Fecal metagenomics, MRE-colonized leukemia, Valencia
216 longitudinal fecal samples from hospitalized acute leukemia patients in Valencia, Spain, who were at some point colonized with multidrug-resistant Enterobacteriaceae. machine-written summary
216 samples · 216 runs · ES · Age unknown · 2022 · 3.25 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,296 sample values (collection date, country, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 216 sample values (location site) · PMC9509339 |
| ✓ Supplementary tables | 176 sample values (subject id) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
47 of 47 people sampled more than once (176 samples; median 2, up to 11 per person).
Genera, mean relative abundance over 196 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 | 216 | 100% | 216 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 176 | 81% | 176 | |||
| collection_date | 216 | 100% | 216 | |||
| detailed_location | 216 | 100% | ||||
| latitude | 216 | 100% | 216 | |||
| location_locality | 216 | 100% | 216 | |||
| location_region | 216 | 100% | 216 | |||
| location_site | 216 | 100% | 216 | |||
| longitude | 216 | 100% | 216 |
- Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae. 2022 PMID 36153315 PMC9509339 own_data
Archive description
Metagenomic shotgun sequencing of fecal samples collected from patients with acute leukemia that were at some point colonized with multidrug-resistant Enterobacteriaceae
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “fecal samples from patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN30723845 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMN30723845 | country | ES | R1 | 0.90 | sample.attr.geo_loc_name | Spain: Valencia |
| SAMN30723845 | latitude | 39.4700 | R1 | 0.90 | biosample.attribute:lat_lon | 39.470 N 0.376 W |
| SAMN30723845 | location_locality | Valencia | R1 | 0.85 | biosample.attribute:geo_loc_name | Spain: Valencia |
| SAMN30723845 | location_region | Valencia | R1 | 0.60 | biosample.attribute:lat_lon | 39.470 N 0.376 W |
| SAMN30723845 | location_site | Hospital La Fe | R3 | 0.70 | paper.fulltext.methods | hospitalized at the Hospital La Fe |
| SAMN30723845 | longitude | -0.3760 | R1 | 0.90 | biosample.attribute:lat_lon | 39.470 N 0.376 W |
| SAMN30723845 | subject_id | 65 | R2 | 0.85 | paper.supp.41467_2022_33313_MOESM4_ESM.xlsx[Supplementary Data file 1!Patient_ID] | Sample_ID 4 | Patient_ID 65 |
Sequencing
216 runs over 216 samples · mean 3.48 Gbp per run (median 3.25 Gbp, total 751.92 Gbp; 216 runs with a base count) · layout PAIRED 216 · platform ILLUMINA 216 · models NextSeq 550 (216) · 91% of runs with a Sandpiper profile · first public 2022-09-10
Authors (22)
Djukovic A first · Garzón MJ · Canlet C · Cabral V · Lalaoui R · García-Garcerá M · Rechenberger J · Tremblay-Franco M · Peñaranda I · Puchades-Carrasco L · Pineda-Lucena A · González-Barberá EM · Salavert M · López-Hontangas JL · Sanz M · Sanz J · Kuster B · Rolain JM · Debrauwer L · Xavier KB · Xavier JB · Ubeda C last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA877821.csv.gz (6.0 KB) · parquet (77.8 KB) — all 216 samples, every field with route and confidence · PRJNA877821_determinations.csv.gz (11.5 KB) — 1,688 evidence rows