Gut microbiota & Pseudomonadota risk in allo-HCT, US
887 gut metagenome samples from allo-HCT (transplant/immunocompromised) patients in New York, USA, examining polysaccharide utilization loci functions linked to gut-derived Gram-negative bloodstream infection risk. machine-written summary
887 samples · 887 runs · US · Age unknown · 2026 · 4.83 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 4,529 sample values (country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 1,774 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 — not resolved
83 of 193 people sampled more than once (392 samples; median 4, up to 20 per person).
Genera, mean relative abundance over 74 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 | 887 | 100% | 887 | |||
| health_condition | 887 | 100% | 887 | |||
| subject_id | 502 | 57% | 502 | |||
| detailed_location | 887 | 100% | ||||
| health_condition_detail | 887 | 100% | 887 | |||
| latitude | 887 | 100% | 887 | |||
| location_region | 887 | 100% | 887 | |||
| longitude | 887 | 100% | 887 | |||
| timepoint_label | 479 | 54% | 479 |
Archive description
We used metagenomics to identify functions encoded by polysaccharide utilization loci underlying microbiota metabiotic potential and link them to gut-derived Gram-negative bacteremia in allo-HCT patients.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07491259 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:New York |
| SAMN07491259 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | study.description | allo-HCT patients |
| SAMN07491259 | health_condition_detail | allogeneic hematopoietic cell transplant recipients | R4 | 0.50 | study.description | allo-HCT patients |
| SAMN07491259 | latitude | 40.7641 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07491259 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:New York |
| SAMN07491259 | longitude | -73.9568 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07491259 | subject_id | 1042 | R1 | 0.85 | sample.attr.patient_id | 1042 |
| SAMN10082069 | timepoint_label | 16 | R1 | 0.85 | sample.attr.day | 16 |
Sequencing
887 runs over 887 samples · mean 4.87 Gbp per run (median 4.83 Gbp, total 4,319.08 Gbp; 887 runs with a base count) · layout PAIRED 887 · platform ILLUMINA 887 · models Illumina NovaSeq 6000 (628), Illumina NovaSeq X (208), Illumina HiSeq 4000 (50), Illumina HiSeq 2500 (1) · 0% of runs with a Sandpiper profile · first public 2026-05-15 – 2026-06-21
Authors (0)
No author record.
Downloads
PRJNA1464738.csv.gz (22.8 KB) · parquet (103.1 KB) — all 887 samples, every field with route and confidence · PRJNA1464738_determinations.csv.gz (34.8 KB) — 6,303 evidence rows