Gut microbiome and MTX response in new-onset RA, USA
92 gut microbiome samples from adults (and a few elderly) in the USA, mostly with autoimmune/inflammatory conditions, studied for methotrexate treatment response in new-onset rheumatoid arthritis; case-control design. machine-written summary
92 samples · 92 runs · US · Adult · 2021 · 2.63 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 552 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 23 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10289814, PMC11293279, PMC9024311 |
| ✓ Supplementary tables | 4 sample values (age, sex) |
| ✓ External resources | 339 sample values (age, antibiotic exposure, 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 — not resolved
23 of 69 people sampled more than once (46 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 83 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 | 92 | 100% | ||||
| country | 92 | 100% | 92 | |||
| health_condition | 69 | 75% | 69 | |||
| subject_id | 92 | 100% | 92 | |||
| collection_date | 92 | 100% | 92 | |||
| detailed_location | 92 | 100% | ||||
| health_condition_detail | 92 | 100% | 69 | 23 | ||
| latitude | 92 | 100% | 92 | |||
| location_region | 92 | 100% | 92 | |||
| longitude | 92 | 100% | 92 | |||
| antibiotic_exposure | 69 | 75% | 69 | |||
| age_at_collection_days | 68 | 74% | 68 | |||
| sex | 68 | 74% | 68 |
- The Pretreatment Gut Microbiome Is Associated With Lack of Response to Methotrexate in New-Onset Rheumatoid Arthritis. 2021 PMID 33314800 PMC11293279 own_data
- The Potential of Gut Microbiota Metabolic Capability to Detect Drug Response in Rheumatoid Arthritis Patients. 2022 PMID 35464950 PMC9024311 unsure
- SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations. 2023 PMID 37306300 PMC10289814 unsure
Archive description
Although oral methotrexate (MTX) remains the anchor drug for RA, up to 50% of patients do not achieve a clinically adequate outcome. Concomitantly, there is a lack of prognostic tools for treatment response prior to drug initiation. Here we study whether inter-individual differences in the human gut microbiome can aid in the prediction of MTX efficacy in new-onset RA (NORA).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “human gut microbiome predicts response”
- life stage study.description · “new-onset RA (NORA)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17006387 | age_at_collection_days | 10227.0 | R2 | 0.75 | external.cmd source | age: 28; age_unit: (empty); age_group: Adult |
| SAMN17006402 | age_at_collection_days | 23741.2 | R2 | 0.85 | paper.supp.elife-82401-fig9-data1.xlsx[Figure9!Age] | 65 |
| SAMN17006387 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN17006387 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN17006387 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN17006387 | health_condition | autoimmune_inflammatory | R2 | 0.75 | external.cmd source | disease: Rheumatoid Arthritis |
| SAMN17006387 | health_condition_detail | Rheumatoid Arthritis | R2 | 0.75 | external.cmd source | disease: Rheumatoid Arthritis |
| SAMN17006456 | health_condition_detail | mixed_case_control: Study includes RA patients (cases) and an independent validation cohort; no explicit statement of co | R4 | 0.50 | paper.abstract | drug-naive patients with new-onset RA |
| SAMN17006387 | latitude | 40.7300 | R1 | 0.90 | biosample.attribute:lat_lon | 40.73 N 74.01 W |
| SAMN17006387 | location_region | New York | R1 | 0.60 | biosample.attribute:lat_lon | 40.73 N 74.01 W |
| SAMN17006387 | longitude | -74.0100 | R1 | 0.90 | biosample.attribute:lat_lon | 40.73 N 74.01 W |
| SAMN17006387 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMN17006456 | sex | female | R2 | 0.85 | paper.supp.elife-82401-fig9-data1.xlsx[Figure9!Gender] | F |
| SAMN17006387 | subject_id | 5 | R1 | 0.70 | sample.name_rule:alias | 5_metagenome_nextseq |
Sequencing
92 runs over 92 samples · mean 2.59 Gbp per run (median 2.63 Gbp, total 238.45 Gbp; 92 runs with a base count) · layout PAIRED 92 · platform ILLUMINA 92 · models NextSeq 550 (69), Illumina MiSeq (23) · 90% of runs with a Sandpiper profile · first public 2021-01-15
Authors (36)
Artacho A first · Isaac S · Nayak R · Flor-Duro A · Alexander M · Koo I · Manasson J · Smith PB · Rosenthal P · Homsi Y · Gulko P · Pons J · Puchades-Carrasco L · Izmirly P · Patterson A · Abramson SB · Pineda-Lucena A · Turnbaugh PJ · Ubeda C · Scher JU last · Han M first · Zhang N · Mao Y · Huang B · Ren M · Peng Z · Bai Z · Chen L · Liu Y · Wang S · Huang S · Cheng Z last · Bustion AE first · Nayak RR · Agrawal A · Pollard KS last
Downloads
PRJNA682730.csv.gz (3.8 KB) · parquet (75.4 KB) — all 92 samples, every field with route and confidence · PRJNA682730_determinations.csv.gz (10.1 KB) — 918 evidence rows