Gut metagenome in Swedish children on ketogenic diet for epilepsy
46 fecal samples from children with drug-resistant epilepsy in Sweden, collected before and after three months on the ketogenic diet, in a longitudinal study of microbiome changes. machine-written summary
46 samples · 46 runs · SE · Child · 2022 · 1.29 Gbp / sample · cohort Association between seizure reduction during ketog
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 138 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 138 sample values (antibiotic exposure, health condition, health condition detail) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Controlled / prescribed diet or feeding regimen design single_arm_before_after · population neurological_psychiatric · Ketogenic diet 3 months for drug-resistant epilepsy
“before starting KD and after three months” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
23 of 23 people sampled more than once (46 samples; median 2, up to 2 per person). Schedule stated by the source: “Before starting KD and after three months on KD” (time origin: intervention_start).
Genera, mean relative abundance over 37 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 | 46 | 100% | ||||
| country | 46 | 100% | 46 | |||
| health_condition | 46 | 100% | 46 | |||
| subject_id | 46 | 100% | 46 | |||
| antibiotic_exposure | 46 | 100% | 46 | |||
| collection_date | 46 | 100% | 46 | |||
| health_condition_detail | 46 | 100% | 46 |
- Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet. 2022 PMID 35598439 PMC9126955 unsure
- Association between seizure reduction during ketogenic diet treatment of epilepsy and changes in circulatory metabolites and gut microbiota composition. 2024 PMID 39500011 PMC11570732 unsure
Archive description
We collected fecal samples from children with therapy-resistant epilepsy before starting KD and after three months on the diet. Applying shotgun metagenomic DNA sequencing we established taxonomic profiles.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by opus_adjudicated with confidence 0.65. Assay shotgun_dna.
- host study.description · “children with therapy-resistant epilepsy”
- body site study.description · “We collected fecal samples”
- life stage study.description · “children with therapy-resistant epilepsy”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA11953700 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 3 months |
| SAMEA11953700 | collection_date | 2016-10-18 | R1 | 0.90 | biosample.attribute:collection_date | 2016-10-18 |
| SAMEA11953700 | country | SE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Sweden |
| SAMEA11953700 | health_condition | neurological_psychiatric | R2 | 0.60 | external.bugsigdb source | Title: children with drug-resistant epilepsy |
| SAMEA11953700 | health_condition_detail | Response to ketogenic diet | R2 | 0.60 | external.bugsigdb source | Condition: Response to ketogenic diet |
| SAMEA11953700 | subject_id | 30 | R1 | 0.70 | sample.name_rule:alias | PA.30 |
Sequencing
46 runs over 46 samples · mean 1.30 Gbp per run (median 1.29 Gbp, total 59.90 Gbp; 46 runs with a base count) · layout PAIRED 46 · platform ILLUMINA 46 · models Illumina MiSeq (46) · 80% of runs with a Sandpiper profile · first public 2022-05-19
Authors (8)
Dahlin M first · Singleton SS · David JA · Basuchoudhary A · Wickström R · Mazumder R · Prast-Nielsen S last · Wheelock CE
Downloads
PRJEB49521.csv.gz (2.1 KB) · parquet (71.0 KB) — all 46 samples, every field with route and confidence · PRJEB49521_determinations.csv.gz (2.8 KB) — 276 evidence rows