The gut microbiota, a complex community of bacteria, is influenced by various factors such as diet, antimicrobials, mucus, and the host immune system. The spatial distribution of these bacteria within the gut, known as gut biogeography, impacts the development and maintenance of a resilient microbial ecosystem. Key microhabitats include the gut lumen, colon mucus layers, and colon crypts, each with distinct microbial communities. Diet plays a crucial role in shaping the microbiota, with breast milk being particularly important during early life. The adult gut microbiota is dominated by Bacteroidetes and Firmicutes, and its composition is stable over time, with a core of ~40 bacterial species persisting for at least a year. The mucus layer, which varies in thickness and density along the gastrointestinal tract, creates protected habitats for specific bacterial ecosystems. Bacteria that can utilize mucus as a carbon and energy source, such as *Akkermansia muciniphila*, have a competitive advantage and can stably colonize the gut. Antimicrobials, secreted by Paneth cells, restrict bacterial growth near the mucosal surface, while the host immune system, particularly through secreted immunoglobulin A (sIgA), mediates homeostasis between the host and the microbiota. Adherence mechanisms, such as the use of pili and lectins, allow bacteria to attach to the epithelial surface and penetrate the mucus barrier. Immunomodulation by beneficial bacteria, such as *Bacteroides fragilis*, contributes to their colonization and persistence. Microbiota dysbiosis, characterized by changes in microbial composition, is associated with various diseases, including inflammatory bowel disease (IBD) and hepatic encephalopathy. Understanding the biogeography of the gut microbiota is essential for developing targeted interventions and therapies.The gut microbiota, a complex community of bacteria, is influenced by various factors such as diet, antimicrobials, mucus, and the host immune system. The spatial distribution of these bacteria within the gut, known as gut biogeography, impacts the development and maintenance of a resilient microbial ecosystem. Key microhabitats include the gut lumen, colon mucus layers, and colon crypts, each with distinct microbial communities. Diet plays a crucial role in shaping the microbiota, with breast milk being particularly important during early life. The adult gut microbiota is dominated by Bacteroidetes and Firmicutes, and its composition is stable over time, with a core of ~40 bacterial species persisting for at least a year. The mucus layer, which varies in thickness and density along the gastrointestinal tract, creates protected habitats for specific bacterial ecosystems. Bacteria that can utilize mucus as a carbon and energy source, such as *Akkermansia muciniphila*, have a competitive advantage and can stably colonize the gut. Antimicrobials, secreted by Paneth cells, restrict bacterial growth near the mucosal surface, while the host immune system, particularly through secreted immunoglobulin A (sIgA), mediates homeostasis between the host and the microbiota. Adherence mechanisms, such as the use of pili and lectins, allow bacteria to attach to the epithelial surface and penetrate the mucus barrier. Immunomodulation by beneficial bacteria, such as *Bacteroides fragilis*, contributes to their colonization and persistence. Microbiota dysbiosis, characterized by changes in microbial composition, is associated with various diseases, including inflammatory bowel disease (IBD) and hepatic encephalopathy. Understanding the biogeography of the gut microbiota is essential for developing targeted interventions and therapies.