High-frequency gut microbiota sampling in BMT patients, NY
Longitudinal study of 174 intestinal microbiota samples from allogeneic bone marrow transplant patients in New York, examining factors influencing antibiotic resistance with focus on Vancomycin-Resistant Enterococcus and Klebsiella pneumoniae. machine-written summary
174 samples · 177 runs · US · Age unknown · 2018 · 4.38 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 870 sample values (country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 348 sample values (health condition, health condition detail) |
| ✓ Full text | 174 sample values (location site) · PMC10527165, PMC6717508 |
| ○ 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
Other administered intervention (see intervention_detail) design observational_with_procedure · population transplant_or_immunocompromised · Allogeneic BMT; high-frequency stool sampling pre/post transplant, no assigned therapy
“allogeneic bone marrow transplant patients” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
18 of 20 people sampled more than once (172 samples; median 2, up to 35 per person). Schedule stated by the source: “fecal samples routinely collected during the initial transplant hospitalization (high-frequency sampling)” (time origin: transplant).
Genera, mean relative abundance over 164 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 | 174 | 100% | 174 | |||
| health_condition | 174 | 100% | 174 | |||
| subject_id | 174 | 100% | 174 | |||
| detailed_location | 174 | 100% | ||||
| health_condition_detail | 174 | 100% | 174 | |||
| latitude | 174 | 100% | 174 | |||
| location_region | 174 | 100% | 174 | |||
| location_site | 174 | 100% | 174 | |||
| longitude | 174 | 100% | 174 |
- Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus. 2019 PMID 31435014 PMC6717508 own_data
- The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia. 2023 PMID 37329880 PMC10527165 unsure
Archive description
High frequency intestinal microbiota sampling in allogeneic bone marrow transplant patients, part of a larger systems biology project examining factors that influence antibiotic resistance, with a focus on the pathogens Vancomycin-Resistant Enterococcus and Klebsiella pneumoniae
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “High frequency intestinal microbiota sampling”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07362074 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:New York |
| SAMN07362074 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | study.title | allogeneic bone marrow transplant patients |
| SAMN07362074 | health_condition_detail | allogeneic bone marrow transplant patients | R4 | 0.50 | study.title | allogeneic bone marrow transplant patients |
| SAMN07362074 | latitude | 40.7641 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07362074 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:New York |
| SAMN07362074 | location_site | Memorial Sloan Kettering Cancer Center | R3 | 0.70 | paper.fulltext.methods | hematopoietic stem cell transplantation at Memorial Sloan Kettering Cancer Center |
| SAMN07362074 | longitude | -73.9568 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07362074 | subject_id | 668 | R1 | 0.85 | sample.attr.patient_id | 668 |
Sequencing
177 runs over 177 samples · mean 5.06 Gbp per run (median 4.38 Gbp, total 895.74 Gbp; 177 runs with a base count) · layout PAIRED 177 · platform ILLUMINA 177 · models Illumina HiSeq 2500 (177) · 84% of runs with a Sandpiper profile · first public 2018-08-18 – 2018-11-10
Authors (41)
Kim SG first · Becattini S · Moody TU · Shliaha PV · Littmann ER · Seok R · Gjonbalaj M · Eaton V · Fontana E · Amoretti L · Wright R · Caballero S · Wang ZX · Jung HJ · Morjaria SM · Leiner IM · Qin W · Ramos RJJF · Cross JR · Narushima S · Honda K · Peled JU · Hendrickson RC · Taur Y · van den Brink MRM · Pamer EG last · Schluter J first · Djukovic A · Taylor BP · Yan J · Duan C · Hussey GA · Liao C · Sharma S · Amoretti LA · Wright RJ · Dai A · Perales MA · Siranosian BA · Bhatt AS · Xavier JB last
Downloads
PRJNA394877.csv.gz (5.1 KB) · parquet (76.2 KB) — all 174 samples, every field with route and confidence · PRJNA394877_determinations.csv.gz (7.5 KB) — 1,392 evidence rows