Abstract: A systems biology approach is used to characterize and relate the intestinal (gut) microbiome of a host organism (e.g. a human) to physiological processes within the host. Information regarding the types and relative amounts of gut microflora is correlated with physiological processes indicative of e.g., a patient's risk of developing a disease or condition, likelihood of responding to a particular treatment, for adjusting treatment protocols, etc. The information is also used to identify novel suitable therapeutic targets and/or to develop and monitor the outcome of therapeutic treatments. An exemplary disease/condition is the development of hepatic encephalopathy (HE), particularly in patients with liver cirrhosis.