Fast genome-based delimitation of Enterobacterales species.

Average Nucleotide Identity (ANI) is becoming a standard measure for bacterial species delimitation. However, its calculation can take orders of magnitude longer than similarity estimates based on sampling of short nucleotides, compiled into so-called sketches. These estimates are widely used.

FastANI, Mash and Dashing equally differentiate between species.

Bacteria of the genus are among the most important multi-drug resistant human pathogens, though they have been isolated from a variety of environments. The importance and ubiquity of these organisms call for quick and accurate methods for their classification. Average Nucleotide Identity (ANI) is becoming a standard for species delimitation based on whole genome sequence comparison.

Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2.

Background: Finding orthologs remains an important bottleneck in comparative genomics analyses. While the authors of software for the quick comparison of protein sequences evaluate the speed of their software and compare their results against the most usual software for the task, it is not common for them to evaluate their software for more particular uses, such as finding orthologs as reciprocal best hits (RBH). Here we compared RBH results obtained using software that runs faster than blastp.

Genome Comparison of UM270 with Related Fluorescent Strains Unveils Genes Involved in Rhizosphere Competence and Colonization.

UM270 is a rhizosphere-colonizing bacterium that produces multiple diffusible and volatile compounds involved in plant growth-promoting activities. Strain UM270 exhibits excellent biocontrol capacities against diverse fungal pathogens In a previous study, the general UM270 genome characteristics were published. Here, we report a deeper analysis of its gene content and compare it to other strains to unveil the genetic elements that might explain UM270's great colonizing and plant growth-promoting capabilities.