Abstracts

Rationale: The human microbiota consists of a complex flora of microorganisms that influence human health by modulating metabolic and neurological pathways, both locally (gut) and systemically (whole body, brain). Bloom Science’s platform, IrisRx^TM, identifies health promoting microbes by starting with clinical samples from patients with demonstrated positive clinical outcomes. We focus on neurological and immune pathways with the ultimate therapeutic goals of treating diseases with unmet medical need, including Dravet syndrome and other rare epilepsies. Here, we showcase the platform path for selecting candidate bacterial strains for BL-001, a live biotherapeutic product (LBP) that traces its origin to the benefits of the ketogenic diet.


Methods: The anti-seizure efficacy of the ketogenic diet is conveyed by gut bacteria, and pre-clinical studies showed that Akkermansia muciniphila and Parabacteroides merdae, in combination, are necessary and sufficient for seizure reduction in two epilepsy disease models. This constituted the starting point for selecting the optimal naturally occurring variants (strains) of the species identified, and the subsequent development of those strains as an LBP. With IrisRx^TM we investigate and discover bioinformatically, select organisms of interest, and use functional screening to identify medically relevant traits. All candidate strains were comprehensively characterized with full length sequencing and bioinformatical analysis, with classic microbiological methods, and secreted bacterial products were tested in in vitro assays to elucidate effects on specific pathways and/ or activity.


Results: The selected strains reduced neuronal inflammation and hyperexcitability in vitro, produced key metabolites and increased GABA in human induced Pluripotent Stem Cell (hiPSC)-derived Glutamatergic neurons in co-culture with hiPSC-derived Astrocytes. No significant antibiotic resistance genes or other mobile genetic elements were identified, and lipopolysaccharide (LPS) immunogenicity was low. Experiments with an in vitro fermentation system, a simplified mimic of the human microbiome, showed that the selected A. muciniphila strain was able to displace another strain of the same species, indicating good engraftment capacity. The BL-001 lead candidate strain combination was tested by twice daily dosing of 1 billion colony forming units in the progressive seizure aggravation model (6Hz, fixed current 32 mA), in mice with a normal microbiome, and BL-001 dosing showed consistent protection against repeated seizures as compared to controls.


Conclusions: From this data we were able to select the strains that exhibited the strongest desirable phenotypes in vitro and in vivo and establish that this combination of bacteria with a high degree of certainty would be safe for human consumption. In conclusion, the strain combination selected by the IrisRx^TM platform methodology to constitute BL-001 was found to be suitable for proceeding to trials in human.


Funding: This study was funded by Bloom Science.