Gut metagenome in ulcerative colitis vs healthy, North India
Case-control study of 41 gut metagenome samples from North India (New Delhi, Delhi, Jind, Hazipur, Rohtak), comparing 27 samples from ulcerative colitis patients with 14 from healthy controls. machine-written summary
41 samples · 41 runs · IN · Adult · 2024 · 13.38 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 491 sample values (age, collection date, country, diet, diet detail, health condition, health condition detail, latitude) |
| ✓ Abstract / description | 47 sample values (location locality, location region, location site) |
| – Full text | no open-access full text linked |
| – 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 36 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 | 41 | 100% | ||||
| country | 41 | 100% | 41 | |||
| health_condition | 41 | 100% | 41 | |||
| subject_id | 41 | 100% | 41 | |||
| age_at_collection_days | 41 | 100% | 41 | |||
| collection_date | 41 | 100% | 41 | |||
| detailed_location | 41 | 100% | ||||
| health_condition_detail | 41 | 100% | 41 | |||
| latitude | 41 | 100% | 41 | |||
| location_locality | 41 | 100% | 36 | 5 | ||
| location_region | 41 | 100% | 40 | 1 | ||
| location_site | 41 | 100% | 41 | |||
| longitude | 41 | 100% | 41 | |||
| sex | 41 | 100% | 41 | |||
| diet | 23 | 56% | 23 | |||
| diet_detail | 23 | 56% | 23 |
Archive description
Metagenomic analysis of north Indian population was conducted in collaboration with medical centre Department of Gastroenterology, All India Institute Of Medical Sciences, New Delhi, India. Patients were recruited in the study after being diagnosed with ulcerative colitis (UC), and the healthy subjects were involved seperately. This study will establish association between healthy and UC patients. Unique patterns of microorganisms and/or presence of bacterial pathogens may be identified that could contribute to the pathogenesis of UC. Significant correlation between micobial composition and clinical disease activities of UC will be explored. Documentation of alterations of the microbiota in healthy and UC patients may provide a basis for targeting future therapies, monitoring disease state, and assessing response to medical therapy.
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 of ulcerative”
- body site external_curation.infant_catalog · “body_site_call gut”
- 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 |
|---|---|---|---|---|---|---|
| SAMN35739953 | age_at_collection_days | 7670.2 | R1 | 0.70 | sample.attr.host_age | 21 |
| SAMN35739953 | collection_date | 2021-02-19 | R1 | 0.90 | biosample.attribute:collection_date | 2021-02-19 |
| SAMN35739953 | country | IN | R1 | 0.90 | sample.attr.geo_loc_name | India:New Delhi |
| SAMN35739954 | diet | vegetarian | R1 | 0.90 | biosample.attribute:host_diet | Indian vegeterarian diet |
| SAMN35739954 | diet_detail | Indian vegeterarian diet | R1 | 0.90 | biosample.attribute:host_diet | Indian vegeterarian diet |
| SAMN35739953 | health_condition | ulcerative_colitis | R1 | 0.90 | biosample_attr | ulcerative colitis |
| SAMN35739980 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:gastrointest_disord | Healthy |
| SAMN35739953 | health_condition_detail | Ulcerative colitis | R1 | 0.90 | sample.attr.gastrointest_disord | Ulcerative colitis |
| SAMN35739953 | latitude | 28.5600 | R1 | 0.90 | biosample.attribute:lat_lon | 28.56 N 77.20 E |
| SAMN35739953 | location_locality | New Delhi | R1 | 0.85 | biosample.attribute:geo_loc_name | India:New Delhi |
| SAMN35739988 | location_locality | New Delhi | R4 | 0.45 | ena.study_description | All India Institute Of Medical Sciences, New Delhi |
| SAMN35739953 | location_region | Delhi | R1 | 0.85 | biosample.attribute:geo_loc_name | India:New Delhi |
| SAMN35739980 | location_region | Haryana | R1 | 0.60 | biosample.attribute:lat_lon | 29.31 N 76.31 E |
| SAMN35739992 | location_region | Northern India | R4 | 0.40 | ena.study_title | stool samples from Northern India |
| SAMN35739953 | location_site | All India Institute of Medical Sciences, Department of Gastroenterology | R4 | 0.45 | ena.study_description | Department of Gastroenterology, All India Institute Of Medical Sciences |
| SAMN35739953 | longitude | 77.2000 | R1 | 0.90 | biosample.attribute:lat_lon | 28.56 N 77.20 E |
| SAMN35739953 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN35739953 | subject_id | AM03 | R1 | 0.85 | sample.attr.host_subject_id | AM03 |
Sequencing
41 runs over 41 samples · mean 14.31 Gbp per run (median 13.38 Gbp, total 586.72 Gbp; 41 runs with a base count) · layout PAIRED 41 · platform ILLUMINA 41 · models Illumina NovaSeq 6000 (41) · 88% of runs with a Sandpiper profile · first public 2024-07-02
Authors (0)
No author record.
Downloads
PRJNA983946.csv.gz (2.7 KB) · parquet (74.2 KB) — all 41 samples, every field with route and confidence · PRJNA983946_determinations.csv.gz (5.0 KB) — 538 evidence rows