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Assessing genetic diversity and similarity of 435 KPC-carrying plasmids.

Brandt C, Viehweger A, Singh A, Pletz MW, Wibberg D, Kalinowski J, Lerch S, Müller B, Makarewicz O.

Sci Rep. 2019 Aug 2;9(1):11223. doi: 10.1038/s41598-019-47758-5.


Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster: They Come in Teams.

Nguyen TV, Wibberg D, Vigil-Stenman T, Berckx F, Battenberg K, Demchenko KN, Blom J, Fernandez MP, Yamanaka T, Berry AM, Kalinowski J, Brachmann A, Pawlowski K.

Genome Biol Evol. 2019 Aug 1;11(8):2273-2291. doi: 10.1093/gbe/evz153.


Bioactive secondary metabolites from new endophytic fungus Curvularia. sp isolated from Rauwolfia macrophylla.

Kaaniche F, Hamed A, Abdel-Razek AS, Wibberg D, Abdissa N, El Euch IZ, Allouche N, Mellouli L, Shaaban M, Sewald N.

PLoS One. 2019 Jun 27;14(6):e0217627. doi: 10.1371/journal.pone.0217627. eCollection 2019.


Codon Usage Heterogeneity in the Multipartite Prokaryote Genome: Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry.

López JL, Lozano MJ, Lagares A Jr, Fabre ML, Draghi WO, Del Papa MF, Pistorio M, Becker A, Wibberg D, Schlüter A, Pühler A, Blom J, Goesmann A, Lagares A.

MBio. 2019 May 28;10(3). pii: e00505-19. doi: 10.1128/mBio.00505-19.


A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani.

Verwaaijen B, Wibberg D, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Pühler A, Schlüter A.

Sci Rep. 2019 May 10;9(1):7221. doi: 10.1038/s41598-019-43706-5.


Biosynthetic reconstitution of deoxysugar phosphoramidate metalloprotease inhibitors using an N-P-bond-forming kinase.

Baulig A, Helmle I, Bader M, Wolf F, Kulik A, Al-Dilaimi A, Wibberg D, Kalinowski J, Gross H, Kaysser L.

Chem Sci. 2019 Mar 21;10(16):4486-4490. doi: 10.1039/c9sc00641a. eCollection 2019 Apr 28.


Insight into the structure, function and conjugative transfer of pLPU83a, an accessory plasmid of Rhizobium favelukesii LPU83.

Castellani LG, Nilsson JF, Wibberg D, Schlüter A, Pühler A, Brom S, Pistorio M, Torres Tejerizo G.

Plasmid. 2019 May;103:9-16. doi: 10.1016/j.plasmid.2019.03.004. Epub 2019 Mar 27.


Harvest of the Oleaginous Microalgae Scenedesmus obtusiusculus by Flocculation From Culture Based on Natural Water Sources.

Bracharz F, Helmdach D, Aschenbrenner I, Funck N, Wibberg D, Winkler A, Bohnen F, Kalinowski J, Mehlmer N, Brück TB.

Front Bioeng Biotechnol. 2018 Dec 18;6:200. doi: 10.3389/fbioe.2018.00200. eCollection 2018.


The genus Borrelia reloaded.

Margos G, Gofton A, Wibberg D, Dangel A, Marosevic D, Loh SM, Oskam C, Fingerle V.

PLoS One. 2018 Dec 26;13(12):e0208432. doi: 10.1371/journal.pone.0208432. eCollection 2018.


Microbiome-Triggered Transformations of Trace Organic Chemicals in the Presence of Effluent Organic Matter in Managed Aquifer Recharge (MAR) Systems.

Hellauer K, Uhl J, Lucio M, Schmitt-Kopplin P, Wibberg D, Hübner U, Drewes JE.

Environ Sci Technol. 2018 Dec 18;52(24):14342-14351. doi: 10.1021/acs.est.8b04559. Epub 2018 Nov 26.


Petroleum hydrocarbon and microbial community structure successions in marine oil-related aggregates associated with diatoms relevant for Arctic conditions.

Netzer R, Henry IA, Ribicic D, Wibberg D, Brönner U, Brakstad OG.

Mar Pollut Bull. 2018 Oct;135:759-768. doi: 10.1016/j.marpolbul.2018.07.074. Epub 2018 Aug 4.


Binning enables efficient host genome reconstruction in cnidarian holobionts.

Celis JS, Wibberg D, Ramírez-Portilla C, Rupp O, Sczyrba A, Winkler A, Kalinowski J, Wilke T.

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy075.


Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions.

Tomazetto G, Hahnke S, Wibberg D, Pühler A, Klocke M, Schlüter A.

Biotechnol Rep (Amst). 2018 Apr 30;18:e00254. doi: 10.1016/j.btre.2018.e00254. eCollection 2018 Jun.


Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species.

Adamek M, Alanjary M, Sales-Ortells H, Goodfellow M, Bull AT, Winkler A, Wibberg D, Kalinowski J, Ziemert N.

BMC Genomics. 2018 Jun 1;19(1):426. doi: 10.1186/s12864-018-4809-4.


Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats.

Salto IP, Torres Tejerizo G, Wibberg D, Pühler A, Schlüter A, Pistorio M.

Sci Rep. 2018 May 17;8(1):7783. doi: 10.1038/s41598-018-26180-3.


Three previously unrecognised classes of biosynthetic enzymes revealed during the production of xenovulene A.

Schor R, Schotte C, Wibberg D, Kalinowski J, Cox RJ.

Nat Commun. 2018 May 17;9(1):1963. doi: 10.1038/s41467-018-04364-9.


A flavin-dependent halogenase from metagenomic analysis prefers bromination over chlorination.

Neubauer PR, Widmann C, Wibberg D, Schröder L, Frese M, Kottke T, Kalinowski J, Niemann HH, Sewald N.

PLoS One. 2018 May 10;13(5):e0196797. doi: 10.1371/journal.pone.0196797. eCollection 2018.


Identification of a novel aminopolycarboxylic acid siderophore gene cluster encoding the biosynthesis of ethylenediaminesuccinic acid hydroxyarginine (EDHA).

Spohn M, Edenhart S, Alanjary M, Ziemert N, Wibberg D, Kalinowski J, Niedermeyer THJ, Stegmann E, Wohlleben W.

Metallomics. 2018 May 23;10(5):722-734. doi: 10.1039/c8mt00009c.


Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing.

Sommermann L, Geistlinger J, Wibberg D, Deubel A, Zwanzig J, Babin D, Schlüter A, Schellenberg I.

PLoS One. 2018 Apr 5;13(4):e0195345. doi: 10.1371/journal.pone.0195345. eCollection 2018.


Characterization of the Actinonin Biosynthetic Gene Cluster.

Wolf F, Leipoldt F, Kulik A, Wibberg D, Kalinowski J, Kaysser L.

Chembiochem. 2018 Mar 30. doi: 10.1002/cbic.201800116. [Epub ahead of print]


Optimization of Δ9-tetrahydrocannabinolic acid synthase production in Komagataella phaffii via post-translational bottleneck identification.

Zirpel B, Degenhardt F, Zammarelli C, Wibberg D, Kalinowski J, Stehle F, Kayser O.

J Biotechnol. 2018 Apr 20;272-273:40-47. doi: 10.1016/j.jbiotec.2018.03.008. Epub 2018 Mar 13.


The secreted metabolome of Streptomyces chartreusis and implications for bacterial chemistry.

Senges CHR, Al-Dilaimi A, Marchbank DH, Wibberg D, Winkler A, Haltli B, Nowrousian M, Kalinowski J, Kerr RG, Bandow JE.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2490-2495. doi: 10.1073/pnas.1715713115. Epub 2018 Feb 20.


Complete Genome Sequencing of Acinetobacter baumannii Strain K50 Discloses the Large Conjugative Plasmid pK50a Encoding Carbapenemase OXA-23 and Extended-Spectrum β-Lactamase GES-11.

Wibberg D, Salto IP, Eikmeyer FG, Maus I, Winkler A, Nordmann P, Pühler A, Poirel L, Schlüter A.

Antimicrob Agents Chemother. 2018 Apr 26;62(5). pii: e00212-18. doi: 10.1128/AAC.00212-18. Print 2018 May.


Single-bacterial genomics validates rich and varied specialized metabolism of uncultivated Entotheonella sponge symbionts.

Mori T, Cahn JKB, Wilson MC, Meoded RA, Wiebach V, Martinez AFC, Helfrich EJN, Albersmeier A, Wibberg D, Dätwyler S, Keren R, Lavy A, Rückert C, Ilan M, Kalinowski J, Matsunaga S, Takeyama H, Piel J.

Proc Natl Acad Sci U S A. 2018 Feb 20;115(8):1718-1723. doi: 10.1073/pnas.1715496115. Epub 2018 Feb 8.


Genome Sequence of the Bile Salt-Degrading Bacterium Novosphingobium sp. Strain Chol11, a Model Organism for Bacterial Steroid Catabolism.

Yücel O, Wibberg D, Philipp B, Kalinowski J.

Genome Announc. 2018 Jan 4;6(1). pii: e01372-17. doi: 10.1128/genomeA.01372-17.


Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing.

Engel K, Sauer J, Jünemann S, Winkler A, Wibberg D, Kalinowski J, Tauch A, Caspers BA.

Microb Ecol. 2018 Aug;76(2):518-529. doi: 10.1007/s00248-017-1130-8. Epub 2017 Dec 27.


Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome.

Verwaaijen B, Wibberg D, Nelkner J, Gordin M, Rupp O, Winkler A, Bremges A, Blom J, Grosch R, Pühler A, Schlüter A.

J Biotechnol. 2018 Feb 10;267:12-18. doi: 10.1016/j.jbiotec.2017.12.021. Epub 2017 Dec 24.


Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri.

Klein B, Wibberg D, Hallmann A.

BMC Biol. 2017 Nov 28;15(1):111. doi: 10.1186/s12915-017-0450-y.


Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes.

Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, König H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Pühler A, Schlüter A.

Biotechnol Biofuels. 2017 Nov 13;10:264. doi: 10.1186/s13068-017-0947-1. eCollection 2017.


N-Acetylborrelidin B: a new bioactive metabolite from Streptomyces mutabilis sp. MII.

Hamed A, Abdel-Razek AS, Frese M, Wibberg D, El-Haddad AF, Ibrahim TMA, Kalinowski J, Sewald N, Shaaban M.

Z Naturforsch C. 2018 Jan 26;73(1-2):49-57. doi: 10.1515/znc-2017-0140.


Isolation and whole genome analysis of endospore-forming bacteria from heroin.

Kalinowski J, Ahrens B, Al-Dilaimi A, Winkler A, Wibberg D, Schleenbecker U, Rückert C, Wölfel R, Grass G.

Forensic Sci Int Genet. 2018 Jan;32:1-6. doi: 10.1016/j.fsigen.2017.10.001. Epub 2017 Oct 4.


Complete Draft Genome Sequence of Escherichia coli K802.

Kleiner-Grote GRM, Wibberg D, Winkler A, Kalinowski J, Friehs K.

Genome Announc. 2017 Sep 28;5(39). pii: e00934-17. doi: 10.1128/genomeA.00934-17.


Complete Draft Genome Sequence of Escherichia coli KRX, a Strain for Efficient Cloning and High-Yield Expression of Proteins under Control of the T7 RNA Polymerase.

Schwarzhans JP, Wibberg D, Winkler A, Kalinowski J, Friehs K.

Genome Announc. 2017 Sep 28;5(39). pii: e00933-17. doi: 10.1128/genomeA.00933-17.


Genome content, metabolic pathways and biotechnological potential of the psychrophilic Arctic bacterium Psychrobacter sp. DAB_AL43B, a source and a host of novel Psychrobacter-specific vectors.

Lasek R, Dziewit L, Ciok A, Decewicz P, Romaniuk K, Jedrys Z, Wibberg D, Schlüter A, Pühler A, Bartosik D.

J Biotechnol. 2017 Dec 10;263:64-74. doi: 10.1016/j.jbiotec.2017.09.011. Epub 2017 Sep 15.


Lifestyle-determining extrachromosomal replicon pAMV1 and its contribution to the carbon metabolism of the methylotrophic bacterium Paracoccus aminovorans JCM 7685.

Czarnecki J, Dziewit L, Puzyna M, Prochwicz E, Tudek A, Wibberg D, Schlüter A, Pühler A, Bartosik D.

Environ Microbiol. 2017 Nov;19(11):4536-4550. doi: 10.1111/1462-2920.13901. Epub 2017 Oct 13.


Highly efficient methane generation from untreated microalgae biomass.

Klassen V, Blifernez-Klassen O, Wibberg D, Winkler A, Kalinowski J, Posten C, Kruse O.

Biotechnol Biofuels. 2017 Jul 17;10:186. doi: 10.1186/s13068-017-0871-4. eCollection 2017.


Linking secondary metabolites to biosynthesis genes in the fungal endophyte Cyanodermella asteris: The anti-cancer bisanthraquinone skyrin.

Jahn L, Schafhauser T, Wibberg D, Rückert C, Winkler A, Kulik A, Weber T, Flor L, van Pée KH, Kalinowski J, Ludwig-Müller J, Wohlleben W.

J Biotechnol. 2017 Sep 10;257:233-239. doi: 10.1016/j.jbiotec.2017.06.410. Epub 2017 Jun 21.


Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3.

Wibberg D, Genzel F, Verwaaijen B, Blom J, Rupp O, Goesmann A, Zrenner R, Grosch R, Pühler A, Schlüter A.

Arch Microbiol. 2017 Sep;199(7):1065-1068. doi: 10.1007/s00203-017-1394-x. Epub 2017 Jun 8.


The completely annotated genome and comparative genomics of the Peptoniphilaceae bacterium str. ING2-D1G, a novel acidogenic bacterium isolated from a mesophilic biogas reactor.

Tomazetto G, Hahnke S, Langer T, Wibberg D, Blom J, Maus I, Pühler A, Klocke M, Schlüter A.

J Biotechnol. 2017 Sep 10;257:178-186. doi: 10.1016/j.jbiotec.2017.05.027. Epub 2017 Jun 6.


A Mitochondrial Autonomously Replicating Sequence from Pichia pastoris for Uniform High Level Recombinant Protein Production.

Schwarzhans JP, Luttermann T, Wibberg D, Winkler A, Hübner W, Huser T, Kalinowski J, Friehs K.

Front Microbiol. 2017 May 2;8:780. doi: 10.3389/fmicb.2017.00780. eCollection 2017.


Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data.

Alkhateeb RS, Rückert C, Rupp O, Pucker B, Hublik G, Wibberg D, Niehaus K, Pühler A, Vorhölter FJ.

J Biotechnol. 2017 Jul 10;253:55-61. doi: 10.1016/j.jbiotec.2017.05.009. Epub 2017 May 12.


The Rhizoctonia solani AG1-IB (isolate 7/3/14) transcriptome during interaction with the host plant lettuce (Lactuca sativa L.).

Verwaaijen B, Wibberg D, Kröber M, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Pühler A, Schlüter A.

PLoS One. 2017 May 9;12(5):e0177278. doi: 10.1371/journal.pone.0177278. eCollection 2017.


Genome improvement of the acarbose producer Actinoplanes sp. SE50/110 and annotation refinement based on RNA-seq analysis.

Wolf T, Schneiker-Bekel S, Neshat A, Ortseifen V, Wibberg D, Zemke T, Pühler A, Kalinowski J.

J Biotechnol. 2017 Jun 10;251:112-123. doi: 10.1016/j.jbiotec.2017.04.013. Epub 2017 Apr 17.


Correction for Zuñiga-Bahamon et al., Draft Genome Sequence of Streptococcus anginosus BVI, a New Vaginal Pathogen Candidate.

Zuñiga-Bahamon A, Tobar-Tosse F, Guillermo-Ortega J, Wibberg D, Tauch A.

Genome Announc. 2017 Mar 9;5(10). pii: e00112-17. doi: 10.1128/genomeA.00112-17. No abstract available.


Evolutionary and biogeographical implications of degraded LAGLIDADG endonuclease functionality and group I intron occurrence in stony corals (Scleractinia) and mushroom corals (Corallimorpharia).

Celis JS, Edgell DR, Stelbrink B, Wibberg D, Hauffe T, Blom J, Kalinowski J, Wilke T.

PLoS One. 2017 Mar 9;12(3):e0173734. doi: 10.1371/journal.pone.0173734. eCollection 2017.


Genome sequence of Methanobacterium congolense strain Buetzberg, a hydrogenotrophic, methanogenic archaeon, isolated from a mesophilic industrial-scale biogas plant utilizing bio-waste.

Tejerizo GT, Kim YS, Maus I, Wibberg D, Winkler A, Off S, Pühler A, Scherer P, Schlüter A.

J Biotechnol. 2017 Apr 10;247:1-5. doi: 10.1016/j.jbiotec.2017.02.015. Epub 2017 Feb 16.


Draft Genome Sequence of Donghicola sp. Strain KarMa, a Model Organism for Monomethylamine-Degrading Nonmethylotrophic Bacteria.

Zecher K, Suleiman M, Wibberg D, Winkler A, Philipp B, Kalinowski J.

Genome Announc. 2017 Feb 16;5(7). pii: e01623-16. doi: 10.1128/genomeA.01623-16.


Transcriptome profiling of the Australian arid-land plant Eremophila serrulata (A.DC.) Druce (Scrophulariaceae) for the identification of monoterpene synthases.

Kracht ON, Ammann AC, Stockmann J, Wibberg D, Kalinowski J, Piotrowski M, Kerr R, Brück T, Kourist R.

Phytochemistry. 2017 Apr;136:15-22. doi: 10.1016/j.phytochem.2017.01.016. Epub 2017 Feb 3.


Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T.

Torres Tejerizo G, Wibberg D, Winkler A, Ormeño-Orrillo E, Martínez-Romero E, Niehaus K, Pühler A, Kalinowski J, Lagares A, Schlüter A, Pistorio M.

Genome Announc. 2017 Jan 26;5(4). pii: e01513-16. doi: 10.1128/genomeA.01513-16.


Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis.

Hersemann L, Wibberg D, Blom J, Goesmann A, Widmer F, Vorhölter FJ, Kölliker R.

BMC Genomics. 2017 Jan 5;18(1):35. doi: 10.1186/s12864-016-3422-7.

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