 | 0.85 | sample.attr.ibd_diagnosis | IC |
| SAMN09907206 | health_condition_detail | C | R1 | 0.90 | sample.attr.diagnosis | C |
| SAMN09907206 | location_locality | Rochester | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Rochester, MN |
| SAMN09907206 | location_region | Minnesota | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Rochester, MN |
| SAMN09907270 | medication | immunosuppressant_or_biologic | R1 | 0.70 | biosample.attribute:Anti-integrin Antibody Type | VEDO |
| SAMN09907278 | medication | corticosteroid | R1 | 0.85 | biosample.attribute:steroids | 1 |
| SAMN09907303 | medication | probiotic_or_prebiotic | R1 | 0.70 | biosample.attribute:Probiotic Type | Probiotic Formula |
| SAMN09907278 | medication_detail | Budesonide,Prednisone | R1 | 0.85 | biosample.attribute:steroids | 1 |
| SAMN09907206 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN09907206 | smoking_status | never | R1 | 0.70 | biosample.attribute:smoking | 0 |
| SAMN09907206 | subject_id | SAMN09907206 | R4 | 0.60 | design.one_sample_per_subject:abstract | One hundred eighty patients were included in the analysis. |
Sequencing
180 runs over 180 samples · mean 0.47 Gbp per run (median 0.51 Gbp, total 85.04 Gbp; 180 runs with a base count) · layout PAIRED 180 · platform ILLUMINA 180 · models Illumina HiSeq 2500 (180) · 0% of runs with a Sandpiper profile · first public 2018-08-25
Authors (36)
Muñiz Pedrogo DA first · Chen J · Hillmann B · Jeraldo P · Al-Ghalith G · Taneja V · Davis JM · Knights D · Nelson H · Faubion WA · Raffals L · Kashyap PC last · Vujkovic-Cvijin I first · Welles HC · Ha CWY · Huq L · Mistry S · Brenchley JM · Trinchieri G · Devkota S · Belkaid Y last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · Elmassry MM first · Sugihara K · Chankhamjon P · Kim Y · Camacho FR · Wang S · Sugimoto Y · Chatterjee S · Chen LA · Kamada N · Donia MS last
Downloads
PRJNA487636.csv.gz (7.1 KB) · parquet (81.1 KB) — all 180 samples, every field with route and confidence · PRJNA487636_determinations.csv.gz (18.4 KB) — 2,220 evidence rows