The human gastrointestinal microbiota is a complex ecosystem that plays a crucial role in systemic metabolism and influences health and disease. Over 1000 microbial species have been identified that can reside in the human gastrointestinal tract, with 1057 species classified into Eukarya, Archaea, and Bacteria. This review provides a systematic overview of these species, based on their small subunit ribosomal RNA gene sequences, and unifies knowledge about their prevalence, abundance, stability, physiology, genetics, and association with human health. The review highlights the importance of these microorganisms and their potential for future research in comparative and functional metagenomics. The study of the human gastrointestinal microbiota has evolved through several turning points, including the isolation of the first bacterial species, the development of anaerobic cultivation techniques, and the introduction of molecular techniques. These advancements have enabled the identification of a wide range of species, including Bacteroides, Clostridium, and Bifidobacterium, which are dominant in the human gastrointestinal tract. However, many species remain uncultivated, and the majority of the microbiota consists of strict anaerobes. The review also discusses the phylogenetic classification of various bacterial groups, including Actinobacteria, Bacteroidetes, and Firmicutes, and highlights the diversity and abundance of these groups in the human gastrointestinal tract. The review emphasizes the importance of these microorganisms in health and disease, and their potential for future research in functional metagenomics. The study also highlights the need for further research to understand the role of these microorganisms in the human gastrointestinal tract and their potential for application in probiotics and other therapeutic approaches. The review concludes that the human gastrointestinal microbiota is a complex and dynamic ecosystem that requires further study to fully understand its role in health and disease.The human gastrointestinal microbiota is a complex ecosystem that plays a crucial role in systemic metabolism and influences health and disease. Over 1000 microbial species have been identified that can reside in the human gastrointestinal tract, with 1057 species classified into Eukarya, Archaea, and Bacteria. This review provides a systematic overview of these species, based on their small subunit ribosomal RNA gene sequences, and unifies knowledge about their prevalence, abundance, stability, physiology, genetics, and association with human health. The review highlights the importance of these microorganisms and their potential for future research in comparative and functional metagenomics. The study of the human gastrointestinal microbiota has evolved through several turning points, including the isolation of the first bacterial species, the development of anaerobic cultivation techniques, and the introduction of molecular techniques. These advancements have enabled the identification of a wide range of species, including Bacteroides, Clostridium, and Bifidobacterium, which are dominant in the human gastrointestinal tract. However, many species remain uncultivated, and the majority of the microbiota consists of strict anaerobes. The review also discusses the phylogenetic classification of various bacterial groups, including Actinobacteria, Bacteroidetes, and Firmicutes, and highlights the diversity and abundance of these groups in the human gastrointestinal tract. The review emphasizes the importance of these microorganisms in health and disease, and their potential for future research in functional metagenomics. The study also highlights the need for further research to understand the role of these microorganisms in the human gastrointestinal tract and their potential for application in probiotics and other therapeutic approaches. The review concludes that the human gastrointestinal microbiota is a complex and dynamic ecosystem that requires further study to fully understand its role in health and disease.