Gut metagenomics in AML patients, Houston, longitudinal
73 baseline stool samples from adult acute myeloid leukemia patients undergoing induction chemotherapy in Houston, USA, examined for links between gut microbiome/resistome features and antimicrobial-resistant infection or colonization; longitudinal design. machine-written summary
73 samples · 73 runs · US · Adult · 2025 · 12.02 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 | 545 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 146 sample values (antibiotic exposure, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC12382674, PMC12408608, PMC12940128 |
| ○ 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 |
longitudinal — not resolved
27 of 46 people sampled more than once (54 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 69 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 | 73 | 100% | ||||
| country | 73 | 100% | 73 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 73 | 100% | 73 | |||
| antibiotic_exposure | 73 | 100% | 73 | |||
| collection_date | 73 | 100% | 73 | |||
| detailed_location | 73 | 100% | ||||
| health_condition_detail | 73 | 100% | 73 | |||
| latitude | 73 | 100% | 73 | |||
| location_locality | 73 | 100% | 73 | |||
| location_region | 73 | 100% | 73 | |||
| longitude | 73 | 100% | 73 | |||
| timepoint_label | 34 | 47% | 34 |
- 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 PA15 AML patients Raw sequence reads
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- life stage study.title · “AML patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN42431304 | antibiotic_exposure | yes | R4 | 0.50 | paper.abstract | prophylactic and empirical antibiotic treatment during chemotherapy |
| SAMN42431304 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN42431304 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Houston |
| SAMN42431304 | health_condition_detail | mixed_case_control: AML patients with/without AR-events | R4 | 0.50 | paper.abstract | acute myeloid leukemia patients |
| SAMN42431304 | latitude | 29.7631 | R1 | 0.90 | biosample.attribute:lat_lon | 29.76305555 N 95.36305555 W |
| SAMN42431304 | location_locality | Houston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Houston |
| SAMN42431304 | location_region | Texas | R1 | 0.60 | biosample.attribute:lat_lon | 29.76305555 N 95.36305555 W |
| SAMN42431304 | longitude | -95.3631 | R1 | 0.90 | biosample.attribute:lat_lon | 29.76305555 N 95.36305555 W |
| SAMN42431304 | subject_id | 001 | R1 | 0.70 | sample.name_rule:alias | 001-BL_S1 |
| SAMN42431304 | timepoint_label | baseline | R1 | 0.70 | sample.name_rule:alias | 001-BL_S1 |
Sequencing
73 runs over 73 samples · mean 12.03 Gbp per run (median 12.02 Gbp, total 878.54 Gbp; 73 runs with a base count) · layout PAIRED 73 · platform ILLUMINA 73 · models Illumina NovaSeq 6000 (73) · 95% 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
PRJNA1128111.csv.gz (2.9 KB) · parquet (73.5 KB) — all 73 samples, every field with route and confidence · PRJNA1128111_determinations.csv.gz (6.0 KB) — 691 evidence rows