Over the last few weeks, I have been having a dialog with a very intelligent parent of a child with epilepsy. There appears to be a combination of SNP mutations and microbiome shifts involved which are largely not explored by conventional researchers.
This post attempts to document what is available on PubMed. I am also adding Epilepsy to the conditions listed on the http://microbiomeprescription.azurewebsites.net site in the hope that other parents can upload the microbiome of people with epilepsy and citizen scientists use the data to find associations.
“Seizures and epilepsy are not the same. An epileptic seizure is a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. Epilepsy is a disease characterized by an enduring predisposition to generate epileptic seizures and by the neurobiological, cognitive, psychological, and social consequences of this condition. Translation: a seizure is an event and epilepsy is the disease involving recurrent unprovoked seizures.”https://www.epilepsy.com/article/2014/4/revised-definition-epilepsy
PubMed and Microbiome
- “Specifically, patients with four seizures per year or fewer showed an increase of Bifidobacteria and Lactobacillus than those with more than four seizures per year.” 
- “The timely work by Zhang et al.  suggests that there are differences in intestinal bacterial composition between pediatric patients with refractory epilepsy that do and not respond to the ketogenic diet. This study raises several questions: 1) How does gut bacteria affect epileptogenesis? 2) Can monitoring gut bacterial composition be used as a marker for treatment efficacy and, as is seen in mouse models, 3) Can altering bacterial composition be used as a therapeutic strategy? ” 
- “After 6 months of treatment, 2 patients were seizure free, 3 had ≥ 90% seizure reduction, 5 had a reduction of 50-89%, and 10 had < 50% reduction. All 10 responders showed an improvement in EEG. Compared with baseline, fecal microbial profiles showed lower alpha diversity after KD therapy and revealed significantly decreased abundance of Firmicutes and increased levels of Bacteroidetes. We also observed that Clostridiales, Ruminococcaceae, Rikenellaceae, Lachnospiraceae, and Alistipes were enriched in the non-responsive group.” 
- Ongoing clinical trial with “twice a day for 4 months (Streptococcus thermophilus, Lactobacillus acidophilus, L.plantarum, L. paracasei, L. delbrueckii subs bulgaricus, Bifidobacterium breve, B.longus y B.infantis. y CD2).” 
- Can epilepsy be treated by antibiotics? “
“We present six patients with drug-resistant epilepsy who attained temporary seizure freedom during antibiotic treatment.”
- “Enrichment of, and gnotobiotic co-colonization with, KD-associated Akkermansia and Parabacteroides restores seizure protection. Moreover, transplantation of the KD gut microbiota and treatment with Akkermansia and Parabacteroides each confer seizure protection to mice fed a control diet… Overall, this study reveals that the gut microbiota modulates host metabolism and seizure susceptibility in mice.” 
- Intestinal Microbiota as an Alternative Therapeutic Target for Epilepsy.
- Fecal microbiota transplantation cured epilepsy in a case with Crohn’s disease: The first report .
DNA – SNP variations:
It is important to remember that DNA and the microbiome are strongly associated. FMT transplant from people with close DNA similarity are more successful than with strangers.
- Identification of new risk factors for rolandic epilepsy: CNV at Xp22.31 and alterations at cholinergic synapses.
- Genetic susceptibility in Juvenile Myoclonic Epilepsy: Systematic review of genetic association studies – full paper.
- TOP3B: A Novel Candidate Gene in Juvenile Myoclonic Epilepsy? 
- ABCC2 rs2273697 is associated with valproic acid concentrations in patients with epilepsy on valproic acid monotherapy. 
- MAP2 – A Candidate Gene for Epilepsy, Developmental Delay and Behavioral Abnormalities in a Patient With Microdeletion 2q34. 
Alas, there is not enough research published yet to create a microbiome profile for epilepsy — but given the number of studies from 2018, I suspect it will be possible in a few months.