This review summarizes the current evidence on the use of prebiotics and probiotics in gastrointestinal (GI) disorders, emphasizing strain-specific effects and potential adverse effects. The gut microbiome plays a crucial role in GI health, and both prebiotics and probiotics can modulate the microbiome and metabolome, influencing host health. Prebiotics are non-digestible, fermentable food components that promote the growth of beneficial bacteria, while probiotics are live microorganisms that confer health benefits when consumed. Synbiotics combine prebiotics and probiotics for synergistic effects. Both prebiotics and probiotics can influence the gut microbiome, immune system, and metabolism, with mechanisms including modulation of the gut barrier, production of short-chain fatty acids (SCFAs), and competition with pathogens. Prebiotics and probiotics have shown benefits in various GI conditions, including diarrhea, constipation, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and small intestinal bacterial overgrowth (SIBO). For diarrhea, probiotics, particularly Saccharomyces boulardii and Lactobacillus strains, have been effective in reducing duration and severity. For constipation, prebiotics like inulin and galacto-oligosaccharides (GOSs) increase beneficial bacteria and improve stool frequency, while probiotics such as Bifidobacterium lactis improve stool frequency and reduce abdominal pain. In IBS, prebiotics and probiotics may help alleviate symptoms, though results are mixed. For IBD, prebiotics like oligofructose-inulin (OF-IN) and probiotics such as VSL#3 have shown potential in inducing remission, though evidence is limited. In SIBO, probiotics like Lacticaseibacillus casei may improve symptoms when used with antibiotics. For celiac disease, probiotics may help reduce GI symptoms, though more research is needed. Overall, while prebiotics and probiotics show promise, strain-specific effects and optimal dosing remain areas requiring further study.This review summarizes the current evidence on the use of prebiotics and probiotics in gastrointestinal (GI) disorders, emphasizing strain-specific effects and potential adverse effects. The gut microbiome plays a crucial role in GI health, and both prebiotics and probiotics can modulate the microbiome and metabolome, influencing host health. Prebiotics are non-digestible, fermentable food components that promote the growth of beneficial bacteria, while probiotics are live microorganisms that confer health benefits when consumed. Synbiotics combine prebiotics and probiotics for synergistic effects. Both prebiotics and probiotics can influence the gut microbiome, immune system, and metabolism, with mechanisms including modulation of the gut barrier, production of short-chain fatty acids (SCFAs), and competition with pathogens. Prebiotics and probiotics have shown benefits in various GI conditions, including diarrhea, constipation, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and small intestinal bacterial overgrowth (SIBO). For diarrhea, probiotics, particularly Saccharomyces boulardii and Lactobacillus strains, have been effective in reducing duration and severity. For constipation, prebiotics like inulin and galacto-oligosaccharides (GOSs) increase beneficial bacteria and improve stool frequency, while probiotics such as Bifidobacterium lactis improve stool frequency and reduce abdominal pain. In IBS, prebiotics and probiotics may help alleviate symptoms, though results are mixed. For IBD, prebiotics like oligofructose-inulin (OF-IN) and probiotics such as VSL#3 have shown potential in inducing remission, though evidence is limited. In SIBO, probiotics like Lacticaseibacillus casei may improve symptoms when used with antibiotics. For celiac disease, probiotics may help reduce GI symptoms, though more research is needed. Overall, while prebiotics and probiotics show promise, strain-specific effects and optimal dosing remain areas requiring further study.