Longitudinal gut metagenomes, US HCT patient on antibiotics
9 longitudinal stool samples from a US hematopoietic cell transplant (HCT) patient, sampled before and after heavy antibiotic exposure, studying E. coli gut domination and a related bloodstream infection. machine-written summary
9 samples · 9 runs · US · Adult · 2019 · 5.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 63 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 18 sample values (health condition, health condition detail) |
| ✓ Full text | 9 sample values (antibiotic exposure) · PMC6886166 |
| ○ 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
1 of 1 people sampled more than once (9 samples; median 9, up to 9 per person) · follow-up median 35 d (max 35 d) · median interval between samples 7 d (time from timepoint labels). Schedule stated by the source: “5 stool time points (A-E) from one HCT patient at days -2, 19, 27, 33, 37 relative to BMT, each sequenced by short read and/or read cloud methods” (time origin: transplant).
Each row is one person (1 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 9 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 | 9 | 100% | ||||
| country | 9 | 100% | 9 | |||
| health_condition | 9 | 100% | 9 | |||
| subject_id | 9 | 100% | 9 | |||
| antibiotic_exposure | 9 | 100% | 9 | |||
| collection_date | 9 | 100% | 9 | |||
| detailed_location | 9 | 100% | ||||
| health_condition_detail | 9 | 100% | 9 | |||
| latitude | 9 | 100% | 9 | |||
| location_region | 9 | 100% | 9 | |||
| longitude | 9 | 100% | 9 | |||
| timepoint_label | 9 | 100% | 9 |
- Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly. 2019 PMID 31787070 PMC6886166 own_data
Archive description
We applied metagenomic read cloud sequencing to four longitudinal stool samples collected from an HCT patient before and after heavy antibiotic exposure. During this time period, the patient experienced Escherichia coli gut domination and an E. coli bloodstream infection. Read clouds improve the completeness and contiguity of genome assemblies for individual organisms, enabling the placement of multiple copies of antibiotic resistance genes both within and across genomes. The presence of resistance genes is shown to correlate with the timing of antibiotics administered to the patient, and comparative genomic analysis of the various E. coli strains across time indicates that the E. coli bloodstream infection likely originated from the gut.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “a human HCT patient”
- body site study.title · “stool samples from a human HCT patient”
- life stage study.description · “HCT patient before and after heavy antibiotic exposure”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10984247 | antibiotic_exposure | yes | R3 | 0.70 | paper.fulltext.abstract | over the course of heavy antibiotic exposure |
| SAMN10984247 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN10984247 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN10984247 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | study.description | HCT patient before and after heavy antibiotic exposure |
| SAMN10984247 | health_condition_detail | Hematopoietic cell transplantation (HCT) patient | R4 | 0.50 | study.description | HCT patient before and after heavy antibiotic exposure |
| SAMN10984247 | latitude | 37.4300 | R1 | 0.90 | biosample.attribute:lat_lon | 37.43 N 122.17 W |
| SAMN10984247 | location_region | California | R1 | 0.60 | biosample.attribute:lat_lon | 37.43 N 122.17 W |
| SAMN10984247 | longitude | -122.1700 | R1 | 0.90 | biosample.attribute:lat_lon | 37.43 N 122.17 W |
| SAMN10984247 | subject_id | 11346 | R1 | 0.85 | biosample.attribute:patient_id | patient_id: 11346 |
| SAMN10984247 | timepoint_label | day -2 | R1 | 0.85 | biosample.attribute:days_relative_bmt | days_relative_bmt: -2 |
Sequencing
9 runs over 9 samples · mean 6.41 Gbp per run (median 5.39 Gbp, total 57.66 Gbp; 9 runs with a base count) · layout PAIRED 9 · platform ILLUMINA 9 · models Illumina HiSeq 4000 (9) · 100% of runs with a Sandpiper profile · first public 2019-03-29
Authors (6)
Kang JB first · Siranosian BA · Moss EL · Banaei N · Andermann TM · Bhatt AS last
Downloads
PRJNA523592.csv.gz (1.2 KB) · parquet (70.8 KB) — all 9 samples, every field with route and confidence · PRJNA523592_determinations.csv.gz (1.4 KB) — 90 evidence rows