Background: The rapid development of next-generation sequencing (NGS) technologies and innovations in mass spectrometry and protein interaction studies have significantly advanced the field of microbial science. This paper explores the latest techniques in microbial genomics and protoplasmics, focusing on their impact on understanding microbial systems and their applications. Objective: To provide a comprehensive overview of recent advances in microbial genomics and protoplasmics, highlighting their contributions to microbial science and practical applications in diverse fields such as medicine, agriculture, and environmental science. Methods: The study integrates findings from recent research on microbial genomics facilitated by NGS technologies and advancements in protoplasmics, particularly in mass spectrometry and protein interaction studies. It examines their applications, challenges, and potential future research directions. Results: The application of NGS technologies in microbial genomics has provided comprehensive insights into microbial genomes and their functional potential. Concurrently, advancements in microbial protoplasmics have improved our understanding of protein expression, function, and interactions within microbial systems. The integration of these approaches reveals synergies that contribute to a more nuanced understanding of microbial science. Conclusion: Recent developments in microbial genomics and protoplasmics have collectively advanced the field of microbial science, providing new perspectives and practical applications across various domains. Continued research and innovation in these areas are essential to overcoming current challenges and unlocking new opportunities for exploration and application.