Rheumatoid arthritis gut/saliva microbiome on DMARD therapy
Longitudinal study of 726 stool and saliva samples from DMARD-naive rheumatoid arthritis patients (adults and elderly), collected at baseline and during the first 12 weeks of DMARD treatment initiation. machine-written summary
726 samples · 726 runs · GB · Adult · 2024 · 8.04 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,066 sample values (age, bmi, health condition, health condition detail, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 2,178 sample values (collection date, country, location region) · PMC11637416 |
| ○ 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 |
longitudinal
119 of 145 people sampled more than once (330 samples; median 3, up to 3 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 42 d (time from visit codes mapped to the stated schedule). Schedule stated by the source: “stool and saliva at baseline, 6 weeks and 12 weeks post-DMARD initiation” (time origin: treatment_start); stated follow-up 3 mo.
Each row is one person (36 shown of 119); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 329 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 | 726 | 100% | ||||
| country | 726 | 100% | 726 | |||
| health_condition | 726 | 100% | 726 | |||
| subject_id | 726 | 100% | 726 | |||
| collection_date | 726 | 100% | 726 | |||
| detailed_location | 726 | 100% | ||||
| health_condition_detail | 726 | 100% | 726 | |||
| location_region | 726 | 100% | 726 | |||
| timepoint_label | 726 | 100% | 726 | |||
| bmi | 723 | 100% | 723 | |||
| sex | 722 | 99% | 722 | |||
| age_at_collection_days | 717 | 99% | 717 |
- Treatment response in rheumatoid arthritis is predicted by the microbiome: a large observational study in UK DMARD-naive patients. 2024 PMID 38291926 PMC11637416 own_data
Archive description
The Influence of Methotrexate on the Rheumatoid Arthritis Microbiome (IMRABIOME) study was a longitudinal, observational study of microbiota changes observed in DMARD-naive newly diagnosed RA patients during the introduction of DMARD treatment. Participants were assessed at baseline (n=144), at six weeks (n=117) and at 12 weeks (n=95) post-DMARD treatment initiation. The study cohort comprised 72.9% females and 63.8% Northern-Europeans demographic, full medical and metagenomic data were available at all three timepoints for 92 participants. Intestinal (stool) and saliva samples were collected at the three timepoints for shotgun metagenomics alongside clinical markers and relevant clinical, demographic and lifestyle information
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult and elderly by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- host study.description · “newly diagnosed RA patients”
- body site study.description · “Intestinal (stool) and saliva samples”
- life stage sample.attr.age · “59 (n=536/726)”
- life stage sample.attr.age · “64 (n=181/726)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN34245922 | age_at_collection_days | 21549.8 | R1 | 0.70 | sample.attr.age | 59 |
| SAMN34245922 | bmi | 23.71 | R1 | 0.90 | sample.attr.bmi | 23.70612 |
| SAMN34245922 | collection_date | 2017-04/2019-07 | R3 | 0.70 | paper.fulltext.methods | Recruitment was undertaken between April 2017 and July 2019 |
| SAMN34245922 | country | GB | R3 | 0.70 | paper.fulltext.methods | 12 outpatient rheumatology clinics in England, UK |
| SAMN34245922 | health_condition | autoimmune_inflammatory | R1 | 0.90 | biosample_attr | Rheumatoid arthritis |
| SAMN34245922 | health_condition_detail | Rheumatoid arthritis | R1 | 0.90 | sample.attr.disease | Rheumatoid arthritis |
| SAMN34245922 | location_region | England | R3 | 0.70 | paper.fulltext.methods | 12 outpatient rheumatology clinics in England, UK |
| SAMN34245922 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN34245922 | subject_id | SITE8-003 | R1 | 0.85 | biosample.attribute:id_and_site | SITE8-003 |
| SAMN34245922 | timepoint_label | BL | R1 | 0.85 | sample.attr.time | BL |
Sequencing
726 runs over 726 samples · mean 8.16 Gbp per run (median 8.04 Gbp, total 5,924.41 Gbp; 726 runs with a base count) · layout PAIRED 726 · platform ILLUMINA 726 · models Illumina NovaSeq 6000 (726) · 92% of runs with a Sandpiper profile · first public 2024-03-01
Authors (9)
Danckert NP first · Freidin MB · Granville Smith I · Wells PM · Naeini MK · Visconti A · Compte R · MacGregor A · Williams FMK last
Downloads
PRJNA957107.csv.gz (20.7 KB) · parquet (98.3 KB) — all 726 samples, every field with route and confidence · PRJNA957107_determinations.csv.gz (47.5 KB) — 7,244 evidence rows