Gut microbiome in allo-HCT patients, New York
344 stool samples from adult allogeneic hematopoietic cell transplant patients in New York, USA, studying nutrition as a predictor of intestinal microbiome disruption during transplantation. machine-written summary
320 samples · 357 runs · US · Adult · 2025 · 6.00 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,793 sample values (country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 320 sample values (health condition) |
| – 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 |
intervention — arms not resolved
Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population transplant_or_immunocompromised · Allogeneic hematopoietic cell transplantation; nutrition observed, not controlled
“allogeneic hematopoietic cell transplantation (allo-HCT)” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
49 of 80 people sampled more than once (286 samples; median 5, up to 22 per person). Schedule stated by the source: “Stool samples collected at multiple timepoints relative to transplant, spanning day -7 to day 8, across 80 subjects (per catalog metadata)” (time origin: transplant); stated follow-up 15 d.
Genera, mean relative abundance over 344 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 | 320 | 100% | ||||
| country | 320 | 100% | 320 | |||
| health_condition | 320 | 100% | 320 | |||
| subject_id | 317 | 99% | 317 | |||
| detailed_location | 320 | 100% | ||||
| latitude | 320 | 100% | 320 | |||
| location_region | 320 | 100% | 320 | |||
| longitude | 320 | 100% | 320 | |||
| timepoint_label | 196 | 61% | 196 |
Archive description
Intestinal microbiome disruption is a risk factor for poor outcomes after allogeneic hematopoietic cell transplantation (allo-HCT), but the factors that contribute to microbiome injury are not well understood. We hypothesized that nutrition contributes to microbiome composition during allo-HCT.
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 · “Intestinal microbiome disruption is”
- body site external_curation.infant_catalog · “body_site_call gut/stool”
- 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 |
|---|---|---|---|---|---|---|
| SAMN07560489 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:New York |
| SAMN07560489 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | study.description | allogeneic hematopoietic cell transplantation (allo-HCT) |
| SAMN07560489 | latitude | 40.7641 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07560489 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:New York |
| SAMN07560489 | longitude | -73.9568 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07560489 | subject_id | 1362 | R1 | 0.85 | sample.attr.patient_id | 1362 |
| SAMN13270460 | subject_id | 1605 | R1 | 0.70 | sample.name_rule:library_name | 1605E |
| SAMN12007069 | timepoint_label | 2 | R1 | 0.85 | sample.attr.bmtday | 2 |
Sequencing
357 runs over 333 samples · mean 6.36 Gbp per run (median 6.00 Gbp, total 2,272.06 Gbp; 357 runs with a base count) · layout PAIRED 357 · platform ILLUMINA 357 · models Illumina NovaSeq 6000 (307), Illumina NovaSeq X (42), Illumina HiSeq 4000 (8) · 100% of runs with a Sandpiper profile · first public 2025-11-11 – 2026-02-10
Authors (0)
No author record.
Downloads
PRJNA878528.csv.gz (8.9 KB) · parquet (81.6 KB) — all 320 samples, every field with route and confidence · PRJNA878528_determinations.csv.gz (14.1 KB) — 2,113 evidence rows