Diarrhea vs healthy stool metagenomes, Kolkata, case-control
75 stool samples from Kolkata, India, including 10 from diarrhea patients and 65 from healthy controls, analyzed by shotgun metagenomics and 16S rRNA amplicon sequencing in a case-control design. machine-written summary
75 samples · 75 runs · IN · Age unknown · 2025 · 12.58 Gbp / sample
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what each source gave
| ✓ Sequence archive | 525 sample values (collection date, country, health condition, health condition detail, location locality, subject id, timepoint) |
| – Abstract / description | no abstract or project description |
| – 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 |
longitudinal
13 of 13 people sampled more than once (75 samples; median 6, up to 6 per person) · follow-up median 15 d (max 2 mo) · median interval between samples 5 d (time from collection dates).
Each row is one person (13 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 72 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 | 0 | 0% | ||||
| country | 75 | 100% | 75 | |||
| health_condition | 75 | 100% | 75 | |||
| subject_id | 75 | 100% | 75 | |||
| collection_date | 75 | 100% | 75 | |||
| detailed_location | 75 | 100% | ||||
| health_condition_detail | 75 | 100% | 75 | |||
| location_locality | 75 | 100% | 75 | |||
| timepoint_label | 75 | 100% | 75 |
Archive description
Many diarrheagenic pathogens are endemic to Kolkata. To know the nature of stool microbial composition of the patients with diarrhea and healthy control people, we planned to perform this metagenomic project. We collected 75 samples, 10 of which were from patients with diarrhea. The extracted DNA samples were used to perform shotgun metagenomic analysis using Illumina NovaSeq6000 and 16S rRNA gene amplicon analysis using Illumina MiSeq.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “patients with diarrhea and healthy control people”
- body site study.description · “stool microbial composition”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00613860 | collection_date | 2021-07-05 | R1 | 0.90 | biosample.attribute:collection_date | 2021-07-05 |
| SAMD00613860 | country | IN | R1 | 0.90 | sample.attr.geo_loc_name | India:Kolkata |
| SAMD00613860 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | healthy |
| SAMD00613860 | health_condition_detail | healthy | R1 | 0.90 | sample.attr.health_state | healthy |
| SAMD00613860 | location_locality | Kolkata | R1 | 0.85 | biosample.attribute:geo_loc_name | India:Kolkata |
| SAMD00613860 | subject_id | C1 | R1 | 0.70 | sample.name_rule:TITLE | C1-1_1 |
| SAMD00613860 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:sample_name | C1-No.1_1 |
| SAMD00613893 | timepoint_label | P | R1 | 0.70 | sample.name_rule:TITLE | C20 P_1 |
Sequencing
75 runs over 75 samples · mean 12.80 Gbp per run (median 12.58 Gbp, total 960.06 Gbp; 75 runs with a base count) · layout PAIRED 75 · platform ILLUMINA 75 · models Illumina NovaSeq 6000 (75) · 96% of runs with a Sandpiper profile · first public 2025-05-23
Authors (0)
No author record.
Downloads
PRJDB15926.csv.gz (3.0 KB) · parquet (73.2 KB) — all 75 samples, every field with route and confidence · PRJDB15926_determinations.csv.gz (4.8 KB) — 525 evidence rows