Gut metagenomics in AML patients, Houston USA
139 baseline stool samples from acute myeloid leukemia patients undergoing induction chemotherapy in Houston, USA, studied longitudinally for gut microbiome and resistome links to antibiotic-resistant infection or colonization. machine-written summary
139 samples · 139 runs · US · Age unknown · 2025 · 10.39 Gbp / sample · cohort Characterization of Antibiotic Administration Fact
One study deposited as 2 BioProjects (212 catalog samples together): PRJNA1128111 · PRJNA1129514 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,112 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 278 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table |
| – 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
Antibiotic given as the study intervention (incl. eradication therapy design observational_with_procedure · population other_cancer · Prophylactic/empirical antibiotics during AML induction chemotherapy
“effects of antibiotic administration on the microbiome” — abstract:40867965 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
39 of 79 people sampled more than once (99 samples; median 2, up to 4 per person).
Genera, mean relative abundance over 136 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 | 139 | 100% | 139 | |||
| health_condition | 139 | 100% | 139 | |||
| subject_id | 139 | 100% | 139 | |||
| collection_date | 139 | 100% | 139 | |||
| detailed_location | 139 | 100% | ||||
| health_condition_detail | 139 | 100% | 139 | |||
| latitude | 139 | 100% | 139 | |||
| location_locality | 139 | 100% | 139 | |||
| location_region | 139 | 100% | 139 | |||
| longitude | 139 | 100% | 139 | |||
| timepoint_label | 139 | 100% | 139 |
- Characterization of Antibiotic Administration Factors Associated with Microbiome Disruption and Subsequent Antibiotic-Resistant Infection and Colonization Events in Acute Myeloid Leukemia Patients Receiving Chemotherapy. 2025 PMID 40867965 PMC12382674 unsure
- Utilization of machine learning to predict antibiotic resistant event outcomes in acute myeloid leukemia patients undergoing induction chemotherapy. 2025 PMID 40918253 PMC12408608 unsure
- Gut microbiome features and resistome elements associated with colonization and infection with antibiotic-resistance threats. 2025 PMID 41909910 PMC12940128 unsure
Archive description
Shotgun metagenomics for PA13 AML patients Raw sequence reads Raw sequence reads
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN42434694 | collection_date | 2013 | R1 | 0.90 | biosample.attribute:collection_date | 2013 |
| SAMN42434694 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Houston |
| SAMN42434694 | health_condition | other_disease | R4 | 0.50 | paper.abstract | patients with hematological malignancies |
| SAMN42434694 | health_condition_detail | Acute myeloid leukemia patients undergoing induction chemotherapy | R4 | 0.50 | paper.abstract | patients with hematological malignancies |
| SAMN42434694 | latitude | 29.7631 | R1 | 0.90 | biosample.attribute:lat_lon | 29.76305555 N 95.36305555 W |
| SAMN42434694 | location_locality | Houston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Houston |
| SAMN42434694 | location_region | Texas | R1 | 0.60 | biosample.attribute:lat_lon | 29.76305555 N 95.36305555 W |
| SAMN42434694 | longitude | -95.3631 | R1 | 0.90 | biosample.attribute:lat_lon | 29.76305555 N 95.36305555 W |
| SAMN42434694 | subject_id | 7 | R1 | 0.70 | sample.name_rule:TITLE | 7 S1 |
| SAMN42434694 | timepoint_label | S1 | R1 | 0.70 | sample.name_rule:TITLE | 7 S1 |
Sequencing
139 runs over 139 samples · mean 10.43 Gbp per run (median 10.39 Gbp, total 1,449.29 Gbp; 139 runs with a base count) · layout PAIRED 139 · platform ILLUMINA 139 · models Illumina NovaSeq 6000 (139) · 98% of runs with a Sandpiper profile · first public 2025-07-25 – 2025-08-26
Authors (14)
Franklin S first · Ramont C · Batool M · McMahon S · Sahasrabhojane P · Blazier JC · Kontoyiannis DP · Ni Y · Galloway-Peña J last · Chang CC · Hayase T · Hayase E · Jenq R · Shelburne S
Downloads
PRJNA1129514.csv.gz (4.5 KB) · parquet (75.9 KB) — all 139 samples, every field with route and confidence · PRJNA1129514_determinations.csv.gz (10.8 KB) — 1,390 evidence rows