A new genomic blueprint of the human gut microbiota has been developed, identifying 1,952 uncultured bacterial species through the reconstruction of 92,143 metagenome-assembled genomes (MAGs) from 11,850 human gut microbiomes. These species significantly expand the known diversity of the gut microbiota, increasing phylogenetic diversity by 281%. Although these species are less prevalent in well-studied populations, they improve classification of understudied samples from Africa and South America by over 200%. The newly identified species encode hundreds of biosynthetic gene clusters and possess unique functional capacities that may explain their elusive nature. The study highlights the importance of comprehensive reference genomes for understanding the intestinal microbiota. The research also reveals that many of the identified species are likely to be more abundant in underrepresented regions, emphasizing the need for global sampling to fully characterize the human gut microbiota. Functional analysis shows that these species have distinct metabolic profiles, including enhanced iron metabolism and transport, suggesting adaptation to specific gut niches. The study underscores the importance of expanding reference genomes to include uncultured species, which could provide new insights into the roles of the gut microbiota in human health and disease.A new genomic blueprint of the human gut microbiota has been developed, identifying 1,952 uncultured bacterial species through the reconstruction of 92,143 metagenome-assembled genomes (MAGs) from 11,850 human gut microbiomes. These species significantly expand the known diversity of the gut microbiota, increasing phylogenetic diversity by 281%. Although these species are less prevalent in well-studied populations, they improve classification of understudied samples from Africa and South America by over 200%. The newly identified species encode hundreds of biosynthetic gene clusters and possess unique functional capacities that may explain their elusive nature. The study highlights the importance of comprehensive reference genomes for understanding the intestinal microbiota. The research also reveals that many of the identified species are likely to be more abundant in underrepresented regions, emphasizing the need for global sampling to fully characterize the human gut microbiota. Functional analysis shows that these species have distinct metabolic profiles, including enhanced iron metabolism and transport, suggesting adaptation to specific gut niches. The study underscores the importance of expanding reference genomes to include uncultured species, which could provide new insights into the roles of the gut microbiota in human health and disease.