A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea was developed by sequencing and analyzing the genomes of 56 culturable species selected to maximize phylogenetic coverage. This project aimed to address the bias in current microbial genome data, which is heavily skewed towards certain phylogenetic groups. The genomes were chosen based on their position in a phylogenetic tree of small subunit (SSU) ribosomal RNA genes, ensuring broad phylogenetic representation. The study demonstrated that phylogenetically diverse genomes provide significant benefits in reconstructing phylogenetic history, discovering new protein families, and predicting gene functions. The results highlight the importance of systematic phylogenomic efforts to compile a comprehensive genomic encyclopedia of Bacteria and Archaea. The project also revealed that phylogenetic diversity is a strong predictor of novel genetic features, even though SSU rRNA genes are not perfect indicators of evolutionary relationships. The GEBA (Genomic Encyclopedia of Bacteria and Archaea) project identified numerous novel protein families and functions, including a bacterial actin-related protein (BARP) in Haliangium ochraceum, which may have a role in eukaryotic actin polymerization. The study also showed that phylogenetically diverse genomes contribute to the discovery of new gene families, gene fusions, and non-coding RNA elements. The findings suggest that a phylogenetically driven approach to genome sequencing can significantly enhance the understanding of microbial diversity and function. The project also highlights the need for further sequencing efforts to capture the remaining unrepresented microbial diversity, which requires new methods for culturing and analyzing uncultured species. The GEBA project represents a key step towards a more comprehensive and balanced genomic representation of the microbial tree of life.A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea was developed by sequencing and analyzing the genomes of 56 culturable species selected to maximize phylogenetic coverage. This project aimed to address the bias in current microbial genome data, which is heavily skewed towards certain phylogenetic groups. The genomes were chosen based on their position in a phylogenetic tree of small subunit (SSU) ribosomal RNA genes, ensuring broad phylogenetic representation. The study demonstrated that phylogenetically diverse genomes provide significant benefits in reconstructing phylogenetic history, discovering new protein families, and predicting gene functions. The results highlight the importance of systematic phylogenomic efforts to compile a comprehensive genomic encyclopedia of Bacteria and Archaea. The project also revealed that phylogenetic diversity is a strong predictor of novel genetic features, even though SSU rRNA genes are not perfect indicators of evolutionary relationships. The GEBA (Genomic Encyclopedia of Bacteria and Archaea) project identified numerous novel protein families and functions, including a bacterial actin-related protein (BARP) in Haliangium ochraceum, which may have a role in eukaryotic actin polymerization. The study also showed that phylogenetically diverse genomes contribute to the discovery of new gene families, gene fusions, and non-coding RNA elements. The findings suggest that a phylogenetically driven approach to genome sequencing can significantly enhance the understanding of microbial diversity and function. The project also highlights the need for further sequencing efforts to capture the remaining unrepresented microbial diversity, which requires new methods for culturing and analyzing uncultured species. The GEBA project represents a key step towards a more comprehensive and balanced genomic representation of the microbial tree of life.