Gut3Gel: A high throughput mucus model to support intestinal microbiome research

The human intestinal microbiota plays a crucial role in health and disease, yet recreating its complex interactions in vitro remains a significant challenge. Gut 3 Gel, introduced herein as a novel in vitro mucus model, is designed for culturing complex microbial communities without the need for anaerobic conditions. Intestinal microbiota samples from five donors were individually inoculated in Gut 3 Gel and cultured for 72 hours. Taxonomic composition assessment revealed that Gut 3 Gel sustains diverse microbial species and particularly enhances the prevalence of mucus-associated bacteria including Bifidobacterium , Lactobacillus , and Faecalibacterium . Microbial metabolic activity within Gut 3 Gel was confirmed by the increased production of acetate and butyrate, as well as of exopolysaccharides. Gut 3 Gel provides microbiota with key physiological features of intestinal mucus, serving as a reproducible and scalable culturing platform. These features make Gut 3 Gel a promising tool for advancing microbiota research with potential applications in drug screening, microbiome mining, and high throughput testing of microbiome-modulating molecules.