A5000733670- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Microbial Natural Products and Biosynthesis
- Bacteriophages and microbial interactions
- Plant Pathogens and Fungal Diseases
- Protist diversity and phylogeny
- Plant Disease Resistance and Genetics
- Actinomycetales infections and treatment
- Mycorrhizal Fungi and Plant Interactions
- Metal Extraction and Bioleaching
- Legume Nitrogen Fixing Symbiosis
- Probiotics and Fermented Foods
- RNA and protein synthesis mechanisms
- Enzyme Production and Characterization
- Infectious Diseases and Mycology
- Plant-Microbe Interactions and Immunity
- Methane Hydrates and Related Phenomena
- Bacterial Identification and Susceptibility Testing
- Bacterial Genetics and Biotechnology
- Identification and Quantification in Food
- Plant Pathogenic Bacteria Studies
- Plant nutrient uptake and metabolism
- Enzyme Structure and Function
- Microbial Metabolic Engineering and Bioproduction
- Mycobacterium research and diagnosis
Newcastle University
2015-2024
Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures
2010-2020
Leibniz Institute for Neurobiology
2016
Leibniz Association
2012-2015
Seoul National University
2015
DSM (Netherlands)
2010-2014
Intelligent Transport Systems Niedersachsen
2014
Helmholtz Centre for Infection Research
2010-2012
Lawrence Livermore National Laboratory
2010-2011
Joint Genome Institute
2010-2011
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...
The complete 1.66-megabase pair genome sequence of an autotrophic archaeon, Methanococcus jannaschii, and its 58- 16-kilobase extrachromosomal elements have been determined by whole-genome random sequencing. A total 1738 predicted protein-coding genes were identified; however, only a minority these (38 percent) could be assigned putative cellular role with high confidence. Although the majority related to energy production, cell division, metabolism in M. jannaschii are most similar those...
The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of overall similarity between genomes two strains, this technique tedious error-prone cannot be used incrementally build up a comparative database. Recent technological progress area genome sequencing calls bioinformatics methods replace wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate...
The bacterial and archaeal genomes that have been sequenced to date were chosen for sequencing based mainly on their physiology, which is fine but has resulted in a distinct phylogenetic bias. An alternative approach taken the Genomic Encyclopedia of Bacteria Archaea (GEBA) project, advocates choosing organism's position, with aim filling gaps along branches tree life. value this demonstrated by pilot study genome sequences 56 culturable species selected maximize coverage. Analysis provides...
Summary Mesophilic crenarchaeota are frequently found in terrestrial and marine habitats worldwide, but despite their considerable abundance the physiology of these as yet uncultivated archaea has remained unknown. From a 1.2 Gb large‐insert environmental fosmid library calcareous grassland soil, 43 kb genomic fragment was isolated with ribosomal RNA that shows its affiliation to group 1.1b repeatedly soils. The insert encoded homologue copper‐containing nitrite reductase an unusual...
The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking software for metagenome assembly, binning and taxonomic profiling. Methods profiling are key to interpreting data, but lack consensus about complicates performance assessment. challenge has engaged the global developer benchmark their programs on highly complex realistic data sets, generated ∼700 newly sequenced microorganisms ∼600 novel viruses...
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...
DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between genomes two organisms. To base species concept for prokaryotes ultimately on DDH was chosen by microbiologists as pragmatic approach deciding about recognition novel species, but also allowed relatively high degree standardization compared other areas taxonomy. However, tedious and error-prone first foremost cannot be used incrementally establish comparative database....
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
The plant growth promoting model bacterium FZB42T was proposed as the type strain of B. amyloliquefaciens subsp. plantarum (Borriss et al., Int J Syst Evol Microbiol. 2011, vol. 61, 1786-801), but has been recently recognized being synonymous to Bacillus velezensis due phylogenomic analysis (Dunlap al. 2016, 66, 1212-1217). However, until now, majority publications consider plant-associated close relatives FZB42 still ´B. amyloliquefaciens´. Here, we reinvestigated taxonomic status and...
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...
Summary By the time complete genome sequence of soil bacterium Pseudomonas putida KT2440 was published in 2002 (Nelson et al ., ) this considered a potential agent for environmental bioremediation industrial waste and good colonizer rhizosphere. However, neither annotation tools available at that nor scarcely omics data—let alone metabolic modeling other nowadays common systems biology approaches—allowed them to anticipate astonishing capacities are encoded genetic complement unique...
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...
Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger for microbial community profiling. The transition to new technologies provided more quantitative information at expense of taxonomic resolution with implications inferring metabolic traits in various ecosystems. We applied single-molecule real-time profiling, generating full-length sequences high throughput, which we propose name PhyloTags. benchmarked and...
The whole-genome-sequenced rhizobacterium Bacillus amyloliquefaciens FZB42(T) (Chen et al., 2007) and other plant-associated strains of the genus described as belonging to species or subtilis are used commercially promote growth improve health crop plants. Previous investigations revealed that a group represented distinct ecotype related B. amyloliquefaciens; however, exact taxonomic position this remains elusive (Reva 2004). In present study, we demonstrated ability closely strain colonize...
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,...
A vast and rich body of information has grown up as a result the world's enthusiasm for 'omics technologies. Finding ways to describe make available this that maximise its usefulness become major effort across world. At heart is Genomic Standards Consortium (GSC), an open-membership organization drives community-based standardization activities, Here we provide short history GSC, overview range current call scientific community join forces improve quality quantity contextual about our public...
The National Genomics Data Center (NGDC) provides a suite of database resources to support worldwide research activities in both academia and industry. With the rapid advancements higher-throughput lower-cost sequencing technologies accordingly huge volume multi-omics data generated at exponential scales rates, NGDC is continually expanding, updating enriching its core through big integration value-added curation. In past year, efforts for update have been mainly devoted BioProject,...
Abstract Summary: opm is an R package designed to analyse multidimensional OmniLog® phenotype microarray (PM) data. provides management, visualization and statistical analysis of PM data, including curve-parameter estimation discretization, dedicated customizable plots, metadata automated generation textual tabular reports, mapping substrates databases, batch conversion files export phylogenetic software in the YAML markup language. Availability: distributed under GPL through Comprehensive...
In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades oligotrophic marine gammaproteobacteria, which originally identified in seawater samples using cultivation independent methods and characterized by high seasonal abundances coastal environments. To date sound taxonomic framework for the classification these ecologically important species accordance with their evolutionary relationships is missing. this study...