Gut metagenome in osteoarthritis, case-control, China
10 fecal metagenome samples from adults in China, studied as a case-control comparison of osteoarthritis patients and healthy volunteers. machine-written summary
10 samples · 10 runs · CN · Adult · 2022 · 8.64 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 | 20 sample values (collection date, country) |
| ✓ Abstract / description | 10 sample values (health condition detail) |
| ✓ Full text | 10 sample values (antibiotic exposure) · PMC9927108 |
| ○ 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 10 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 | 10 | 100% | ||||
| country | 10 | 100% | 10 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 10 | 100% | 10 | |||
| collection_date | 10 | 100% | 10 | |||
| health_condition_detail | 10 | 100% | 10 |
- Characterizations of the Gut Bacteriome, Mycobiome, and Virome in Patients with Osteoarthritis. 2023 PMID 36515546 PMC9927108 own_data
- Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis. 2024 PMID 38872164 PMC11170907 unsure
Archive description
The gut microbiota plays an essential role in the regulation of the immune system and the etiology of human autoimmune diseases. However, a holistic understanding of the gut bacteriome, mycobiome, and virome in patients with osteoarthritis (OA) remains lacking. Here we explored the gut microbiota of 20 OA patients and 28 healthy volunteers via deep whole-metagenome shotgun sequencing of their fecal samples. The gut bacteriome and mycobiome were analyzed using a reference-based strategy. Gut viruses were identified from the metagenomic assembled contigs, and the gut virome was profiled based on 9,140 non-redundance viral operational taxonomic units. We showed that the multi-kingdom signatures are effective in discriminating the OA patients from healthy controls, suggesting the potential of gut microbiota in the prediction of OA and related diseases.
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.description · “The gut microbiota plays an”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “and 28 healthy volunteers via deep whole-metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA14270344 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | received antibiotics, antifungals, or probiotic treatment within 1 month |
| SAMEA14270344 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMEA14270344 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA14270344 | health_condition_detail | mixed_case_control: osteoarthritis patients vs healthy controls | R4 | 0.50 | study.description | 20 OA patients and 28 healthy volunteers |
Sequencing
10 runs over 10 samples · mean 9.10 Gbp per run (median 8.64 Gbp, total 90.97 Gbp; 10 runs with a base count) · layout PAIRED 10 · platform ILLUMINA 10 · models Illumina HiSeq X (10) · 100% of runs with a Sandpiper profile · first public 2022-04-29 – 2022-04-30
Authors (33)
Chen C first · Zhang Y · Yao X · Li S · Wang G · Huang Y · Yang Y · Zhang A · Liu C · Zhu D · Li H · Yan Q · Ma W last · Chen CM first · Yan QL · Guo RC · Tang F · Wang MH · Yi HZ · Huang CX · Wang QY · Lan WY · Jiang Z · Yang YZ · Wang GY · Zhang AQ · Ma J · You W · Ullah H · Li SH · Yao XM · Sun W · Ma WK last
Downloads
PRJEB52499.csv.gz (1.1 KB) · parquet (69.4 KB) — all 10 samples, every field with route and confidence · PRJEB52499_determinations.csv.gz (854 B) — 40 evidence rows