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Artikelaktionen

Publications

Publications with relation to Tools developed at the Bielefeld-Gießen Resource Center for Microbial Bionformatics (BiGi)


  • Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A (2021) Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 7(11):000685. doi: 10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.
  • Dieckmann MA, Beyvers S, Nkouamedjo-Fankep RC, Hanel PHG, Jelonek L, Blom J, Goesmann A (2021) EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure. Nucleic Acids Res. 49(W1): W185-W192. doi: 10.1093/nar/gkab341. PMID: 33988716; PMCID: PMC8262741.
  • Hoek A, Maibach K, Özmen E, Vazquez-Armendariz AI, Mengel JP, Hain T, Herold S, Goesmann A (2021) WASP: a versatile, web-accessible single cell RNA-Seq processing platform. BMC Genomics. 22(1):195. doi: 10.1186/s12864-021-07469-6. PMID: 33736596; PMCID: PMC7977290.
  • Schwengers O, Barth P, Falgenhauer L, Hain T, Chakraborty T, Goesmann A (2020) Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microb Genom. 6(10): mgen000398. doi: 10.1099/mgen.0.000398. PMID: 32579097; PMCID: PMC7660248.
  • Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A (2020) ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS Comput Biol. 16(3): e1007134. doi: 10.1371/journal.pcbi.1007134. PMID: 32134915; PMCID: PMC7077848.
  • Blom J, Glaeser SP, Juhre T, Kreis J, Hanel PHG, Schrader JG, Kämpfer P, Goesmann A (2019) EDGAR: A Versatile Tool for Phylogenomics. Bergey's Manual of Systematics of Archaea and Bacteria (eds Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P, Rainey FA, Whitman WB). doi: 10.1002/9781118960608.bm00038
  • Jaenicke S, Albaum SP, Blumenkamp P, Linke B, Stoye J, Goesmann A (2018) Flexible metagenome analysis using the MGX framework. Microbiome. 6(1):76. doi: 10.1186/s40168-018-0460-1. PMID: 29690922; PMCID: PMC5937802.
  • Yu J, Blom J, Glaeser SP, Jaenicke S, Juhre T, Rupp O, Schwengers O, Spänig S, Goesmann A (2017) A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies. J Biotechnol. 261:2-9. doi: 10.1016/j.jbiotec.2017.07.010. Epub 2017 Jul 10. PMID: 28705636.
  • Yu J, Blom J, Sczyrba A, Goesmann A (2017) Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism. J Biotechnol. 257:58-60. doi: 10.1016/j.jbiotec.2017.02.020. Epub 2017 Feb 21. PMID: 28232083.
  • Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A (2016) ReadXplorer 2-detailed read mapping analysis and visualization from one single source. Bioinformatics. 32(24):3702-3708. doi: 10.1093/bioinformatics/btw541. Epub 2016 Aug 18. PMID: 27540267; PMCID: PMC5167064.
  • Blom J, Kreis J, Spänig S, Juhre T, Bertelli C, Ernst C, Goesmann A (2016) EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res. 44(Web Server issue): W22–W28. doi: 10.1093/nar/gkw255. PMID: 27098043; PMCID: PMC4987874.
  • Sobetzko P, Jelonek L, Strickert M, Han W, Goesmann A, Waldminghaus T (2016) DistAMo: A Web-Based Tool to Characterize DNA-Motif Distribution on Bacterial Chromosomes. Front Microbiol. 7:283. doi: 10.3389/fmicb.2016.00283. PMID: 27014208; PMCID: PMC4786541.
  • Langenkämper D, Jakobi T, Feld D, Jelonek L, Goesmann A, Nattkemper TW (2016) Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations. Front Genet. 7:5. doi: 10.3389/fgene.2016.00005. PMID: 26904094; PMCID: PMC4748744.
  • Kessler N, Bonte A, Albaum SP, Mäder P, Messmer M, Goesmann A, Niehaus K, Langenkämper G, Nattkemper TW (2015) Learning to Classify Organic and Conventional Wheat - A Machine Learning Driven Approach Using the MeltDB 2.0 Metabolomics Analysis Platform. Front Bioeng Biotechnol. 3:35. doi: 10.3389/fbioe.2015.00035. PMID: 25853128; PMCID: PMC4371749.

 

Publications with contributions of BiGi personnel

 

  • Fenske L, Noll I, Blom J, Ewers C, Semmler T, Fawzy A, Eisenberg T (2022) A dominant clonal lineage of Streptococcus uberis in cattle in Germany. Antonie Van Leeuwenhoek. 115(7):857-870. doi: 10.1007/s10482-022-01740-w. Epub 2022 Apr 30. PMID: 35489013; PMCID: PMC9206625.
  • Breuer J, Barth P, Noe Y, Shalamova L, Goesmann A, Weber F, Rossbach O (2022) What goes around comes around: Artificial circular RNAs bypass cellular antiviral responses. Mol Ther Nucleic Acids. 28:623-635. doi: 10.1016/j.omtn.2022.04.017. Epub 2022 Apr 27. PMID: 35497503; PMCID: PMC9042720.
  • Djahanschiri B, Di Venanzio G, Distel JS, Breisch J, Dieckmann MA, Goesmann A, Averhoff B, Göttig S, Wilharm G, Feldman MF, Ebersberger I (2022) Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PLoS Genet. 18(6): e1010020. doi: 10.1371/journal.pgen.1010020. PMID: 35653398; PMCID: PMC9162365.
  • Rafiqi M, Jelonek L, Diouf AM, Mbaye A, Rep M, Diarra A (2022) Profile of the in silico secretome of the palm dieback pathogen, Fusarium oxysporum f. sp. albedinis, a fungus that puts natural oases at risk. PLoS One. 17(5): e0260830. doi: 10.1371/journal.pone.0260830. PMID: 35617325; PMCID: PMC9135196.
  • Hurka S, Brinkrolf K, Özbek R, Förster F, Billion A, Heep J, Timm T, Lochnit G, Vilcinskas A, Lüddecke T (2022) Venomics of the Central European Myrmicine Ants Myrmica rubra and Myrmica ruginodis. Toxins (Basel). 14(5):358. doi: 10.3390/toxins14050358. PMID: 35622604; PMCID: PMC9147725.
  • Neuzil-Bunesova V, Ramirez Garcia A, Modrackova N, Makovska M, Sabolova M, Spröer C, Bunk B, Blom J, Schwab C (2022) Feed Insects as a Reservoir of Granadaene- Producing Lactococci. Front Microbiol. 13:848490. doi: 10.3389/fmicb.2022.848490. PMID: 35615513; PMCID: PMC9125021.
  • Ruinelli M, Blom J, Smits THM, Pothier JF (2022) Comparative Genomics of Prunus-Associated Members of the Pseudomonas syringae Species Complex Reveals Traits Supporting Co-evolution and Host Adaptation. Front Microbiol. 13:804681. doi: 10.3389/fmicb.2022.804681. PMID: 35592008; PMCID: PMC9111521.
  • Lau Vetter MCY, Huang B, Fenske L, Blom J (2022) Metabolism of the Genus Guyparkeria Revealed by Pangenome Analysis. Microorganisms. 10(4):724. doi: 10.3390/microorganisms10040724. PMID: 35456775; PMCID: PMC9032823.
  • Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Schwengers O, Heider D (2022) Multi-label classification for multi-drug resistance prediction of Escherichia coli. Comput Struct Biotechnol J. 20:1264-1270. doi: 10.1016/j.csbj.2022.03.007. PMID: 35317240; PMCID: PMC8918850.
  • Blumenscheit C, Jähne J, Schneider A, Blom J, Schweder T, Lasch P, Borriss R (2022) Genome sequence data of Bacillus velezensis BP1.2A and BT2.4. Data Brief. 41:107978. doi: 10.1016/j.dib.2022.107978. PMID: 35242952; PMCID: PMC8885614.
  • Volokhov DV, Furtak VA, Blom J, Zagorodnyaya TA, Gao Y, Gulland FM (2022) Mycoplasma miroungirhinis sp. nov. and Mycoplasma miroungigenitalium sp. nov., isolated from northern elephant seals (Mirounga angustirostris), Mycoplasma phocoenae sp. nov., isolated from harbour porpoise (Phocoena phocoena), and Mycoplasma phocoeninasale sp. nov., isolated from harbour porpoise and California sea lions (Zalophus californianus). Int J Syst Evol Microbiol. 72(1). doi: 10.1099/ijsem.0.005224. PMID: 35073252.
  • Dia NC, Van Vaerenbergh J, Van Malderghem C, Blom J, Smits THM, Cottyn B, Pothier JF (2021) Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens. Int J Syst Evol Microbiol. 71(12). doi: 10.1099/ijsem.0.005163. PMID: 34913859.
  • Mahmoud W, Perniss A, Poharkar K, Soultanova A, Pfeil U, Hoek A, Bhushan S, Hain T, Gärtner U, Kummer W (2021) CXCL13 is expressed in a subpopulation of neuroendocrine cells in the murine trachea and lung. Cell Tissue Res. doi: 10.1007/s00441-021-03552-2. Epub ahead of print. PMID: 34762185.
  • Le VV, Ko SR, Lee SA, Jin L, Blom J, Ahn CY, Oh HM (2021) Cochlodiniinecator piscidefendens gen. nov., sp. nov., an algicidal bacterium against the ichthyotoxic dinoflagellate Cochlodinium polykrikoides. Int J Syst Evol Microbiol. 71(11). doi: 10.1099/ijsem.0.005124. PMID: 34846282.
  • Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Hauschild AC, Schwengers O, Heider D (2021) Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. Bioinformatics. 38(2):325–34. doi: 10.1093/bioinformatics/btab681. Epub ahead of print. PMID: 34613360; PMCID: PMC8722762.
  • Stitz M, Chaparro C, Lu Z, Olzog VJ, Weinberg CE, Blom J, Goesmann A, Grunau C, Grevelding CG (2021) Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni. Genome Biol Evol. 13(10): evab204. doi: 10.1093/gbe/evab204. PMID: 34469545; PMCID: PMC8490949.
  • Shaban MS, Müller C, Mayr-Buro C, Weiser H, Meier-Soelch J, Albert BV, Weber A, Linne U, Hain T, Babayev I, Karl N, Hofmann N, Becker S, Herold S, Schmitz ML, Ziebuhr J, Kracht M (2021) Multi-level inhibition of coronavirus replication by chemical ER stress. Nat Commun. 12(1):5536. doi: 10.1038/s41467-021-25551-1. PMID: 34545074; PMCID: PMC8452654.
  • Šečić E, Zanini S, Wibberg D, Jelonek L, Busche T, Kalinowski J, Nasfi S, Thielmann J, Imani J, Steinbrenner J, Kogel KH (2021) A novel plant-fungal association reveals fundamental sRNA and gene expression reprogramming at the onset of symbiosis. BMC Biol. 19(1):171. doi: 10.1186/s12915-021-01104-2. PMID: 34429124; PMCID: PMC8385953.
  • Werner BT, Koch A, Šečić E, Engelhardt J, Jelonek L, Steinbrenner J, Kogel KH (2021) Fusarium graminearum DICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulence. PLoS One. 16(8): e0252365. doi: 10.1371/journal.pone.0252365. PMID: 34351929; PMCID: PMC8341482.
  • Hudec C, Biessy A, Novinscak A, St-Onge R, Lamarre S, Blom J, Filion M (2021) Comparative Genomics of Potato Common Scab-Causing Streptomyces spp. Displaying Varying Virulence. Front Microbiol. 12:716522. doi: 10.3389/fmicb.2021.716522. PMID: 34413844; PMCID: PMC8369830.
  • Schwabe M, Griep S, Schmidtberg H, Plarre R, Goesmann A, Vilcinskas A, Vogel H, Brinkrolf K (2021) Next-Generation Sequencing Analysis of the Tineola bisselliella Larval Gut Transcriptome Reveals Candidate Enzymes for Keratin Digestion. Genes (Basel). 12(8):1113. doi: 10.3390/genes12081113. PMID: 34440287; PMCID: PMC8394580.
  • Kwon S, Rupp O, Brachmann A, Blum CF, Kraege A, Goesmann A, Feldbrügge M (2021) mRNA Inventory of Extracellular Vesicles from Ustilago maydis. J Fungi (Basel). 7(7):562. doi: 10.3390/jof7070562. PMID: 34356940; PMCID: PMC8306574.
  • Schlemmer T, Barth P, Weipert L, Preußer C, Hardt M, Möbus A, Busche T, Koch A (2021) Isolation and Characterization of Barley (Hordeum vulgare) Extracellular Vesicles to Assess Their Role in RNA Spray-Based Crop Protection. Int J Mol Sci. 22(13):7212. doi: 10.3390/ijms22137212. PMID: 34281265; PMCID: PMC8268707.
  • Lick S, Wibberg D, Winkler A, Blom J, Grimmler C, Goesmann A, Kalinowski J, Kröckel L (2021) Pseudomonas paraversuta sp. nov. isolated from refrigerated dry-aged beef. Int J Syst Evol Microbiol. 71(6). doi: 10.1099/ijsem.0.004822. PMID: 34097596.
  • Masello JF, Barbosa A, Kato A, Mattern T, Medeiros R, Stockdale JE, Kümmel MN, Bustamante P, Belliure J, Benzal J, Colominas-Ciuró R, Menéndez-Blázquez J, Griep S, Goesmann A, Symondson WOC, Quillfeldt P (2021) How animals distribute themselves in space: energy landscapes of Antarctic avian predators. Mov Ecol. 9(1):24. doi: 10.1186/s40462-021-00255-9. PMID: 34001240; PMCID: PMC8127181.
  • Brinkrolf K, Shukla SP, Griep S, Rupp O, Heise P, Goesmann A, Heckel DG, Vogel H, Vilcinskas A (2021) Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides. BMC Genomics. 22(1):323. doi: 10.1186/s12864-021-07597-z. PMID: 33941076; PMCID: PMC8091737.
  • Volokhov DV, Zagorodnyaya TA, Shen Z, Blom J, Furtak VA, Eisenberg T, Fan P, Jeong KC, Gao Y, Zhang S, Amselle M (2021) Streptococcus vicugnae sp. nov., isolated from faeces of alpacas (Vicugna pacos) and cattle (Bos taurus), Streptococcus zalophi sp. nov., and Streptococcus pacificus sp. nov., isolated from respiratory tract of California sea lions (Zalophus californianus). Int J Syst Evol Microbiol. 71(5). doi: 10.1099/ijsem.0.004826. PMID: 33999792.
  • Panthee S, Paudel A, Hamamoto H, Ogasawara AA, Iwasa T, Blom J, Sekimizu K (2021) Complete genome sequence and comparative genomic analysis of Enterococcus faecalis EF-2001, a probiotic bacterium. Genomics. 113(3):1534-1542. doi: 10.1016/j.ygeno.2021.03.021. Epub 2021 Mar 24. PMID: 33771633.
  • Nechitaylo TY, Sandoval-Calderón M, Engl T, Wielsch N, Dunn DM, Goesmann A, Strohm E, Svatoš A, Dale C, Weiss RB, Kaltenpoth M (2021) Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont. Proc Natl Acad Sci U S A. 118(17): e2023047118. doi: 10.1073/pnas.2023047118. PMID: 33883280; PMCID: PMC8092579.
  • Tegtmeier D, Hurka S, Klüber P, Brinkrolf K, Heise P, Vilcinskas A (2021) Cottonseed Press Cake as a Potential Diet for Industrially Farmed Black Soldier Fly Larvae Triggers Adaptations of Their Bacterial and Fungal Gut Microbiota. Front Microbiol. 12: 634503. doi: 10.3389/fmicb.2021.634503. PMID: 33854488; PMCID: PMC8039154.
  • Fernandes C, Martins L, Teixeira M, Blom J, Pothier JF, Fonseca NA, Tavares F (2021) Comparative Genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis Strains Isolated from a Single Walnut Host Tree. Microorganisms. 9(3):624. doi: 10.3390/microorganisms9030624. PMID: 33803052; PMCID: PMC8003016.
  • Cantrell K, Fedarko MW, Rahman G, McDonald D, Yang Y, Zaw T, Gonzalez A, Janssen S, Estaki M, Haiminen N, Beck KL, Zhu Q, Sayyari E, Morton JT, Armstrong G, Tripathi A, Gauglitz JM, Marotz C, Matteson NL, Martino C, Sanders JG, Carrieri AP, Song SJ, Swafford AD, Dorrestein PC, Andersen KG, Parida L, Kim HC, Vázquez-Baeza Y, Knight R (2021) EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets. mSystems. 6(2): e01216-20. doi: 10.1128/mSystems.01216-20. PMID: 33727399; PMCID: PMC8546999.
  • Pulami D, Schauss T, Eisenberg T, Blom J, Schwengers O, Bender JK, Wilharm G, Kämpfer P, Glaeser SP (2021) Acinetobacter stercoris sp. nov. isolated from output source of a mesophilic german biogas plant with anaerobic operating conditions. Antonie Van Leeuwenhoek. 114(3):235-251. doi: 10.1007/s10482-021-01517-7. Epub 2021 Feb 16. PMID: 33591460; PMCID: PMC7902594.
  • Khilyas IV, Sorokina AV, Markelova MI, Belenikin M, Shafigullina L, Tukhbatova RI, Shagimardanova EI, Blom J, Sharipova MR, Cohen MF (2021) Genomic and phenotypic analysis of siderophore-producing Rhodococcus qingshengii strain S10 isolated from an arid weathered serpentine rock environment. Arch Microbiol. 203(2):855-860. doi: 10.1007/s00203-020-02057-w. Epub 2020 Oct 6. PMID: 33025059.
  • Herbert DB, Gross T, Rupp O, Becker A (2021) Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense). BMC Plant Biol. 21(1):95. doi: 10.1186/s12870-021-02867-0. PMID: 33588756; PMCID: PMC7885512.
  • Lick S, Wibberg D, Winkler A, Blom J, Grimmler C, Goesmann A, Kalinowski J, Kröckel L (2021) Pseudomonas paracarnis sp. nov., isolated from refrigerated beef. Int J Syst Evol Microbiol. 71(2). doi: 10.1099/ijsem.0.004652. PMID: 33480838.
  • Casas-Pastor D, Müller RR, Jaenicke S, Brinkrolf K, Becker A, Buttner MJ, Gross CA, Mascher T, Goesmann A, Fritz G (2021) Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family. Nucleic Acids Res. 49(2):986-1005. doi: 10.1093/nar/gkaa1229. PMID: 33398323; PMCID: PMC7826278.
  • Blifernez-Klassen O, Klassen V, Wibberg D, Cebeci E, Henke C, Rückert C, Chaudhari S, Rupp O, Blom J, Winkler A, Al-Dilaimi A, Goesmann A, Sczyrba A, Kalinowski J, Bräutigam A, Kruse O (2021) Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia. Sci Rep. 11(1):1726. doi: 10.1038/s41598-021-81082-1. PMID: 33462312; PMCID: PMC7813871.
  • Berger C, Rückert C, Blom J, Rabaey K, Kalinowski J, Rosenbaum MA (2021) Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics. Sci Rep. 11(1):1370. doi: 10.1038/s41598-020-80592-8. PMID: 33446769; PMCID: PMC7809047.
  • Naorem RS, Blom J, Fekete C (2021) Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary. PeerJ. 9: e10185. doi: 10.7717/peerj.10185. PMID: 33520430; PMCID: PMC7811285.
  • Eisenberg T, Gronow S, Falgenhauer J, Imirzalioglu C, Mühldorfer K, Rau J, Blom J, Fawzy A, Glaeser SP, Kämpfer P (2021) Sneathia vaginalis sp. nov. (Fusobacteriales, Leptotrichiaceae) as a replacement of the species 'Sneathia amnii' Harwich et al. 2012 and 'Leptotrichia amnionii' Shukla et al. 2002, and emended description of Sneathia Collins et al. 2001. Int J Syst Evol Microbiol. 71(3). doi: 10.1099/ijsem.0.004663. Epub 2021 Feb 22. PMID: 33616512.
  • Glaeser SP, Rückert C, Abdelmohsen UR, Winkler A, Blom J, Goesmann A, Kalinowski J, Hentschel U, Busse HJ, Kämpfer P (2021) Streptomyces dysideae sp. nov., isolated from a marine Mediterranean sponge Dysidea tupha. Int J Syst Evol Microbiol. 71(3). doi: 10.1099/ijsem.0.004672. Epub 2021 Jan 29. PMID: 33512313.
  • Wibberg D, Price-Carter M, Rückert C, Blom J, Möbius P (2020) Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes. Microorganisms. 9(1):70. doi: 10.3390/microorganisms9010070. PMID: 33383865; PMCID: PMC7823733.
  • Martins L, Fernandes C, Blom J, Dia NC, Pothier JF, Tavares F (2020) Xanthomonas euroxanthea sp. nov., a new xanthomonad species including pathogenic and non-pathogenic strains of walnut. Int J Syst Evol Microbiol. 70(12):6024-6031. doi: 10.1099/ijsem.0.004386. PMID: 32924921; PMCID: PMC8049493.
  • Rocha DJP, Azevedo V, Brenig B, Silva A, Blom J, Ramos RT, Aguiar ERG, Chapartegui-González I, Fernández-Martínez M, Martínez-Martínez L, Pacheco LGC, Navas J (2020) Whole-genome sequencing reveals misidentification of a multidrug- resistant urine clinical isolate as Corynebacterium urealyticum. J Glob Antimicrob Resist. 23:16-19. doi: 10.1016/j.jgar.2020.07.020. Epub 2020 Aug 8. PMID: 32777440.
  • Bathke J, Gauernack AS, Rupp O, Weber L, Preusser C, Lechner M, Rossbach O, Goesmann A, Evguenieva-Hackenberg E, Klug G (2020) iCLIP analysis of RNA substrates of the archaeal exosome. BMC Genomics. 21(1):797. doi: 10.1186/s12864-020-07200-x. PMID: 33198623; PMCID: PMC7667871.
  • Vazquez-Armendariz AI, Heiner M, El Agha E, Salwig I, Hoek A, Hessler MC, Shalashova I, Shrestha A, Carraro G, Mengel JP, Günther A, Morty RE, Vadász I, Schwemmle M, Kummer W, Hain T, Goesmann A, Bellusci S, Seeger W, Braun T, Herold S (2020) Multilineage murine stem cells generate complex organoids to model distal lung development and disease. EMBO J. 39(21): e103476. doi: 10.15252/embj.2019103476. Epub 2020 Sep 28. PMID: 32985719; PMCID: PMC7604576.
  • Herrera-Belaroussi A, Normand P, Pawlowski K, Fernandez MP, Wibberg D, Kalinowski J, Brachmann A, Berckx F, Lee N, Blom J, Pozzi AC, Fournier P, Bethencourt L, Dubost A, Abrouk D, Sellstedt A (2020) Candidatus Frankia nodulisporulans sp. nov., an Alnus glutinosa-infective Frankia species unable to grow in pure culture and able to sporulate in-planta. Syst Appl Microbiol. 43(6):126134. doi: 10.1016/j.syapm.2020.126134. Epub 2020 Sep 28. PMID: 33059155.
  • Mühldorfer K, Szentiks CA, Wibbelt G, van der Linden M, Ewers C, Semmler T, Akimkin V, Blom J, Rau J, Eisenberg T (2020) Streptococcus catagoni sp. nov., isolated from the respiratory tract of diseased Chacoan peccaries (Catagonus wagneri). Int J Syst Evol Microbiol. 70(11):5734-5739. doi: 10.1099/ijsem.0.004471. Epub 2020 Sep 17. PMID: 32941130.
  • Pulami D, Schauss T, Eisenberg T, Wilharm G, Blom J, Goesmann A, Kämpfer P, Glaeser SP (2020) Acinetobacter baumannii in manure and anaerobic digestates of German biogas plants. FEMS Microbiol Ecol. 96(10): fiaa176. doi: 10.1093/femsec/fiaa176. PMID: 32832994.
  • Fawzy A, Rau J, Riße K, Schauerte N, Geiger C, Blom J, Imirzalioglu C, Falgenhauer J, Bach A, Herden C, Eisenberg T (2020) Streptobacillus felis, a member of the oropharynx microbiota of the Felidae, isolated from a tropical rusty-spotted cat. Antonie Van Leeuwenhoek. 113(10):1455-1465. doi: 10.1007/s10482-020-01454-x. Epub 2020 Aug 9. PMID: 32776203; PMCID: PMC7415334.
  • Clawson ML, Schuller G, Dickey AM, Bono JL, Murray RW, Sweeney MT, Apley MD, DeDonder KD, Capik SF, Larson RL, Lubbers BV, White BJ, Blom J, Chitko-McKown CG, Brichta-Harhay DM, Smith TPL (2020) Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica. BMC Microbiol. 20(1):250. doi: 10.1186/s12866-020-01932-2. PMID: 32787780; PMCID: PMC7424683.
  • Eisenberg T, Schlez K, Fawzy A, Völker I, Hechinger S, Curić M, Schauerte N, Geiger C, Blom J, Scholz HC (2020) Expanding the host range: infection of a reptilian host (Furcifer pardalis) by an atypical Brucella strain. Antonie Van Leeuwenhoek. 113(10):1531-1537. doi: 10.1007/s10482-020-01448-9. Epub 2020 Jul 22. PMID: 32699967; PMCID: PMC7481142.
  • Ayeni FA, Falgenhauer J, Schmiedel J, Schwengers O, Chakraborty T, Falgenhauer L (2020) Detection of blaCTX-M-27-encoding Escherichia coli ST206 in Nigerian poultry stocks. J Antimicrob Chemother. 75(10):3070-3072. doi: 10.1093/jac/dkaa293. PMID: 32688376.
  • Franco A, Rückert C, Blom J, Busche T, Reichert J, Schubert P, Goesmann A, Kalinowski J, Wilke T, Kämpfer P, Glaeser SP (2020) High diversity of Vibrio spp. associated with different ecological niches in a marine aquaria system and description of Vibrio aquimaris sp. nov. Syst Appl Microbiol. 43(5):126123. doi: 10.1016/j.syapm.2020.126123. Epub 2020 Jul 18. PMID: 32847789.
  • Glaeser SP, Pulami D, Blom J, Eisenberg T, Goesmann A, Bender J, Wilharm G, Kämpfer P (2020) The status of the genus Prolinoborus (Pot et al. 1992) and the species Prolinoborus fasciculus (Pot et al. 1992). Int J Syst Evol Microbiol. 70(9):5165-5171. doi: 10.1099/ijsem.0.004404. Epub 2020 Aug 26. PMID: 32845831.
  • Liou JS, Huang CH, Ikeyama N, Lee AY, Chen IC, Blom J, Chen CC, Chen CH, Lin YC, Hsieh SY, Huang L, Ohkuma M, Watanabe K, Sakamoto M (2020) Prevotella hominis sp. nov., isolated from human faeces. Int J Syst Evol Microbiol. 70(8):4767-4773. doi: 10.1099/ijsem.0.004342. PMID: 32697186.
  • Tekedar HC, Arick MA 2nd, Hsu CY, Thrash A, Blom J, Lawrence ML, Abdelhamed H (2020) Identification of Antimicrobial Resistance Determinants in Aeromonas veronii Strain MS-17-88 Recovered From Channel Catfish (Ictalurus punctatus). Front Cell Infect Microbiol. 10:348. doi: 10.3389/fcimb.2020.00348. PMID: 32766165; PMCID: PMC7379393.
  • Liu A, Zhang YJ, Cheng P, Peng YJ, Blom J, Xue QJ (2020) Whole genome analysis calls for a taxonomic rearrangement of the genus Colwellia. Antonie Van Leeuwenhoek. 113(7):919-931. doi: 10.1007/s10482-020-01405-6. Epub 2020 Mar 26. PMID: 32219666.
  • Lüddecke T, von Reumont BM, Förster F, Billion A, Timm T, Lochnit G, Vilcinskas A, Lemke S (2020) An Economic Dilemma Between Molecular Weapon Systems May Explain an Arachno-atypical Venom in Wasp Spiders (Argiope bruennichi). Biomolecules. 10(7):978. doi: 10.3390/biom10070978. PMID: 32630016; PMCID: PMC7407881.
  • Huang CH, Chen CC, Liou JS, Lee AY, Blom J, Lin YC, Huang L, Watanabe K (2020) Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae. Int J Syst Evol Microbiol. 70(6):3755-3762. doi: 10.1099/ijsem.0.003969. PMID: 32421490.
  • Rothen J, Sapugahawatte DN, Li C, Lo N, Vogel G, Foucault F, Pflüger V, Pothier JF, Blom J, Daubenberger C, Ip M (2020) A simple, rapid typing method for Streptococcus agalactiae based on ribosomal subunit proteins by MALDI-TOF MS. Sci Rep. 10(1):8788. doi: 10.1038/s41598-020-65707-5. PMID: 32472028; PMCID: PMC7260235.
  • Volokhov DV, Blom J, Amselle M, Delmonte P, Gao Y, Shen Z, Zhang S, Gulland FM, Chizhikov VE, Eisenberg T (2020) Oceanivirga miroungae sp. nov., isolated from oral cavity of northern elephant seal (Mirounga angustirostris). Int J Syst Evol Microbiol. 70(5):3037-3048. doi: 10.1099/ijsem.0.004127. PMID: 32223835.
  • Lori M, Piton G, Symanczik S, Legay N, Brussaard L, Jaenicke S, Nascimento E, Reis F, Sousa JP, Mäder P, Gattinger A, Clément JC, Foulquier A (2020) Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change- induced rain regimes. Sci Rep. 10(1):7296. doi: 10.1038/s41598-020-64279-8. PMID: 32350402; PMCID: PMC7190635.
  • Palmer M, Steenkamp ET, Blom J, Hedlund BP, Venter SN (2020) All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy. Int J Syst Evol Microbiol. 70(4):2937-2948. doi: 10.1099/ijsem.0.004124. Epub 2020 Apr 3. PMID: 32242793.
  • Liu Y, Rao Q, Blom J, Lin Q, Luo T (2020) Pseudomonas piscis sp. nov., isolated from the profound head ulcers of farmed Murray cod (Maccullochella peelii peelii). Int J Syst Evol Microbiol. 70(4):2732-2739. doi: 10.1099/ijsem.0.004101. Epub 2020 Mar 26. PMID: 32213249.
  • Eisenberg T, Heydel C, Prenger-Berninghoff E, Fawzy A, Kling U, Akimkin V, Semmler T, Mühldorfer K, Kämpfer P, Blom J, Ewers C (2020) Streptobacillus canis sp. nov. isolated from a dog. Int J Syst Evol Microbiol. 70(4):2648-2656. doi: 10.1099/ijsem.0.004086. Epub 2020 Mar 25. PMID: 32209168.
  • Eisenberg T, Glaeser SP, Blom J, Kämpfer P (2020) Proposal to reclassify Streptobacillus hongkongensis into a novel genus as Pseudostreptobacillus hongkongensis gen. nov., comb. nov. Int J Syst Evol Microbiol. 70(4):2366-2368. doi: 10.1099/ijsem.0.004051. Epub 2020 Mar 3. PMID: 32125261.
  • Höfle L, Biedenkopf D, Werner BT, Shrestha A, Jelonek L, Koch A (2020) Study on the efficiency of dsRNAs with increasing length in RNA-based silencing of the Fusarium CYP51 genes. RNA Biol. 17(4):463-473. doi: 10.1080/15476286.2019.1700033. Epub 2020 Jan 13. PMID: 31814508; PMCID: PMC7237133.
  • Maus I, Klocke M, Derenkó J, Stolze Y, Beckstette M, Jost C, Wibberg D, Blom J, Henke C, Willenbücher K, Rumming M, Rademacher A, Pühler A, Sczyrba A, Schlüter A (2020) Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics. Environ Microbiome. 15(1):7. doi: 10.1186/s40793-020-00354-x. PMID: 33902713; PMCID: PMC8067321.
  • Eisenberg T, Glaeser SP, Blom J, Kämpfer P (2020) Proposal to reclassify Leptotrichia goodfellowii into a novel genus as Pseudoleptotrichia goodfellowii gen. nov., comb. nov. Int J Syst Evol Microbiol. 70(3):2084-2088. doi: 10.1099/ijsem.0.004024. PMID: 32228774.
  • Wu L, Li X, Ma L, Blom J, Wu H, Gu Q, Borriss R, Gao X (2020) The "pseudo- pathogenic" effect of plant growth-promoting Bacilli on starchy plant storage organs is due to their α-amylase activity which is stimulating endogenous opportunistic pathogens. Appl Microbiol Biotechnol. 104(6):2701-2714. doi: 10.1007/s00253-020-10367-8. Epub 2020 Jan 30. PMID: 32002598.
  • Lick S, Kröckel L, Wibberg D, Winkler A, Blom J, Bantleon A, Goesmann A, Kalinowski J (2020) Pseudomonas carnis sp. nov., isolated from meat. Int J Syst Evol Microbiol. 70(3):1528-1540. doi: 10.1099/ijsem.0.003928. PMID: 31922466.
  • Kumru S, Tekedar HC, Blom J, Lawrence ML, Karsi A (2020) Genomic diversity in flavobacterial pathogens of aquatic origin. Microb Pathog. 42:104053. doi: 10.1016/j.micpath.2020.104053. Epub ahead of print. PMID: 32058022.
  • Tekedar HC, Blom J, Kalindamar S, Nho S, Karsi A, Lawrence ML (2020) Comparative genomics of the fish pathogens Edwardsiella ictaluri 93-146 and Edwardsiella piscicida C07-087. Microb Genom. 6(2): e000322. doi: 10.1099/mgen.0.000322. PMID: 32108566; PMCID: PMC7067208.
  • Lick S, Kröckel L, Wibberg D, Winkler A, Blom J, Goesmann A, Kalinowski J (2020) Pseudomonas bubulae sp. nov., isolated from beef. Int J Syst Evol Microbiol. 70(1):292-301. doi: 10.1099/ijsem.0.003751. PMID: 31622235.
  • Kämpfer P, Fuglsang-Damgaard D, Overballe-Petersen S, Hasman H, Hammerum AM, Fuursted K, Blom J, Glaeser SP, Hansen F (2019) Taxonomic reassessment of the genus Pseudocitrobacter using whole genome sequencing: Pseudocitrobacter anthropi is a later heterotypic synonym of Pseudocitrobacter faecalis and description of Pseudocitrobacter vendiensis sp. nov. Int J Syst Evol Microbiol. 70(2):1315-1320. doi: 10.1099/ijsem.0.003918. PMID: 31860429.
  • Madhaiyan M, Saravanan VS, Blom J, Smits THM, Rezzonico F, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L (2019) Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.). Int J Syst Evol Microbiol. 70(2):841-848. doi: 10.1099/ijsem.0.003834. PMID: 31829916.
  • Alexandraki V, Kazou M, Blom J, Pot B, Papadimitriou K, Tsakalidou E (2019) Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species. Front Microbiol. 10:2916. doi: 10.3389/fmicb.2019.02916. PMID: 31956321; PMCID: PMC6951406.
  • Özbek R, Wielsch N, Vogel H, Lochnit G, Foerster F, Vilcinskas A, von Reumont BM (2019) Proteo-Transcriptomic Characterization of the Venom from the Endoparasitoid Wasp Pimpla turionellae with Aspects on Its Biology and Evolution. Toxins (Basel). 11(12):721. doi: 10.3390/toxins11120721. PMID: 31835557; PMCID: PMC6950128.
  • Koch A, Höfle L, Werner BT, Imani J, Schmidt A, Jelonek L, Kogel KH (2019) SIGS vs HIGS: a study on the efficacy of two dsRNA delivery strategies to silence Fusarium FgCYP51 genes in infected host and non-host plants. Mol Plant Pathol. 20(12):1636-1644. doi: 10.1111/mpp.12866. Epub 2019 Oct 11. PMID: 31603277; PMCID: PMC6859480.
  • Falgenhauer L, Schwengers O, Schmiedel J, Baars C, Lambrecht O, Heß S, Berendonk TU, Falgenhauer J, Chakraborty T, Imirzalioglu C (2019) Multidrug-Resistant and Clinically Relevant Gram-Negative Bacteria Are Present in German Surface Waters. Front Microbiol. 10:2779. doi: 10.3389/fmicb.2019.02779. PMID: 31849911; PMCID: PMC6896662.
  • Wibberg D, Batut B, Belmann P, Blom J, Glöckner FO, Grüning B, Hoffmann N, Kleinbölting N, Rahn R, Rey M, Scholz U, Sharan M, Tauch A, Trojahn U, Usadel B, Kohlbacher O (2019) The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Res. 8: ELIXIR-1877. doi: 10.12688/f1000research.20244.2. PMID: 33163154; PMCID: PMC7607484.
  • Huang CH, Wang CL, Liou JS, Lee AY, Blom J, Huang L, Watanabe K (2019) Reclassification of Micrococcus aloeverae and Micrococcus yunnanensis as later heterotypic synonyms of Micrococcus luteus. Int J Syst Evol Microbiol. 69(11):3512-3518. doi: 10.1099/ijsem.0.003654. PMID: 31454307.
  • Silva SG, Blom J, Keller-Costa T, Costa R (2019) Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host-associated and free-living Aquimarina (Bacteroidetes, Flavobacteriaceae) species. Environ Microbiol. 21(11):4002-4019. doi: 10.1111/1462-2920.14747. Epub 2019 Aug 5. PMID: 31314938.
  • Paterson ML, Ranasinghe D, Blom J, Dover LG, Sutcliffe IC, Lopes B, Sangal V (2019) Genomic analysis of a novel Rhodococcus (Prescottella) equi isolate from a bovine host. Arch Microbiol. 201(9):1317-1321. doi: 10.1007/s00203-019-01695-z. Epub 2019 Jul 13. PMID: 31302711; PMCID: PMC6790187.
  • Chen S, Soehnlen M, Blom J, Terrapon N, Henrissat B, Walker ED (2019) Comparative genomic analyses reveal diverse virulence factors and antimicrobial resistance mechanisms in clinical Elizabethkingia meningoseptica strains. PLoS One. 14(10): e0222648. doi: 10.1371/journal.pone.0222648. PMID: 31600234; PMCID: PMC6786605.
  • Smits THM, Rezzonico F, Frasson D, Vesga P, Vacheron J, Blom J, Pothier JF, Keel C, Maurhofer M, Sievers M (2019) Updated Genome Sequence and Annotation for the Full Genome of Pseudomonas protegens CHA0. Microbiol Resour Announc. 8(39): e01002-19. doi: 10.1128/MRA.01002-19. PMID: 31558637; PMCID: PMC6763652.
  • Suarez C, Ratering S, Hain T, Fritzenwanker M, Goesmann A, Blom J, Chakraborty T, Bunk B, Spröer C, Overmann J, Schnell S (2019) Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19T. Int J Genomics. 2019:7586430. doi: 10.1155/2019/7586430. PMID: 31583244; PMCID: PMC6754898.
  • Tekedar HC, Kumru S, Blom J, Perkins AD, Griffin MJ, Abdelhamed H, Karsi A, Lawrence ML (2019) Comparative genomics of Aeromonas veronii: Identification of a pathotype impacting aquaculture globally. PLoS One. 14(8): e0221018. doi: 10.1371/journal.pone.0221018. PMID: 31465454; PMCID: PMC6715197.
  • 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 (2019) Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster: They Come in Teams. Genome Biol Evol. 11(8):2273-2291. doi: 10.1093/gbe/evz153. PMID: 31368478; PMCID: PMC6735867.
  • Smits THM, Duffy B, Blom J, Ishimaru CA, Stockwell VO (2019) Pantocin A, a peptide-derived antibiotic involved in biological control by plant-associated Pantoea species. Arch Microbiol. 201(6):713-722. doi: 10.1007/s00203-019-01647-7. Epub 2019 Mar 13. PMID: 30868174.
  • Panthee S, Paudel A, Blom J, Hamamoto H, Sekimizu K (2019) Complete Genome Sequence of Weissella hellenica 0916-4-2 and Its Comparative Genomic Analysis. Front Microbiol. 10:1619. doi: 10.3389/fmicb.2019.01619. PMID: 31396169; PMCID: PMC6667553.
  • Falgenhauer J, Imirzalioglu C, Falgenhauer L, Yao Y, Hauri AM, Erath B, Schwengers O, Goesmann A, Seifert H, Chakraborty T, Doijad S (2019) Whole-Genome Sequences of Clinical Enterobacter bugandensis Isolates from Germany. Microbiol Resour Announc. 8(29): e00465-19. doi: 10.1128/MRA.00465-19. PMID: 31320432; PMCID: PMC6639611.
  • Solovey M, Wang Y, Michel C, Metzeler KH, Herold T, Göthert JR, Ellenrieder V, Hessmann E, Gattenlöhner S, Neubauer A, Pavlinic D, Benes V, Rupp O, Burchert A (2019) Nuclear factor of activated T-cells, NFATC1, governs FLT3ITD-driven hematopoietic stem cell transformation and a poor prognosis in AML. J Hematol Oncol. 12(1):72. doi: 10.1186/s13045-019-0765-y. PMID: 31286998; PMCID: PMC6615262.
  • Avontuur JR, Palmer M, Beukes CW, Chan WY, Coetzee MPA, Blom J, Stępkowski T, Kyrpides NC, Woyke T, Shapiro N, Whitman WB, Venter SN, Steenkamp ET (2019) Genome- informed Bradyrhizobium taxonomy: where to from here? Syst Appl Microbiol. 42(4):427-439. doi: 10.1016/j.syapm.2019.03.006. Epub 2019 Apr 4. PMID: 31031014.
  • Ludueña LM, Anzuay MS, Angelini JG, McIntosh M, Becker A, Rupp O, Goesmann A, Blom J, Fabra A, Taurian T (2019) Genome sequence of the endophytic strain Enterobacter sp. J49, a potential biofertilizer for peanut and maize. Genomics. 111(4):913-920. doi: 10.1016/j.ygeno.2018.05.021. Epub 2018 May 29. PMID: 29857118.
  • Riedlinger T, Bartkuhn M, Zimmermann T, Hake SB, Nist A, Stiewe T, Kracht M, Schmitz ML (2019) Chemotherapeutic Drugs Inhibiting Topoisomerase 1 Activity Impede Cytokine-Induced and NF-κB p65-Regulated Gene Expression. Cancers (Basel). 11(6):883. doi: 10.3390/cancers11060883. PMID: 31242600; PMCID: PMC6627772.
  • Wu H, Gu Q, Xie Y, Lou Z, Xue P, Fang L, Yu C, Jia D, Huang G, Zhu B, Schneider A, Blom J, Lasch P, Borriss R, Gao X (2019) Cold-adapted Bacilli isolated from the Qinghai-Tibetan Plateau are able to promote plant growth in extreme environments. Environ Microbiol. doi: 10.1111/1462-2920.14722. Epub ahead of print. PMID: 31233661.
  • Nelkner J, Henke C, Lin TW, Pätzold W, Hassa J, Jaenicke S, Grosch R, Pühler A, Sczyrba A, Schlüter A (2019) Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. Genes (Basel). 10(6):424. doi: 10.3390/genes10060424. PMID: 31163637; PMCID: PMC6627896.
  • Farr M, Ferreira S, Al-Dilaimi A, Bögeholz S, Goesmann A, Kalinowski J, Knabbe C, Faber L, Oliveira JP, Rudolph V (2019) Fabry disease: Detection of Alu-mediated exon duplication by NGS. Mol Cell Probes. 45:79-83. doi: 10.1016/j.mcp.2019.03.008. Epub 2019 Mar 29. PMID: 30936019.
  • 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 (2019) Codon Usage Heterogeneity in the Multipartite Prokaryote Genome: Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry. mBio. 10(3): e00505-19. doi: 10.1128/mBio.00505-19. PMID: 31138741; PMCID: PMC6538778.
  • Liou JS, Huang CH, Wang CL, Lee AY, Mori K, Tamura T, Watanabe M, Blom J, Huang L, Watanabe K (2019) Lactobacillus suantsaii sp. nov., isolated from suan-tsai, a traditional Taiwanese fermented mustard green. Int J Syst Evol Microbiol. 69(5):1484-1489. doi: 10.1099/ijsem.0.003346. Epub 2019 Mar 19. PMID: 30888315.
  • Ramdhan ND, Blom J, Sutcliffe IC, Pereira-Ribeiro PMA, Santos CS, Mattos- Guaraldi AL, Burkovski A, Sangal V (2019) Genomic analysis of a novel nontoxigenic Corynebacterium diphtheriae strain isolated from a cancer patient. New Microbes New Infect. 30:100544. doi: 10.1016/j.nmni.2019.100544. PMID: 31061711; PMCID: PMC6488682.
  • Jaswal R, Pathak A, Edwards B III, Lewis R III, Seaman JC, Stothard P, Krivushin K, Blom J, Rupp O, Chauhan A (2019) Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA. Genes (Basel). 10(5):325. doi: 10.3390/genes10050325. PMID: 31035394; PMCID: PMC6562407.
  • Bouhired S, Rupp O, Blom J, Schäberle TF, Schiefer A, Kehraus S, Pfarr K, Goesmann A, Hoerauf A, König G (2019) Complete Genome Sequence of the Corallopyronin A-Producing Myxobacterium Corallococcus coralloides B035. Microbiol Resour Announc. 8(17): e00050-19. doi: 10.1128/MRA.00050-19. PMID: 31023790; PMCID: PMC6486236.
  • Guan Y, Ngugi DK, Vinu M, Blom J, Alam I, Guillot S, Ferry JG, Stingl U (2019) Comparative Genomics of the Genus Methanohalophilus, Including a Newly Isolated Strain From Kebrit Deep in the Red Sea. Front Microbiol. 10:839. doi: 10.3389/fmicb.2019.00839. PMID: 31068917; PMCID: PMC6491703.
  • Palmer M, Venter SN, McTaggart AR, Coetzee MPA, Van Wyk S, Avontuur JR, Beukes CW, Fourie G, Santana QC, Van Der Nest MA, Blom J, Steenkamp ET (2019) The synergistic effect of concatenation in phylogenomics: the case in Pantoea. PeerJ. 7: e6698. doi: 10.7717/peerj.6698. PMID: 31024760; PMCID: PMC6474361.
  • Gerresheim GK, Bathke J, Michel AM, Andreev DE, Shalamova LA, Rossbach O, Hu P, Glebe D, Fricke M, Marz M, Goesmann A, Kiniry SJ, Baranov PV, Shatsky IN, Niepmann M (2019) Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling. Int J Mol Sci. 20(6):1321. doi: 10.3390/ijms20061321. PMID: 30875926; PMCID: PMC6470931.
  • Rothen J, Pothier JF, Foucault F, Blom J, Nanayakkara D, Li C, Ip M, Tanner M, Vogel G, Pflüger V, Daubenberger CA (2019) Subspecies Typing of Streptococcus agalactiae Based on Ribosomal Subunit Protein Mass Variation by MALDI-TOF MS. Front Microbiol. 10:471. doi: 10.3389/fmicb.2019.00471. PMID: 30915057; PMCID: PMC6421976.
  • Ruinelli M, Blom J, Smits THM, Pothier JF (2019) Comparative genomics and pathogenicity potential of members of the Pseudomonas syringae species complex on Prunus spp. BMC Genomics. 20(1):172. doi: 10.1186/s12864-019-5555-y. PMID: 30836956; PMCID: PMC6402114.
  • Baal N, Cunningham S, Obermann HL, Thomas J, Lippitsch A, Dietert K, Gruber AD, Kaufmann A, Michel G, Nist A, Stiewe T, Rupp O, Goesmann A, Zukunft S, Fleming I, Bein G, Lohmeyer J, Bauer S, Hackstein H (2019) ADAR1 Is Required for Dendritic Cell Subset Homeostasis and Alveolar Macrophage Function. J Immunol. 202(4):1099-1111. doi: 10.4049/jimmunol.1800269. Epub 2019 Jan 16. PMID: 30651342.
  • Rutz D, Frasson D, Sievers M, Blom J, Rezzonico F, Pothier JF, Smits THM (2019) High-Quality Draft Genome Sequence of Pseudomonas reidholzensis Strain CCOS 865T. Microbiol Resour Announc. 8(3): e01502-18. doi: 10.1128/MRA.01502-18. PMID: 30687835; PMCID: PMC6346167.
  • Tekedar HC, Abdelhamed H, Kumru S, Blom J, Karsi A, Lawrence ML (2019) Comparative Genomics of Aeromonas hydrophila Secretion Systems and Mutational Analysis of hcp1 and vgrG1 Genes From T6SS. Front Microbiol. 9:3216. doi: 10.3389/fmicb.2018.03216. PMID: 30687246; PMCID: PMC6333679.
  • Biessy A, Novinscak A, Blom J, Léger G, Thomashow LS, Cazorla FM, Josic D, Filion M (2018) Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp. Environ Microbiol. 21(1):437-455. doi: 10.1111/1462-2920.14476. Epub 2018 Dec 17. PMID: 30421490.
  • Amiri Moghaddam J, Crüsemann M, Alanjary M, Harms H, Dávila-Céspedes A, Blom J, Poehlein A, Ziemert N, König GM, Schäberle TF (2018) Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites. Sci Rep. 8(1):16600. doi: 10.1038/s41598-018-34954-y. PMID: 30413766; PMCID: PMC6226438.
  • Shibl AA, Ngugi DK, Talarmin A, Thompson LR, Blom J, Stingl U (2018) The genome of a novel isolate of Prochlorococcus from the Red Sea contains transcribed genes for compatible solute biosynthesis. FEMS Microbiol Ecol. 94(12). doi: 10.1093/femsec/fiy182. PMID: 30188995.
  • Fernandes C, Blom J, Pothier JF, Tavares F (2018) High-Quality Draft Genome Sequence of Xanthomonas arboricola pv. juglandis CPBF 1521, Isolated from Leaves of a Symptomatic Walnut Tree in Portugal without a Past of Phytosanitary Treatment. Microbiol Resour Announc. 7(16): e00887-18. doi: 10.1128/MRA.00887-18. PMID: 30533738; PMCID: PMC6256574.
  • Rutz D, Frasson D, Sievers M, Blom J, Rezzonico F, Pothier JF, Smits THM (2018) High-Quality Draft Genome Sequence of Pseudomonas wadenswilerensis CCOS 864T. Microbiol Resour Announc. 7(16): e01059-18. doi: 10.1128/MRA.01059-18. PMID: 30533735; PMCID: PMC6256571.
  • Fernandes C, Blom J, Pothier JF, Tavares F (2018) High-Quality Draft Genome Sequence of Xanthomonas sp. Strain CPBF 424, a Walnut-Pathogenic Strain with Atypical Features. Microbiol Resour Announc. 7(15): e00921-18. doi: 10.1128/MRA.00921-18. PMID: 30533728; PMCID: PMC6256435.
  • Sangal V, Goodfellow M, Blom J, Tan GYA, Klenk HP, Sutcliffe IC (2018) Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach. Front Microbiol. 9:2281. doi: 10.3389/fmicb.2018.02281. PMID: 30319584; PMCID: PMC6171478.
  • Weirick T, Müller R, Uchida S (2018) Increasing workflow development speed and reproducibility with Vectools. F1000Res. 7:1499. doi: 10.12688/f1000research.16301.2. PMID: 30631441; PMCID: PMC6281013.
  • Aliyu H, Lebre P, Blom J, Cowan D, De Maayer P (2018) Corrigendum to "Phylogenomic re-assessment of the thermophilic genus Geobacillus" [Syst. Appl. Microbiol. 39 (2016) 527-533]. Syst Appl Microbiol. 41(5):529-530. doi: 10.1016/j.syapm.2018.07.001. Epub 2018 Jul 10. Erratum for: Syst Appl Microbiol. 39(8):527-533. PMID: 30006234.
  • Schult F, Le TN, Albersmeier A, Rauch B, Blumenkamp P, van der Does C, Goesmann A, Kalinowski J, Albers SV, Siebers B (2018) Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response. Nucleic Acids Res. 46(14):7179-7192. doi: 10.1093/nar/gky527. PMID: 29982548; PMCID: PMC6101591.
  • Zanini S, Šečić E, Jelonek L, Kogel KH (2018) A Bioinformatics Pipeline for the Analysis and Target Prediction of RNA Effectors in Bidirectional Communication During Plant-Microbe Interactions. Front Plant Sci. 9:1212. doi: 10.3389/fpls.2018.01212. PMID: 30177942; PMCID: PMC6109766.
  • Argemi X, Matelska D, Ginalski K, Riegel P, Hansmann Y, Bloom J, Pestel- Caron M, Dahyot S, Lebeurre J, Prévost G (2018) Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer. BMC Genomics. 19(1):621. doi: 10.1186/s12864-018-4978-1. PMID: 30126366; PMCID: PMC6102843.
  • Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, Lewis NE, Borth N, Lee KH (2018) A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnol Bioeng. 115(8):2087-2100. doi: 10.1002/bit.26722. Epub 2018 May 29. PMID: 29704459; PMCID: PMC6045439.
  • Celis JS, Wibberg D, Ramírez-Portilla C, Rupp O, Sczyrba A, Winkler A, Kalinowski J, Wilke T (2018) Binning enables efficient host genome reconstruction in cnidarian holobionts. Gigascience. 7(7): giy075. doi: 10.1093/gigascience/giy075. PMID: 29917104; PMCID: PMC6049006.
  • Riesco R, Carro L, Román-Ponce B, Prieto C, Blom J, Klenk HP, Normand P, Trujillo ME (2018) Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics. Front Microbiol. 9:1360. doi: 10.3389/fmicb.2018.01360. PMID: 29988535; PMCID: PMC6026663.
  • Maus I, Rumming M, Bergmann I, Heeg K, Pohl M, Nettmann E, Jaenicke S, Blom J, Pühler A, Schlüter A, Sczyrba A, Klocke M (2018) Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. Biotechnol Biofuels. 11:167. doi: 10.1186/s13068-018-1162-4. PMID: 29951113; PMCID: PMC6010159.
  • Kazou M, Alexandraki V, Blom J, Pot B, Tsakalidou E, Papadimitriou K (2018) Comparative Genomics of Lactobacillus acidipiscis ACA-DC 1533 Isolated From Traditional Greek Kopanisti Cheese Against Species Within the Lactobacillus salivarius Clade. Front Microbiol. 9:1244. doi: 10.3389/fmicb.2018.01244. PMID: 29942291; PMCID: PMC6004923.
  • Wei Y, Mao H, Xu Y, Zou W, Fang J, Blom J (2018) Pseudomonas abyssi sp. nov., isolated from the abyssopelagic water of the Mariana Trench. Int J Syst Evol Microbiol. 68(8):2462-2467. doi: 10.1099/ijsem.0.002785. Epub 2018 Jun 21. PMID: 29927369.
  • Karimi E, Slaby BM, Soares AR, Blom J, Hentschel U, Costa R (2018) Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges. FEMS Microbiol Ecol. 94(6). doi: 10.1093/femsec/fiy074. PMID: 29701776.
  • Palmer M, Steenkamp ET, Coetzee MPA, Avontuur JR, Chan WY, van Zyl E, Blom J, Venter SN (2018) Mixta gen. nov., a new genus in the Erwiniaceae. Int J Syst Evol Microbiol. 68(4):1396-1407. doi: 10.1099/ijsem.0.002540. Epub 2018 Feb 27. PMID: 29485394.
  • Åvall-Jääskeläinen S, Taponen S, Kant R, Paulin L, Blom J, Palva A, Koort J (2018) Comparative genome analysis of 24 bovine-associated Staphylococcus isolates with special focus on the putative virulence genes. PeerJ. 6: e4560. doi: 10.7717/peerj.4560. PMID: 29610707; PMCID: PMC5880176.
  • Pati NB, Doijad SP, Schultze T, Mannala GK, Yao Y, Jaiswal S, Ryan D, Suar M, Gwozdzinski K, Bunk B, Mraheil MA, Marahiel MA, Hegemann JD, Spröer C, Goesmann A, Falgenhauer L, Hain T, Imirzalioglu C, Mshana SE, Overmann J, Chakraborty T (2018) Enterobacter bugandensis: a novel enterobacterial species associated with severe clinical infection. Sci Rep. 8(1):5392. doi: 10.1038/s41598-018-23069-z. PMID: 29599516; PMCID: PMC5876403.
  • Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR, van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET (2018) Corrigendum: Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato. Front Microbiol. 9:373. doi: 10.3389/fmicb.2018.00373. Erratum for: Front Microbiol. 8:1154. PMID: 29576763; PMCID: PMC5863518.
  • Bartz JO, Blom J, Busse HJ, Mvie JB, Hardt M, Schubert P, Wilke T, Goesmann A, Wilharm G, Bender J, Kämpfer P, Glaeser SP (2018) Parendozoicomonas haliclonae gen. nov. sp. nov. isolated from a marine sponge of the genus Haliclona and description of the family Endozoicomonadaceae fam. nov. comprising the genera Endozoicomonas, Parendozoicomonas, and Kistimonas. Syst Appl Microbiol. 41(2):73-84. doi: 10.1016/j.syapm.2017.11.004. Epub 2017 Dec 22. PMID: 29398077.
  • Gétaz M, Baeyen S, Blom J, Maes M, Cottyn B, Pothier JF (2018) High-Quality Draft Genome Sequences of Five Xanthomonas arboricola pv. fragariae Isolates. Genome Announc. 6(7): e01585-17. doi: 10.1128/genomeA.01585-17. PMID: 29449402; PMCID: PMC5814503.
  • Verwaaijen B, Wibberg D, Nelkner J, Gordin M, Rupp O, Winkler A, Bremges A, Blom J, Grosch R, Pühler A, Schlüter A (2018) 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. J Biotechnol. 267:12-18. doi: 10.1016/j.jbiotec.2017.12.021. Epub 2017 Dec 24. PMID: 29278726.
  • Palmer M, Steenkamp ET, Coetzee MPA, Blom J, Venter SN (2018) Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria. Front Microbiol. 9:113. doi: 10.3389/fmicb.2018.00113. PMID: 29467735; PMCID: PMC5808187.
  • Ruinelli M, Blom J, Pothier JF (2017) Complete Genome Sequence of Pseudomonas viridiflava CFBP 1590, Isolated from Diseased Cherry in France. Genome announcements. 5(30). doi: 10.1128/genomeA.00662-17
  • Rezzonico F, Rupp O, Fahrentrapp J (2017) Pathogen recognition in compatible plant-microbe interactions. Scientific reports. 7(1): 6383. doi: 10.1038/s41598-017-04792-5
  • Jeong DW, Heo S, Ryu S, Blom J, Lee JH (2017) Genomic insights into the virulence and salt tolerance of Staphylococcus equorum. Scientific reports. 7(1): 5383. doi: 10.1038/s41598-017-05918-5
  • Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR, van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET (2017) Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato. Frontiers in microbiology. 8: 1154. doi: 10.3389/fmicb.2017.01154
  • Jimenez-Infante F, Ngugi DK, Vinu M, Blom J, Alam I, Bajic VB, Stingl U (2017) Genomic Characterization of Two Novel SAR11 Isolates From the Red Sea, Including the First Strain of the SAR11 Ib clade. FEMS microbiology ecology. 93(7). doi: 10.1093/femsec/fix083
  • Golyshina OV, Tran H, Reva ON, Lemak S, Yakunin AF, Goesmann A, Nechitaylo TY, LaCono V, Smedile F, Slesarev A, Rojo D, Barbas C, Ferrer M, Yakimov MM, Golyshin PN (2017) Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT. Scientific reports. 7(1): 3682. doi: 10.1038/s41598-017-03904-5
  • Wibberg D, Genzel F, Verwaaijen B, Blom J, Rupp O, Goesmann A, Zrenner R, Grosch R, Pühler A, Schlüter A (2017) Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3. Archives of microbiology. 199, pages1065–1068. doi: 10.1007/s00203-017-1394-x
  • Tomazetto G, Hahnke S, Langer T, Wibberg D, Blom J, Maus I, Pühler A, Klocke M, Schlüter A (2017) The completely annotated genome and comparative genomics of the Peptoniphilaceae bacterium str. ING2-D1G, a novel acidogenic bacterium isolated from a mesophilic biogas reactor. Journal of biotechnology. 257, pages178-186. doi: 10.1016/j.jbiotec.2017.05.027
  • Wöchtl B, Gunzer F, Gerner W, Gasse H, Koch M, Bagó Z, Ganter M, Weissenböck H, Dinhopl N, Coldewey SM, von Altrock A, Waldmann KH, Saalmüller A, Zimmermann K, Steinmann J, Kehrmann J, Klein-Hitpass L, Blom J, Ehricht R, Engelmann I, Hennig-Pauka I (2017) Comparison of clinical and immunological findings in gnotobiotic piglets infected with Escherichia coli O104:H4 outbreak strain and EHEC O157:H7. Gut pathogens. 9: 30. doi: 10.1186/s13099-017-0179-8
  • Alkhateeb RS, Rückert C, Rupp O, Pucker B, Hublik G, Wibberg D, Niehaus K, Pühler A, Vorhölter FJ (2017) Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data. Journal of biotechnology. 253: 55-61. doi: 10.1016/j.jbiotec.2017.05.009
  • Stadermann KB, Blom J, Borgmeier C, Sciberras N, Herbold S, Kipker M, Meurer G, Molck S, Petri D, Pelzer S, Schneider J (2017) First complete genome sequence of Bacillus glycinifermentans B-27. Journal of biotechnology. 257:187-191. doi: 10.1016/j.jbiotec.2017.04.021
  • Duar RM, Frese SA, Lin XB, Fernando SC, Burkey TE, Tasseva G, Peterson DA, Blom J, Wenzel CQ, Szymanski CM, Walter J (2017) Experimental Evaluation of Host Adaptation of Lactobacillus reuteri to Different Vertebrate Species. Applied and environmental microbiology. 83(12). doi: 10.1128/AEM.00132-17
  • Ampattu BJ, Hagmann L, Liang C, Dittrich M, Schlüter A, Blom J, Krol E, Goesmann A, Becker A, Dandekar T, Müller T, Schoen C (2017) Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence. BMC genomics. 18(1): 282. doi: 10.1186/s12864-017-3616-7
  • Celis JS, Edgell DR, Stelbrink B, Wibberg D, Hauffe T, Blom J, Kalinowski J, Wilke T (2017) Evolutionary and biogeographical implications of degraded LAGLIDADG endonuclease functionality and group I intron occurrence in stony corals (Scleractinia) and mushroom corals (Corallimorpharia). PloS one. 12(3): e0173734. doi: 10.1371/journal.pone.0173734
  • Entfellner E, Frei M, Christiansen G, Deng L, Blom J, Kurmayer R (2017) Evolution of Anabaenopeptin Peptide Structural Variability in the Cyanobacterium Planktothrix. Frontiers in microbiology. 8: 219. doi: 10.3389/fmicb.2017.00219
  • Palmer M, Steenkamp ET, Coetzee MP, Chan WY, van Zyl E, De Maayer P, Coutinho TA, Blom J, Smits TH, Duffy B, Venter SN (2017) Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella. Antonie van Leeuwenhoek. 110:1287-1309. doi: 10.1007/s10482-017-0852-4
  • Serrania J, Johner T, Rupp O, Goesmann A, Becker A (2017) Massive parallel insertion site sequencing of an arrayed Sinorhizobium meliloti signature-tagged mini-Tn 5 transposon mutant library. Journal of biotechnology. 257:9-12. doi: 10.1016/j.jbiotec.2017.02.019
  • Alexandraki V, Kazou M, Blom J, Pot B, Tsakalidou E, Papadimitriou K (2017) The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2. Standards in genomic sciences. 12: 18. doi: 10.1186/s40793-017-0227-5
  • Fan B, Blom J, Klenk HP, Borriss R (2017) Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an "Operational Group B. amyloliquefaciens" within the B. subtilis Species Complex. Frontiers in microbiology. 8: 22. doi: 10.3389/fmicb.2017.00022
  • Langlois PA, Snelling J, Hamilton JP, Bragard C, Koebnik R, Verdier V, Triplett LR, Blom J, Tisserat NA, Leach JE (2017) Characterization of the Xanthomonas translucens Complex Using Draft Genomes, Comparative Genomics, Phylogenetic Analysis, and Diagnostic LAMP Assays. Phytopathology. 107(5): 519-527. doi: 10.1094/PHYTO-08-16-0286-R
  • Pfannebecker KC, Lange M, Rupp O, Becker A (2017) Seed Plant-Specific Gene Lineages Involved in Carpel Development. Molecular biology and evolution. 34(4): 925-942. doi: 10.1093/molbev/msw297
  • Klughammer J, Dittrich M, Blom J, Mitesser V, Vogel U, Frosch M, Goesmann A, Müller T, Schoen C (2017) Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease. PloS one. 12(1): e0169892. doi: 10.1371/journal.pone.0169892
  • Schmautz Z, Graber A, Jaenicke S, Goesmann A, Junge R, Smits TH (2017) Microbial diversity in different compartments of an aquaponics system. Archives of microbiology. 199(4): 613-620. doi: 10.1007/s00203-016-1334-1
  • Hersemann L, Wibberg D, Blom J, Goesmann A, Widmer F, Vorhölter FJ, Kölliker R (2017) Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis. BMC genomics. 18(1): 35. doi: 10.1186/s12864-016-3422-7
  • Makarewicz O, Lucas M, Brandt C, Herrmann L, Albersmeier A, Rückert C, Blom J, Goesmann A, van der Linden M, Kalinowski J, Pletz MW (2017) Whole Genome Sequencing of 39 Invasive Streptococcus pneumoniae Sequence Type 199 Isolates Revealed Switches from Serotype 19A to 15B. PloS one. 12(1): e0169370. doi: 10.1371/journal.pone.0169370
  • Petkauskaite R, Blom J, Goesmann A, Kuisiene N (2017) Draft genome sequence of pectic polysaccharide-degrading moderate thermophilic bacterium Geobacillus thermodenitrificans DSM 101594. Brazilian journal of microbiology. 48(1): 7-8. doi: 10.1016/j.bjm.2016.06.013
  • Pfannebecker KC, Lange M, Rupp O, Becker A (2016) An Evolutionary Framework for Carpel Developmental Control Genes. Molecular biology and evolution. 34(2): 330-348. doi: 10.1093/molbev/msw229
  • Aliyu H, Lebre P, Blom J, Cowan D, De Maayer P (2016) Phylogenomic re-assessment of the thermophilic genus Geobacillus. Systematic and applied microbiology. 39(8): 527-533. doi: 10.1016/j.syapm.2016.09.004
  • Scholz HC, Mühldorfer K, Shilton C, Benedict S, Whatmore AM, Blom J, Eisenberg T (2016) The Change of a Medically Important Genus: Worldwide Occurrence of Genetically Diverse Novel Brucella Species in Exotic Frogs. PloS one. 11(12): e0168872. doi: 10.1371/journal.pone.0168872
  • Sangal V, Goodfellow M, Jones AL, Schwalbe EC, Blom J, Hoskisson PA, Sutcliffe IC (2016) Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa. Scientific reports. 6: 38392. doi: 10.1038/srep38392
  • Wegmann U, Goesmann A, Carding SR (2016) Complete Genome Sequence of Bacteroides ovatus V975. Genome announcements. 4(6). doi: 10.1128/genomeA.01335-16
  • Jaenicke S, Bunk B, Wibberg D, Spröer C, Hersemann L, Blom J, Winkler A, Schatschneider S, Albaum SP, Kölliker R, Goesmann A, Pühler A, Overmann J, Vorhölter FJ (2016) Complete Genome Sequence of the Barley Pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T). Genome announcements. 4(6). doi: 10.1128/genomeA.01334-16
  • Wippermann A, Rupp O, Brinkrolf K, Hoffrogge R, Noll T (2016) Integrative analysis of DNA methylation and gene expression in butyrate-treated CHO cells. Journal of biotechnology. 257:150-161. doi: 10.1016/j.jbiotec.2016.11.020
  • Morales M, Sentchilo V, Bertelli C, Komljenovic A, Kryuchkova-Mostacci N, Bourdilloud A, Linke B, Goesmann A, Harshman K, Segers F, Delapierre F, Fiorucci D, Seppey M, Trofimenco E, Berra P, El Taher A, Loiseau C, Roggero D, Sulfiotti M, Etienne A, Ruiz Buendia G, Pillard L, Escoriza A, Moritz R, Schneider C, Alfonso E, Ben Jeddou F, Selmoni O, Resch G, Greub G, Emery O, Dubey M, Pillonel T, Robinson-Rechavi M, van der Meer JR (2016) The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand. PloS one. 11(11): e0165850. doi: 10.1371/journal.pone.0165850
  • Eisenberg T, Riße K, Schauerte N, Geiger C, Blom J, Scholz HC (2016) Isolation of a novel 'atypical' Brucella strain from a bluespotted ribbontail ray (Taeniura lymma). Antonie van Leeuwenhoek. 110(2): 221-234. doi: 10.1007/s10482-016-0792-4
  • Barbeyron T, Thomas F, Barbe V, Teeling H, Schenowitz C, Dossat C, Goesmann A, Leblanc C, Oliver Glöckner F, Czjzek M, Amann R, Michel G (2016) Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans DsijT. Environmental microbiology. 18(12): 4610-4627. doi: 10.1111/1462-2920.13584
  • Koch A, Biedenkopf D, Furch A, Weber L, Rossbach O, Abdellatef E, Linicus L, Johannsmeier J, Jelonek L, Goesmann A, Cardoza V, McMillan J, Mentzel T, Kogel KH (2016) An RNAi-Based Control of Fusarium graminearum Infections Through Spraying of Long dsRNAs Involves a Plant Passage and Is Controlled by the Fungal Silencing Machinery. PLoS pathogens. 12(10): e1005901. doi: 10.1371/journal.ppat.1005901
  • Nguyen TV, Wibberg D, Battenberg K, Blom J, Vanden Heuvel B, Berry AM, Kalinowski J, Pawlowski K (2016) An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH. BMC genomics. 17(1): 796. doi: 10.1186/s12864-016-3140-1
  • Kupferschmied P, Chai T, Flury P, Blom J, Smits TH, Maurhofer M, Keel C (2016) Specific surface glycan decorations enable antimicrobial peptide resistance in plant-beneficial pseudomonads with insect-pathogenic properties. Environmental microbiology. 18(11): 4265-4281. doi: 10.1111/1462-2920.13571
  • Hersemann L, Wibberg D, Blom J, Widmer F, Kölliker R (2016) Draft Genome Sequence of the Xanthomonas bromi Type Strain LMG 947. Genome announcements. 4(5). doi: 10.1128/genomeA.00961-16
  • Anton BP, Harhay GP, Smith TP, Blom J, Roberts RJ (2016) Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi. PloS one. 11(8): e0161499. doi: 10.1371/journal.pone.0161499
  • Pathak A, Chauhan A, Blom J, Indest KJ, Jung CM, Stothard P, Bera G, Green SJ, Ogram A (2016) Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation. PloS one. 11(8): e0161032. doi: 10.1371/journal.pone.0161032
  • Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, Jaenicke S, Goesmann A, Sczyrba A, Scherer P, König H, Schwarz WH, Zverlov VV, Liebl W, Pühler A, Schlüter A, Klocke M (2016) Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates. Biotechnology for biofuels. 9: 171. doi: 10.1186/s13068-016-0581-3
  • Bertelli C, Cissé OH, Rusconi B, Kebbi-Beghdadi C, Croxatto A, Goesmann A, Collyn F, Greub G (2016) CRISPR System Acquisition and Evolution of an Obligate Intracellular Chlamydia-Related Bacterium. Genome biology and evolution. 8(8): 2376-86. doi: 10.1093/gbe/evw138
  • Falgenhauer L, Waezsada SE, Gwozdzinski K, Ghosh H, Doijad S, Bunk B, Spröer C, Imirzalioglu C, Seifert H, Irrgang A, Fischer J, Guerra B, Käsbohrer A, Overmann J, Goesmann A, Chakraborty T (2016) Chromosomal Locations of mcr-1 and blaCTX-M-15 in Fluoroquinolone-Resistant Escherichia coli ST410. Emerging infectious diseases. 22(9): 1689-91. doi: 10.3201/eid2209.160692. PMID: 27322919. PMCID: PMC4994348
  • Martini MC, Wibberg D, Lozano M, Torres Tejerizo G, Albicoro FJ, Jaenicke S, van Elsas JD, Petroni A, Garcillán-Barcia MP, de la Cruz F, Schlüter A, Pühler A, Pistorio M, Lagares A, Del Papa MF (2016) Genomics of high molecular weight plasmids isolated from an on-farm biopurification system. Scientific reports. 6: 28284. doi: 10.1038/srep28284
  • Ortseifen V, Stolze Y, Maus I, Sczyrba A, Bremges A, Albaum SP, Jaenicke S, Fracowiak J, Pühler A, Schlüter A (2016) An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of biotechnology. 231: 268-79. doi: 10.1016/j.jbiotec.2016.06.014
  • Blifernez-Klassen O, Wibberg D, Winkler A, Blom J, Goesmann A, Kalinowski J, Kruse O (2016) Complete Chloroplast and Mitochondrial Genome Sequences of the Hydrocarbon Oil-Producing Green Microalga Botryococcus braunii Race B (Showa). Genome announcements. 4(3). doi: 10.1128/genomeA.00524-16
  • Barbuddhe SB, Doijad SP, Goesmann A, Hilker R, Poharkar KV, Rawool DB, Kurkure NV, Kalorey DR, Malik SS, Shakuntala I, Chaudhari S, Waskar V, D'Costa D, Kolhe R, Arora R, Roy A, Raorane A, Kale S, Pathak A, Negi M, Kaur S, Waghmare R, Warke S, Shoukat S, Harish B, Poojary A, Madhavaprasad C, Nagappa K, Das S, Zende R, Garg S, Bhosle S, Radriguez S, Paturkar A, Fritzenwanker M, Ghosh H, Hain T, Chakraborty T (2016) Presence of a widely disseminated Listeria monocytogenes serotype 4b clone in India. Emerging microbes & infections. 5(1) 1-4. doi: 10.1038/emi.2016.55
  • Falgenhauer L, Imirzalioglu C, Ghosh H, Gwozdzinski K, Schmiedel J, Gentil K, Bauerfeind R, Kämpfer P, Seifert H, Michael GB, Schwarz S, Pfeifer Y, Werner G, Pietsch M, Roesler U, Guerra B, Fischer J, Sharp H, Käsbohrer A, Goesmann A, Hille K, Kreienbrock L, Chakraborty T (2016) Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany. International journal of antimicrobial agents. 47(6): 457-65. doi: 10.1016/j.ijantimicag.2016.03.019
  • Maus I, Cibis KG, Bremges A, Stolze Y, Wibberg D, Tomazetto G, Blom J, Sczyrba A, König H, Pühler A, Schlüter A (2016) Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment. Journal of biotechnology. 232: 50-60. doi: 10.1016/j.jbiotec.2016.05.001
  • Franta Z, Vogel H, Lehmann R, Rupp O, Goesmann A, Vilcinskas A (2016) Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots. BioMed research international. 2016: 8285428. doi: 10.1155/2016/8285428
  • Ghatak S, Blom J, Das S, Sanjukta R, Puro K, Mawlong M, Shakuntala I, Sen A, Goesmann A, Kumar A, Ngachan SV (2016) Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila. Antonie van Leeuwenhoek. 109(7): 945-56. doi: 10.1007/s10482-016-0693-6
  • Papadimitriou K, Baharidis PK, Georgoulis A, Engel M, Louka M, Karamolegkou G, Tsoka A, Blom J, Pot B, Malecki P, Rypniewski W, Huber H, Schloter M, Vorgias C (2016) Analysis of the complete genome sequence of the archaeon Pyrococcus chitonophagus DSM 10152 (formerly Thermococcus chitonophagus). Extremophiles: life under extreme conditions. 20(3): 351-61. doi: 10.1007/s00792-016-0826-x
  • Wibberg D, Andersson L, Tzelepis G, Rupp O, Blom J, Jelonek L, Pühler A, Fogelqvist J, Varrelmann M, Schlüter A, Dixelius C (2016) Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes. BMC genomics. 17: 245. doi: 10.1186/s12864-016-2561-1
  • Scholz HC, Revilla-Fernández S, Al Dahouk S, Hammerl JA, Zygmunt MS, Cloeckaert A, Koylass M, Whatmore AM, Blom J, Vergnaud G, Witte A, Aistleitner K, Hofer E (2016) Brucella vulpis sp. nov., isolated from mandibular lymph nodes of red foxes (Vulpes vulpes). International journal of systematic and evolutionary microbiology. 66(5): 2090-8. doi: 10.1099/ijsem.0.000998
  • Flury P, Aellen N, Ruffner B, Péchy-Tarr M, Fataar S, Metla Z, Dominguez-Ferreras A, Bloemberg G, Frey J, Goesmann A, Raaijmakers JM, Duffy B, Höfte M, Blom J, Smits TH, Keel C, Maurhofer M (2016) Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. The ISME Journal. 10(10): 2527-42. doi: 10.1038/ismej.2016.5
  • Dickey AM, Loy JD, Bono JL, Smith TP, Apley MD, Lubbers BV, DeDonder KD, Capik SF, Larson RL, White BJ, Blom J, Chitko-McKown CG, Clawson ML (2016) Large genomic differences between Moraxella bovoculi isolates acquired from the eyes of cattle with infectious bovine keratoconjunctivitis versus the deep nasopharynx of asymptomatic cattle. Veterinary research. 47: 31. doi: 10.1186/s13567-016-0316-2
  • Wibberg D, Andersson L, Rupp O, Goesmann A, Pühler A, Varrelmann M, Dixelius C, Schlüter A (2016) Draft genome sequence of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB strain BBA69670. Journal of biotechnology, 222: 11-2. doi: 10.1016/j.jbiotec.2016.02.001
  • Rezzonico F, Smits TH, Born Y, Blom J, Frey JE, Goesmann A, Cleenwerck I, de Vos P, Bonaterra A, Duffy B, Montesinos E (2016) Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees. International journal of systematic and evolutionary microbiology. 66(3). doi: 10.1099/ijsem.0.000920
  • Falgenhauer L, Waezsada SE, Yao Y, Imirzalioglu C, Käsbohrer A, Roesler U, Michael GB, Schwarz S, Werner G, Kreienbrock L, Chakraborty T, RESET consortium. (2016) Colistin resistance gene mcr-1 in extended-spectrum β-lactamase-producing and carbapenemase-producing Gram-negative bacteria in Germany. The Lancet. Infectious diseases. 16(3): 282-283. doi: 10.1016/S1473-3099(16)00009-8
  • Fischer S, Klockgether J, Morán Losada P, Chouvarine P, Cramer N, Davenport CF, Dethlefsen S, Dorda M, Goesmann A, Hilker R, Mielke S, Schönfelder T, Suerbaum S, Türk O, Woltemate S, Wiehlmann L, Tümmler B (2016) Intraclonal genome diversity of the major Pseudomonas aeruginosa clones C and PA14. Environmental microbiology reports. 8(2): 227-34. doi: 10.1111/1758-2229.12372
  • Ngugi DK, Blom J, Stepanauskas R, Stingl U (2016) Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines. The ISME Journal. 10(6): 1383-99. doi: 10.1038/ismej.2015.214
  • Glaeser SP, Imani J, Alabid I, Guo H, Kumar N, Kämpfer P, Hardt M, Blom J, Goesmann A, Rothballer M, Hartmann A, Kogel KH (2016) Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. The ISME Journal. 10(4): 871-84. doi: 10.1038/ismej.2015.163
  • Gómez-Consarnau L, González JM, Riedel T, Jaenicke S, Wagner-Döbler I, Sañudo-Wilhelmy SA, Fuhrman JA (2016) Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. The ISME Journal. 10(5): 1102-12. doi: 10.1038/ismej.2015.196
  • Humphreys CM, McLean S, Schatschneider S, Millat T, Henstra AM, Annan FJ, Breitkopf R, Pander B, Piatek P, Rowe P, Wichlacz AT, Woods C, Norman R, Blom J, Goesmann A, Hodgman C, Barrett D, Thomas NR, Winzer K, Minton NP (2015) Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. BMC genomics. 16: 1085. doi: 10.1186/s12864-015-2287-5
  • Wibberg D, Rupp O, Blom J, Jelonek L, Kröber M, Verwaaijen B, Goesmann A, Albaum S, Grosch R, Pühler A, Schlüter A (2015) Development of a Rhizoctonia solani AG1-IB Specific Gene Model Enables Comparative Genome Analyses between Phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 Isolates. PloS one. 10(12): e0144769. doi: 10.1371/journal.pone.0144769
  • Smits TH, Rezzonico F, Blom J, Goesmann A, Abelli A, Kron Morelli R, Vanneste JL, Duffy B (2015) Draft Genome Sequence of the Commercial Biocontrol Strain Pantoea agglomerans P10c. Genome announcements. 3(6). doi: 10.1128/genomeA.01448-15
  • Jimenez-Infante F, Ngugi DK, Vinu M, Alam I, Kamau AA, Blom J, Bajic VB, Stingl U (2015) Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs. Applied and environmental microbiology. 82(4): 1215-26. doi: 10.1128/AEM.02852-15
  • Pauli M, Chakarov N, Rupp O, Kalinowski J, Goesmann A, Sorenson MD, Krüger O, Hoffman JI (2015) De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite. BMC genomics. 16:1038. doi: 10.1186/s12864-015-2254-1
  • Wegmann U, MacKenzie DA, Zheng J, Goesmann A, Roos S, Swarbreck D, Walter J, Crossman LC, Juge N (2015) The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. BMC genomics. 16:1023. doi: 10.1186/s12864-015-2216-7
  • Schultze T, Hilker R, Mannala GK, Gentil K, Weigel M, Farmani N, Windhorst AC, Goesmann A, Chakraborty T, Hain T (2015) A detailed view of the intracellular transcriptome of Listeria monocytogenes in murine macrophages using RNA-seq. Frontiers in microbiology. 6: 1199. doi: 10.3389/fmicb.2015.01199
  • Schäper S, Krol E, Skotnicka D, Kaever V, Hilker R, Søgaard-Andersen L, Becker A (2015) Cyclic Di-GMP Regulates Multiple Cellular Functions in the Symbiotic Alphaproteobacterium Sinorhizobium meliloti. Journal of bacteriology. 198(3): 521-35. doi: 10.1128/JB.00795-15
  • Sangal V, Blom J, Sutcliffe IC, von Hunolstein C, Burkovski A, Hoskisson PA (2015) Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated and secreted proteome. BMC genomics. 16: 765. doi: 10.1186/s12864-015-1980-8
  • Heggelund L, Gaustad P, Håvelsrud OE, Blom J, Borgen L, Sundset A, Sørum H, Frøland SS (2015) Corynebacterium pseudotuberculosis Pneumonia in a Veterinary Student Infected During Laboratory Work. Open forum infectious diseases. 2(2): ofv053. doi: 10.1093/ofid/ofv053
  • Fatykhova D, Rabes A, Machnik C, Guruprasad K, Pache F, Berg J, Toennies M, Bauer TT, Schneider P, Schimek M, Eggeling S, Mitchell TJ, Mitchell AM, Hilker R, Hain T, Suttorp N, Hippenstiel S, Hocke AC, Opitz B (2015) Serotype 1 and 8 Pneumococci Evade Sensing by Inflammasomes in Human Lung Tissue. PloS one. 10(8): e0137108. doi: 10.1371/journal.pone.0137108
  • Doijad S, Weigel M, Barbuddhe S, Blom J, Goesmann A, Hain T, Chakraborty T (2015) Phylogenomic grouping of Listeria monocytogenes. Canadian journal of microbiology. 61(9): 637-46. doi: /10.1139/cjm-2015-0281
  • Rückert C, Kriete M, Jaenicke S, Winkler A, Tauch A (2015) Complete Genome Sequence of the Type Strain Corynebacterium testudinoris DSM 44614, Recovered from Necrotic Lesions in the Mouth of a Tortoise. Genome announcements. 3(4). doi: 10.1128/genomeA.00784-15
  • Rückert C, Kriete M, Jaenicke S, Winkler A, Tauch A (2015) Virulence Factor Genes Detected in the Complete Genome Sequence of Corynebacterium uterequi DSM 45634, Isolated from the Uterus of a Maiden Mare. Genome announcements. 3(4). doi: 10.1128/genomeA.00783-15
  • Wibberg D, Tielen P, Narten M, Schobert M, Blom J, Schatschneider S, Meyer AK, Neubauer R, Albersmeier A, Albaum S, Jahn M, Goesmann A, Vorhölter FJ, Pühler A, Jahn D (2015) Genome Sequence of the Urethral Isolate Pseudomonas aeruginosa RN21. Genome announcements. 3(4). doi: 10.1128/genomeA.00788-15
  • Rupp O, Brinkrolf K, Buerth C, Kunigo M, Schneider J, Jaenicke S, Goesmann A, Pühler A, Jaeger KE, Ernst JF (2015) The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms. Journal of biotechnology. 211: 20-30. doi: 10.1016/j.jbiotec.2015.06.423
  • Arnold M, Wibberg D, Blom J, Schatschneider S, Winkler A, Kutter Y, Rückert C, Albersmeier A, Albaum S, Goesmann A, Zange S, Heesemann J, Pühler A, Hogardt M, Vorhölter FJ (2015) Draft Genome Sequence of Pseudomonas aeruginosa Strain WS136, a Highly Cytotoxic ExoS-Positive Wound Isolate Recovered from Pyoderma Gangrenosum. Genome announcements. 3(4). doi: 10.1128/genomeA.00680-15
  • De Maayer P, Chan WY, Martin DA, Blom J, Venter SN, Duffy B, Cowan DA, Smits TH, Coutinho TA (2015) Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis. Frontiers in microbiology. 6: 576. doi: 10.3389/fmicb.2015.00576
  • Smits TH, Pothier JF, Ruinelli M, Blom J, Frasson D, Koechli C, Fabbri C, Brandl H, Duffy B, Sievers M (2015) Complete Genome Sequence of the Cyanogenic Phosphate-Solubilizing Pseudomonas sp. Strain CCOS 191, a Close Relative of Pseudomonas mosselii. Genome announcements. 3(3). doi: 10.1128/genomeA.00616-15
  • Li X, Blom J, Zeng Y (2015) Whole genome sequences of a free-living Pseudomonas sp. strain ML96 isolated from a freshwater Maar Lake. Marine genomics. 24 Pt 3: 219-21. doi: 10.1016/j.margen.2015.05.016
  • Guimarães L, Soares S, Trost E, Blom J, Ramos R, Silva A, Barh D, Azevedo V (2015) Genome informatics and vaccine targets in Corynebacterium urealyticum using two whole genomes, comparative genomics, and reverse vaccinology. BMC genomics. 16 Suppl 5: S7. doi: 10.1186/1471-2164-16-S5-S7
  • Burgsdorf I, Slaby BM, Handley KM, Haber M, Blom J, Marshall CW, Gilbert JA, Hentschel U, Steindler L (2015) Lifestyle evolution in cyanobacterial symbionts of sponges. mBio. 6(3): e00391-15. doi: 10.1128/mBio.00391-15
  • Zischka M, Künne CT, Blom J, Wobser D, Sakιnç T, Schmidt-Hohagen K, Dabrowski PW, Nitsche A, Hübner J, Hain T, Chakraborty T, Linke B, Goesmann A, Voget S, Daniel R, Schomburg D, Hauck R, Hafez HM, Tielen P, Jahn D, Solheim M, Sadowy E, Larsen J, Jensen LB, Ruiz-Garbajosa P, Quiñones Pérez D, Mikalsen T, Bender J, Steglich M, Nübel U, Witte W, Werner G (2015) Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40. BMC genomics. 16: 175. doi: 10.1186/s12864-015-1367-x
  • Kweon O, Kim SJ, Blom J, Kim SK, Kim BS, Baek DH, Park SI, Sutherland JB, Cerniglia CE (2015) Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium. BMC evolutionary biology. 15: 21. doi: 10.1186/s12862-015-0302-8
  • Wibberg D, Rupp O, Jelonek L, Kröber M, Verwaaijen B, Blom J, Winkler A, Goesmann A, Grosch R, Pühler A, Schlüter A (2015) Improved genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 as established by deep mate-pair sequencing on the MiSeq (Illumina) system. Journal of biotechnology. 203: 19-21. doi: 10.1016/j.jbiotec.2015.03.005
  • Morley L, McNally A, Paszkiewicz K, Corander J, Méric G, Sheppard SK, Blom J, Manning G (2015) Gene Loss and Lineage-Specific Restriction-Modification Systems Associated with Niche Differentiation in the Campylobacter jejuni Sequence Type 403 Clonal Complex. Applied and environmental microbiology. 81(11): 3641-7. doi: 10.1128/AEM.00546-15
  • Vorhölter FJ, Tielen P, Wibberg D, Narten M, Schobert M, Tüpker R, Blom J, Schatschneider S, Winkler A, Albersmeier A, Goesmann A, Pühler A, Jahn D (2015) Genome Sequence of the Urethral Catheter Isolate Pseudomonas aeruginosa MH19. Genome announcements. 3(2). doi: 10.1128/genomeA.00115-15
  • Maier LK, Benz J, Fischer S, Alstetter M, Jaschinski K, Hilker R, Becker A, Allers T, Soppa J, Marchfelder A (2015) Deletion of the Sm1 encoding motif in the lsm gene results in distinct changes in the transcriptome and enhanced swarming activity of Haloferax cells. Biochimie. 117: 129-37. doi: 10.1016/j.biochi.2015.02.023
  • Bertelli C, Aeby S, Chassot B, Clulow J, Hilfiker O, Rappo S, Ritzmann S, Schumacher P, Terrettaz C, Benaglio P, Falquet L, Farinelli L, Gharib WH, Goesmann A, Harshman K, Linke B, Miyazaki R, Rivolta C, Robinson-Rechavi M, van der Meer JR, Greub G (2015) Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. Frontiers in microbiology. 6: 101. doi: 10.3389/fmicb.2015.00101
  • Zschüttig A, Auerbach C, Meltke S, Eichhorn C, Brandt M, Blom J, Goesmann A, Jarek M, Scharfe M, Zimmermann K, Wassenaar TM, Gunzer F (2015) Complete Sequence of Probiotic Symbioflor 2 Escherichia coli Strain G3/10 and Draft Sequences of Symbioflor 2 E. coli Strains G1/2, G4/9, G5, G6/7, and G8. Genome announcements. 3(2). doi: 10.1128/genomeA.01330-14
  • Wippermann A, Rupp O, Brinkrolf K, Hoffrogge R, Noll T (2015) The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells. Journal of biotechnology. 199: 38-46. doi: 10.1016/j.jbiotec.2015.02.014
  • Chakarov N, Linke B, Boerner M, Goesmann A, Krüger O, Hoffman JI (2015) Apparent vector-mediated parent-to-offspring transmission in an avian malaria-like parasite. Molecular ecology. 24(6): 1355-63. doi: 10.1111/mec.13115
  • Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A (2015) Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. Biotechnology for biofuels. 8: 14. doi: 10.1186/s13068-014-0193-8
  • Rückert C, Albersmeier A, Busche T, Jaenicke S, Winkler A, Friðjónsson ÓH, Hreggviðsson GÓ, Lambert C, Badcock D, Bernaerts K, Anne J, Economou A, Kalinowski J (2015) Complete genome sequence of Streptomyces lividans TK24. Journal of biotechnology. 199: 21-2. doi: 10.1016/j.jbiotec.2015.02.004
  • Vinardell JM, Acosta-Jurado S, Zehner S, Göttfert M, Becker A, Baena I, Blom J, Crespo-Rivas JC, Goesmann A, Jaenicke S, Krol E, McIntosh M, Margaret I, Pérez-Montaño F, Schneiker-Bekel S, Serranía J, Szczepanowski R, Buendía AM, Lloret J, Bonilla I, Pühler A, Ruiz-Sainz JE, Weidner S (2015) The Sinorhizobium fredii HH103 Genome: A Comparative Analysis With S. fredii Strains Differing in Their Symbiotic Behavior With Soybean. Molecular plant-microbe interactions (MPMI). 28(7): 811-24. doi: 10.1094/MPMI-12-14-0397-FI
  • Huja S, Oren Y, Trost E, Brzuszkiewicz E, Biran D, Blom J, Goesmann A, Gottschalk G, Hacker J, Ron EZ, Dobrindt U (2015) Genomic Avenue to Avian Colisepticemia. mBio. 6(1). doi: 10.1128/mBio.01681-14
  • Maus I, Wibberg D, Stantscheff R, Stolze Y, Blom J, Eikmeyer FG, Fracowiak J, König H, Pühler A, Schlüter A (2015) Insights into the annotated genome sequence of Methanoculleus bourgensis MS2T, related to dominant methanogens in biogas-producing plants. Journal of biotechnology. 201: 43-53. doi: 10.1016/j.jbiotec.2014.11.020
  • Hilker R, Munder A, Klockgether J, Losada PM, Chouvarine P, Cramer N, Davenport CF, Dethlefsen S, Fischer S, Peng H, Schönfelder T, Türk O, Wiehlmann L, Wölbeling F, Gulbins E, Goesmann A, Tümmler B (2015) Interclonal gradient of virulence in the Pseudomonas aeruginosa pangenome from disease and environment. Environmental microbiology. 17(1): 29-46. doi: 10.1111/1462-2920.12606
  • Kamanda Ngugi D, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang G, Hikmawan T, Guan Y, Antunes A, Siam R, El Dorry H, Bajic V, Stingl U (2015) Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. The ISME Journal. 9(2): 396-411. doi: 10.1038/ismej.2014.137
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Descriptions of families / genera as book chapters in Bergey's Manual of Systematics of Archaea and Bacteria (eds M.E. Trujillo, S. Dedysh, P. DeVos, B. Hedlund, P. Kämpfer, F.A. Rainey and W.B. Whitman) with BiGi-participation:


  • Caviibacter
    DOI: 10.1002/9781118960608.gbm01523

  • Leptotrichiaceae
    DOI: 10.1002/9781118960608.fbm00155.pub2

  • Leptotrichia
    DOI: 10.1002/9781118960608.gbm00771.pub2

  • Oceanivirga
    DOI: 10.1002/9781118960608.gbm01524

  • Sebaldella
    DOI: 10.1002/9781118960608.gbm00772.pub2

  • Sneathia
    DOI: 10.1002/9781118960608.gbm00773.pub2

  • Streptobacillus
    DOI: 10.1002/9781118960608.gbm00774.pub2