High-throughput workflow for cultivation and functional characterization of novel gut microbiota strains with metabolic signatures associated with gut-brain communication

Nearly one and a half billion people suffer from neurological and psychiatric disorders globally, with Alzheimer's disease, Parkinson's disease, multiple sclerosis, autism spectrum disorder, and major depressive disorder as the most prevalent, representing a huge burden on society. Recently, all these diseases have been associated with chronic inflammation, gut microbiota dysbiosis, and alterations in the functioning of the microbiota-gut-brain axis (MGBA). Hence, culturing novel human gut microbiota (HGM) strains, and characterization of their safety status, anti-inflammatory potential, and production of MGBA-related metabolites could contribute to deciphering the molecular mechanisms staying behind the MGBA host-microbe interactions and discovering the novel biotherapeutic agents (next-generation probiotics) for prevention and treatment of neuropsychiatric diseases. At the moment, research on the gut microbiota is challenged by expanding the collections of cultivable HGM members and the development of the methods and workflows for their isolation. Here we report a novel high-throughput workflow based on targeted culturing linked to metagenome sequencing, combined with the bioinformatic search for HGM members producing MGBA-related microbial-related metabolites and phenotypic analyses. With this approach, we isolated 141 bacterial strains, and 41 of them were characterized for their safety status and potential as MGBA-related probiotics. Our workflow enabled the culturing, archiving, phenotyping, and probiotic characterization of novel HGM bacteria, significantly expanded the resources for the MGBA cross-talk research, and revealed novel safety and probiotic information of 22 extremely oxygen-sensitive strains.