Gut microbiome and methotrexate response in early RA
113 gut microbiome samples from treatment-naive rheumatoid arthritis patients, studying gut microbiome associations with methotrexate response using a cross-sectional design. machine-written summary
113 samples · 113 runs · US · Adult · 2026 · 15.81 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 678 sample values (collection date, country, latitude, location region, longitude, timepoint) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design observational_with_procedure · population autoimmune_inflammatory · Oral methotrexate in treatment-naive RA patients
“Oral methotrexate (MTX) is the first-line treatment for newly diagnosed rheumatoid arthritis” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Baseline and Follow-up stool samples per patient (per sample titles/descriptions, e.g. RA-MTX27-Baseline, RA-MTX84-Follow-up)” (time origin: treatment_start).
Genera, mean relative abundance over 106 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 | 113 | 100% | ||||
| country | 113 | 100% | 113 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 113 | 100% | 113 | |||
| detailed_location | 113 | 100% | ||||
| latitude | 113 | 100% | 113 | |||
| location_region | 113 | 100% | 113 | |||
| longitude | 113 | 100% | 113 | |||
| timepoint_label | 113 | 100% | 113 |
Archive description
Oral methotrexate (MTX) is the first-line treatment for newly diagnosed rheumatoid arthritis (RA) patients. However, up to 50% of patients do not respond adequately to MTX and need other therapeutic interventions. Failure to respond to MTX during the first three months, which is known as the critical window of opportunity for effective RA treatment, can significantly impact disease progression. Therefore, accurately predicting MTX response is crucial for managing RA disease progression. Recent studies have revealed an association between the gut microbiome and the response to MTX in treatment-naive RA patients. However, most of these studies primarily used 16S rRNA gene amplicon sequencing data, which primarily provides taxonomic resolution at the genus level. One study utilized whole-genome shotgun (WGS) sequencing data, but it did not employ WGS-based taxonomic profiles to identify its association with the MTX response. Additionally, this study applied an arbitrary criterion to determine MTX response instead of using the standardized EULAR response criteria, which limits the clinical translation of its findings. Our study aims to address these limitations and more thoroughly investigate whether the gut microbiome can reliably predict MTX response in treatment-naive RA patients.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut Microbiome Signatures Forecast”
- body site study.description · “association between the gut microbiome and the”
- body site study.description · “Oral methotrexate (MTX) is”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN55926658 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN55926658 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN55926658 | latitude | 44.0193 | R1 | 0.90 | biosample.attribute:lat_lon | 44.0193 N 92.4588 W |
| SAMN55926658 | location_region | Minnesota | R1 | 0.60 | biosample.attribute:lat_lon | 44.0193 N 92.4588 W |
| SAMN55926658 | longitude | -92.4588 | R1 | 0.90 | biosample.attribute:lat_lon | 44.0193 N 92.4588 W |
| SAMN55926658 | timepoint_label | Baseline | R1 | 0.85 | biosample.attribute:description | Baseline |
Sequencing
113 runs over 113 samples · mean 15.36 Gbp per run (median 15.81 Gbp, total 1,735.94 Gbp; 113 runs with a base count) · layout PAIRED 113 · platform ILLUMINA 113 · models Illumina HiSeq 4000 (113) · 94% of runs with a Sandpiper profile · first public 2026-03-04
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1427647.csv.gz (3.6 KB) · parquet (73.9 KB) — all 113 samples, every field with route and confidence · PRJNA1427647_determinations.csv.gz (4.1 KB) — 678 evidence rows