Oral and gut microbiota in AML patients on chemotherapy, Seattle
283 longitudinal saliva, plaque, and fecal samples from 39 adult cancer patients undergoing intensive chemotherapy at Fred Hutch Cancer Center, Seattle, WA, collected at baseline and weeks 2–4. machine-written summary
283 samples · 283 runs · Adult · 2025 · 2.51 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 566 sample values (subject id, timepoint) |
| ✓ Abstract / description | 849 sample values (location locality, location region, location site) |
| ✓ Full text | 566 sample values (health condition, health condition detail) · PMC12106833 |
| ○ 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 |
intervention — arms not resolved
design observational_with_procedure
longitudinal — not resolved
38 of 39 people sampled more than once (282 samples; median 8, up to 15 per person). Schedule stated by the source: “Samples collected at baseline (bl), week 2 (w2), week 3 (w3), and week 4 (w4) of chemotherapy from saliva, plaque, and stool per patient; median interval between consecutive same-type samples was 7.5 ” (time origin: chemotherapy start); stated follow-up 30 d.
Genera, mean relative abundance over 220 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 | 283 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 283 | 100% | 283 | |||
| subject_id | 283 | 100% | 283 | |||
| detailed_location | 283 | 100% | ||||
| health_condition_detail | 283 | 100% | 283 | |||
| location_locality | 283 | 100% | 283 | |||
| location_region | 283 | 100% | 283 | |||
| location_site | 283 | 100% | 283 | |||
| timepoint_label | 283 | 100% | 283 |
- Distal gut colonization by oral bacteria during intensive chemotherapy: direct evidence from strain-level analysis of paired samples. 2025 PMID 40419513 PMC12106833 own_data
Archive description
We profiled the microbiota in longitudinal salivary, supragingival plaque, and fecal samples from patients undergoing intensive chemotherapy at Fred Hutch Cancer Center, Seattle, WA. Samples were collected at baseline, week 2, week 3, and week 4 of chemotherapy. Shotgun metagenomes and clinical data were analyzed.
How this project entered the registry
Classified as human oral cavity / gut / stool / multiple sites shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.71. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “salivary, supragingival plaque, and fecal samples”
- life stage study.description · “patients undergoing intensive chemotherapy”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN48634546 | health_condition | other_cancer | R3 | 0.70 | paper.fulltext.methods | high-grade myeloid malignancies receiving frontline or salvage intensive chemotherapy |
| SAMN48634546 | health_condition_detail | high-grade myeloid malignancies receiving intensive chemotherapy | R3 | 0.70 | paper.fulltext.methods | high-grade myeloid malignancies receiving frontline or salvage intensive chemotherapy |
| SAMN48634546 | location_locality | Seattle | R4 | 0.45 | ena.study_description | Fred Hutch Cancer Center, Seattle, WA |
| SAMN48634546 | location_region | Washington | R4 | 0.45 | ena.study_description | Fred Hutch Cancer Center, Seattle, WA |
| SAMN48634546 | location_site | Fred Hutch Cancer Center | R4 | 0.45 | ena.study_description | patients undergoing intensive chemotherapy at Fred Hutch Cancer Center |
| SAMN48634546 | subject_id | AML002 | R1 | 0.70 | sample.name_rule:library_names | AML002_plaque_bl_2022-11-21 |
| SAMN48634546 | timepoint_label | bl | R1 | 0.70 | sample.name_rule:library_names | AML002_plaque_bl_2022-11-21 |
Sequencing
283 runs over 283 samples · mean 2.54 Gbp per run (median 2.51 Gbp, total 719.00 Gbp; 283 runs with a base count) · layout SINGLE 283 · platform ILLUMINA 283 · models Illumina NovaSeq 6000 (283) · 78% of runs with a Sandpiper profile · first public 2025-05-23
Authors (15)
Raychaudhuri S first · Gem H · Chung K · McLean JS · Kerns KA · Hullar MAJ · Elmorr E · Appelbaum JB · Percival MM · Walter RB · Halpern AB · Minot SS · Kim K · Zevin AS · Rashidi A last
Downloads
PRJNA1265886.csv.gz (7.5 KB) · parquet (79.3 KB) — all 283 samples, every field with route and confidence · PRJNA1265886_determinations.csv.gz (13.9 KB) — 1,981 evidence rows