Leibniz Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Recent publications
In the Anthropocene, plastic pollution is a worldwide concern that must be tackled from different viewpoints, bringing together different areas of science. Microbial transformation of polymers is a broad-spectrum research topic that has become a keystone in the circular economy of fossil-based and biobased plastics. To have an open discussion about these themes, experts in the synthesis of polymers and biodegradation of lignocellulose and plastics convened within the framework of The Transnational Network for Research and Innovation in Microbial Biodiversity, Enzymes Technology and Polymer Science (MENZYPOL-NET), which was recently created by early-stage scientists from Colombia and Germany. In this context, the international workshop "Microbial Synthesis and Degradation of Polymers: Toward a Sustainable Bioeconomy" was held on 27 September 2021 via Zoom. The workshop was divided into two sections, and questions were raised for discussion with panelists and expert guests. Several key points and relevant perspectives were delivered, mainly related to (i) the microbial evolution driven by plastic pollution; (ii) the relevance of and interplay between polymer structure/composition, enzymatic mechanisms, and assessment methods in plastic biodegradation; (iii) the recycling and valorization of plastic waste; (iv) engineered plastic-degrading enzymes; (v) the impact of (micro)plastics on environmental microbiomes; (vi) the isolation of plastic-degrading (PD) microbes and design of PD microbial consortia; and (vii) the synthesis and applications of biobased plastics. Finally, research priorities from these key points were identified within the microbial, enzyme, and polymer sciences.
Immortalized or continuous cell lines are invaluable tools in basic and preclinical research. However, the widespread use of misidentified cell lines is a serious threat to scientific reproducibility. Based on the experiences of mandatory cell line authentication at the International Journal of Cancer (IJC), we provide an overview of the issues pertinent to misidentified cell lines and discuss available solutions. We also summarize the lessons learned, revealing that at least 5% of the human cell lines used in manuscripts considered for peer review are misidentified. About 4% of the considered manuscripts are rejected for severe cell line problems, and most are subsequently published in other journals. In order to diminish such malpractice and its consequences for the scientific record, we postulate that strict multi-layered quality control is essential. Besides journals and publishers, we encourage scientists, research institutions, and funders to take action on the matter and revise their respective policies. Hence, we provide concrete recommendations on introducing regular authentication schemes and staff training, and discuss future steps for enhancing good cell culture practices.
A new actinobacterium strain, designated BMG 823 T , was isolated from a limestone sample collected in Tunisia. Its taxonomic position was scrutinized using a polyphasic approach. Colonies of strain BMG 823 T were pink orange-coloured, regular and had a moist surface. Cells are Gram-stain-positive, catalase-negative and oxidase-negative. The strain grew at pH 5.5–9, 10–40 °C and in presence of up to 4 % NaCl (w/v). Chemotaxonomically, strain BMG 823 T was characterized by cell-wall type III containing meso -diaminopimelic acid as diamino acid, glucose, ribose and rhamnose as whole-cell sugars, MK-9(H 4 ) as predominant menaquinone, and phosphatidylcholine, diphosphadidylglycerol, phosphatidethanolamine, phosphatidylcholine, phosphatidylinositol, unidentified glycolipid, unidentified aminophospholipids and unidentified glycophospholipid as major polar lipids. The fatty acid profile consisted of iso-C 16 : 0 and iso-C 17 : 1 ω 9. Phylogenetic trees based on 16S rRNA gene and genome sequences placed strain BMG 823 T within the genus Blastococcus and separated it from all type strains of validly published species. Comparison of 16S rRNA gene sequence similarity, digital DNA–DNA hybridization and average nucleotide identity indicated that strain BMG 823 T was most closely related to Blastococcus litoris DSM 106127 T and Blastococcus colisei BMG 822 T with pairwise values well below the species differentiation thresholds. The distinct phenotypic and genotypic features of strain BMG 823 T (=DSM 46838 T =CECT 8881 T ) within the genus Blastococcus warrant its recognition as the type strain for the new species for which we propose the name Blastococcus tunisiensis sp. nov.
Background Allorhizobium vitis (formerly named Agrobacterium vitis or Agrobacterium biovar 3) is the primary causative agent of crown gall disease of grapevine worldwide. We obtained and analyzed whole-genome sequences of diverse All. vitis strains to get insights into their diversification and taxonomy. Results Pairwise genome comparisons and phylogenomic analysis of various All. vitis strains clearly indicated that All. vitis is not a single species, but represents a species complex composed of several genomic species. Thus, we emended the description of All. vitis , which now refers to a restricted group of strains within the All. vitis species complex (i.e. All. vitis sensu stricto ) and proposed a description of a novel species, All. ampelinum sp. nov. The type strain of All. vitis sensu stricto remains the current type strain of All. vitis , K309 T . The type strain of All. ampelinum sp. nov. is S4 T . We also identified sets of gene clusters specific to the All. vitis species complex, All. vitis sensu stricto and All. ampelinum, respectively, for which we predicted the biological function and infer the role in ecological diversification of these clades, including some we could experimentally validate. All. vitis species complex-specific genes confer tolerance to different stresses, including exposure to aromatic compounds. Similarly, All. vitis sensu stricto -specific genes confer the ability to degrade 4-hydroxyphenylacetate and a putative compound related to gentisic acid. All. ampelinum -specific genes have putative functions related to polyamine metabolism and nickel assimilation. Congruently with the genome-based classification, All. vitis sensu stricto and All. ampelinum were clearly delineated by MALDI-TOF MS analysis. Moreover, our genome-based analysis indicated that Allorhizobium is clearly separated from other genera of the family Rhizobiaceae . Conclusions Comparative genomics and phylogenomic analysis provided novel insights into the diversification and taxonomy of Allorhizobium vitis species complex, supporting our redefinition of All. vitis sensu stricto and description of All. ampelinum. Our pan-genome analyses suggest that these species have differentiated ecologies, each relying on specialized nutrient consumption or toxic compound degradation to adapt to their respective niche.
Clostridioides difficile (previously Clostridium difficile ) causes life-threatening gut infections. The central metabolism of the bacterium is strongly influencing toxin production and consequently the infection progress. In this context, the composition and potential origin of the volatile metabolome was investigated, showing a large number of sulfur-containing volatile metabolites. Gas chromatography/mass spectrometry (GC/MS)-based headspace analyses of growing C. difficile 630Δ erm cultures identified 105 mainly sulfur-containing compounds responsible of the typical C. difficile odor. Major components were identified to be 2-methyl-1-propanol, 2-methyl-1-propanethiol, 2-methyl-1-butanethiol, 4-methyl-1-pentanethiol, and as well as their disulfides. Structurally identified were 64 sulfur containing volatiles. In order to determine their biosynthetic origin, the concentrations of the sulfur-containing amino acids methionine and cysteine were varied in the growth medium. The changes observed in the volatile metabolome profile indicated that cysteine plays an essential role in the formation of the sulfur-containing volatiles. We propose that disulfides are derived from cysteine via formation of cystathionine analogs, which lead to corresponding thiols. These thiols may then be oxidized to disulfides. Moreover, methionine may contribute to the formation of short-chain disulfides through integration of methanethiol into the disulfide biosynthesis. In summary, the causative agents of the typical C. difficile odor were identified and first hypotheses for their biosynthesis were proposed.
In vitro models of the peripheral nervous system would benefit from further refinements to better support studies on neuropathies. In particular, the assessment of pain-related signals is still difficult in human cell cultures. Here, we harnessed induced pluripotent stem cells (iPSCs) to generate peripheral sensory neurons enriched in nociceptors. The objective was to generate a culture system with signaling endpoints suitable for pharmacological and toxicological studies. Neurons generated by conventional differentiation protocols expressed moderate levels of P2X3 purinergic receptors and only low levels of TRPV1 capsaicin receptors, when maturation time was kept to the upper practically useful limit of 6 weeks. As alternative approach, we generated cells with an inducible NGN1 transgene. Ectopic expression of this transcription factor during a defined time window of differentiation resulted in highly enriched nociceptor cultures, as determined by functional (P2X3 and TRPV1 receptors) and immunocytochemical phenotyping, complemented by extensive transcriptome profiling. Single cell recordings of Ca2+-indicator fluorescence from >9000 cells were used to establish the "fraction of reactive cells" in a stimulated population as experimental endpoint, that appeared robust, transparent and quantifiable. To provide an example of application to biomedical studies, functional consequences of prolonged exposure to the chemotherapeutic drug oxaliplatin were examined at non-cytotoxic concentrations. We found (i) neuronal (allodynia-like) hypersensitivity to otherwise non-activating mechanical stimulation that could be blocked by modulators of voltage-gated sodium channels; (ii) hyper-responsiveness to TRPV1 receptor stimulation. These findings and several other measured functional alterations indicate that the model is suitable for pharmacological and toxicological studies related to peripheral neuropathies.
Two bacterial strains, 9H-EGSE T and 15D-MOB T , were isolated from small freshwater habitats located near Salzburg, Austria. They showed the highest 16S rRNA sequence similarities of 100% and 99.9%, respectively, with type strains of species of the genus Aquirufa ( Bacteroidota ). Genome-based phylogenetic reconstructions with 119 amino acid sequences assigned the new taxa to the two distinct branches of the genus Aquirufa . Whole-genome average nucleotide identities were calculated with all possible pairs belonging to the genus. Values between 75.4% and 88.6% revealed that the two new strains represent each a new species. Like all, so far described members of the genus, they grew aerobically and chemoorganotrophically, were rod-shaped, red-pigmented, and motile by gliding, and showed genome sizes of about 3 Mbp and G + C values of about 40%. They could be distinguished by some phenotypic and chemotaxonomic features from their nearest related species. Until now, strain 9H-EGSE T is the only one among the Aquirufa strains which contained traces of MK8 as respiratory quinone, and strain 15D-MOB T is the only one that formed tiny orange globules in liquid medium. The genome of strain 9H-EGSE T comprised genes for the complete light-harvesting rhodopsin / retinal system, in the case of 15D-MOB T genes predicted for a nitrous oxide reductase were present. For the two new species of the genus Aquirufa , we propose to establish the names Aquirufa lenticrescens for strain 9H-EGSE T (= JCM 34077 T = CIP 111926 T ) and Aquirufa aurantiipilula for strain 15D-MOB T (= JCM 34078 T = CIP 111925 T ).
Background The need for replacing conventional plastics has led to an increase of the use biodegradable plastics. Most biodegradable plastic materials are certified for compostability, and their degradation mechanisms by marine bacterial communities, are still largely unknown. Methods Bacterial communities that degrade a poly (butylene adipate-co-terephthalate)-based biodegradable film (PF) were enriched from marine samples. DNA, RNA and proteins were extracted simultaneously from the biofilm and free-living bacteria. Genes of hydrolases similar to the ones involved in polyethylene terephthalate (PET) and monoester mono-2-hydroxyethyl terephthalate (MHET) degradation (PETase and MHETases, respectively) were detected. A MHETase-like gene (Mle046) was then recombinantly expressed. The activity of Mle046 was tested against the end product of PET and PF degradation: MHET and 4-(4-hydroxybutoxycarbonyl) benzoic acid (Bte), respectively. The optimal incubation temperature and pH of Mle046 activity was determined. Results PETase-like (Ples) and MHETase-like (Mles) hydrolases and other enzymes needed for PF degradation were expressed within the microbial community. Within the biofilm, Ples were abundant and upregulated while Mles and terephthalate dioxygenases were abundant in the free-living fraction. Mle046 was the only Mle produced in this fraction and it was highly expressed. The purified Mle046 could degrade MHET and Bte. The optimum temperature of Mle046 activity was 20°C. Conclusion PF degradation is achieved synergistically by labour division among film-attached and free-living bacteria. Understanding the biodegradability of these plastics will facilitate the development of more degradable materials. In addition, the discovery of new PETases- and MHETases-like enzymes will enable their future use in plastic recycling.
Strain San01, isolated from an ant-nest found in the tea estate of Darjeeling, India, was the subject of polyphasic taxonomic studies. Phylogenetic studies based on multilocus sequence analysis ( atpK , gyrA , ftsZ , dnaK and secA ) showed that isolate San01 forms a separate branch within the genus Streptomyces with Streptomyces avermitilis MA-4680 T (ATTC 31267 T =NCIMB 12804 T =NRRL 8165 T ) as the closest neighbour. The average nucleotide identity (ANI) value (83.52%) between the genome sequence of the studied strain and its closest phylogenetic neighbour is below the threshold for assigning prokaryotic strain to a novel species. Strain San01 could also be distinguished from its closest neighbour using a broad range of phenotypic data. The draft genome sequence of isolate San01(NZ_RZYA00000000.1) was estimated to be 9.12 Mbp in size with 71.2% of GC content and it encompasses 39 biosynthetic gene clusters that emphasizes the biotechnological potential of this isolate . Based on the phenotypic, genetic and genomic data, isolate San01 (=JCM 34633 = NCTC 14543) merits to be recognized as a type strain of a novel species and hereby propose the name Streptomyces antnestii sp.nov. Incidentally, this is the first report on Streptomyces genomes from Darjeeling, India.
Living in extremely metal-rich environments requires specific adaptations, and often, specific metal tolerance genes are encoded on a transferable plasmid. Here, Streptomyces mirabilis P16B-1, isolated from a former mining area and able to grow with up to 130 mM NiSO 4 , was investigated.
The minutes of the online meeting of the Judicial Commission of the International Committee on Systematics of Prokaryotes that was held on 3 March 2022 per video conference are presented.
Yam (Dioscorea spp.) is an important crop for smallholder farmers in the Northeast region of Brazil. Wherever yam is grown, diseases caused by yam mosaic virus (YMV) are prevalent. In the present study, the diversity of YMV infecting Dioscorea cayennensis-rotundata was analyzed. In addition, five species of Dioscorea (D. alata, D. altissima, D. bulbifera, D. subhastata, and D. trifida) commonly found in Brazil were analyzed using ELISA and high-throughput sequencing (HTS). YMV was detected only in D. cayennensis-rotundata, of which 66.7% of the samples tested positive in ELISA. Three YMV genome sequences were assembled from HTS and one by Sanger sequencing to group the sequences in a clade phylogenetically distinct from YMV from other origins. Temporal phylogenetic analyses estimated the mean evolutionary rate for the CP gene of YMV as 1.76 × 10–3 substitutions per site per year, and the time to the most recent common ancestor as 168.68 years (95% Highest Posterior Density, HPD: 48.56–363.28 years), with a most likely geographic origin in the African continent. The data presented in this study contribute to reveal key aspects of the probable epidemiological history of YMV in Brazil.
Insects are a component of the diet of different animal species and have been suggested as the major source of human dietary protein for the future. However, insects are also carriers of potentially pathogenic microbes that constitute a risk to food and feed safety. In this study, we reported the occurrence of a hemolytic orange pigmented producing phenotype of Lactococcus garvieae/petauri/formosensis in the fecal microbiota of golden lion tamarins ( Leontopithecus rosalia ) and feed larvae ( Zophobas atratus ). Feed insects were identified as a regular source of L. garvieae/petauri/formosensis based on a reanalysis of available 16S rRNA gene libraries. Pan-genome analysis suggested the existence of four clusters within the L. garvieae/petauri/formosensis group. The presence of cyl cluster indicated that some strains of the L. garvieae/petauri/formosensis group produced a pigment similar to granadaene, an orange cytotoxic lipid produced by group B streptococci, including Streptococcus agalactiae . Pigment production by L. garvieae/petauri/formosensis strains was dependent on the presence of the fermentable sugars, with no pigment being observed at pH <4.7. The addition of buffering compounds or arginine, which can be metabolized to ammonium, restored pigment formation. In addition, pigment formation might be related to the source of peptone. These data suggest that edible insects are a possible source of granadaene-producing lactococci, which can be considered a pathogenic risk with zoonotic potential.
Background Bhendi or okra ( Abelmoschus esculentus ) is an important crop widely cultivated in the Indian subcontinent. The production of okra in tropical regions is constrained by several abiotic and biotic factors. Among biotic stresses, yellow vein mosaic disease (YVMD), transmitted by the whitefly ( Bemisia tabaci Genn.), causes significant production losses. Results Leaves showing symptoms of YVMD were collected from okra plants in the district of Mardan, Pakistan, from which the total nucleic acid was extracted. It was found that the viral genome was 2739 bp in the length and had seven conserved open reading frames, comparable to those of monopartite begomovirus species from the Old World. Nucleotide sequence comparison revealed that the genome has 97.7% identity with bhendi yellow vein mosaic virus (BYVMV). Additionally, alpha- and betasatellite DNA components were amplified and sequenced. The alpha- and betasatellite DNA sequences were 1367 and 1346 nt in length, respectively. Sequence analysis revealed that the alpha- and betasatellite sequences shared 97.9 and 98.7% similarity with cotton leaf curl Multan alphasatellite DNA (CLCuMuA) and croton yellow vein mosaic betasatellite DNA (CroYVMB), respectively. Conclusions Based on the prevailing classification system, the isolate was identified as a variant of BYVMV, CLCuMuA, and CroYVB. Alphasatellite presence in the begomovirus betasatellite complex detected in the present study indicated a recent mobilization into the viral complex infecting okra in this region. The study findings may facilitate the design of new management strategies to protect this valuable crop against begomovirus infection.
Predation by phages is a major driver of bacterial evolution. As a result, elucidating antiphage strategies is crucial from both fundamental and therapeutic standpoints.
A genome-based polyphasic study was undertaken to establish the taxonomic status of an actinobacterium strain isolated from an actinorhizal root nodule. Strain ncl1T was found to have chemotaxonomic, cultural and morphological properties characteristic of members of the genus Nocardia. The strain was closely related to Nocardia aurea in the phylogenetic trees based on 16S rRNA gene and genome sequences. The draft genome of the strain is 8.9 Mbp in size, has a genomic DNA G + C content of 67.0% and was predicted to contain at least 19 biosynthetic gene clusters encoding for specialized metabolites. Strain ncl1T was distinguished from its closest neighbour, N. aurea DSM 103986T, by a broad range of phenotypic properties and by low average nucleotide identity and digital DNA-DNA hybridization scores. Consequently, the strain represents a novel Nocardia species for which the name Nocardia noduli sp. nov. is proposed. The type strain is ncl1T (CECT 30123T = DSM 110878T). The present study provides further evidence that actinorhizal nodules are a source of novel species of Nocardia.
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92 members
Vera Thiel
  • Department of Microbiology
Andrey M Yurkov
  • Bioresources for Bioeconomy and Health Research
Boyke Bunk
  • Bioinformatics
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Prof. Dr. Jörg Overmann
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