This is a practical review written by a clinician for other clinicians. It draws from an extensive body of evidence on the links between the gut microbes (bacteria amongst them), called the microbiota, both in health and in a variety of human diseases. The author, who is also a researcher in the communication between the gut and the brain (the gut-brain axis), focuses on the translation of science into simple clinical applications that result in measurable health outcomes, and in particular in neurodegenerative conditions such as Alzheimer's and Parkinson's, but also other less well studied such as Chronic Fatigue Syndrome (CFS). The paper also covers mental health / mood conditions such as anxiety, and depression. Practitioners who work in the area of gut health and use stool tests to assess various imbalances their patients may be experiencing will get the most out this paper. The author takes a look at the physiological processes that influence gastrointestinal as well as brain health and discusses how tools such as the characterisation or "mapping" of commensal bacteria (the bacteria that lives inside our guts normally), along with the identification of potential opportunistic and pathogenic bacteria and parasites, together with knowledge of molecules such as short chain fatty acids or zonulin can enable better clinical decision making by nutrition and lifestyle medicine practitioners. The paper also includes a valuable discussion on patient-reported outcome measures (PROMs), and particularly on the use of MYMOP by practitioners as a validated tool to collect insight from exposure to real world data in clinical practice.