Shotgun metagenomic analysis reveals gut dysbiosis in epilepsy patients

14 Jun 2024

Despite the increasing availability of anti-seizure medication options, a substantial proportion of epilepsy patients, estimated at 30%-40%, continue to have drug-resistant disease.1 As such, treatment approaches beyond just pharmacotherapy have garnered increasing interest in recent years.1 Dietary interventions, such as the ketogenic diets, have demonstrated efficacy in managing certain epilepsy subtypes, suggesting a potential role of the bidirectional gut-brain axis in the management of this neurological disorder.1 Further study of the gut microbiome and its role in drug-resistant epilepsy may thus offer new insights into the pathogenesis and potential novel therapeutic targets.1 During the AAN 2024 Annual Meeting, Dr. Leung, Chun-Yin William from Queen Mary Hospital, Hong Kong, presented the results of a shotgun metagenomics study which aimed to study the role of gut dysbiosis in drug-resistant epilepsy.1

In this single-center, case-control, observational study, patients aged >18 years with known focal epilepsy were recruited.1 Stool samples were collected with the OMNIgene•GUT collection device for shotgun metagenomic sequencing, which allows for a more comprehensive characterization of taxonomic composition and relative abundance of gut microbiota compared to the usual 16S RNA sequencing.1 Exclusion criteria included a known history of gastrointestinal disorders, any form of gastrointestinal surgery, recent history of febrile illness or gastroenteritis within 4 weeks, recent use of oral or intravenous antibiotics, probiotics, and/or steroids within 4 weeks, travel to tropical areas within the past 3 months or pregnant women.1 In total, 169 samples were accepted, including 20 from drug-sensitive epilepsy (DSE) patients, 17 from drug-resistant epilepsy (DRE) patients and 132 from healthy controls (HC).1  

Alpha diversity, which reflects the species-level diversity within an individual subject, is considered favorable as it is associated with increased resilience of the gut ecosystem to withstand disturbances.1 Compared with healthy controls, both the DRE (DRE vs. HC: 3.0 vs. 3.34; p=0.00227) and DSE (DSE vs. HC: 2.85 vs. 3.34; p=0.00235) groups had reduced alpha diversity indices.1 However, no statistically significant differences in alpha diversity were observed between the DRE and DSE groups (p=0.98).1 Regarding beta diversity, which reflects the overall bacteria diversity across all 3 study populations, similar compositional and abundance patterns were observed in the DSE and DRE groups, with both displaying significant inter-variability compared with the healthy controls.1

Analysis at the species level revealed significant heterogeneity in the relative taxonomic abundance of 9 bacterial species between the DSE and DRE groups.1 Specifically, the Linear discriminant analysis Effect Size (LEfSE) analysis and individual Wilcoxon tests consistently identified Clostridium sp. AT4, Acidaminococcus intestini, and Bilophila wadsworthia as having statistically significant differences in relative abundance between the two groups.1 Clostridium sp. AT4 and A. intestini were found to have higher relative abundance in the DRE group, while B. wadsworthia had a higher relative abundance in the DSE group.1 Logistic regression models adjusting for age and sex on the 9 species identified through the Wilcoxon tests further confirmed that the DRE cohort had an increased abundance of Phocaeicola vulgatus and A. intestini, but decreased abundance of B. wadsworthia.1 Similar abundance patterns persisted after adjusting for all anti-seizure medications.1

In summary, this study found a reduction in gut microbiome alpha diversity in gut microbiota populations in both DSE and DRE patients compared with healthy controls.1 An increase in relative abundance of Clostridium sp. AT4, P. vulgatus, A. intestine and a decrease in relative abundance in B. wadsworthia were significantly associated with DRE, even after adjusting for age, sex, and anti-seizure medications.1 Further downstream analysis and interventional studies in a larger sample are needed to establish a causal relationship between individual gut microbiota species and different epilepsy subgroups.1

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