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. Gut3Gel, 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 Gut3Gel and cultured for 72 h. Taxonomic composition assessment revealed that Gut3Gel sustains diverse microbial species and particularly enhances the prevalence of mucus-associated bacteria including Bifidobacterium, Lactobacillus, and Faecalibacterium. Microbial metabolic activity within Gut3Gel was confirmed by the increased production of acetate and butyrate, as well as of exopolysaccharides. Gut3Gel provides microbiota with key physiological features of intestinal mucus, serving as a reproducible and scalable culturing platform. These features make Gut3Gel a promising tool for advancing microbiome research with potential applications in drug screening, microbiome mining, and high throughput testing of microbiome-modulating molecules.