The pathophysiology of human diseases has been shown to be strongly connected to a variety of microorganisms. The microbiome that inhabits the human bodies has a significant impact on our health, yet its relationship to disease remains poorly understood. Now, various microbial-based human illness networks have been created, examining the micro-to-macro link between microorganisms and disease. In addition, microbial-based disease analysis can anticipate new disease-microbe-drug correlations and processes. The prediction techniques and scientific achievements given could be used to solve intractable medical problems. On the basis of evidence that microbes have either been demonstrated to play pathogenic roles in promoting obesity, NAFLD, and cardiovascular illnesses, a link has been established between gut bacteria and the development of numerous diseases, both positively and negatively. How to better systematically comprehend the intricate connections between bacteria and hosts within the human body and develop novel tailored medications to tackle metabolic illnesses. Reduce the number or activity of dangerous microorganisms by encouraging the reconfiguration of the gut microbiota, or utilizing their activity to stimulate the growth of beneficial bacteria. Analyzing the pathogenic logic chain of microbes in various diseases, identifying the metabolic mechanism at the micro level, and developing more accurate methods for disease prediction.