Gut microbiome strain dynamics in HCT patient, longitudinal
4 longitudinal stool samples from an adult hematopoietic cell transplantation patient, used to study gut microbiome strain-level dynamics and antibiotic resistance during treatment. machine-written summary
4 samples · 12 runs · Age unknown · 2019 · 29.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 8 sample values (collection date, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 20 sample values (antibiotic exposure, health condition, health condition detail, location site, sex) · PMC7260799 |
| ○ 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
Schedule stated by the source: “4 stool samples (timepoints A, B, C, D) collected over 56 days during HCT treatment course, starting prior to/around antibiotic exposure”; stated follow-up 56 d.
Genera, mean relative abundance over 4 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 | 4 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 4 | 100% | 4 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 4 | 100% | 4 | |||
| collection_date | 4 | 100% | 4 | |||
| detailed_location | 4 | 100% | ||||
| health_condition_detail | 4 | 100% | 4 | |||
| location_site | 4 | 100% | 4 | |||
| sex | 4 | 100% | 4 | |||
| timepoint_label | 4 | 100% | 4 |
- Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale. 2020 PMID 32471482 PMC7260799 own_data
Archive description
Read cloud sequencing and assembly of the human gut microbiome in clinical subject
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “human gut microbiome in clinical subject”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09058614 | antibiotic_exposure | yes | R3 | 0.60 | paper.fulltext.results | exposed to a course of therapy with azithromycin |
| SAMN09058614 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN09058614 | health_condition | transplant_or_immunocompromised | R3 | 0.70 | paper.fulltext.methods | hematopoietic cell transplantation (HCT) patient |
| SAMN09058614 | health_condition_detail | hematopoietic cell transplantation patient with myelodysplastic syndrome and myelofibrosis | R3 | 0.70 | paper.fulltext.methods | hematopoietic cell transplantation (HCT) patient |
| SAMN09058614 | location_site | Stanford Hospital | R3 | 0.60 | paper.fulltext.results | underwent HCT at the Stanford Hospital |
| SAMN09058614 | sex | male | R3 | 0.60 | paper.fulltext.results | was a 46-year-old man who underwent HCT |
| SAMN09058614 | timepoint_label | A | R1 | 0.85 | sample.attr.timepoint | A |
Sequencing
12 runs over 4 samples · mean 12.30 Gbp per run (median 6.50 Gbp, total 147.59 Gbp; 12 runs with a base count) · layout PAIRED 12 · platform ILLUMINA 12 · models Illumina HiSeq 4000 (8), NextSeq 500 (4) · 83% of runs with a Sandpiper profile · first public 2019-11-21
Authors (13)
Zlitni S first · Bishara A · Moss EL · Tkachenko E · Kang JB · Culver RN · Andermann TM · Weng Z · Wood C · Handy C · Ji HP · Batzoglou S · Bhatt AS last
Downloads
PRJNA434731.csv.gz (1.1 KB) · parquet (70.1 KB) — all 4 samples, every field with route and confidence · PRJNA434731_determinations.csv.gz (894 B) — 28 evidence rows