Author: Jan

I’m delighted to announce the launch of our novel web service VICTOR. It allows for the comparison of up to 100 bacterial and archaeal viruses (“phages”) using either their genome or proteome sequences. The results include phylogenomic trees inferred using the Genome-BLAST Distance Phylogeny method (GBDP), with branch support, as well as suggestions for the classification at the species, genus and family level. The methods were validated against a comprehensive taxonomic reference dataset accepted by the ICTV with respect to phylogenetic as well as clustering algorithms. We are confident that this service will be beneficial for phage taxonomy in particular […]

A number of highly anticipated works have been accepted in recent weeks. These include (but not limited to): Our very extensive work (Simon et al.) on the phylogenomics of the Rhodobacteraceae which revealed evolutionary adaptation to marine and non-marine habitats A large-scale phylogenomic study (Hahnke et al.) on the genome-based taxonomic classification of Bacteroidetes – a work which elucidated and corrected many previous misclassifications and suggested the emendation of countless species descriptions.  

The highly diverse Ascomycete yeasts have enormous biotechnological potential. Collectively, these yeasts convert a broad range of substrates into useful compounds, such as ethanol, lipids, and vitamins, and can grow in extremes of temperature, salinity, and pH. We compared 29 yeast genomes with the goal of correlating genetics to useful traits. In one rare species, we discovered a genetic code that translates CUG codons to alanine rather than canonical leucine. Genome comparison enabled correlation of genes to useful metabolic properties and showed the synteny of the mating-type locus to be conserved over a billion years of evolution. Our study provides […]

The entirety of bacteria in the mouse intestine–the so-called gut microbiota–can have a significant impact on scientific results in the context of the mouse model. But there is still only little known about the precise composition of gut bacteria in mice for a proper assessment of their influence. The composition of the gut microbiota was now comprehensively assessed via a collection of cultivable bacteria: 100 strains were characterized, including fifteen new species. Here, my whole genome sequence-based phylogenomic analyses using the GBDP method were able to provide exciting insights via precise phylogenies including both new and already known species. The […]

The article was published in Frontieres in Microbiology.

The article was published in BMC Standards in Genomic Sciences.

We investigated the phylogeny of 93 sequenced strains within the Pseudomonas fluorescens complex using state-of-the-art whole-genome sequence-based methods such as the Genome Blast Distance Phylogeny approach. As a result we divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH; http://ggdc.dsmz.de) identified 69 species and 75 subspecies among the 93 strains. The eight groups corresponded to clustering with a threshold of 31.8% dDDH. The article was published in PLoS ONE.

I want to draw your attention to one of my recent articles [1] in the well known German BIOspektrum journal. The article was published in the category “Karriere, Köpfe & Konzepte” (i.e., “careers, heads and concepts”) and summarizes our recent work on the E. coli type strain [2] as well as the suite of modern, computer-assisted taxonomic tools we applied to shed further light on the taxonomy of this important group. The article also covers our new method for a genome sequence-based subspecies delineation (of all bacterial and archaeal strains!) as published in the original article [2]. References: [1] http://dx.doi.org/10.1007/s12268-015-0600-0 […]