Gut multi-kingdom microbiome in gouty arthritis, China
Case-control study of 26 stool samples from adults in China, comparing gut bacteriome, mycobiome, and virome between gouty arthritis patients and healthy controls via whole-metagenome shotgun sequencing. machine-written summary
26 samples · 26 runs · CN · Adult · 2023 · 9.42 Gbp / sample · cohort Distinct characteristics of the gut virome in pati
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 156 sample values (collection date, country, health condition, health condition detail, latitude, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 78 sample values (antibiotic exposure, location site, subject id) · PMC10668524 |
| ○ 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 |
Genera, mean relative abundance over 24 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 | 26 | 100% | ||||
| country | 26 | 100% | 26 | |||
| health_condition | 26 | 100% | 26 | |||
| subject_id | 26 | 100% | 26 | |||
| antibiotic_exposure | 26 | 100% | 26 | |||
| collection_date | 26 | 100% | 26 | |||
| detailed_location | 26 | 100% | ||||
| health_condition_detail | 26 | 100% | 26 | |||
| latitude | 26 | 100% | 26 | |||
| location_site | 26 | 100% | 26 | |||
| longitude | 26 | 100% | 26 |
- Characterizations of the multi-kingdom gut microbiota in Chinese patients with gouty arthritis. 2023 PMID 38001408 PMC10668524 own_data
- Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis. 2024 PMID 38872164 PMC11170907 unsure
Archive description
The dysbiotic gut microbial composition has been associated with autoimmune diseases in humans, especially patients with arthritis. However, the holistic investigation of the gut bacteriome, mycobiome, and virome in patients with gouty arthritis (GA) remains unclear. In this study, we characterized the multi-kingdom gut microbiome of 25 GA patients and 28 healthy subjects via whole-metagenome shotgun sequencing of their stool samples. We found that the gut bacteriome, mycobiome, and virome of GA patients were substantially altered, characterized by a panel of 1,117 differentially abundant bacterial species, 23 fungal species, and 4,115 viral operational taxonomic units. Our findings uncovered the fecal bacteriome, mycobiome, and virome features of the GA microbiota, which may promote future mechanistic and therapeutic works.
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 · “characterization of the gut microbiota in patients”
- body site study.description · “The dysbiotic gut microbial composition has”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA113939220 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | received antibiotics, antifungals, or probiotics treatment in 1 month |
| SAMEA113939220 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMEA113939220 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA113939220 | health_condition | autoimmune_inflammatory | R1 | 0.85 | biosample.attribute:description | gouty arthritis (GA) |
| SAMEA113939220 | health_condition_detail | gouty arthritis (GA) | R1 | 0.85 | biosample.attribute:description | gouty arthritis (GA) |
| SAMEA113939220 | latitude | 39.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39 122 |
| SAMEA113939220 | location_site | Second Affiliated Hospital of Guizhou University of Chinese Medicine | R3 | 0.70 | paper.fulltext.methods | Second Affiliated Hospital of Guizhou University of Chinese Medicine, China |
| SAMEA113939220 | longitude | 122.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 39 122 |
| SAMEA113939220 | subject_id | SAMEA113939220 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Twenty-six gouty arthritis patients admitted to the Department of Rheumatology and Immunology |
Sequencing
26 runs over 26 samples · mean 9.57 Gbp per run (median 9.42 Gbp, total 248.90 Gbp; 26 runs with a base count) · layout PAIRED 26 · platform ILLUMINA 26 · models Illumina NovaSeq 6000 (26) · 92% of runs with a Sandpiper profile · first public 2023-06-26 – 2023-06-29
Authors (43)
Chen C first · Zhang Y · Yao X · Yan Q · Li S · Zhong Q · Liu Z · Tang F · Liu C · Li H · Zhu D · Lan W · Ling Y · Lu D · Xu H · Ning Q · Wang Y · Jiang Z · Zhang Q · Gu G · Sun L · Wang N · Wang G · Zhang A · Ullah H · Sun W · Ma W last · Chen CM first · Yan QL · Guo RC · Wang MH · Yi HZ · Huang CX · Wang QY · Lan WY · Yang YZ · Wang GY · Zhang AQ · Ma J · You W · Li SH · Yao XM · Ma WK last
Downloads
PRJEB58696.csv.gz (1.7 KB) · parquet (71.7 KB) — all 26 samples, every field with route and confidence · PRJEB58696_determinations.csv.gz (2.4 KB) — 234 evidence rows