A method for reducing the likelihood of developing liver cancer in an individual diagnosed with non-alcoholic fatty liver disease involves providing in the gut of an individual a population of beneficial bacteria selected from the group consisting of Lactobacillus species, and administering fiber to the individual to maintain a therapeutically effective amount of the beneficial bacteria in the gut of the individual. In certain embodiments, monoacylglycerolacyltransferase-3 (MGAT3) synthesis is inhibited to lower triacylglycerol (TAG) production, while in others, expression of diacylglycerolacyltransferase-2 (DGAT-2) is inhibited. The beneficial bacteria are preferably modified to produce increased amounts of butyrate and may also be encapsulated in a frangible enclosure. Levels of Roseburia are preferably increased while the levels of Akkermansia spp. in the individual's gut microbiome are reduced. In other embodiments, a therapeutically effective amount of a bacterial formulation comprising Faecalibacterium prausnitzii is administered, or a composition comprising modified L. reuteri bacteria having the ability to survive conditions in the duodenum or jejunum of the individual's small intestine. Other embodiments include the administration of a bacterial formulation comprising at least one of Coprococcus, Veillonella, Roseburia, Bifidobacterium, Faecalibacterium prausnitzii and Prevotella.