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PRJNA1247145 SRP576740

Gut microbiome in stem cell transplant patients, USA

Intestinal permeability of stem cell transplant patients

149 samples from stem cell transplant patients in the USA, examining how intestinal permeability relates to systemic acute phase responses and gut dysbiosis. machine-written summary

149 samples · 149 runs · US · Age unknown · 2025 · 2.89 Gbp / sample

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Sources
✓Sequence archive 1,043✓Abstract / description 149○Full text○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive1,043 sample values (collection date, country, health condition detail, latitude, location region, longitude, timepoint)
✓ Abstract / description149 sample values (health condition)
○ Full textread; no usable statement or table · PMC10480541
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet · share metadata
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention — arms not resolved

design observational_with_procedure

Samples at a glance
1 sampling locations · 1 country
Age
unknown149
Condition
transplant_or_immunocompromised149
Country
US149
Body site
primary149
Collected 2019–2021
2019: 15 samples2020: 91 samples2021: 43 samples20192021
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 6 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 1 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 7 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 66 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 67 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 2 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 2.89 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal — not resolved

Schedule stated by the source: “stool/urine before transplant (baseline), day +7, and day +30” (time origin: transplant); stated follow-up 6 mo.

How longitudinal and relatedness information is derived

Community composition
Bacteroides 12.4%Phocaeicola 8.5%Blautia_A 8.2%Bifidobacterium 7.6%Enterocloster 5.6%Akkermansia 5.6%Mediterraneibacter 2.8%Roseburia 2.5%Klebsiella 2.1%Parabacteroides 2.0%Prevotella 1.9%Streptococcus 1.8%not assigned to a genus 5.3%other genera 33.6%

Genera, mean relative abundance over 133 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category0 0%
country149 100%149
health_condition149 100%149
subject_id0 0%
collection_date149 100%149
detailed_location149 100%
health_condition_detail149 100%149
latitude149 100%149
location_region149 100%149
longitude149 100%149
timepoint_label149 100%149
Papers (1)
  • Intestinal permeability in patients undergoing stem cell transplantation correlates with systemic acute phase responses and dysbiosis. 2023 PMID 37083597 PMC10480541 own_data
Details
Archive description

Intestinal permeability of stem cell transplant patients correlates with systemic acute phase responses and dysbiosis

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site study.title · “Intestinal permeability of stem cell transplant patients”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN47805064collection_date2019-09-22R10.90biosample.attribute:collection_date2019-09-22
SAMN47805064countryUSR10.90sample.attr.geo_loc_nameUSA
SAMN47805064health_conditiontransplant_or_immunocompromisedR40.50study.titlestem cell transplant patients
SAMN47805064health_condition_detailBLR10.90sample.attr.conditionBL
SAMN47805064latitude39.1031R10.90biosample.attribute:latitude_and_longitude39.1031 N 84.5120 W
SAMN47805065latitude39.1031R10.90biosample.attribute:lat_lon39.1031 N 84.5120 W
SAMN47805064location_regionKentuckyR10.60biosample.attribute:latitude_and_longitude39.1031 N 84.5120 W
SAMN47805065location_regionKentuckyR10.60biosample.attribute:lat_lon39.1031 N 84.5120 W
SAMN47805064longitude-84.5120R10.90biosample.attribute:latitude_and_longitude39.1031 N 84.5120 W
SAMN47805065longitude-84.5120R10.90biosample.attribute:lat_lon39.1031 N 84.5120 W
SAMN47805064timepoint_labelBLR10.85biosample.attribute:conditionBL
Sequencing

149 runs over 149 samples · mean 3.21 Gbp per run (median 2.89 Gbp, total 478.00 Gbp; 149 runs with a base count) · layout PAIRED 149 · platform ILLUMINA 149 · models Illumina NovaSeq 6000 (149) · 89% of runs with a Sandpiper profile · first public 2025-04-07

Authors (0)

No author record.

Help complete this project

2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata

Downloads

PRJNA1247145.csv.gz (4.9 KB) · parquet (76.4 KB) — all 149 samples, every field with route and confidence · PRJNA1247145_determinations.csv.gz (8.2 KB) — 1,192 evidence rows

Samples (149 · every field this project has values for · hover a cell for its source)
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