Gut microbiome in pediatric ALL patients, Canada
44 gut microbiome samples (16S rRNA and metagenomic shotgun sequencing) from pediatric acute lymphoblastic leukemia patients treated in Canada, in a cross-sectional study examining links between microbiome composition and infectious complications during treatment. machine-written summary
44 samples · 44 runs · CA · Child · 2018 · 0.36 Gbp / sample · cohort Antibiotic and antifungal use in pediatric leukemi
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 396 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 88 sample values (location locality, location site) · PMC6389711 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 44 sample values (antibiotic exposure) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
10 of 16 people sampled more than once (38 samples; median 3, up to 7 per person). Schedule stated by the source: “Multiple stool samples per patient (16 subjects, 44 samples) collected over first 6 months of ALL therapy; baseline sample within 10 days of therapy start.” (time origin: intervention_start); stated follow-up 6 mo.
Genera, mean relative abundance over 8 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 | 44 | 100% | ||||
| country | 44 | 100% | 44 | |||
| health_condition | 44 | 100% | 44 | |||
| subject_id | 44 | 100% | 44 | |||
| antibiotic_exposure | 44 | 100% | 44 | |||
| collection_date | 44 | 100% | 44 | |||
| detailed_location | 44 | 100% | ||||
| health_condition_detail | 44 | 100% | 44 | |||
| latitude | 44 | 100% | 44 | |||
| location_locality | 44 | 100% | 44 | |||
| location_region | 44 | 100% | 44 | |||
| location_site | 44 | 100% | 44 | |||
| longitude | 44 | 100% | 44 | |||
| timepoint_label | 44 | 100% | 44 |
- Infectious Complications Are Associated With Alterations in the Gut Microbiome in Pediatric Patients With Acute Lymphoblastic Leukemia. 2019 PMID 30838178 PMC6389711 own_data
- Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria responsible for activities that enhance colonic defense. 2022 PMID 35967843 PMC9363618 unsure
- The gastrointestinal antibiotic resistome in pediatric leukemia and lymphoma patients. 2023 PMID 36909730 PMC9998685 unsure
Archive description
Numerous studies have linked shifts in the gut microbiome composition to infection events in various hematological malignances including acute lymphoblastic leukemia (ALL). In order to get a view of the gut microbiome of pediatriac ALL patients we completed both 16S rRNA gene sequencing and metagenomic shotgun sequencing from individuals with ALL being treated at the IWK. Metadata that goes along with these samples will be uploaded with the final publication of our findings on this cohort.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and adolescent by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host study.description · “gut microbiome of pediatriac ALL patients”
- body site study.description · “gut microbiome of pediatriac ALL patients”
- life stage study.title · “pediatric acute lymphoblastic leukemia cohort”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4982918 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 2 weeks |
| SAMEA4982918 | collection_date | 2015/2018 | R1 | 0.90 | biosample.attribute:collection_date | 2015/2018 |
| SAMEA4982918 | country | CA | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Canada |
| SAMEA4982918 | health_condition | other_cancer | R1 | 0.85 | biosample.attribute:environment (feature) | Paediatric Acute Lymphoblastic Leukemia |
| SAMEA4982918 | health_condition_detail | Paediatric Acute Lymphoblastic Leukemia | R1 | 0.85 | biosample.attribute:environment (feature) | Paediatric Acute Lymphoblastic Leukemia |
| SAMEA4982918 | latitude | 44.6373 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.6373° N 63.5842° W |
| SAMEA4982918 | location_locality | Halifax | R3 | 0.70 | paper.fulltext.methods | IWK Health Center in Halifax, Nova Scotia, Canada |
| SAMEA4982918 | location_region | Nova Scotia | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.6373° N 63.5842° W |
| SAMEA4982918 | location_site | IWK Health Center | R3 | 0.70 | paper.fulltext.methods | treated at the IWK Health Center in Halifax |
| SAMEA4982918 | longitude | -63.5842 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.6373° N 63.5842° W |
| SAMEA4982918 | subject_id | MALL-001 | R1 | 0.70 | sample.name_rule:alias | MALL-001 |
| SAMEA4982918 | timepoint_label | S1 | R1 | 0.70 | sample.name_rule:alias | S1 |
Sequencing
44 runs over 44 samples · mean 0.55 Gbp per run (median 0.36 Gbp, total 24.36 Gbp; 44 runs with a base count) · layout SINGLE 44 · platform ILLUMINA 44 · models NextSeq 550 (44) · 18% of runs with a Sandpiper profile · first public 2018-10-18
Authors (13)
Nearing JT first · Connors J · Whitehouse S · Van Limbergen J · Macdonald T · Kulkarni K · Langille MGI last · Dunn KA first · Rodrigues GJ · Forbrigger Z · Bielawski JP · MacDonald J · Van Limbergen JE
Downloads
PRJEB29237.csv.gz (2.1 KB) · parquet (72.3 KB) — all 44 samples, every field with route and confidence · PRJEB29237_determinations.csv.gz (4.3 KB) — 528 evidence rows