At present, it is already known that many gastrointestinal tract diseases are caused by disorders of the intestinal ecosystem. The contribution of microbiota disorders to the development and sustaining of inlammatory bowel diseases, irritable bowel syndrome, necrotizing enterocolitis, constipation or bloating has been demonstrated in numerous scientiic studies. Another matter is bacterial imbalance in food allergy and atopic diseases. The effectiveness of probiotics and prebiotics in these diseases has been repeatedly conirmed, which made researchers search for new diseases in which probiotics could be an eficient therapeutic solution. Reports have also been published on microbiota disturbances in children with a spectrum of autistic disorders, depression or metabolic syndrome, and in obese patients. New micro -organisms have been discovered, which in addition to Lactobacillus or Biidobacterium bacteria, may signiicantly inluence the improvement of human health. Especially promising are two bacterial species, Akkermansia muciniphila and Faecalibacterium prausnitzii, which seem to interact in continuity regeneration of the intestinal epithelium. A. muciniphila has the ability to degrade mucin, while producing acetic acid, propionic acid and oligosaccharides. These products become the substrate for F. prausnitzii, one of the main producers of butyrate in the intestine. The anaerobic butyrate -producing bacterium helps to inhibit inlammation in the gastrointestinal tract, while preventing increased intestinal permeability. Growth stimulation in bacteria (e.g. towards prebiotic therapy) may therefore prove to be a valuable nutritional option and an eficient way to restore the intestinal epithelium. While A. muciniphila is extensively studied in the context of obesity and diabetes, F. prausnitzii may become an interesting marker for Crohn’s disease activity. The aim of this paper is to present new and promising aspects of intestinal microbiota restoration in the treatment of selected diseases.