HSCT patients' gut microbiomes, longitudinal, Vellore, India
262 MacConkey-enriched stool samples from adult patients undergoing allogenic or haploidentical haematopoietic stem cell transplantation at a single centre in Vellore, India, collected longitudinally. machine-written summary
262 samples · 262 runs · IN · Adult · 2024 · 3.94 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,092 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 524 sample values (health condition, health condition detail) |
| – 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
71 of 89 people sampled more than once (242 samples; median 3, up to 7 per person) · follow-up median 35 d (max 6 mo) · median interval between samples 10 d (time from collection dates). Schedule stated by the source: “before and after transplant timepoints (e.g. BT/AT codes); specific day offsets not stated” (time origin: transplant).
Each row is one person (36 shown of 71); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 229 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 | 262 | 100% | ||||
| country | 262 | 100% | 262 | |||
| health_condition | 262 | 100% | 262 | |||
| subject_id | 260 | 99% | 260 | |||
| collection_date | 262 | 100% | 262 | |||
| detailed_location | 262 | 100% | ||||
| health_condition_detail | 262 | 100% | 262 | |||
| latitude | 262 | 100% | 262 | |||
| location_locality | 262 | 100% | 262 | |||
| location_region | 262 | 100% | 262 | |||
| longitude | 262 | 100% | 262 | |||
| timepoint_label | 260 | 99% | 260 |
- Gut translocation of antimicrobial resistant pathogens in patients undergoing haematopoietic stem cell transplantation in India 2025 own_data
- Stool-based genomic surveillance identifies post-engraftment expansion of multidrug-resistant pathogens in haematopoietic stem cell transplant patients in India 2026 own_data
Archive description
MacConkey-enriched plate-sweeps of longitudinal stool samples collected from patients undergoing allogenic or haploidentical haematopoietic stem cell transplantation at a single centre in India.
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 · “plate-sweeps of longitudinal stool samples collected from”
- 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 |
|---|---|---|---|---|---|---|
| SAMN39752622 | collection_date | 2022-06-13 | R1 | 0.90 | biosample.attribute:collection_date | 2022-06-13 |
| SAMN39752622 | country | IN | R1 | 0.90 | sample.attr.geo_loc_name | India: Vellore |
| SAMN39752622 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | study.description | patients undergoing allogenic or haploidentical haematopoietic stem cell transplantation |
| SAMN39752622 | health_condition_detail | Patients undergoing haematopoietic stem cell transplantation (allogeneic or haploidentical) | R4 | 0.50 | study.description | patients undergoing allogenic or haploidentical haematopoietic stem cell transplantation |
| SAMN39752622 | latitude | 12.9165 | R1 | 0.90 | biosample.attribute:lat_lon | 12.9165 N 79.1325 E |
| SAMN39752622 | location_locality | Vellore | R1 | 0.85 | biosample.attribute:geo_loc_name | India: Vellore |
| SAMN39752622 | location_region | Tamil Nadu | R1 | 0.60 | biosample.attribute:lat_lon | 12.9165 N 79.1325 E |
| SAMN39752622 | longitude | 79.1325 | R1 | 0.90 | biosample.attribute:lat_lon | 12.9165 N 79.1325 E |
| SAMN39752622 | subject_id | 01 | R1 | 0.70 | sample.name_rule:alias | P01BT0041 |
| SAMN39752622 | timepoint_label | BT0041 | R1 | 0.70 | sample.name_rule:alias | P01BT0041 |
Sequencing
262 runs over 262 samples · mean 4.09 Gbp per run (median 3.94 Gbp, total 1,070.70 Gbp; 262 runs with a base count) · layout PAIRED 262 · platform ILLUMINA 262 · models Illumina NovaSeq 6000 (262) · 87% of runs with a Sandpiper profile · first public 2024-02-07
Authors (12)
Madhav A first · Jacob JJ · Selvarajan S · Kulkarni S · Murugan D · Narayanan PS · Muniyandi Y · Mohan K · Das S · George B · Veeraraghavan B · Baker S last
Downloads
PRJNA1072756.csv.gz (9.1 KB) · parquet (82.4 KB) — all 262 samples, every field with route and confidence · PRJNA1072756_determinations.csv.gz (21.4 KB) — 2,616 evidence rows