Ketogenic diet, gut microbiota, childhood epilepsy, Sweden
48 fecal samples from Sweden, from children with therapy-resistant epilepsy and their non-diet parent controls, studied in a diet intervention design comparing gut microbiota before and after 3 months on a ketogenic diet. machine-written summary
48 samples · 48 runs · SE · Child · 2018 · 1.25 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 | 326 sample values (collection date, country, health condition, health condition detail, intervention, subject id, timepoint) |
| ✓ Abstract / description | 4 sample values (health condition, health condition detail) |
| ✓ Full text | 142 sample values (family role, location locality, location site) · PMC11570732, PMC6344533, PMC9126955 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 48 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 |
Controlled / prescribed diet or feeding regimen · population neurological_psychiatric · Ketogenic diet for 3 months vs parent diet controls
“fecal samples from 12 children with therapy-resistant epilepsy before starting KD and” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinalparent–child — not resolved
23 of 23 people sampled more than once (46 samples; median 2, up to 2 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 3 mo (time from timepoint labels). Schedule stated by the source: “stool before starting KD and again after 3 months on the diet” (time origin: intervention_start); stated follow-up 3 mo.
Each row is one person (23 shown); dots are samples at days since that person's first sample.
12 children on ketogenic diet and 11 healthy parents of the patients (same household); no pair key published.
Genera, mean relative abundance over 36 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 | 48 | 100% | ||||
| country | 48 | 100% | 48 | |||
| health_condition | 48 | 100% | 46 | 2 | ||
| subject_id | 46 | 96% | 46 | |||
| antibiotic_exposure | 48 | 100% | 48 | |||
| collection_date | 48 | 100% | 48 | |||
| detailed_location | 48 | 100% | ||||
| health_condition_detail | 48 | 100% | 46 | 2 | ||
| location_locality | 48 | 100% | 48 | |||
| location_site | 48 | 100% | 48 | |||
| family_role | 46 | 96% | 46 | |||
| intervention | 46 | 96% | 46 | |||
| timepoint_label | 46 | 96% | 46 |
- The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy. 2019 PMID 30701077 PMC6344533 own_data
- 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
The gut microbiota has been linked to various neurological disorders via the gut-brain-axis. Diet, in turn, influences the composition of the gut microbiota. The ketogenic diet (KD) is a high-fat, adequate-protein, low-carbohydrate diet established for treatment of therapy-resistant epilepsy in children. Its efficacy in reducing seizures has been confirmed, but the mechanisms remain elusive. The diet has also shown positive effects in a wide range of other diseases, including Alzheimer´s, depression, autism, cancer, and type 2 diabetes. We collected fecal samples from 12 children with therapy-resistant epilepsy before starting KD and after three months on the diet. Parents did not start KD and served as diet controls. Applying shotgun metagenomic DNA sequencing we established both taxonomic and functional profiles. While alpha diversity was not changed significantly during the diet, differences in both taxonomic and functional composition were detected. Bifidobacteria were significantly diminished during the intervention as well as E. rectale and Dialister. An increase in E. coli was observed on KD. Functional analysis revealed changes in 29 SEED subsystems including the reduction of seven pathways involved in carbohydrate metabolism. Decomposition of these shifts indicated that bifidobacteria and Escherichia were important contributors to the observed functional shifts. As health-promoting, fiber-consuming bacteria become less abundant during KD we raise concern about the effects of the diet on the gut microbiota and overall health. Further studies need to investigate whether these changes are necessary for the therapeutic effect of KD.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.title · “composition of the gut microbiota in children”
- body site study.description · “The gut microbiota has been”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “gut microbiota in children with severe epilepsy”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4947578 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 3 months |
| SAMEA4947578 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMEA4947578 | country | SE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Sweden |
| SAMEA4947578 | family_role | parent | R3 | 0.60 | biosample.attribute:alias | alias: CA.01 |
| SAMEA4947578 | health_condition | neurological_psychiatric | R1 | 0.70 | sample.name_rule:alias | CA.01 |
| SAMEA4947600 | health_condition | neurological_psychiatric | R4 | 0.50 | study.description | children with therapy-resistant epilepsy |
| SAMEA4947578 | health_condition_detail | C | R1 | 0.70 | sample.name_rule:alias | CA.01 |
| SAMEA4947600 | health_condition_detail | therapy-resistant epilepsy | R4 | 0.50 | study.description | children with therapy-resistant epilepsy |
| SAMEA4947578 | intervention | diet_intervention | R1 | 0.70 | sample.name_rule:alias | CA.01 |
| SAMEA4947578 | location_locality | Stockholm | R3 | 0.70 | paper.fulltext.methods | Regionala etikprövningsnämden i Stockholm |
| SAMEA4947578 | location_site | Astrid Lindgren Children's Hospital, Karolinska Hospital, Neuropediatric Department | R3 | 0.70 | paper.fulltext.methods | Neuropediatric Department, Astrid Lindgren Children's Hospital, Karolinska Hospital |
| SAMEA4947578 | subject_id | C.01 | R1 | 0.70 | sample.name_rule:alias | CA.01 |
| SAMEA4947578 | timepoint_label | baseline | R1 | 0.70 | sample.name_rule:alias | CA.01 |
Sequencing
48 runs over 48 samples · mean 1.28 Gbp per run (median 1.25 Gbp, total 61.48 Gbp; 48 runs with a base count) · layout PAIRED 48 · platform ILLUMINA 48 · models Illumina MiSeq (48) · 75% of runs with a Sandpiper profile · first public 2018-12-20
Authors (16)
Lindefeldt M first · Eng A · Darban H · Bjerkner A · Zetterström CK · Allander T · Andersson B · Borenstein E · Dahlin M · Prast-Nielsen S last · Singleton SS · David JA · Basuchoudhary A · Wickström R · Mazumder R · Wheelock CE
Downloads
PRJEB28847.csv.gz (2.4 KB) · parquet (73.1 KB) — all 48 samples, every field with route and confidence · PRJEB28847_determinations.csv.gz (5.6 KB) — 520 evidence rows