Diet-induced obesity is the most widely used animal model for studying nonalcoholic fatty liver disease (NAFLD). However, the physiological effects of a high-fat diet (HFD) are inconsistent between different studies. To elucidate this mystery, mice raised with conventional (CONV), specific pathogen-free (SPF) and gentamicin (G) treatments and fed with standard diet (STD) or HFD were analyzed in terms of their physiology, gut microbiota composition, hepatic steatosis and inflammation. Serum biochemistry showed increased levels of cholesterol and aspartate aminotransferase in the G-STD and CONV-HFD groups, respectively. The CONV-HFD group exhibited more inflammatory foci compared to the SPF-HFD and G-HFD groups. Furthermore, immunohistochemistry staining revealed the infiltration of Kupffer cells in the liver, consistent with increased mRNA levels of MCP-1, CD36 and TLR4. Principal coordinate analysis and the cladogram of LEfSe showed that the distinguished clusters of gut microbiota were dependent on housing conditions. The Rikenellaceae, F16 and Desulfovibrionaceae were strongly correlated with hepatic inflammation. Otherwise, higher NAFLD activity score correlated with altered relative abundances of Bacteroidetes and Firmicutes. In conclusion, gut microbiota varying with housing condition may be pivotal for the host response to HFD.Copyright © 2020 Elsevier Inc. All rights reserved.