Gut microbiome & clinical improvement in RA, US, long.
32 stool samples from adult and elderly rheumatoid arthritis patients in the USA, studied longitudinally to identify gut microbiome features associated with minimum clinically important improvement in disease activity. machine-written summary
32 samples · 32 runs · US · Adult · 2021 · 6.64 Gbp / sample · cohort Gut microbial determinants of clinically important
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 192 sample values (age, collection date, country, sex, subject id, timepoint) |
| ✓ Abstract / description | 64 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC8439035 |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 30 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 | 32 | 100% | ||||
| country | 32 | 100% | 32 | |||
| health_condition | 32 | 100% | 32 | |||
| subject_id | 32 | 100% | 32 | |||
| age_at_collection_days | 32 | 100% | 32 | |||
| collection_date | 32 | 100% | 32 | |||
| health_condition_detail | 32 | 100% | 32 | |||
| sex | 32 | 100% | 32 | |||
| timepoint_label | 32 | 100% | 32 |
- Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis. 2021 PMID 34517888 PMC8439035 unsure
Archive description
Within the past decade, several studies have shown that dysbiosis of the gut microbiome is a key hallmark of rheumatoid arthritis (RA). Yet, the relationship between gut microbiome and clinical improvement in the disease activity of patients with RA remains. In this study, we explored the gut microbiome of patients with RA to identify features that are associated with, as well as predictive of, minimum clinically important improvement (MCII) in disease activity.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly 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 Microbial Determinants of”
- body site study.description · “dysbiosis of the gut microbiome is a”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.host_age · “65 (n=18/32)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17161291 | age_at_collection_days | 20434.0 | R1 | 0.85 | sample.attr.host_age | 56 |
| SAMN17161291 | collection_date | 2014-12-23 | R1 | 0.90 | biosample.attribute:collection_date | 2014-12-23 |
| SAMN17161291 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN17161291 | health_condition | autoimmune_inflammatory | R4 | 0.50 | study.description | patients with RA |
| SAMN17161291 | health_condition_detail | Rheumatoid arthritis | R4 | 0.50 | study.description | patients with RA |
| SAMN17161291 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN17161291 | subject_id | RHB_RAM_0004_V-2 | R1 | 0.85 | sample.attr.host_subject_id | RHB_RAM_0004_V-2 |
| SAMN17161291 | timepoint_label | V-2 | R1 | 0.70 | sample.name_rule:host_subject_id | RHB_RAM_0004_V-2 |
Sequencing
32 runs over 32 samples · mean 6.62 Gbp per run (median 6.64 Gbp, total 211.73 Gbp; 32 runs with a base count) · layout PAIRED 32 · platform ILLUMINA 32 · models Illumina HiSeq 4000 (32) · 94% of runs with a Sandpiper profile · first public 2021-04-02
Authors (10)
Gupta VK first · Cunningham KY · Hur B · Bakshi U · Huang H · Warrington KJ · Taneja V · Myasoedova E · Davis JM · Sung J last
Downloads
PRJNA687957.csv.gz (2.1 KB) · parquet (71.6 KB) — all 32 samples, every field with route and confidence · PRJNA687957_determinations.csv.gz (2.8 KB) — 256 evidence rows