Gut microflora as biomarkers for the prognosis of cirrhosis and brain dysfunction

A treatment method for a patient with a liver disease, comprising the steps of

• analyzing gut microflora of said patient in order to determine a gut microbiome signature for said patient;
• comparing said gut microbiome signature of said patient to one or more gut microbiome reference signatures;
• and, based on said step of comparing,
• concluding whether or not said patient has or is at risk for developing at least one of said one or more conditions of interest;
• and
• if said patient has or is at risk for developing at least one of said one or more conditions of interest, then selecting from one or more treatment protocols appropriate for said one or more conditions of interest, and treating the patient according to said one or more treatment protocols selected.

A method of monitoring the efficacy of a treatment protocol in a patient with liver disease or a condition associated with liver disease, comprising the steps of

• analyzing gut microflora of said patient in order to determine a gut microbiome signature for said patient;
• comparing said gut microbiome signature of said patient to one or more gut microbiome reference signatures, wherein said one or more gut microbiome reference signatures include one or more of a positive gut microbiome reference signature based on results from control subjects with encephalopathy and a negative gut microbiome reference signature based on results from control subjects without encephalopathy;
• and
• if said gut microbiome signature for said patient statistically significantly matches said positive gut microbiome reference signature, then concluding that said treatment protocol is not efficacious;
• and/or
• if said gut microbiome signature for said patient deviates statistically significantly from said negative gut microbiome reference signature, then concluding that said treatment protocol is efficacious,
• wherein said analyzing and comparing steps are performed a plurality of times with samples collected from said patient at a plurality of time periods during said treatment protocol.