Gut microbiota in allo-HSCT patients, auto-FMT, New York
140 adult samples from allo-HSCT patients in New York, USA, studying autologous fecal microbiota transplant (auto-FMT) as an intervention. machine-written summary
140 samples · 301 runs · US · Adult · 2020 · 3.40 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 759 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 140 sample values (location site) |
| – Full text | no open-access full text linked · PMC9725748 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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
Faecal microbiota transplantation design single_arm_before_after · population transplant_or_immunocompromised · Autologous fecal microbiota transplant in allo-HSCT patients
“Autologous Fecal Microbiota Transplant (auto-FMT) at MSKCC” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
23 of 53 people sampled more than once (109 samples; median 3, up to 16 per person). Schedule stated by the source: “Stool sampled repeatedly per patient at variable days relative to transplant (bmtday/day fields, no fixed schedule)” (time origin: transplant).
Genera, mean relative abundance over 135 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 | 140 | 100% | ||||
| country | 140 | 100% | 140 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 139 | 99% | 139 | |||
| detailed_location | 140 | 100% | ||||
| latitude | 140 | 100% | 140 | |||
| location_region | 140 | 100% | 140 | |||
| location_site | 140 | 100% | 140 | |||
| longitude | 140 | 100% | 140 | |||
| timepoint_label | 59 | 42% | 59 | |||
| collection_date | 1 | 1% | 1 |
- Metagenome analysis using the Kraken software suite. 2022 PMID 36171387 PMC9725748 unsure
Archive description
Microbiota of allo-HSCT patients and in the setting of Autologous Fecal Microbiota Transplant (auto-FMT) at MSKCC Raw sequence reads
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 study.title · “setting of Autologous Fecal Microbiota Transplant (auto-FMT)”
- body site study.description · “setting of Autologous Fecal Microbiota Transplant (auto-FMT)”
- 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 |
|---|---|---|---|---|---|---|
| SAMN17862032 | collection_date | 2019-06-13 | R1 | 0.90 | biosample.attribute:collection_date | 2019-06-13T00:00:00Z |
| SAMN07491402 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:New York |
| SAMN07491402 | latitude | 40.7641 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07491402 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:New York |
| SAMN07491402 | location_site | Memorial Sloan Kettering Cancer Center | R4 | 0.40 | ena.study_title | Autologous Fecal Microbiota Transplant (auto-FMT) at MSKCC |
| SAMN07491402 | longitude | -73.9568 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN07491402 | subject_id | 1107 | R1 | 0.85 | sample.attr.patient_id | 1107 |
| SAMN13270709 | subject_id | 1392 | R1 | 0.70 | sample.name_rule:alias | 1392M |
| SAMN10082787 | timepoint_label | 11 | R1 | 0.85 | sample.attr.day | 11 |
Sequencing
301 runs over 227 samples · mean 3.23 Gbp per run (median 2.22 Gbp, total 971.84 Gbp; 301 runs with a base count) · layout PAIRED 301 · platform ILLUMINA 301 · models Illumina HiSeq 1000 (207), Illumina MiSeq (94) · 84% of runs with a Sandpiper profile · first public 2020-12-10 – 2021-04-07
Authors (8)
Lu J first · Rincon N · Wood DE · Breitwieser FP · Pockrandt C · Langmead B · Salzberg SL · Steinegger M last
Downloads
PRJNA491657.csv.gz (4.8 KB) · parquet (76.2 KB) — all 140 samples, every field with route and confidence · PRJNA491657_determinations.csv.gz (6.5 KB) — 899 evidence rows