For millions of years, prokaryotic organisms have functioned as a vital selective force shaping eukaryotic evolution. It is now widely accepted that gut bacteria play a vital role in various physiological and metabolic activities of hosts, and thus, it is essential to maintain their homeostasis. Previous studies have shown an association of gut bacterial imbalance (dysbiosis) associated with several pathologies. However, very little is known about possible mechanisms involved between bacteria and hosts to maintain their homeostasis in the gut. Bacterial activities, such as cooperation (biofilm formation, horizontal gene transfer, quorum sensing, etc.), antagonism, and combination, and host responses of their immune system, gut barrier functions, and different dietary components have been identified as crucial factors for maintaining bacterial homeostasis in the gut. Our understanding of several possible mechanisms involved in gut bacterial homeostasis should be widened to modulate their composition or treat diseases. The objective of this chapter is to provide an overview of different factors involved in gut bacterial homeostasis with an emphasis on host intestinal barrier and immune system, dietary components, and quorum sensing. Also, brief information regarding roles of microbiota on gut-brain axis has also been included.