Research and development of therapeutics, consumer products, diagnostic and prognostic tools and methods consisting of designed ecologies of combinations of microorganisms, or individually selected microorganisms for the treatment and prevention of immune diseases, including food allergy desensitization, asthma, and inflammation, infections, including sepsis and surgery-associated infections, and infections with Clostridium difficile, oncology, including colon cancer and carcinomas, and neurological conditions, such as Alzheimer's disease, autism spectrum disorder, dementia, Parkinson's disease, and pre- and post-natal depression