Trillions of microbes majorly bacteria dwell in various parts of the human body, and play crucial roles in health and illness as well. About equal proportion of microbe cells compared with human cells estimated” with “With an estimated population of almost the same size as human cells, trillions of microorganisms, primarily bacteria, live in different regions of the human body and are essential to both health and illness. The microbiota of newborns is initially acquired via their mothers, and it continues to be altered by nursing. Adulthood brings the microbiome into equilibrium, and as people get older, its microbiota diversity can decrease and inflammation may rise, making them more vulnerable to disease. There are various factors including genetic, environmental, lifestyle and others that can alter the human microbiota, and this imbalance in human microbiota called dysbiosis is responsible for various metabolic and chronic diseases. Recently, the whole microbial genome has been sequenced using whole-genome shotgun-based metagenomics, which provides both functional along with taxonomic information. Research on the human microbiome is currently in its third phase. Personalized medicine is the main emphasis of this phase, which uses each person’s unique microbiome profile to customize medicinal and nutritional treatments. Technological developments in areas such as artificial intelligence (AI), machine learning, as well as high-throughput culturomics are essential for managing big datasets and detecting important signals in the microbiome. Enhancing clinical trial strategies and controlling the hype towards microbiome research by highlighting strong, data-driven methodologies are a few of the problems faced by the area. In this chapter, we focus on the challenges related to standardization in microbiota profiling methods, ethical issues and quality control data along with the significance of human microbiota research in integrated personalized medicines.