Gut microbiome in melioidosis patients vs controls, India
86 fecal samples from melioidosis patients and community controls in Manipal, Karnataka, India, profiling gut microbiota and resistome longitudinally from diagnosis through 6 months postinfection; case-control design. machine-written summary
86 samples · 86 runs · IN · Adult · 2025 · 5.44 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 704 sample values (age, collection date, country, health condition, health condition detail, location locality, location region, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 86 sample values (location site) · PMC11568386 |
| ○ 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 |
intervention — arms not resolved
design observational_with_procedure
longitudinal
24 of 44 people sampled more than once (66 samples; median 3, up to 3 per person) · follow-up median 5 mo (max 4.0 y) · median interval between samples 12 d (time from collection dates). Schedule stated by the source: “Cases sampled at diagnosis (Day 1), Day 14, and Month 6; controls sampled once.”; stated follow-up 6 mo.
Each row is one person (24 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 85 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 | 86 | 100% | ||||
| country | 86 | 100% | 86 | |||
| health_condition | 16 | 19% | 16 | |||
| subject_id | 86 | 100% | 86 | |||
| age_at_collection_days | 86 | 100% | 86 | |||
| collection_date | 86 | 100% | 86 | |||
| detailed_location | 86 | 100% | ||||
| location_locality | 86 | 100% | 86 | |||
| location_region | 86 | 100% | 86 | |||
| location_site | 86 | 100% | 86 | |||
| sex | 86 | 100% | 86 | |||
| timepoint_label | 70 | 81% | 70 | |||
| health_condition_detail | 16 | 19% | 16 |
- Gut Microbiome in Human Melioidosis: Composition and Resistome Dynamics from Diagnosis to Discovery. 2024 PMID 39553288 PMC11568386 own_data
Archive description
The goal is to evaluate the longitudinal alterations in the gut microbiome of melioidosis patients following antibiotic treatment, in comparison to healthy individuals in India.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Human Fecal Sample: Melioidosis”
- life stage sample.attr.age · “43 (n=79/86)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40560872 | age_at_collection_days | 6574.5 | R1 | 0.70 | sample.attr.age | 18 |
| SAMN40560872 | collection_date | 2020-06-27 | R1 | 0.90 | biosample.attribute:collection_date | 2020-06-27 |
| SAMN40560872 | country | IN | R1 | 0.90 | sample.attr.geo_loc_name | India: Karnataka, Manipal |
| SAMN40560942 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | Control SP 1 |
| SAMN40560942 | health_condition_detail | Control SP | R1 | 0.70 | sample.name_rule:alias | Control SP 1 |
| SAMN40560872 | location_locality | Manipal | R1 | 0.85 | biosample.attribute:geo_loc_name | India: Karnataka, Manipal |
| SAMN40560872 | location_region | Karnataka | R1 | 0.85 | biosample.attribute:geo_loc_name | India: Karnataka, Manipal |
| SAMN40560872 | location_site | Kasturba Hospital | R3 | 0.70 | paper.fulltext.methods | prospective observational study at Kasturba Hospital (Manipal, India) |
| SAMN40560872 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN40560872 | subject_id | Case 1 | R1 | 0.70 | sample.name_rule:alias | Case 1 Day 1 |
| SAMN40560872 | timepoint_label | Day 1 | R1 | 0.70 | sample.name_rule:alias | Case 1 Day 1 |
Sequencing
86 runs over 86 samples · mean 5.99 Gbp per run (median 5.44 Gbp, total 515.44 Gbp; 86 runs with a base count) · layout PAIRED 86 · platform ILLUMINA 86 · models Illumina NovaSeq X (86) · 99% of runs with a Sandpiper profile · first public 2025-05-28
Authors (9)
Chowdhury S first · Kullberg RFJ · Haak BW · Duran C · Earny VA · Eshwara VK · Lawley TD · Wiersinga WJ · Mukhopadhyay C last
Downloads
PRJNA1090271.csv.gz (3.8 KB) · parquet (75.3 KB) — all 86 samples, every field with route and confidence · PRJNA1090271_determinations.csv.gz (7.4 KB) — 790 evidence rows