Gut microbiome in allo-HSCT patients, Valencia, longitudinal
102 longitudinal gut microbiome samples from adult allogeneic hematopoietic stem cell transplant patients in Valencia, Spain, studying microbiome changes via 16S rRNA, shotgun sequencing, and metabolomics around transplantation and GVHD. machine-written summary
102 samples · 102 runs · ES · Adult · 2024 · 1.56 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 816 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 204 sample values (health condition, health condition detail) |
| ✓ Full text | 102 sample values (location site) · PMC11542268 |
| ✓ Supplementary tables | 112 sample values (age, sex) |
| – 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
Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population transplant_or_immunocompromised · Allogeneic hematopoietic stem cell transplantation, sampled following procedure
“microbiome changes following allo-HSCT at multiple modalities” — abstract:39511587 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
46 of 56 people sampled more than once (92 samples; median 2, up to 2 per person). Schedule stated by the source: “before allo-HSCT (avg 4.49±4.24 days before) and after allo-HSCT, around engraftment (14.01±1.15 days after)” (time origin: transplant).
Genera, mean relative abundance over 72 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 | 102 | 100% | ||||
| country | 102 | 100% | 102 | |||
| health_condition | 102 | 100% | 102 | |||
| subject_id | 102 | 100% | 102 | |||
| collection_date | 102 | 100% | 102 | |||
| detailed_location | 102 | 100% | ||||
| health_condition_detail | 102 | 100% | 102 | |||
| latitude | 102 | 100% | 102 | |||
| location_locality | 102 | 100% | 102 | |||
| location_region | 102 | 100% | 102 | |||
| location_site | 102 | 100% | 102 | |||
| longitude | 102 | 100% | 102 | |||
| sex | 102 | 100% | 102 | |||
| timepoint_label | 102 | 100% | 102 | |||
| age_at_collection_days | 10 | 10% | 10 |
- Multimodal analysis identifies microbiome changes linked to stem cell transplantation-associated diseases. 2024 PMID 39511587 PMC11542268 own_data
Archive description
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is one of the most efficient therapeutic options available to cure many haematological malignancies. However, severe complications derived from this procedure, including graft-versus-host disease (GVHD) and infections, can limit its success and negatively impact on survival. Previous studies have shown that alterations in bacterial communities inhabiting our gut (the microbiome) are associated with the development of allo-HSCT derived complications. However, most studies relied on single techniques that can only analyse a unique aspect of the microbiome (e.g. taxonomic composition), which hinders our ability to understand how microbiome alterations drive allo-HSCT associated diseases. Here, we have applied multiple omic techniques (16S rRNA and shotgun sequencing, targeted and un-targeted metabolomics) in combination with machine learning approaches to define the most significant microbiome changes following allo-HSCT at multiple modalities (bacterial taxa, encoded functions and derived metabolites).
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.description · “communities inhabiting our gut (the microbiome) are”
- body site external_curation.infant_catalog · “body_site_call gut/feces”
- 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 |
|---|---|---|---|---|---|---|
| SAMN40573537 | age_at_collection_days | 16688.0 | R2 | 0.75 | paper.supp.40168_2024_1948_MOESM2_ESM.xlsx[Suppl.Table.1!Age] | 45.68925394 |
| SAMN40573537 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMN40573537 | country | ES | R1 | 0.90 | sample.attr.geo_loc_name | Spain: Valencia |
| SAMN40573537 | health_condition | transplant_or_immunocompromised | R4 | 0.50 | study.description | Allogeneic hematopoietic stem cell transplantation (allo-HSCT) |
| SAMN40573537 | health_condition_detail | allogeneic hematopoietic stem cell transplantation patients | R4 | 0.50 | study.description | Allogeneic hematopoietic stem cell transplantation (allo-HSCT) |
| SAMN40573537 | latitude | 39.4600 | R1 | 0.90 | biosample.attribute:lat_lon | 39.46 N 0.46 W |
| SAMN40573537 | location_locality | Valencia | R1 | 0.85 | biosample.attribute:geo_loc_name | Spain: Valencia |
| SAMN40573537 | location_region | Valencia | R1 | 0.60 | biosample.attribute:lat_lon | 39.46 N 0.46 W |
| SAMN40573537 | location_site | Hospital La Fe | R3 | 0.70 | paper.fulltext.methods | Hospital La Fe (Valencia, Spain) |
| SAMN40573537 | longitude | -0.4600 | R1 | 0.90 | biosample.attribute:lat_lon | 39.46 N 0.46 W |
| SAMN40573537 | sex | male | R2 | 0.75 | paper.supp.40168_2024_1948_MOESM2_ESM.xlsx[Suppl.Table.1!Gender (a)] | M |
| SAMN40573537 | subject_id | 100 | R1 | 0.70 | sample.name_rule:source_material_id | patient_100_post_transplant |
| SAMN40573537 | timepoint_label | post-transplant | R1 | 0.70 | sample.name_rule:source_material_id | patient_100_post_transplant |
Sequencing
102 runs over 102 samples · mean 2.35 Gbp per run (median 1.56 Gbp, total 239.45 Gbp; 102 runs with a base count) · layout PAIRED 102 · platform ILLUMINA 102 · models NextSeq 550 (102) · 71% of runs with a Sandpiper profile · first public 2024-03-23
Authors (14)
Artacho A first · González-Torres C · Gómez-Cebrián N · Moles-Poveda P · Pons J · Jiménez N · Casanova MJ · Montoro J · Balaguer A · Villalba M · Chorão P · Puchades-Carrasco L · Sanz J · Ubeda C last
Downloads
PRJNA1088414.csv.gz (3.8 KB) · parquet (75.7 KB) — all 102 samples, every field with route and confidence · PRJNA1088414_determinations.csv.gz (9.4 KB) — 1,234 evidence rows