A5041087984- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Genetic diversity and population structure
- Gut microbiota and health
- Plant Pathogens and Fungal Diseases
- Protist diversity and phylogeny
- Plant Pathogenic Bacteria Studies
- Actinomycetales infections and treatment
- Viral gastroenteritis research and epidemiology
- Probiotics and Fermented Foods
- Plant and fungal interactions
- Legume Nitrogen Fixing Symbiosis
- Clostridium difficile and Clostridium perfringens research
- Microbial Natural Products and Biosynthesis
- Evolution and Paleontology Studies
- Microbial infections and disease research
- Bacterial Identification and Susceptibility Testing
- Identification and Quantification in Food
- Microbial Metabolites in Food Biotechnology
- Yeasts and Rust Fungi Studies
- Enzyme Production and Characterization
- Alcohol Consumption and Health Effects
- Plant-Microbe Interactions and Immunity
- Plant Disease Resistance and Genetics
University of Augsburg
2024
Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures
2014-2023
German Center for Infection Research
2017
Leibniz Association
2013
University of Tübingen
2007-2011
Abstract Background For the last 25 years species delimitation in prokaryotes ( Archaea and Bacteria ) was to a large extent based on DNA-DNA hybridization (DDH), tedious lab procedure designed early 1970s that served its purpose astonishingly well absence of deciphered genome sequences. With rapid progress sequencing time has come directly use now available easy generate sequences for species. (Genome Blast Distance Phylogeny) infers genome-to-genome distances between pairs entirely or...
The application of phylogenetic taxonomic procedures led to improvements in the classification bacteria assigned phylum Actinobacteria but even so there remains a need further clarify relationships within taxon that encompasses organisms agricultural, biotechnological, clinical and ecological importance. Classification morphologically diverse belonging this large based on limited number features has proved be difficult, not least when decisions rested heavily interpretation poorly resolved...
Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for prokaryote taxonomy, connected to large, continuously growing database of genomic, taxonomic nomenclatural information. It infers genome-scale phylogenies state-of-the-art estimates species subspecies boundaries from user-defined automatically...
The class
The List of Prokaryotic names with Standing in Nomenclature (LPSN) was acquired November 2019 by the DSMZ and relaunched using an entirely new production system February 2020. This article describes detail structure site, navigation, page layout, search facilities features.
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to phylum Bacteroidetes, there remains a need further clarify taxonomic relationships within diverse assemblage that includes organisms clinical, piscicultural, and ecological importance. Bacteroidetes proved be difficult, not least when decisions rested heavily on interpretation poorly resolved 16S rRNA gene trees limited number phenotypic features. Here, draft genome sequences...
Abstract Microbial systematics is heavily influenced by genome-based methods and challenged an ever increasing number of taxon names associated sequences in public data repositories. This poses a challenge for database systems, particularly since it obviously advantageous if such are based on globally recognized approach to manage names, as the International Code Nomenclature Prokaryotes. The amount can only be handled accurate reliable high-throughput platforms available that able both...
The G+C content of a genome is frequently used in taxonomic descriptions species and genera. In the past it has been determined using conventional, indirect methods, but nowadays reasonable to calculate DNA directly from increasingly available affordable sequences. expected increase accuracy, however, might alter way which for drawing conclusions. We here re-estimate literature assumption that can vary up 3-5 % within genomic datasets. resulting differences are compared with DNA-DNA...
Abstract Intestinal bacteria influence mammalian physiology, but many types of are still uncharacterized. Moreover, reference strains mouse gut not easily available, although models extensively used in medical research. These major limitations for the investigation intestinal microbiomes and their interactions with diet host. It is thus important to study detail diversity functions microbiota members, including those colonizing intestine. To address these issues, we aimed at establishing...
Although Escherichia coli is the most widely studied bacterial model organism and often considered to be bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of G enomic E ncyclopedia B acteria A rchaea project, we here describe features E. DSM 30083T together with genome sequence annotation as well novel aspects phenotype. The 5,038,133 bp containing includes 4,762 protein-coding genes 175 RNA single plasmid. Affiliation set 250 genome-sequenced...
The bacterial phylum
Abstract Motivation Bacterial and archaeal viruses are crucial for global biogeochemical cycles might well be game-changing therapeutic agents in the fight against multi-resistant pathogens. Nevertheless, it is still unclear how to best use genome sequence data a fast, universal accurate taxonomic classification of such viruses. Results We here present novel silico framework phylogeny prokaryotic viruses, line with principles phylogenetic systematics, using large reference dataset officially...
Significance The highly diverse Ascomycete yeasts have enormous biotechnological potential. Collectively, these convert a broad range of substrates into useful compounds, such as ethanol, lipids, and vitamins, can grow in extremes temperature, salinity, pH. We compared 29 yeast genomes with the goal correlating genetics to traits. In one rare species, we discovered genetic code that translates CUG codons alanine rather than canonical leucine. Genome comparison enabled correlation genes...
Abstract Marine Rhodobacteraceae (Alphaproteobacteria) are key players of biogeochemical cycling, comprise up to 30% bacterial communities in pelagic environments and often mutualists eukaryotes. As ‘Roseobacter clade’, these ‘roseobacters’ assumed be monophyletic, but non-marine have not yet been included phylogenomic analyses. Therefore, we analysed 106 genome sequences, particularly emphasizing gene sampling its effect on phylogenetic stability, investigated relationships between marine...
The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining taxonomic affiliations these strains using whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. GBDP analysis clearly separated 224 into 30 clusters, representing eleven known, partially merged species accordingly 19-20 putative novel species. Additionally, 16S rRNA gene analysis, a variant multi-locus sequence (nMLSA)...
Abstract We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage phylogenetic space. These double number existing type strains expand their overall diversity by 25%. Comparative analyses with previously available finished draft reveal a 10.5% increase in novel protein families function diversity. The GEBA recruit 25 million unassigned metagenomic proteins from 4,650 samples,...
The Pseudomonas fluorescens complex includes strains that have been taxonomically assigned to more than fifty different species, many of which described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny this has analyzed according phenotypic traits, 16S rDNA, MLSA inferred by whole-genome analysis. However, since most type not fully sequenced new species are frequently described, correlation between taxonomy...
The order Methylococcales constitutes the methanotrophs – bacteria that can metabolize methane, a potent greenhouse gas, as their sole source of energy. These are significant players in global carbon cycle and produce value-added products from such biopolymers, biofuels, single-cell proteins for animal feed, among others. Previous studies using single-gene phylogenies have shown inconsistencies currently established taxonomic structure this group. This study aimed to determine resolve these...
A universal taxonomy of viruses is essential for a comprehensive view the virus world and communicating complicated evolutionary relationships among viruses. However, there are major differences in conceptualisation approaches to classification nomenclature virologists, clinicians, agronomists, other interested parties. Here, we provide recommendations guide construction coherent taxonomy, based on expert scientific consensus. Firstly, assignments should be congruent with best attainable...
Partial gyrB gene sequence analysis of 17 isolates from human and environmental sources revealed 13 clusters strains identified them as Burkholderia glathei clade (BGC) bacteria. The taxonomic status these was examined by whole-genome analysis, determination the G+C content, whole-cell fatty acid biochemical characterization. sequence-based phylogeny assessed using Genome Blast Distance Phylogeny (GBDP) method an extended multilocus (MLSA) approach. results demonstrated that BGC represented...
Abstract There is a need to clarify relationships within the actinobacterial genus Micromonospora , type of family Micromonosporaceae given its biotechnological and ecological importance. Here, draft genomes 40 strains two non-type are made available through Genomic Encyclopedia Bacteria Archaea project used generate phylogenomic tree which showed they could be assigned well supported phyletic lines that were not evident in corresponding trees based on single concatenated sequences conserved...
The aim of this study was to gain further insight into the diversity Escherichia coli phagesfollowed by enhanced work on taxonomic issues in that field. Therefore, we present genomiccharacterization and classification 50 bacteriophages against E. isolated fromvarious sources, such as manure or sewage. All phages were examined for their host range a setof different strains, originating, e.g., from human diagnostic laboratories poultry farms.Transmission electron microscopy revealed...
Geodermatophilaceae (order Geodermatophilales, class Actinobacteria) form a comparatively isolated family within the phylum Actinobacteria and harbour many strains adapted to extreme ecological niches tolerant against reactive oxygen species. Clarifying evolutionary history of was so far mainly hampered by insufficient resolution main phylogenetic marker in use, 16S rRNA gene. In conjunction with taxonomic characterisation motile aerobic strain, designated YIM M13156T phylogenetically...
In the course of screening surface soils ancient copper mines and smelters (East Harz, Germany) an aerobic, non-motile halotolerant actinobacterium forming small rods or cocci was isolated. The strain designated F300 T developed creamy to yellow colonies on tryptone soy agar grew optimally at 28 °C, pH 7–8 with 0.5–2 % (m/v) NaCl. Its peptidoglycan type A4α l -Lys –l -Glu (A11.54). menaquinone profile dominated by MK-8(II, III-H 4 ) contained minor amounts MK-8(H 2 ), 6 MK-9(H ). polar...