Enterococcus and allo-HCT outcomes in adults, New York
Longitudinal study of 118 gut microbiome samples from adult allogeneic hematopoietic cell transplant patients in New York, USA, examining Enterococcus expansion in relation to graft-versus-host disease and mortality. machine-written summary
118 samples · 208 runs · US · Adult · 2020 · 6.04 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 708 sample values (country, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 236 sample values (health condition, health condition detail) · PMC10527165, PMC7003985 |
| ○ 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
24 of 37 people sampled more than once (105 samples; median 4, up to 11 per person). Schedule stated by the source: “Serial stool samples per patient labeled by day relative to transplant (e.g. bmtday, day); study window day -20 to +80 relative to allo-HCT” (time origin: transplant).
Genera, mean relative abundance over 115 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 | 118 | 100% | ||||
| country | 118 | 100% | 118 | |||
| health_condition | 118 | 100% | 118 | |||
| subject_id | 118 | 100% | 118 | |||
| detailed_location | 118 | 100% | ||||
| health_condition_detail | 118 | 100% | 118 | |||
| latitude | 118 | 100% | 118 | |||
| location_region | 118 | 100% | 118 | |||
| longitude | 118 | 100% | 118 | |||
| timepoint_label | 118 | 100% | 118 |
- Lactose drives Enterococcus expansion to promote graft-versus-host disease. 2019 PMID 31780560 PMC7003985 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
This study investigated the role of Enterococcus in the outcome of allogeneic hematopoietic cell transplantation (allo-HCT). Enterococcus expansion is highly prevalent in allo-HCT patients, associated with graft-versus-host disease and mortality.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07491416 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:New York |
| SAMN07491416 | health_condition | transplant_or_immunocompromised | R3 | 0.70 | paper.fulltext.other | adult allo-HCT recipients at four HCT centers |
| SAMN07491416 | health_condition_detail | Allogeneic hematopoietic cell transplant recipients | R3 | 0.60 | paper.fulltext.other | adult allo-HCT recipients at four HCT centers |
| SAMN07491416 | latitude | 40.7641 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07491416 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:New York |
| SAMN07491416 | longitude | -73.9568 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07491416 | subject_id | 1110 | R1 | 0.85 | sample.attr.patient_id | 1110 |
| SAMN11884969 | subject_id | 1197 | R1 | 0.70 | sample.name_rule:alias | 1197A |
| SAMN07491416 | timepoint_label | H | R1 | 0.70 | sample.name_rule:alias | 1110H |
| SAMN10085989 | timepoint_label | 29 | R1 | 0.85 | sample.attr.day | 29 |
Sequencing
208 runs over 208 samples · mean 6.54 Gbp per run (median 6.04 Gbp, total 1,359.76 Gbp; 208 runs with a base count) · layout PAIRED 208 · platform ILLUMINA 208 · models Illumina HiSeq 1000 (196), Illumina HiSeq 2500 (12) · 93% of runs with a Sandpiper profile · first public 2020-01-06 – 2021-03-30
Authors (64)
Stein-Thoeringer CK first · Nichols KB · Lazrak A · Docampo MD · Slingerland AE · Slingerland JB · Clurman AG · Armijo G · Gomes ALC · Shono Y · Staffas A · Burgos da Silva M · Devlin SM · Markey KA · Bajic D · Pinedo R · Tsakmaklis A · Littmann ER · Pastore A · Taur Y · Monette S · Arcila ME · Pickard AJ · Maloy M · Wright RJ · Amoretti LA · Fontana E · Pham D · Jamal MA · Weber D · Sung AD · Hashimoto D · Scheid C · Xavier JB · Messina JA · Romero K · Lew M · Bush A · Bohannon L · Hayasaka K · Hasegawa Y · Vehreschild MJGT · Cross JR · Ponce DM · Perales MA · Giralt SA · Jenq RR · Teshima T · Holler E · Chao NJ · Pamer EG · Peled JU · van den Brink MRM last · Schluter J first · Djukovic A · Taylor BP · Yan J · Duan C · Hussey GA · Liao C · Sharma S · Dai A · Siranosian BA · Bhatt AS
Downloads
PRJNA545312.csv.gz (4.2 KB) · parquet (75.1 KB) — all 118 samples, every field with route and confidence · PRJNA545312_determinations.csv.gz (7.5 KB) — 944 evidence rows