Low-grade systemic inflammation in adipose tissues or liver, is an important etiologic factor in insulin resistance. LPS is an important element causing such metabolic inflammation, and intestinal flora is considered a major source of systemic LPS. We studied changes of intestinal microbiota associated with high-fat diet (HFD) that causes insulin resistance and metabolic stress. 16S rRNA gene sequencing showed that HFD significantly decreased the abundance of a mucin-degrading bacterium Akkermansia muciniphila compared to control diet. Reduced abundance of Akkermansia in HFD-fed mice was reversed by metformin, a widely prescribed anti-diabetic medicine. Oral administration of Akkermansia to HFD-fed mice significantly enhanced insulin sensitivity and attenuated adipose tissue inflammation probably by inducing Foxp3+ regulatory T cells (Tregs) in the visceral adipose tissue. We also studied Paneth cells, specialized intestinal epithelial cells that produce antimicrobial peptides (AMP) and shape gut microbial milieu. We studied whether high-fat diet (HFD) impairs the function of Paneth cells and interferes with intestinal microbial homeostasis, potentially contributing to the development of metabolic syndrome. HFD-fed mice exhibited reduced expressions of some AMP and defective antimicrobial activity, which led to loss of epithelial integrity and a significantly higher content of LPS in the liver and serum of HFD-fed mice compared to chow-fed mice. Antibiotic treatment reduced translocation of bacterial components, steatosis, and inflammation in the liver of HFD-fed mice, which in turn improved systemic glucose metabolism. HFD-fed mice were also more susceptible to dextran sodium sulfate-induced colitis, probably due to impaired Paneth cell function. Our data suggest that Paneth cell dysfunction may be one of the underlying mechanisms of glucose intolerance and inflammatory bowel disease associated with western diet. These results suggest that high-fat diet could be a risk factor not only for metabolic syndrome but also for colitis, and modulation of the gut microbiota or Paneth cell function could be a new therapeutic modality against metabolic syndrome or colitis associated with western diet.