Bacteria that are important for nutrition and health predominantly live in a healthy gut. Gut dysbiosis results from alterations in gut homeostasis. Contemporary probiotics are used to treat gastrointestinal (GI) problems. Probiotic-producing genera include Lactobacillus, Clostridium, Bifidobacterium, and Streptococcus, which account for many probiotic strains currently in use. Recent improvements in culturomics, using new methods combined with gnotobiotic animal models, offer a solid foundation for the development of innovative host-specific probiotic treatments. The GI tract begins from the mouth and ends at the anus, and it controls food consumption and digestion. Along with aiding food digestion, the GI tract acts as an immune system and a physical barrier against potentially hazardous germs, foreign objects, and antigens. The principal location of nutritional absorption is the gut, which includes the stomach and the small and large intestines. Contemporary probiotics contain well-characterized live microbes that can manipulate the gut and provide health benefits. Based on the available literature, the normal gut microbiota can be restored to preserve gut integrity and host health. Changes or dysfunctions in the microbiome can lead to various illnesses, such as inflammatory bowel disease, obesity, and autoimmune disorders. Prebiotics, probiotics, and fecal microbiota transplantation are only a few of the treatment strategies discussed in this article, along with their advantages, drawbacks, and potential future research areas. Furthermore, it highlights the current studies linking the gut microbiota to COVID-19 and their potential implications for disease treatment and prevention. A topic on the future of microbiome research and how it will enhance general wellness is presented in the article’s conclusion.