Development of a high throughput in vivo screening platform for identifying novel pro-and postbiotic bacterial strains

Project Abstract Recent advances in metagenomic sampling have revealed the diversity of bacterial species in the human gut microbiome. Dysbiosis within the gut microbiome is a major driver of human health disorders. These conditions include obesity, leaky gut, sarcopenia, and neurodegenerative diseases. Conversely, supplementing with beneficial bacteria may treat many health conditions associated with gut dysbiosis. This dietary supplementation is being commercially pursued as probiotics or postbiotics. Probiotics deliver live bacteria to the gut, which actively colonize to deliver a health benefit. Postbiotics involve using inactivated bacteria or material derived from them which confer a health benefit. Postbiotics are emerging as attractive dietary supplements since they provide a means to bring anerobic strains into the market, given that a vast majority of gut microbes are anerobic. However, a significant challenge in selecting beneficial bacteria is identifying which isolates might positively impact health from the thousands of strains that are being collected from either human gut or food sources. Such a screening task would be very challenging in rodent models as gnotobiotic maintenance is complex, slow, and expensive. Likewise, in vitro models are limited in relevance and difficult to phenotype human health benefits. In this study, we propose to develop a fast in vivo screening pipeline using NemaLife’s proprietary high-throughput platform. Caenorhabditis elegans is a microscopic nematode that feeds on bacteria, which then colonize the worm’s gut and establish its microbiome. This natural aspect of worm biology allows us to perform life-long and straightforward gnotobiotic maintenance. In Aim 1, we will take 50 representative bacteria species from four genera that have proven beneficial effects on human health disorders and test them in worm models of the same condition. We will examine four phenotypic readouts: healthy aging, sarcopenia, obesity, and leaky gut. These studies will establish the biological contexts of where the worm is an excellent translatable model for human microbiome research. In Aim 2, we will build a database of fully sequenced gut microbiome species associated with positive health outcomes. We will then identify and obtain the 100 most promising strains for human health, based on their metabolic gene annotations, from this database and screen them in our worm models from Aim 1. This screen will allow us to functionally characterize these strains and identify those with therapeutic potential. We will then determine how these beneficial strains impact host physiology to elicit their health effects using transcriptomics. When taken together, the results of this project will validate our screening platform as a cost- effective and high-throughput in vivo tool for discovering, translating, and commercializing novel probiotics and postbiotics with high therapeutic potential and known mechanism of action.