Table 2.

Experimental Mouse models for liver disease

Model	Description	Liver pathology	Microbiome Features
Diet
High Fat diet	Diet using higher saturated fat, or supplemented with cholesterol compared to chow	Induces fatty liver and hepatic steatosis. Associated with metabolic syndrome phenotype.238	Common model for inducing dysbiosis; associated with changes in the microbiome
Choline Deficient Diet	A high fat diet with choline and methionine omitted.	Induces fatty liver, steatosis and inflammation and fibrosis. The model does not contribute to metabolic syndrome.5	Small study suggests diet- induced changes239
Ethanol supplemented liquid diet	A model of chronic alcohol abuse administered as an isocaloric diet where ethanol or maltose and dextrose are supplemented. Diet can be administered orally (Lieber-DeCarli240) or intragastrically (Tsukamoto-French241)	Oral supplementation leads to inflammation and fatty liver, representing a good model for early ALD Intragastric administration leads to severe steatosis and mild fibrosis4	Diet affects the abundance of several taxa and is associated with changes in the microbiome57
Genetic Manipulations
Knock out model	A mouse line where both copies of a gene have been removed	This depends on the gene. For example, FxR−/− mice have more fatty liver accumulation on a high fat diet.31 Muc2−/− are protected from diet- induced liver injury.107 GSTA4−/−, PPAR-α−/− double knockout mice have increased inflammation and fibrosis compared to either single mutant or WT242	The microbiome of lineage- derived mice is distinct from wild type mice. This is likely to be an effect of microbiome drift within the colonies, rather than a direct effect of the genotype.243
Littermate controls	Mice from a heterozygous cross that lead to Wild Type and knockout littermates.		Much of the mouse microbiome is acquired through vertical transmission; littermates are better microbial controls.244
Cre-Lox localized mutation	A genetic cross that allows for tissue-specific knockout of a gene	This is gene dependent on the gene. A Cre/Lox model of liver specific E-cadherin knockout shows pathology like primary sclerosing cholangitis, and increases susceptibility to cancer.245 The loss of TLR 5 in hepatocytes leads to increased inflammation and fibrosis in a high fat diet induced model of NASH246	Microbiome considerations depend on the how the controls are selected.
Avatar Mice	Mice transplanted with solid state tumors from cancer patients.	Human hepatocellular carcinoma can be transplanted into the mouse.247	There is no specific effect on the microbiome.
Microbiome
Antibiotic treatment	Treatment with a broad- spectrum antibiotic	No direct effect on liver disease; Antibiotics can moderate the effect of other interventions.	Antibiotics can have off target effects and significantly alter the microbial community in addition to decreasing the bacterial load194
Probiotic manipulation	Microbial supplementation to modify the microbiome	No direct effect on liver disease; probiotics can modulate the effect of other treatments:  Lactobacillus to ameliorate alcohol-induced liver injury)106	Can lead to the over- abundance of a specific organism or correct defects in the community. However, not all probiotics colonize.
Germ-Free Mice	Raised without any bacterial community	Germ free mice have immune defects.248 These mice are also more susceptible to alcohol- induced liver injury.86	Useful to demonstrate the importance of bacterial communities for a phenotype.
Monoculture gnotobiotic mice	Germ free mice that have been colonized with a single bacterium or defined bacterial community	No direct effect; depends on the community transplanted and challenge	Can test whether the defined community can modulate the phenotype
Mouse transplant	Bacterial communities from mice transplanted into germ free mice	No direct effect; depends on the community transplanted and challenge	Demonstrates whether mouse phenotype is transferable or can be modulated through the microbial community.
Humanized mice	Germ free mice which have been gavage with the microbiome from a human donor	No direct effect; depends on the community transplanted and challenge	Demonstrates whether human phenotype is transferable or can be through the microbial community.