Gut microbiome in ankylosing spondylitis, China
97 fecal samples from Chinese individuals with ankylosing spondylitis, part of a case-control shotgun metagenomics study comparing patients (97) and healthy controls (104) to identify differentially abundant genes and metagenomic species. machine-written summary
97 samples · 97 runs · CN · Age unknown · 2016 · 4.13 Gbp / sample · cohort Quantitative metagenomics reveals unique gut micro
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 582 sample values (collection date, country, health condition, health condition detail, latitude, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC5530561 |
| ✓ Supplementary tables | 290 sample values (age, bmi, sex) |
| – 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 89 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 | 97 | 100% | ||||
| country | 97 | 100% | 97 | |||
| health_condition | 97 | 100% | 97 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 97 | 100% | 97 | |||
| collection_date | 97 | 100% | 97 | |||
| health_condition_detail | 97 | 100% | 97 | |||
| latitude | 97 | 100% | 97 | |||
| longitude | 97 | 100% | 97 | |||
| sex | 97 | 100% | 97 | |||
| bmi | 96 | 99% | 96 |
- Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis. 2017 PMID 28750650 PMC5530561 own_data
Archive description
To reveal the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study that was based on deep shotgun sequencing of the gut microbial DNA from 211 Chinese individuals (97 patients and 104 healthy controls) was carried out. A total of 23,709 genes and 16 metagenomic species that were differentially abundant in the two groups were identified.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “Human gut microbiome in AS”
- body site study.description · “gut microbial DNA from 211 Chinese individuals”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06016327 | age_at_collection_days | 14975.0 | R2 | 0.85 | paper.supp.13059_2017_1271_MOESM1_ESM.xlsx[Table S1!Age] | AS100: 41 |
| SAMN06016327 | bmi | 19.72 | R2 | 0.85 | paper.supp.13059_2017_1271_MOESM1_ESM.xlsx[Table S1!BMI (kg/m2)] | AS100: 19.721036967980208 |
| SAMN06016327 | collection_date | 2015-04 | R1 | 0.90 | biosample.attribute:collection_date | 2015-04 |
| SAMN06016327 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China |
| SAMN06016327 | health_condition | autoimmune_inflammatory | R1 | 0.85 | biosample.attribute:env_feature | env_feature: ankylosing spondylitis patient |
| SAMN06016327 | health_condition_detail | ankylosing spondylitis patient | R1 | 0.85 | biosample.attribute:env_feature | env_feature: ankylosing spondylitis patient |
| SAMN06016327 | latitude | 30.3000 | R1 | 0.90 | biosample.attribute:lat_lon | 30.3 N 120.2 E |
| SAMN06016327 | longitude | 120.2000 | R1 | 0.90 | biosample.attribute:lat_lon | 30.3 N 120.2 E |
| SAMN06016327 | sex | male | R2 | 0.85 | paper.supp.13059_2017_1271_MOESM1_ESM.xlsx[Table S1!Gender] | AS100: M |
Sequencing
97 runs over 97 samples · mean 4.37 Gbp per run (median 4.13 Gbp, total 423.78 Gbp; 97 runs with a base count) · layout PAIRED 97 · platform ILLUMINA 97 · models Illumina HiSeq 2000 (97) · 92% of runs with a Sandpiper profile · first public 2016-11-25
Authors (0)
No author record.
Downloads
PRJNA353560.csv.gz (3.9 KB) · parquet (75.0 KB) — all 97 samples, every field with route and confidence · PRJNA353560_determinations.csv.gz (8.0 KB) — 872 evidence rows