Gut metagenome in rheumatoid arthritis, Hangzhou, China
168 gut metagenome samples from Hangzhou, China (90 autoimmune/inflammatory, 78 healthy controls), studied as a case-control design to examine associations between rheumatoid arthritis, gut microbiome enterotypes, and methotrexate drug-metabolism gene composition. machine-written summary
168 samples · 168 runs · CN · Adult · 2016 · 6.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,152 sample values (collection date, country, health condition, health condition detail, latitude, location locality, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11009399, PMC9024311 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 832 sample values (age, antibiotic exposure, bmi, 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 |
health condition: curatedMetagenomicData and GMrepo disagree for 6 samples (e.g. healthy_control vs autoimmune_inflammatory) — withheld.
The sources disagree on 6 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (6)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN06112084 | health condition | healthy_control (curatedMetagenomicData) | autoimmune_inflammatory (GMrepo) | withheld: neither value published |
| SAMN06112085 | health condition | healthy_control (curatedMetagenomicData) | autoimmune_inflammatory (GMrepo) | withheld: neither value published |
| SAMN06112092 | health condition | healthy_control (curatedMetagenomicData) | autoimmune_inflammatory (GMrepo) | withheld: neither value published |
| SAMN06112093 | health condition | healthy_control (curatedMetagenomicData) | autoimmune_inflammatory (GMrepo) | withheld: neither value published |
| SAMN06112094 | health condition | healthy_control (curatedMetagenomicData) | autoimmune_inflammatory (GMrepo) | withheld: neither value published |
| SAMN06112095 | health condition | healthy_control (curatedMetagenomicData) | autoimmune_inflammatory (GMrepo) | withheld: neither value published |
Genera, mean relative abundance over 149 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 | 168 | 100% | ||||
| country | 168 | 100% | 168 | |||
| health_condition | 162 | 96% | 72 | 90 | ||
| subject_id | 168 | 100% | 168 | |||
| collection_date | 168 | 100% | 168 | |||
| detailed_location | 168 | 100% | ||||
| health_condition_detail | 168 | 100% | 72 | 96 | ||
| latitude | 168 | 100% | 168 | |||
| location_locality | 168 | 100% | 168 | |||
| longitude | 168 | 100% | 168 | |||
| antibiotic_exposure | 162 | 96% | 162 | |||
| sex | 162 | 96% | 162 | |||
| age_at_collection_days | 161 | 96% | 161 | |||
| bmi | 161 | 96% | 161 |
- The Potential of Gut Microbiota Metabolic Capability to Detect Drug Response in Rheumatoid Arthritis Patients. 2022 PMID 35464950 PMC9024311 unsure
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. 2024 PMID 38605009 PMC11009399 unsure
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023 unsure
Archive description
Gut microbiome make contributions to human host, and intestinal dysbiosis is associated with rheumatoid arthritis. Here we firstly demonstrated that the human gut microbiome related to rheumatoid arthritis could be divided into subtyping groups under different human enterotypes, which indicate the associations between rheumatoid arthritis and gut microbiome were diverse. In rheumatoid arthritis-related microbiota, Prevotella could be an indicator of early rheumatoid arthritis patients but insufficient to differentiate RA patients from healthy controls, and Bacteroides coprocola enriched in group 3 and Bacteroides dorei enriched in group 4 were considered to be as indicators of serious rheumatoid arthritis patients. Our findings provide additional evidences supporting that rheumatoid arthritis is a heterogeneous disease. Thus, the study of association between disease and gut microbiome should be conducted under different human gut enterotypes.
How this project entered the registry
Classified as human gut / stool 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 · “human gut metagenome in RA”
- body site study.description · “Gut microbiome make contributions”
- 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 |
|---|---|---|---|---|---|---|
| SAMN06111928 | age_at_collection_days | 9131.25 | R2 | 0.75 | external.cmd source | age: 25; age_unit: (empty); age_group: Adult |
| SAMN06111928 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN06111928 | bmi | 22.21 | R2 | 0.75 | external.cmd source | bmi: 22.21 |
| SAMN06111928 | collection_date | 2015-10 | R1 | 0.90 | biosample.attribute:collection_date | 2015-10 |
| SAMN06111928 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China:Hangzhou |
| SAMN06111928 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:env_material | healthy_person |
| SAMN06111978 | health_condition | autoimmune_inflammatory | R2 | 0.75 | external.cmd source | disease: Rheumatoid Arthritis |
| SAMN06111928 | health_condition_detail | healthy_person | R1 | 0.85 | biosample.attribute:env_material | healthy_person |
| SAMN06111978 | health_condition_detail | Rheumatoid Arthritis | R2 | 0.75 | external.cmd source | disease: Rheumatoid Arthritis |
| SAMN06111928 | latitude | 30.3000 | R1 | 0.90 | biosample.attribute:lat_lon | 30.3 N 120.2 E |
| SAMN06111928 | location_locality | Hangzhou | R1 | 0.85 | biosample.attribute:geo_loc_name | China:Hangzhou |
| SAMN06111928 | longitude | 120.2000 | R1 | 0.90 | biosample.attribute:lat_lon | 30.3 N 120.2 E |
| SAMN06111928 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMN06111928 | subject_id | N005 | R1 | 0.85 | biosample.attribute:alias | N005 |
Sequencing
168 runs over 168 samples · mean 7.14 Gbp per run (median 6.39 Gbp, total 1,198.73 Gbp; 168 runs with a base count) · layout PAIRED 168 · platform ILLUMINA 168 · models Illumina HiSeq 2000 (168) · 89% of runs with a Sandpiper profile · first public 2016-12-15
Authors (54)
Pasolli E first · Asnicar F · Manara S · Zolfo M · Karcher N · Armanini F · Beghini F · Manghi P · Tett A · Ghensi P · Collado MC · Rice BL · DuLong C · Morgan XC · Golden CD · Quince C · Huttenhower C · Segata N 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 · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · Zorea A first · Pellow D · Levin L · Pilosof S · Friedman J · Shamir R · Mizrahi I last
Downloads
PRJNA356102.csv.gz (6.3 KB) · parquet (79.4 KB) — all 168 samples, every field with route and confidence · PRJNA356102_determinations.csv.gz (19.1 KB) — 1,984 evidence rows