Obesity alters gut microbial ecology. This study analyzed 5,088 bacterial 16S rRNA gene sequences from the distal intestinal microbiota of genetically obese ob/ob mice, lean ob/+ mice, and their ob/+ mothers, all fed the same polysaccharide-rich diet. The majority of gut species are unique to mice, but the mouse and human microbiota are similar at the division level, with Firmicutes and Bacteroidetes dominating. Microbial community composition is inherited from mothers. However, compared with lean mice, ob/ob animals have a 50% reduction in Bacteroidetes and a proportional increase in Firmicutes, indicating that obesity affects gut microbiota diversity. These changes suggest that manipulating microbial community structure may help regulate energy balance in obese individuals. The gut microbiota plays a crucial role in extracting calories from indigestible polysaccharides in the diet. Microbial fermentation of dietary polysaccharides produces short-chain fatty acids, which stimulate triglyceride synthesis in the liver. Microbial suppression of fasting-induced adipocyte protein (Fiaf) in the gut epithelium reduces LPL inhibition, increasing fat storage. Differences in gut microbial ecology between humans may influence energy homeostasis, with individuals predisposed to obesity having microbial communities that promote more efficient energy extraction and storage. The study found that kinship significantly affects microbial diversity, with mothers and their offspring sharing similar microbiotas. Obesity correlates with a shift in the abundance of Bacteroidetes and Firmicutes, with obese mice showing a 50% reduction in Bacteroidetes and a greater proportion of Firmicutes. These changes occur at the division level and are independent of kinship and gender. The findings suggest that gut microbial ecology is influenced by host genotype, maternal exposure, diet, and energy balance. The study also identified a deep-branching clade of Cyanobacteria in the guts of mice and other animals, possibly representing descendants of nonphotosynthetic ancestral cyanobacteria adapted to life in animal gastrointestinal tracts. The results highlight the importance of gut microbial diversity in obesity and suggest that understanding the role of gut microbiota in energy homeostasis could lead to new treatment strategies for obesity. The study underscores the need for further research into the relationship between gut microbial ecology and obesity in humans.Obesity alters gut microbial ecology. This study analyzed 5,088 bacterial 16S rRNA gene sequences from the distal intestinal microbiota of genetically obese ob/ob mice, lean ob/+ mice, and their ob/+ mothers, all fed the same polysaccharide-rich diet. The majority of gut species are unique to mice, but the mouse and human microbiota are similar at the division level, with Firmicutes and Bacteroidetes dominating. Microbial community composition is inherited from mothers. However, compared with lean mice, ob/ob animals have a 50% reduction in Bacteroidetes and a proportional increase in Firmicutes, indicating that obesity affects gut microbiota diversity. These changes suggest that manipulating microbial community structure may help regulate energy balance in obese individuals. The gut microbiota plays a crucial role in extracting calories from indigestible polysaccharides in the diet. Microbial fermentation of dietary polysaccharides produces short-chain fatty acids, which stimulate triglyceride synthesis in the liver. Microbial suppression of fasting-induced adipocyte protein (Fiaf) in the gut epithelium reduces LPL inhibition, increasing fat storage. Differences in gut microbial ecology between humans may influence energy homeostasis, with individuals predisposed to obesity having microbial communities that promote more efficient energy extraction and storage. The study found that kinship significantly affects microbial diversity, with mothers and their offspring sharing similar microbiotas. Obesity correlates with a shift in the abundance of Bacteroidetes and Firmicutes, with obese mice showing a 50% reduction in Bacteroidetes and a greater proportion of Firmicutes. These changes occur at the division level and are independent of kinship and gender. The findings suggest that gut microbial ecology is influenced by host genotype, maternal exposure, diet, and energy balance. The study also identified a deep-branching clade of Cyanobacteria in the guts of mice and other animals, possibly representing descendants of nonphotosynthetic ancestral cyanobacteria adapted to life in animal gastrointestinal tracts. The results highlight the importance of gut microbial diversity in obesity and suggest that understanding the role of gut microbiota in energy homeostasis could lead to new treatment strategies for obesity. The study underscores the need for further research into the relationship between gut microbial ecology and obesity in humans.