The human gut microbiome has become a focal point of research over the past 15 years, with increasing attention on its role in health and disease. The gut microbiota is now viewed as a potential source of novel therapeutics, with over 12,900 publications between 2013 and 2017 focusing on its impact. This review discusses recent evidence of the gut microbiota's influence on metabolic disorders and highlights key mechanisms. It also critically examines current knowledge, identifying potential issues and misinterpretations. The abundance of metagenomic data can lead to erroneous conclusions about causation, as environmental factors like diet, drugs, and stool characteristics also influence microbiota composition. The gut microbiota interacts with host cells, particularly through the innate immune system, which recognizes microbial components. This interaction is crucial for immune defense and metabolism. Specific microbial metabolites, such as short-chain fatty acids (SCFAs), influence host metabolism by binding to receptors and modulating immune responses. For example, butyrate and propionate have roles in maintaining gut barrier function and immune defense. The review also discusses the importance of considering microbial quantity, not just composition, in understanding microbiome function. Studies on bacteria like Prevotella copri and Akkermansia muciniphila show conflicting results, highlighting the need for careful analysis. A. muciniphila has been associated with improved metabolic health and immune function, but its role in neurodegenerative diseases is less clear. The presence of A. muciniphila in stool samples does not necessarily indicate its beneficial effects, as other factors like diet and drug treatments can influence its abundance. The review emphasizes the need for rigorous studies to establish causality, as many findings are based on correlations. It also highlights the importance of multiomics approaches to better understand microbiome-host interactions. The role of the gut microbiome in cancer therapy is also discussed, with evidence suggesting that A. muciniphila may enhance the effectiveness of immunotherapy. However, further research is needed to confirm these findings and to develop targeted therapies. In conclusion, while the gut microbiome holds great promise for therapeutic applications, careful analysis and validation are essential to avoid misinterpretation of data. The field requires continued research to fully understand the complex interactions between the microbiome and host health.The human gut microbiome has become a focal point of research over the past 15 years, with increasing attention on its role in health and disease. The gut microbiota is now viewed as a potential source of novel therapeutics, with over 12,900 publications between 2013 and 2017 focusing on its impact. This review discusses recent evidence of the gut microbiota's influence on metabolic disorders and highlights key mechanisms. It also critically examines current knowledge, identifying potential issues and misinterpretations. The abundance of metagenomic data can lead to erroneous conclusions about causation, as environmental factors like diet, drugs, and stool characteristics also influence microbiota composition. The gut microbiota interacts with host cells, particularly through the innate immune system, which recognizes microbial components. This interaction is crucial for immune defense and metabolism. Specific microbial metabolites, such as short-chain fatty acids (SCFAs), influence host metabolism by binding to receptors and modulating immune responses. For example, butyrate and propionate have roles in maintaining gut barrier function and immune defense. The review also discusses the importance of considering microbial quantity, not just composition, in understanding microbiome function. Studies on bacteria like Prevotella copri and Akkermansia muciniphila show conflicting results, highlighting the need for careful analysis. A. muciniphila has been associated with improved metabolic health and immune function, but its role in neurodegenerative diseases is less clear. The presence of A. muciniphila in stool samples does not necessarily indicate its beneficial effects, as other factors like diet and drug treatments can influence its abundance. The review emphasizes the need for rigorous studies to establish causality, as many findings are based on correlations. It also highlights the importance of multiomics approaches to better understand microbiome-host interactions. The role of the gut microbiome in cancer therapy is also discussed, with evidence suggesting that A. muciniphila may enhance the effectiveness of immunotherapy. However, further research is needed to confirm these findings and to develop targeted therapies. In conclusion, while the gut microbiome holds great promise for therapeutic applications, careful analysis and validation are essential to avoid misinterpretation of data. The field requires continued research to fully understand the complex interactions between the microbiome and host health.