Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...

A comprehensive resource of viruses from the human gut microbiome that includes thoroughly annotated genomes, protein structures, and a novel hierarchical classification system that systematically org...

An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.

Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data

In this Journal Club, Luis Orellana recalls a 2005 publication by Konstantinidis and Tiedje that introduced average nucleotide identity as a sequence-based metric to determine the relatedness between ...

Our up-to-date sources of the man-known microbiology are publicly available, and include, as the most complete repository, the Genome Taxonomy Database GTDB https://gtdb.ecogenomic.org/, encompassing, on one end, 196 phyla, across which, at the other end, 107,235 bacterial species have been currently defined. The intermediate ranks feature 541 classes, 1,863 orders, 4,896 families, and 23,112 genera. Such a dataset is hereby used, not as a source of DNA sequences but rather as the handiest and presently most exhaustive checklist matrix of our current taxonomical notions. In the mathematical 'zero assumption' of an equal opportunity chance for each taxon throughout a parallel evolution, a 'perfectly even' community featuring those values would display today, within each of the 196 phyla, the mean values that would result by dividing the actual observed ones by the number of phyla. Such a virtual assemblage would therefore have the following numbers per phylum in each of them: 2.76 classes, 9.51 orders, 24.98 families, 117.92 genera, and 547.12 species. The deltas between these set-point null hypothesis values and the truly observed and described numbers for each lineage member featured by the database (numbers of species per genus, genera per family, families per order, orders per class, and classes per phylum) can reveal how much, and in which lineages, their evolution differed from each of those mere ranks' means. The comparison among the actual data also allows one to answer a series of questions: 1) What is the actually occurred uneven dynamics of evolutionary differentiation across each lineage?; 2) Which taxa are, at present, the 'winners' of the evolutionary race?, And, have they always led the run, or when did they overtake their formerly faster competitors? 3) Are there chronological bottlenecks that violate the assumption of either a constant or of a progressive speed of evolution (i.e. is speciation to each deeper, and more 'modern' rank, consistently faster than its former step, or is there evidence of evolutionary congestion 'jams'?); 4) which past step turns out to have been the most determinant to shape the modern assemblages? Which ones, among the taxa dominating today's diversity, have risen up just recently (e.g. by a massive radiation from genera), and which ones had instead started or accomplished the critical expansion that still keeps them as leaders, in remote times (e.g. by class or order radiations?; 5) Which patterns characterize in this respect the lineages of the most relevant bacterial agents in food, soil, industrial, clinical and environmental microbiology? Corresponding queries are addressed for the 5,869 species of Archaea. The methods and the results of this database-mined in silico analysis are hereby presented and discussed. The dataset provided as supplementary material allows the reader to address the above aspects for any taxon of interest within the 107,235 species covered by this analysis. ### Competing Interest Statement The authors have declared no competing interest.

Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

Human host-associated cellular products may act as induction agents for bacteriophages.

MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l