Marker genes used in microbial phylogenomics are limited to fixed gene sets selected from complete genomes. TMarSel is a flexible yet robust method for selecting any number of markers from genomes or ...

It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core genomes across 50 major bacte...

Abstract. Although microbial eukaryotes comprise the majority of eukaryotic phylogenetic diversity and inhabit nearly all ecosystems globally, most researc

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...

Abstract. The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportuniti

A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.

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

Abstract. The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomi

Rapid and economical DNA sequencing has resulted in a revolution in phylogenomics. The impact of changes in nomenclature can be perceived as an absolute necessity of scientific rigour, coupled with th...

The School of Chemistry and Molecular Biosciences The Australian Centre for Ecogenomics (ACE) Full-time (100%), fixed-term position for up to 2 years Academic Level A / Level B Based at our St Lucia l...

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.

Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

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

Candidatus Acidulodesulfobacterales, a formerly proposed bacterial order within the Deltaproteobacteria lineage, represents an ecologically significant group in sulfur-rich environments. Their diversity and functional potential in artificial acid mine drainage (AMD) ecosystems have been well studied; however, their distribution and ecological role in marine hydrothermal sulfides remain poorly understood. Here we integrated publicly available metagenome-assembled genomes (MAGs) with a newly reconstructed MAG from hydrothermal sulfides to perform comprehensive phylogenetic, metabolic, and host-virus interaction analyses. Phylogenomic and 16S rRNA gene analyses indicated that this lineage represents a distinct phylum-level clade, leading us to propose the designation Ca. Acidulodesulfobacteriota. Metabolic reconstructions indicated a versatile lifestyle, encompassing pathways for carbon fixation, nitrogen fixation, sulfur metabolism, iron oxidation, and hydrogen oxidation. Notably, the concatenated DsrAB protein phylogeny and the mixed enzyme types involved in Dsr-dependent dissimilatory sulfur metabolism suggest that Ca. Acidulodesulfobacteriota may represent a transitional lineage in the evolutionary shift from reductive to oxidative Dsr metabolism. Viral auxiliary metabolic genes (AMGs) associated with this phylum were predicted to modulate host metabolic pathways, including folate biosynthesis and sulfur metabolism, highlighting intricate host-virus interactions. These findings advance our understanding of the evolution, metabolic potential, and ecological roles of Ca. Acidulodesulfobacteriota in biogeochemical cycling.

Life on Earth has existed for nearly 4 billion years, and for most of that time, it was microbial (1). The diverse world we see around us today owes its entire existence to a few foundational events c...

PhD Project - The genomic basis of symbiotic integration at University of Bath, listed on FindAPhD.com

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