Abstract: A composition of fecal material is prepared and administered to a subject suffering from alcohol craving, alcohol consumption and/or alcohol use disorder. The donor fecal material is enriched in beneficial microbiota associated with reduced alcohol craving and/or consumption and supplies beneficial microbiota in which the recipient is deficient, and reduces harmful microbes. Methods of preparing and administering are disclosed, along with the identification of beneficial and harmful microbiota families. The treatment is also useful for delivery of microbiota that are short chain fatty acid producers to reduce alcohol craving and/or consumption in subjects deficient in short chain fatty acids.

Abstract: Disclosed herein are compositions and methods for diagnosing fungal dysbiosis in the gut of a subject with cirrhosis that involves assaying a sample from the subject for bacterial taxa. These compositions and methods are based on the discovery that there is significant correlation between fungal and bacterial diversity in gut microbiota of cirrhotic patients. Therefore, disclosed herein is a method for treating a subject with liver cirrhosis that involves assaying a gut sample from the subject for bacterial taxa to generate a bacterial profile, comparing the bacterial profile to control profiles to predict fungal dysbiosis; and treating the subject for fungal dysbiosis.

Abstract: Methods of detecting and treating cognitive impairment are provided. The methods involve determining, via a metagenomic analysis, the salivary and/or gut microbiota signature of the subject, e.g. a subject with an illness such as chronic liver disease and/or post-traumatic stress disorder (PTSD), and based in the microbiota signature, identifying subjects who have cognitive impairment.

Abstract: Disclosed herein are compositions and methods for diagnosing fungal dysbiosis in the gut of a subject with cirrhosis that involves assaying a sample from the subject for bacterial taxa. These compositions and methods are based on the discovery that there is significant correlation between fungal and bacterial diversity in gut microbiota of cirrhotic patients. Therefore, disclosed herein is a method for treating a subject with liver cirrhosis that involves assaying a gut sample from the subject for bacterial taxa to generate a bacterial profile, comparing the bacterial profile to control profiles to predict fungal dysbiosis; and treating the subject for fungal dysbiosis.

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.