Gut microbiome in HCT patients, California, longitudinal
320 stool samples from adults undergoing hematopoietic cell transplantation, hospitalized in California, were sequenced longitudinally to study gut microbiome strain sharing and potential pathogen transmission between patients. machine-written summary
320 samples · 320 runs · US · Adult · 2021 · 1.75 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,238 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 640 sample values (location locality, location site) · PMC12358190, PMC8803835 |
| ✓ Supplementary tables | 60 sample values (age, subject id) |
| – 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
Other administered intervention (see intervention_detail) design observational_with_procedure · population transplant_or_immunocompromised · Hematopoietic cell transplantation, stool sampled around procedure
“human hematopoietic cell transplantation patients” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal — not resolvedhospital ward
66 of 126 people sampled more than once (260 samples; median 4, up to 8 per person). Schedule stated by the source: “Weekly stool samples collected from adult patients undergoing HCT, days relative to HCT recorded (date_rel_HCT)” (time origin: transplant).
149 HCT patients on one ward (14 single, 4 double rooms); 83 roommate pairs among 85 catalog patients from Supplementary Data 11.
household member · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 17 linked groups from explicit relations. 126 people in the project overall.
Genera, mean relative abundance over 279 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 | 0 | 0% | ||||
| subject_id | 320 | 100% | 319 | 1 | ||
| collection_date | 320 | 100% | 320 | |||
| detailed_location | 320 | 100% | ||||
| latitude | 320 | 100% | 320 | |||
| location_locality | 320 | 100% | 320 | |||
| location_region | 320 | 100% | 320 | |||
| location_site | 320 | 100% | 320 | |||
| longitude | 320 | 100% | 320 | |||
| timepoint_label | 319 | 100% | 319 | |||
| age_at_collection_days | 59 | 18% | 59 |
- Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults. 2022 PMID 35102136 PMC8803835 own_data
- The prototypic crAssphage is a linear phage-plasmid. 2025 PMID 40730160 PMC12358190 unsure
Archive description
We studied the microbiome of patients undergoing and recovering from hematopoietic cell transplantation (HCT). These data were include standard short-read metagenomic sequencing, as well as "linked-read" sequencing libraries prepared on the 10X Genomics Chromium. This dataset is linked to a study of transmission of pathogens in the microbiome of HCT patients.
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.title · “Metagenomic sequencing of stool samples from human”
- 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 |
|---|---|---|---|---|---|---|
| SAMN18206646 | age_at_collection_days | 11322.8 | R2 | 0.75 | paper.supp.41467_2022_28048_MOESM4_ESM.xlsx[patient metadata!AGE] | 31 |
| SAMN18206638 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN18206638 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:California |
| SAMN18206638 | latitude | 37.4354 | R1 | 0.90 | biosample.attribute:lat_lon | 37.435391 N 122.176510 W |
| SAMN18206638 | location_locality | Stanford | R3 | 0.70 | paper.fulltext.methods | recruited at the Stanford Hospital Blood and Marrow Transplant Unit |
| SAMN18206638 | location_region | California | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:California |
| SAMN18206638 | location_site | Stanford Hospital Blood and Marrow Transplant Unit | R3 | 0.70 | paper.fulltext.methods | Stanford Hospital Blood and Marrow Transplant Unit |
| SAMN18206638 | longitude | -122.1765 | R1 | 0.90 | biosample.attribute:lat_lon | 37.435391 N 122.176510 W |
| SAMN18206639 | subject_id | 11303 | R1 | 0.85 | sample.attr.patient_id | 11303 |
| SAMN18206638 | subject_id | 00000 | R2 | 0.85 | paper.supp.41467_2022_28048_MOESM5_ESM.xlsx[sequence metadata!patient_id] | 00000 |
| SAMN18206639 | timepoint_label | -2 | R1 | 0.85 | sample.attr.date_rel_hct | -2 |
Sequencing
320 runs over 320 samples · mean 8.39 Gbp per run (median 1.75 Gbp, total 2,684.75 Gbp; 320 runs with a base count) · layout PAIRED 320 · platform ILLUMINA 320 · models Illumina HiSeq 4000 (320) · 87% of runs with a Sandpiper profile · first public 2021-12-10
Authors (13)
Siranosian BA first · Brooks EF · Andermann T · Rezvani AR · Banaei N · Tang H · Bhatt AS last · Schmidtke DT first · Hickey AS · Wirbel J · Lin JD · Liachko I · Sherlock G
Downloads
PRJNA707487.csv.gz (10.1 KB) · parquet (83.8 KB) — all 320 samples, every field with route and confidence · PRJNA707487_determinations.csv.gz (21.9 KB) — 2,938 evidence rows