Gut microbiomes play central roles in health and disease. For example, the early-life gut microbiome is a simple yet rapidly changing ecosystem crucial for infant development. Early-life events, such as feeding, influence the succession of the gut microbiome. Breast milk is considered the preferred food source for infants due to its protection against infections and allergy development, among other benefits. It remains unknown how to best recover a healthy microbiome following disturbance.
UC Berkeley researchers have developed a method of generating an in vitro microbiome that allows the discovery of treatments that enable recovery of infant gut microbiomes from a dysbiotic state. The invention provides the advantage of finding personalized treatments, thus minimizing side effects. A novel component is the use of microbial genome editing to eliminate specific microbial strains or to modify the capacities of specific members of personalized microbiomes to improve their performance or to eliminate pathogenicity factors. This will increase the chances of successful microbiome manipulation compared to more disruptive treatments, such as antibiotics or addition of organisms not normally resident in the native microbiome (e.g., probiotics).