Leibniz Institute DSMZ

Braunschweig, Germany

Leibniz Institute DSMZ

Braunschweig, Germany
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Steglich M.,Leibniz Institute DSMZ | Nubel U.,Leibniz Institute DSMZ | Nubel U.,German Center for Infection Research
Journal of Biotechnology | Year: 2017

We tested the capabilities of four different software tools to detect insertions and deletions (indels) in a bacterial genome on the basis of short sequencing reads. We included tools applying the gapped-alignment (VarScan, FreeBayes) or split-read (Pindel) methods, respectively, and a combinatorial approach with local de-novo assembly (ScanIndel). Tests were performed with 151-basepair, paired-end sequencing reads simulated from a bacterial (Clostridioides difficile R20291) genome sequence with predefined indels (indel length, 1-2321. bp). Results achieved with the different tools varied widely, and the specific sensitivity and false-discovery rates strongly depended on indel size. All tools tested were able to detect short indels (≤29 basepairs) at sensitivities close to 100%, albeit Pindel reported up to 20% false calls. In contrast, gapped-alignment and split-read tools failed to recover large proportions of long indels (>29. bp) even at 120-fold coverage, and again, Pindel produced significant numbers of false-positive calls. Outstandingly, ScanIndel detected and reconstructed 97% of long indels on average (95% confidence intervals, 88%-99%) and, at the same time, produced negligible amounts of false calls. Hence, the combinatorial approach implemented in ScanIndel was able to recover the positions, types and sequences of indels with excellent sensitivity and false-discovery rate, by encompassing the full indel length spectrum present in the datasets. © 2017.

Bajerski F.,Alfred Wegener Institute for Polar and Marine Research | Bajerski F.,Leibniz Institute DSMZ | Wagner D.,Helmholtz Center Potsdam | Mangelsdorf K.,Helmholtz Center Potsdam
Frontiers in Microbiology | Year: 2017

Microorganisms in Antarctic glacier forefields are directly exposed to the hostile environment of their habitat characterized by extremely low temperatures and changing geochemical conditions. To survive under those stress conditions microorganisms adapt, among others, their cell membrane fatty acid inventory. However, only little is known about the adaptation potential of microorganisms from Antarctic soil environments. In this study, we examined the adaptation of the cell membrane polar lipid fatty acid inventory of Chryseobacterium frigidisoli PB4T in response to changing temperature (0°C to 20°C) and pH (5.5 to 8.5) regimes, because this new strain isolated from an Antarctic glacier forefield showed specific adaptation mechanisms during its detailed physiological characterization. Flavobacteriaceae including Chryseobacterium species occur frequently in extreme habitats such as ice-free oases in Antarctica. C. frigidisoli shows a complex restructuring of membrane derived fatty acids in response to different stress levels. Thus, from 20°C to 10°C a change from less iso-C15:0 to more iso-C17:1ω7 is observed. Below 10°C temperature adaptation is regulated by a constant increase of anteiso-FAs and decrease of iso-FAs. An anteiso- and bis-unsaturated fatty acid, anteiso-heptadeca-9,13-dienoic acid, shows a continuous increase with decreasing cultivation temperatures underlining the particular importance of this fatty acid for temperature adaptation in C. frigidisoli. Concerning adaptation to changing pH conditions, most of the dominant fatty acids reveal constant relative proportions around neutral pH (pH 6-8). Strong variations are mainly observed at the pH extremes (pH 5.5 and 8.5). At high pH short chain saturated iso- and anteiso-FAs increase while longer chain unsaturated iso- and anteiso-FAs decrease. At low pH the opposite trend is observed. The study shows a complex interplay of different membrane components and provides, therefore, deep insights into adaptation strategies of microorganisms from extreme habitats to changing environmental conditions. © 2017 Bajerski, Wagner and Mangelsdorf.

Montero-Calasanz M.C.,Leibniz Institute DSMZ | Montero-Calasanz M.C.,IFAPA Institute Investigacion y Formacion Agraria y Pesquera | Goker M.,Leibniz Institute DSMZ | Rohde M.,Helmholtz Center for Infection Research | And 7 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2013

A novel non-motile, Gram-staining-negative, yellow-pigmented bacterium, designated AG13T, isolated from a rain water pond at a plant nursery in Spain and characterized as a plant-growth-promoting bacterium, was investigated to determine its taxonomic status. The isolate grew best over a temperature range of 15-40 °C, at pH 5.0-8.0 and with 0-4 % (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Chryseobacterium. The DNA G+C content of the novel strain was 37.2 mol%. The strain had a polyamine pattern with sym-homospermidine as the major compound and produced flexirubin-type pigments. MK-6 was the dominant menaquinone and the major cellular fatty acids were iso-C15: 0, C17: 1ω9c and iso-C17: 0 3-OH. The main polar lipids were phosphatidylethanolamine, aminolipids and several unidentified lipids. The 16S rRNA gene showed 92.0-97.2 % sequence similarity with those of the members of the genus Chryseobacterium. Based on chemotaxonomic and phenotypic traits, and DNA-DNA hybridizations with the type strains of the most closely related species, the isolate is proposed to represent a novel species, Chryseobacterium hispalense, type strain AG13T (= DSM 25574T = CCUG 63019T). Emended descriptions of the species Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium are also provided. © 2013 IUMS.

Wittmann J.,Leibniz Institute DSMZ | Dreiseikelmann B.,Bielefeld University | Rohde M.,Helmholtz Center for Infection Research | Meier-Kolthoff J.P.,Leibniz Institute DSMZ | And 2 more authors.
Virology Journal | Year: 2014

Background: Multi-resistant Achromobacter xylosoxidans has been recognized as an emerging pathogen causing nosocomially acquired infections during the last years. Phages as natural opponents could be an alternative to fight such infections. Bacteriophages against this opportunistic pathogen were isolated in a recent study. This study shows a molecular analysis of two podoviruses and reveals first insights into the genomic structure of Achromobacter phages so far. Methods. Growth curve experiments and adsorption kinetics were performed for both phages. Adsorption and propagation in cells were visualized by electron microscopy. Both phage genomes were sequenced with the PacBio RS II system based on single molecule, real-time (SMRT) technology and annotated with several bioinformatic tools. To further elucidate the evolutionary relationships between the phage genomes, a phylogenomic analysis was conducted using the genome Blast Distance Phylogeny approach (GBDP). Results: In this study, we present the first detailed analysis of genome sequences of two Achromobacter phages so far. Phages JWAlpha and JWDelta were isolated from two different waste water treatment plants in Germany. Both phages belong to the Podoviridae and contain linear, double-stranded DNA with a length of 72329 bp and 73659 bp, respectively. 92 and 89 putative open reading frames were identified for JWAlpha and JWDelta, respectively, by bioinformatic analysis with several tools. The genomes have nearly the same organization and could be divided into different clusters for transcription, replication, host interaction, head and tail structure and lysis. Detailed annotation via protein comparisons with BLASTP revealed strong similarities to N4-like phages. Conclusions: Analysis of the genomes of Achromobacter phages JWAlpha and JWDelta and comparisons of different gene clusters with other phages revealed that they might be strongly related to other N4-like phages, especially of the Escherichia group. Although all these phages show a highly conserved genomic structure and partially strong similarities at the amino acid level, some differences could be identified. Those differences, e.g. the existence of specific genes for replication or host interaction in some N4-like phages, seem to be interesting targets for further examination of function and specific mechanisms, which might enlighten the mechanism of phage establishment in the host cell after infection. © 2014 Wittmann et al.; licensee BioMed Central Ltd.

Spring S.,Leibniz Institute DSMZ | Riedel T.,Helmholtz Center for Infection Research | Riedel T.,French National Center for Scientific Research | Sproer C.,Leibniz Institute DSMZ | And 4 more authors.
BMC Microbiology | Year: 2013

Background: Aerobic gammaproteobacteria affiliated to the OM60/NOR5 clade are widespread in saline environments and of ecological importance in several marine ecosystems, especially the euphotic zone of coastal areas. Within this group a close relationship between aerobic anoxygenic photoheterotrophs and non-phototrophic members has been found. Results: Several strains of aerobic red-pigmented bacteria affiliated to the OM60/NOR5 clade were obtained from tidal flat sediment samples at the island of Sylt (North Sea, Germany). Two of the novel isolates, Rap1red and Ivo14§ssup§T§esup§, were chosen for an analysis in detail. Strain Rap1red shared a 16S rRNA sequence identity of 99% with the type strain of Congregibacter litoralis and was genome-sequenced to reveal the extent of genetic microheterogeneity among closely related strains within this clade. In addition, a draft genome sequence was obtained from the isolate Ivo14§ssup§T§esup§, which belongs to the environmental important NOR5-1 lineage that contains so far no cultured representative with a comprehensive description. Strain Ivo14§ssup§T§esup§ was characterized using a polyphasic approach and compared with other red-pigmented members of the OM60/NOR5 clade, including Congregibacter litoralis DSM 17192§ssup§T§esup§, Haliea rubra DSM 19751§ssup§T§esup§ and Chromatocurvus halotolerans DSM 23344§ssup§T§esup§. All analyzed strains contained bacteriochlorophyll a and spirilloxanthin as photosynthetic pigments. Besides a detailed phenotypic characterization including physiological and chemotaxonomic traits, sequence information based on protein-coding genes and a comparison of draft genome data sets were used to identify possible features characteristic for distinct taxa within this clade. Conclusions: Comparative sequence analyses of the pufLM genes of genome-sequenced representatives of the OM60/NOR5 clade indicated that the photosynthetic apparatus of these species was derived from a common ancestor and not acquired by multiple horizontal gene transfer from phylogenetically distant species. An affiliation of the characterized bacteriochlorophyll a-containing strains to different genera was indicated by significant phenotypic differences and pufLM nucleotide sequence identity values below 82%. The revealed high genotypic and phenotypic diversity of closely related strains within this phylogenetic group reflects a rapid evolution and frequent niche separation in the OM60/NOR5 clade, which is possibly driven by the necessities of an adaptation to oligotrophic marine habitats. © 2013 Spring et al.; licensee BioMed Central Ltd.

Meier-Kolthoff J.P.,Leibniz Institute DSMZ | Auch A.F.,University of Tübingen | Klenk H.-P.,Leibniz Institute DSMZ | Goker M.,Leibniz Institute DSMZ
BMC Bioinformatics | Year: 2013

Background: For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its purpose astonishingly well in the absence of deciphered genome sequences. With the rapid progress in genome sequencing time has come to directly use the now available and easy to generate genome sequences for delimitation of species. GBDP (Genome Blast Distance Phylogeny) infers genome-to-genome distances between pairs of entirely or partially sequenced genomes, a digital, highly reliable estimator for the relatedness of genomes. Its application as an in-silico replacement for DDH was recently introduced. The main challenge in the implementation of such an application is to produce digital DDH values that must mimic the wet-lab DDH values as close as possible to ensure consistency in the Prokaryotic species concept.Results: Correlation and regression analyses were used to determine the best-performing methods and the most influential parameters. GBDP was further enriched with a set of new features such as confidence intervals for intergenomic distances obtained via resampling or via the statistical models for DDH prediction and an additional family of distance functions. As in previous analyses, GBDP obtained the highest agreement with wet-lab DDH among all tested methods, but improved models led to a further increase in the accuracy of DDH prediction. Confidence intervals yielded stable results when inferred from the statistical models, whereas those obtained via resampling showed marked differences between the underlying distance functions.Conclusions: Despite the high accuracy of GBDP-based DDH prediction, inferences from limited empirical data are always associated with a certain degree of uncertainty. It is thus crucial to enrich in-silico DDH replacements with confidence-interval estimation, enabling the user to statistically evaluate the outcomes. Such methodological advancements, easily accessible through the web service at http://ggdc.dsmz.de, are crucial steps towards a consistent and truly genome sequence-based classification of microorganisms. © 2013 Meier-Kolthoff et al.; licensee BioMed Central Ltd.

Jogler C.,Leibniz Institute DSMZ
Molecular Microbiology | Year: 2014

Organelles are membrane-enclosed compartments that serve a dedicated physiological purpose. While eukaryotic organelles are common textbook knowledge, bacteria were long thought to lack such subcellular organization. However, Planctomycetes were proposed to comprise a compartmentalized cell plan, including membrane-enclosed organelles such as the paryphoplasm, the pirellulosome, a nucleus-like membrane system and the anammoxosome. The latter is the hallmark of anaerobic ammonium oxidizing (anammox) bacteria, which gain energy by coupling the oxidation of ammonium to the reduction of nitrite. Since calculations indicate that 50% of nitrogen gas in the earth atmosphere results from anammox activity, this process is key for the global nitrogen cycle. Despite strong evidence for a confined compartment housing this reaction, the concept of planctomycetal compartmentalization in general is currently under debate and the presence of organelles in these bacteria was questioned. However, Neumann etal. (2014) report the isolation of physiological functional anammoxosomes from 'CandidatusKuenenia stuttgartiensis'. Subsequent proteomic and microscopic analysis revealed a confined organelle, paralleling eukaryotic mitochondria. This advance is of major importance for the understanding of bacterial compartmentalization in general and of the Planctomycetes in particular. Furthermore, the work of Neumann etal. leads to a better understanding of the anammox process. © 2014 John Wiley & Sons Ltd.

Spring S.,Leibniz Institute DSMZ | Scheuner C.,Leibniz Institute DSMZ | Goker M.,Leibniz Institute DSMZ | Klenk H.-P.,Leibniz Institute DSMZ | Klenk H.-P.,Northumbria University
Frontiers in Microbiology | Year: 2015

In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov. © 2015 Spring, Scheuner, Göker and Klenk.

Jeske O.,Leibniz Institute DSMZ | Jogler M.,Leibniz Institute DSMZ | Petersen J.,Leibniz Institute DSMZ | Sikorski J.,Leibniz Institute DSMZ | Jogler C.,Leibniz Institute DSMZ
Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology | Year: 2013

Most members of the phylum Planctomycetes share many unusual traits that are unique for bacteria, since they divide independent of FtsZ through asymmetric budding, possess a complex life cycle and comprise a compartmentalized cell plan. Besides their complex cell biological features Planctomycetes are environmentally important and play major roles in global matter fluxes. Such features have been successfully employed in biotechnological applications such as the anaerobic oxidation of ammonium in wastewater treatment plants or the utilization of enzymes for biotechnological processes. However, little is known about planctomycetal secondary metabolites. This is surprising as Planctomycetes have several key features in common with known producers of small bioactive molecules such as Streptomycetes or Myxobacteria: a complex life style and large genome sizes. Planctomycetal genomes with an average size of 6.9 MB appear as tempting targets for drug discovery approaches. To enable the hunt for bioactive molecules from Planctomycetes, we performed a comprehensive genome mining approach employing the antiSMASH secondary metabolite identification pipeline and found 102 candidate genes or clusters within the analyzed 13 genomes. However, as most genes and operons related to secondary metabolite production are exclusively expressed under certain environmental conditions, we optimized Phenotype MicroArray protocols for Rhodopirellula baltica and Planctomyces limnophilus to allow high throughput screening of putative stimulating carbon sources. Our results point towards a previously postulated relationship of Planctomycetes with algae or plants, which secrete compounds that might serve as trigger to stimulate the secondary metabolite production in Planctomycetes. Thus, this study provides the necessary starting point to explore planctomycetal small molecules for drug development. © 2013 Springer Science+Business Media Dordrecht.

Meier-Kolthoff J.P.,Leibniz Institute DSMZ | Auch A.F.,University of Tübingen | Klenk H.-P.,Leibniz Institute DSMZ | Goker M.,Leibniz Institute DSMZ
Concurrency Computation Practice and Experience | Year: 2014

Genome Blast Distance Phylogeny (GBDP) infers distances and phylogenetic relationships between organisms from completely or partially sequenced genomes. It is well suited for parallelization as pairwise distances are calculated independently. As exemplar data for a high-performance cluster implementation that executes many pairwise genome comparisons in parallel, we here used sequences from the Genomic Encyclopedia of Bacteria and Archaea project. Phylogenies were inferred from genome-scale nucleotide and amino acid data with all variants of GBDP, including novel adaptations to amino acid sequences and approaches yielding trees with branch support. The dependency of phylogenetic accuracy, average branch support as well as performance indicators such as running time and disk space consumption on details of genome comparison, distance calculation, and phylogenetic inference was examined in detail. If combined with conservative measures for branch support, GBDP appears to infer reasonable phylogenetic relationships of microorganisms with a comparatively low computational cost. Due to the linear speed-up of the cluster, benchmarks reveal an overall computation time of less than 24 h required for the 7750 pairwise genome/proteome comparisons of the Genomic Encyclopedia of Bacteria and Archaea data set that is opposed to an estimated running time of about 30 days for the non-parallelized version. Copyright © 2013 John Wiley & Sons, Ltd.

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