Gut metagenomics in recovered acute leukemia patients, Spain
30 gut metagenome samples from patients in Asturias, Spain, who had recovered from acute leukemia and were previously colonized with ESBL/carbapenemase-producing Enterobacterales; case-control design. machine-written summary
30 samples · 30 runs · ES · Adult · 2023 · 4.88 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 210 sample values (age, collection date, country, health condition, health condition detail, location region, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 30 sample values (location site) · PMC9964539 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
Genera, mean relative abundance over 27 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 | 30 | 100% | ||||
| country | 30 | 100% | 30 | |||
| health_condition | 30 | 100% | 30 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 30 | 100% | 30 | |||
| collection_date | 30 | 100% | 30 | |||
| detailed_location | 30 | 100% | ||||
| health_condition_detail | 30 | 100% | 30 | |||
| location_region | 30 | 100% | 30 | |||
| location_site | 30 | 100% | 30 | |||
| sex | 30 | 100% | 30 |
- Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales in Culture Negative Patients Recovered from Acute Leukemia. 2023 PMID 36838367 PMC9964539 own_data
- Study of the intestinal microbiota composition and the effect of treatment with intensive chemotherapy in patients recovered from acute leukemia. 2024 PMID 38454103 PMC10920697 unsure
Archive description
Shotgun metagenomics sequencing data for the article "Evaluation of a shotgun metagenomics approach for detection of ESBL- and/or carbapenemase-producing Enterobacterales in culture negative patients recovered from acute leukemia"
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.host_age · “69 (n=8/30)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN32318268 | age_at_collection_days | 19358.2 | R1 | 0.70 | sample.attr.host_age | 53 |
| SAMN32318268 | collection_date | 2021-01-11 | R1 | 0.90 | biosample.attribute:collection_date | 2021-01-11 |
| SAMN32318268 | country | ES | R1 | 0.90 | sample.attr.geo_loc_name | Spain: Asturias |
| SAMN32318268 | health_condition | other_cancer | R1 | 0.85 | biosample_attr | Patient recovered from acute leukemia |
| SAMN32318268 | health_condition_detail | Patient recovered from acute leukemia | R1 | 0.90 | sample.attr.host_disease | Patient recovered from acute leukemia |
| SAMN32318268 | location_region | Asturias | R1 | 0.85 | biosample.attribute:geo_loc_name | Spain: Asturias |
| SAMN32318268 | location_site | Hospital Universitario Central de Asturias | R3 | 0.70 | paper.fulltext.methods | tertiary Spanish hospital, the “Hospital Universitario Central de Asturias” |
| SAMN32318268 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
Sequencing
30 runs over 30 samples · mean 4.82 Gbp per run (median 4.88 Gbp, total 144.53 Gbp; 30 runs with a base count) · layout PAIRED 30 · platform ILLUMINA 30 · models Illumina NovaSeq 6000 (30) · 90% of runs with a Sandpiper profile · first public 2023-04-14
Authors (12)
Lumbreras-Iglesias P first · Sabater C · Fernández Moreno A · López de Ugarriza P · Fernández-Verdugo A · Margolles A · Rodicio MR · Bernal T · Fernández J last · Vázquez X first · Moreno AF · de Ugarriza PL
Downloads
PRJNA914091.csv.gz (2.0 KB) · parquet (71.7 KB) — all 30 samples, every field with route and confidence · PRJNA914091_determinations.csv.gz (2.5 KB) — 240 evidence rows