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Artikelaktionen

Personal Homepage of Dr. Jochen Blom

Contact

Jochen Blom

Heinrich-Buff-Ring 58

Raum: 0003.B

Tel.: +49 (0)641 99 35-803
Tel.: +49 (0)641 99 35-801 (Sekr.)

CV

2013 - present PostDoc at Justus-Liebig-University Gießen, Germany
2013

PhD - Faculty of Technology, Bielefeld University, Bielefeld, Germany

PhD thesis: "Comparative genomics on gene and single nucleotide level" LINK

2010-2013

Scientific assistant in the research program "Application-oriented Research on
Non-Pathogenic Microorganisms for Health, Nutrition and Ressource-Efficient
Industry Production" (BMBF grant 0315599B ”Genomik-Transfer“)

2006-2010 Scientific assistant in the research program "Genome Research on Microorganisms
for Industrial Production, Nutrition, Environment and Health" (BMBF grant 0313805A "Genomik-Plus")
2006

Diploma - Informatics in the Natural Sciences, Faculty of Technology, Bielefeld University, Bielefeld, Germany

Diploma thesis: "CAmpER - Calculation of Amplification Efficiencies for RT-PCR-experiments"

1999

School leaving examination (Abitur), Städtisches Gymnasium Goch

1980 Born in Kleve, Germany

Publications

2020

Lick S, Kröckel L, Wibberg D, Winkler A, Blom J, Goesmann A, Kalinowski J (2020) Pseudomonas bubulae sp. nov., isolated from beef. International journal of systematic and evolutionary microbiology 70(1): 292-301.

Madhaiyan M, Saravanan VS, Blom J, Smits TH, Rezzonico F, Kim S, Weon H, Kwon S, Whitman WB, Ji L (2020) Phytobacter palmae sp. nov., a novel endophytic, N2 fixing, plant growth promoting Gammaproteobacterium isolated from oil palm (Elaeis guineensis Jacq.). International Journal of Systematic and Evolutionary Microbiology 70(2): 841-848.

Kämpfer P, Fuglsang-Damgaard D, Overballe-Petersen S, Hasman H, Hammerum AM, Fuursted K, Blom J, Glaeser SP, Hansen F (2020) 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. International Journal of Systematic and Evolutionary Microbiology 70(2): 1315-1320.

Lick S, Kröckel L, Wibberg D, Winkler A, Blom J, Bantleon A, Goesmann A, Kalinowski J (2020) Pseudomonas carnis sp. nov., isolated from meat. International journal of systematic and evolutionary microbiology 70(3): 1528-1540.

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. Applied Microbiology and Biotechnology 104(6): 2701-2714.

Kumru S, Tekedar HC, Blom J, Lawrence ML, Karsi A (2020) Genomic diversity in flavobacterial pathogens of aquatic origin. Microbial Pathogenesis: 104053.

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. Microbial Genomics 6(2).

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. International Journal of Systematic and Evolutionary Microbiology 70(3): 2084-2088.

Maus I, Klocke M, Derenkó J, Stolze Y, Beckstette M, Jost C, Wibberg D, Blom J, Henke C, Willenbücher K, others (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. Environmental Microbiome 15(1): 1-21.

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. International Journal of Systematic and Evolutionary Microbiology 70(4): 2366-2368.

Eisenberg T, Heydel C, Prenger-Berninghoff E, Fawzy A, Kling U, Akimkin V, Semmler T, Mühldorfer K, Kämpfer P, Blom J, others (2020) Streptobacillus canis sp. nov. isolated from a dog. International Journal of Systematic and Evolutionary Microbiology 70(4): 2648-2656.

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). International Journal of Systematic and Evolutionary Microbiology 70(4): 2732-2739.

Liu A, Zhang Y, Cheng P, Peng Y, Blom J, Xue Q (2020) Whole genome analysis calls for a taxonomic rearrangement of the genus Colwellia. Antonie van Leeuwenhoek: 1-13.

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). International Journal of Systematic and Evolutionary Microbiology 70(5): 3037-3048.

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. International Journal of Systematic and Evolutionary Microbiology 70(4): 2937-2948.

Huang C, Chen C, Liou J, Lee A, Blom J, Lin Y, Huang L, Watanabe K (2020) Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae. International Journal of Systematic and Evolutionary Microbiology: ijsem003969.

Rothen J, Sapugahawatte DN, Li C, Lo N, Vogel G, Foucault F, Pflüger V, Pothier JF, Blom J, Daubenberger C, others (2020) A simple, rapid typing method for Streptococcus agalactiae based on ribosomal subunit proteins by MALDI-TOF MS. Scientific Reports 10(1): 1-8.

Berger C, Rückert C, Blom J, Rabaey K, Kalinowski J, Rosenbaum MA (2020) Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics..

Tekedar HC, Arick T, Hsu C, 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). Frontiers in Cellular and Infection Microbiology: 348.

Filippidou S, Fatton M, Junier T, Bergé M, Poppleton D, Blum TB, Kaminek M, Odriozola A, Blom J, Johnson SL, others (2020) Cryptosporulation in Kurthia spp. forces a rethinking of asporogenesis in Firmicutes. BioRxiv.

2019

Biessy A, Novinscak A, Blom J, Léger G, Thomashow LS, Cazorla FM, Josic D, Filion M (2019) Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp. Environmental microbiology 21(1): 437-455.

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. Frontiers in Microbiology: 3216.

Rutz D, Frasson D, Sievers M, Blom J, Rezzonico F, Pothier JF, Smits TH (2019) High-quality draft genome sequence of Pseudomonas reidholzensis strain CCOS 865T. Microbiology Resource Announcements 8(3).

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.

Amiri Moghaddam J, Dávila-Céspedes A, Alanjary M, Blom J, König GM, Schäberle TF (2019) Genome analysis of the marine bacterium Labrenzia sp. strain 011, a potential protective agent of mollusks. Data 4(1): 33.

Rothen J, Pothier JF, Foucault F, Blom J, Nanayakkara D, Li C, Ip M, Tanner M, Vogel G, Pflüger V, others (2019) Subspecies typing of Streptococcus agalactiae based on ribosomal subunit protein mass variation by MALDI-TOF MS. Frontiers in microbiology: 471.

Ruinelli M, Blom J, Smits TH, Pothier JF (2019) Comparative genomics and pathogenicity potential of members of the Pseudomonas syringae species complex on Prunus spp. BMC genomics 20(1): 172.

Smits TH, Duffy B, Blom J, Ishimaru CA, Stockwell VO (2019) Pantocin A, a peptide-derived antibiotic involved in biological control by plant-associated Pantoea species. Archives of microbiology 201(6): 713-722.

Liou J, Huang C, Wang C, Lee A, 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. International journal of systematic and evolutionary microbiology 69(5): 1484-1489.

Avontuur JR, Palmer M, Beukes CW, Chan WY, Coetzee MP, Blom J, Stępkowski T, Kyrpides NC, Woyke T, Shapiro N, others (2019) Genome-informed Bradyrhizobium taxonomy: where to from here? Systematic and applied microbiology 42(4): 427-439.

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. Frontiers in microbiology: 839.

Ramdhan ND, Blom J, Sutcliffe I, 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 and new infections: 100544.

Palmer M, Venter SN, McTaggart AR, Coetzee MP, Van Wyk S, Avontuur JR, Beukes CW, Fourie G, Santana QC, Van Der Nest MA, others (2019) The synergistic effect of concatenation in phylogenomics: the case in Pantoea. PeerJ: e6698.

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. Microbiology Resource Announcements 8(17).

López J, Lozano M, Lagares A, Fabre M, Draghi W, Del Papa M, Pistorio M, Becker A, Wibberg D, Schlüter A, others (2019) Codon usage heterogeneity in the multipartite prokaryote genome: Selection-based coding bias associated with gene location, expression level, and ancestry. Mbio 10(3).

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.

Wu H, Gu Q, Xie Y, Lou Z, Xue P, Fang L, Yu C, Jia D, Huang G, Zhu B, others (2019) Cold-adapted Bacilli isolated from the Qinghai-Tibetan Plateau are able to promote plant growth in extreme environments. Environmental microbiology 21(9): 3505-3526.

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. Frontiers in microbiology: 1619.

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. Archives of microbiology 201(9): 1317-1321.

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. Environmental microbiology 21(11): 4002-4019.

Nguyen TV, Wibberg D, Vigil-Stenman T, Berckx F, Battenberg K, Demchenko KN, Blom J, Fernandez MP, Yamanaka T, Berry AM, others (2019) Frankia-enriched metagenomes from the earliest diverging symbiotic Frankia cluster: They come in teams. Genome biology and evolution 11(8): 2273-2291.

Blom J, Glaeser SP, Juhre T, Kreis J, Hanel PH, Schrader JG, Kämpfer P, Goesmann A (2019) EDGAR: a versatile tool for phylogenomics. Bergey's Manual of Systematics of Archaea and Bacteria: 1-15.

Huang C, Wang C, Liou J, Lee A, Blom J, Huang L, Watanabe K (2019) Reclassification of Micrococcus aloeverae and Micrococcus yunnanensis as later heterotypic synonyms of Micrococcus luteus. International Journal of Systematic and Evolutionary Microbiology 69(11): 3512-3518.

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.

Suarez C, Ratering S, Hain T, Fritzenwanker M, Goesmann A, Blom J, Chakraborty T, Bunk B, Spröer C, Overmann J, others (2019) Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19T. International journal of genomics.

Smits TH, 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. Microbiology Resource Announcements 8(39): e01002-19.

Rutz D, Frasson D, Sievers M, Blom J, Rezzonico F, Pothier JF, Smits TH (2019) Comparative genomic analysis of the biotechnological potential of the novel species Pseudomonas wadenswilerensis CCOS 864T and Pseudomonas reidholzensis CCOS 865T. Diversity 11(11): 204.

Wibberg D, Batut B, Belmann P, Blom J, Glöckner FO, Grüning B, Hoffmann N, Kleinbölting N, Rahn R, Rey M, others (2019) The de. NBI/ELIXIR-DE training platform-Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research 8(1877): 1877.

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. Frontiers in microbiology: 2916.

Blifernez-Klassen O, Klassen V, Wibberg D, Cebeci E, Henke C, Rueckert C, Chaudhari S, Rupp O, Blom J, Winkler A, others (2019) Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems: Biocoenosis of Botryococcus consortia. bioRxiv: 476887.

2018

Landwehr W, Kämpfer P, Glaeser SP, Rückert C, Kalinowski J, Blom J, Goesmann A, Mack M, Schumann P, Atasayar E, others (2018) Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov. International journal of systematic and evolutionary microbiology 68(1): 382-393.

Ludueña LM, Anzuay MS, Angelini JG, McIntosh M, Becker A, Rupp O, Goesmann A, Blom J, Fabra A, Taurian T (2018) Strain Serratia sp. S119: A potential biofertilizer for peanut and maize and a model bacterium to study phosphate solubilization mechanisms. Applied Soil Ecology: 107-112.

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. Frontiers in microbiology: 1244.

Verwaaijen B, Wibberg D, Nelkner J, Gordin M, Rupp O, Winkler A, Bremges A, Blom J, Grosch R, Pühler A, others (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. Journal of biotechnology: 12-18.

Maus I, Rumming M, Bergmann I, Heeg K, Pohl M, Nettmann E, Jaenicke S, Blom J, Pühler A, Schlüter A, others (2018) Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. Biotechnology for biofuels 11(1): 167.

Eisenberg T, Glaeser SP, Blom J, Kämpfer P (2018) Leptotrichiaceae. Bergey's Manual of Systematics of Archaea and Bacteria: 1-9.

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 announcements 6(7).

Douriet-Gámez NR, Maldonado-Mendoza IE, Ibarra-Laclette E, Blom J, Calderón-Vázquez CL (2018) Genomic analysis of Bacillus sp. strain B25, a biocontrol agent of maize pathogen Fusarium verticillioides. Current microbiology 75(3): 247-255.

Pillonetto M, Arend LN, Faoro H, D’Espindula HR, Blom J, Smits TH, Mira MT, Rezzonico F (2018) Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov. International journal of systematic and evolutionary microbiology 68(1): 176-184.

Riesco R, Carro L, Román-Ponce B, Prieto C, Blom J, Klenk H, Normand P, Trujillo ME (2018) Defining the species Micromonospora saelicesensis and Micromonospora noduli under the framework of genomics. Frontiers in microbiology: 1360.

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..

Bartz J, Blom J, Busse H, Mvie JB, Hardt M, Schubert P, Wilke T, Goessmann A, Wilharm G, Bender J, others (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. Systematic and applied microbiology 41(2): 73-84.

Palmer M, Steenkamp ET, Coetzee M, Blom J, Venter SN (2018) Genome-based characterization of biological processes that differentiate closely related bacteria. Frontiers in Microbiology: 113.

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 microbiology ecology 94(6): fiy074.

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. International journal of systematic and evolutionary microbiology 68(8): 2462-2467.

Kämpfer P, Rückert C, Blom J, Goesmann A, Wink J, Kalinowski J, Glaeser SP (2018) Streptomyces ciscaucasicus Sveshnikova et al. 1983 is a later subjective synonym of Streptomyces canus Heinemann et al. 1953. International journal of systematic and evolutionary microbiology 68(1): 42-46.

Eisenberg T, Glaeser SP, Blom J, Kämpfer P (2018) Sebaldella. Bergey's Manual of Systematics of Archaea and Bacteria: 1-4.

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: e4560.

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: 529-530.

Eisenberg L, Johnson S, Grodowitz MJ (2018) The reproductive morphology and physiological age grading of the female salvinia weevil, Cyrtobagous salviniae Calder and Sands. International journal of insect science: 1179543317751909.

Eisenberg T, Glaeser SP, Blom J, Rau J, Kämpfer P (2018) Streptobacillus. Bergey's Manual of Systematics of Archaea and Bacteria: 1-13.

Sangal V, Goodfellow M, Blom J, Tan GYA, Klenk H, Sutcliffe IC (2018) Revisiting the taxonomic status of the biomedically and industrially important genus Amycolatopsis, using a phylogenomic approach. Frontiers in microbiology: 2281.

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 microbiology ecology 94(12): fiy182.

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. Microbiology Resource Announcements 7(15).

Rutz D, Frasson D, Sievers M, Blom J, Rezzonico F, Pothier JF, Smits TH (2018) High-quality draft genome sequence of Pseudomonas wadenswilerensis CCOS 864T. Microbiology Resource Announcements 7(16).

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. Microbiology Resource Announcements 7(16).

Moghaddam JA, 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. Scientific reports 8(1): 1-14.

Blifernez-Klassen O, Klassen V, Wibberg D, Chaudhari S, Henke C, Winkler A, Al-Dilaimi A, Rupp O, Blom J, Goesmann A, others (2018) The ‘zoo’accompanying Botryococcus braunii: Unraveling the fundamentals of algae-bacteria biocoenosis. bioRxiv: 476887.

Eisenberg T, Glaeser SP, Blom J, Kämpfer P (2018) Leptotrichia. Bergey's Manual of Systematics of Archaea and Bacteria: 1-10.

Eisenberg T, Glaeser SP, Blom J, Kämpfer P (2018) Caviibacter. Bergey's Manual of Systematics of Archaea and Bacteria: 1-7.

Eisenberg T, Glaeser SP, Blom J, Kämpfer P (2018) Oceanivirga. Bergey's Manual of Systematics of Archaea and Bacteria: 1-7.

Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR, van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, others (2018) Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato (vol 8, 1154, 2017). FRONTIERS IN MICROBIOLOGY.

Palazzo AF, Celis JS, Edgell DR, Stelbrink B, Wibberg D, Hauffe T, Blom J, Kalinowski J, Wilke T (2018) Evolutionary and Biogeographical Implications of Degraded LAGLIDADG Endonuclease Functionality and Group I Intron Occurrence in Stony Corals (Scleractinia) and Mushroom Corals (Corallimorpharia)..

2017

Ngugi DK, Miyake S, Cahill M, Vinu M, Hackmann TJ, Blom J, Tietbohl MD, Berumen ML, Stingl U (2017) Genomic diversification of giant enteric symbionts reflects host dietary lifestyles. Proceedings of the National Academy of Sciences 114(36): E7592-E7601.

Palmer M, Steenkamp ET, Coetzee MP, Chan W, Van Zyl E, De Maayer P, Coutinho TA, Blom J, Smits TH, Duffy B, others (2017) Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella. Antonie Van Leeuwenhoek 110(10): 1287-1309.

Duar RM, Frese SA, Lin XB, Fernando SC, Burkey TE, Tasseva G, Peterson DA, Blom J, Wenzel CQ, Szymanski CM, others (2017) Experimental evaluation of host adaptation of Lactobacillus reuteri to different vertebrate species. Applied and environmental microbiology 83(12).

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.

Lopes R, Cerdeira L, Tavares GS, Ruiz JC, Blom J, Horácio EC, Mantovani HC, de Queiroz MV (2017) Genome analysis reveals insights of the endophytic Bacillus toyonensis BAC3151 as a potentially novel agent for biocontrol of plant pathogens. World Journal of Microbiology and Biotechnology 33(10): 185.

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.

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: 178-186.

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.

Eisenberg T, Riße K, Schauerte N, Geiger C, Blom J, Scholz HC (2017) Isolation of a novel ‘atypical’Brucella strain from a bluespotted ribbontail ray (Taeniura lymma). Antonie Van Leeuwenhoek 110(2): 221-234.

Wöchtl B, Gunzer F, Gerner W, Gasse H, Koch M, Bagó Z, Ganter M, Weissenböck H, Dinhopl N, Coldewey SM, others (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(1): 30.

Kämpfer P, Rückert C, Blom J, Goesmann A, Wink J, Kalinowski J, Glaeser SP (2017) Streptomyces phaeopurpureus Shinobu 1957 (Approved Lists 1980) and Streptomyces griseorubiginosus (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958 (Approved Lists 1980) are heterotypic subjective synonyms. International journal of systematic and evolutionary microbiology 67(8): 3111-3116.

Chen S, Blom J, Walker ED (2017) Genomic, physiologic, and symbiotic characterization of Serratia marcescens strains isolated from the mosquito Anopheles stephensi. Frontiers in microbiology: 1483.

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(7): 1065-1068.

Makarewicz O, Lucas M, Brandt C, Herrmann L, Albersmeier A, Rückert C, Blom J, Goesmann A, van der Linden M, Kalinowski J, others (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.

De Maayer P, Aliyu H, Vikram S, Blom J, Duffy B, Cowan DA, Smits TH, Venter SN, Coutinho TA (2017) Phylogenomic, pan-genomic, pathogenomic and evolutionary genomic insights into the agronomically relevant enterobacteria Pantoea ananatis and Pantoea stewartii. Frontiers in Microbiology: 1755.

Gétaz M, van der Wolf JM, Blom J, Pothier JF (2017) Complete genome sequences of three isolates of Xanthomonas fragariae, the bacterium responsible for angular leaf spots on strawberry plants. Genome announcements 5(32).

Glaeser SP, Alabid I, Guo H, Kumar N, Imani J, Kämpfer P, Hardt M, Busche T, Kalinowski J, Blom J, others (2017) Detection and Characterization of Endobacteria in the Fungal Endophyte Piriformospora indica.: 237-250.

Stadermann KB, Blom J, Borgmeier C, Sciberras N, Herbold S, Kipker M, Meurer G, Molck S, Petri D, Pelzer S, others (2017) First complete genome sequence of Bacillus glycinifermentans B-27. Journal of biotechnology: 187-191.

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(1): 18.

Chen S, Blom J, Loch TP, Faisal M, Walker ED (2017) The emerging fish pathogen Flavobacterium spartansii isolated from chinook salmon: comparative genome analysis and molecular manipulation. Frontiers in microbiology: 2339.

Fan B, Blom J, Klenk H, 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: 22.

Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter F (2017) Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology 163(8): 1117-1144.

Hersemann L, Wibberg D, Blom J, Goesmann A, Widmer F, Vorhölter F, Kölliker R (2017) Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis. BMC genomics 18(1): 1-18.

Jeong D, Heo S, Ryu S, Blom J, Lee J (2017) Genomic insights into the virulence and salt tolerance of Staphylococcus equorum. Scientific reports 7(1): 1-11.

Yu J, Blom J, Sczyrba A, Goesmann A (2017) Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism. Journal of biotechnology: 58-60.

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.

Yu J, Blom J, Glaeser S, 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. Journal of Biotechnology: 2-9.

Grosse-Kock S, Kolodkina V, Schwalbe EC, Blom J, Burkovski A, Hoskisson PA, Brisse S, Smith D, Sutcliffe IC, Titov L, others (2017) Genomic analysis of endemic clones of toxigenic and non-toxigenic Corynebacterium diphtheriae in Belarus during and after the major epidemic in 1990s. BMC genomics 18(1): 873.

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).

Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR, van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, others (2017) Genome data provides high support for generic boundaries in Burkholderia sensu lato. Frontiers in microbiology: 1154.

Ampattu BJ, Hagmann L, Liang C, Dittrich M, Schlüter A, Blom J, Krol E, Goesmann A, Becker A, Dandekar T, others (2017) Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence. BMC genomics 18(1): 282.

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: 219.

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).

Heberling MM, Postema CP, Meijer TJ, Otzen M, Wibberg D, Blom J, Schlüter A, Janssen DB (2017) Genome mining..

Taponen SS, Åvall-Jääskeläinen ST, Kant R, Paulin LG, Blom J, Palva AM, Koort JMK (2017) Virulence genes of bovine mastitis-associated Staphylococcus isolates..

Petkauskaite R, Blom J, Goesmann A, Kuisiene N (2017) Portal de Pesquisa da BVS Veterinária. Braz. J. Microbiol 48(1): 7-8.

2016

Jimenez-Infante F, Ngugi DK, Vinu M, Alam I, Kamau AA, Blom J, Bajic VB, Stingl U (2016) 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): 1215-1226.

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.

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.

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.

Van Nguyen T, Wibberg D, Battenberg K, Blom J, Heuvel BV, 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.

Dickey AM, Loy JD, Bono JL, Smith TP, Apley MD, Lubbers BV, DeDonder KD, Capik SF, Larson RL, White BJ, others (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(1): 1-11.

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): 1383-1399.

Scholz HC, Revilla-Fernández S, Al Dahouk S, Hammerl JA, Zygmunt MS, Cloeckaert A, Koylass M, Whatmore AM, Blom J, Vergnaud G, others (2016) Brucella vulpis sp. nov., isolated from mandibular lymph nodes of red foxes (Vulpes vulpes). International journal of systematic and evolutionary microbiology 66(5): 2090-2098.

Sun Y, Wang Z, Zhang S, Li X, Gao H, Zhang C, Abdel-Shafy H, Mansour M, Kuppusamy S, Thavamani P, others (2016) Purification and properties of NADH-ferredoxinNAP reductase, a component of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816. Biotechnology 16(4-6): 107-123.

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.

Ghatak S, Blom J, Das S, Sanjukta R, Puro K, Mawlong M, Shakuntala I, Sen A, Goesmann A, Kumar A, others (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): 945-956.

Gonzalez-Perez M, Murcia M, Parra-Lopez C, Blom J, Tauch A (2016) Deciphering the virulence factors of the opportunistic pathogen Mycobacterium colombiense. New microbes and new infections: 98-105.

Papadimitriou K, Baharidis PK, Georgoulis A, Engel M, Louka M, Karamolegkou G, Tsoka A, Blom J, Pot B, Malecki P, others (2016) Analysis of the complete genome sequence of the archaeon Pyrococcus chitonophagus DSM 10152 (formerly Thermococcus chitonophagus). Extremophiles 20(3): 351-361.

Maus I, Cibis KG, Bremges A, Stolze Y, Wibberg D, Tomazetto G, Blom J, Sczyrba A, König H, Pühler A, others (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: 50-60.

Hofer E, Hammerl JA, Zygmunt MS, Cloeckaert A, Koylass M, Whatmore AM, Blom J, Revilla-Fernández S, Witte A, Scholz HC, others (2016) Brucella vulpis sp. nov., a novel Brucella species isolated from mandibular lymph nodes of red foxes (Vulpes vulpes) in Austria. International Journal of Systematic and Evolutionary Microbiology.

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 research 44(W1): W22-W28.

Azarbaijani R, Yeganeh LP, Blom J, Younesi H, Fazeli SAS, Tabatabaei M, Salekdeh GH (2016) Comparative genome analysis of Oceanimonas sp. GK1, a halotolerant bacterium with considerable xenobiotics degradation potentials. Annals of Microbiology 66(2): 703-716.

Fernández-Natal I, Sáez-Nieto J, Rodrı́guez-Lázaro D, Valdezate-Ramos S, Parras-Padilla T, Medina M, Rodr\ǵuez-Pollán R, Blom J, Tauch A, Soriano F (2016) Phenotypic, molecular characterization, antimicrobial susceptibility and draft genome sequence of Corynebacterium argentoratense strains isolated from clinical samples. New Microbes and New Infections: 116-121.

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).

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.

Glaeser SP, Imani J, Alabid I, Guo H, Kumar N, Kämpfer P, Hardt M, Blom J, Goesmann A, Rothballer M, others (2016) Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. The ISME journal 10(4): 871-884.

Wibberg D, Andersson L, Tzelepis G, Rupp O, Blom J, Jelonek L, Pühler A, Fogelqvist J, Varrelmann M, Schlüter A, others (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(1): 245.

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(1): 1-12.

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).

Rezzonico F, Smits TH, Born Y, Blom J, Frey JE, Goesmann A, Cleenwerck I, De Vos P, Bonaterra A, Duffy B, others (2016) Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees. International Journal of Systematic and Evolutionary Microbiology 66(3): 1583-1592.

Flury P, Aellen N, Ruffner B, Péchy-Tarr M, Fataar S, Metla Z, Dominguez-Ferreras A, Bloemberg G, Frey J, Goesmann A, others (2016) Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. The ISME journal 10(10): 2527-2542.

Jaenicke S, Bunk B, Wibberg D, Spröer C, Hersemann L, Blom J, Winkler A, Schatschneider S, Albaum SP, Kölliker R, others (2016) Complete genome sequence of the barley pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T). Genome announcements 4(6).

2015

Zischka M, Kuenne CT, Blom J, Wobser D, Sak$ıota$nç T, Schmidt-Hohagen K, Dabrowski PW, Nitsche A, Hübner J, Hain T, others (2015) Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40. BMC genomics 16(1): 175.

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): 637-646.

Ngugi DK, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang G, Hikmawan T, Guan Y, Antunes A, Siam R, others (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.

De Maayer P, Chan W, 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: 576.

Maus I, Wibberg D, Stantscheff R, Stolze Y, Blom J, Eikmeyer F, 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: 43-53.

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).

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. 2(2): ofv053.

Wibberg D, Rupp O, Jelonek L, Kröber M, Verwaaijen B, Blom J, Winkler A, Goesmann A, Grosch R, Pühler A, others (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: 19-21.

Wibberg D, Rupp O, Blom J, Jelonek L, Kröber M, Verwaaijen B, Goesmann A, Albaum S, Grosch R, Pühler A, others (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.

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: 219-221.

Arnold M, Wibberg D, Blom J, Schatschneider S, Winkler A, Kutter Y, Rückert C, Albersmeier A, Albaum S, Goesmann A, others (2015) Draft genome sequence of Pseudomonas aeruginosa strain WS136, a highly cytotoxic ExoS-positive wound isolate recovered from pyoderma gangrenosum. Genome announcements 3(4).

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).

Guimarães LC, de Castro Soares S, Trost E, Blom J, Ramos RTJ, 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(S5): S7.

Kweon O, Kim S, Blom J, Kim S, Kim B, Baek D, 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(1): 21.

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): 3641-3647.

Vorhölter F, Tielen P, Wibberg D, Narten M, Schobert M, Tüpker R, Blom J, Schatschneider S, Winkler A, Albersmeier A, others (2015) Genome sequence of the urethral catheter isolate Pseudomonas aeruginosa MH19. Genome Announcements 3(2).

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(1): 765.

Huja S, Oren Y, Trost E, Brzuszkiewicz E, Biran D, Blom J, Goesmann A, Gottschalk G, Hacker J, Ron EZ, others (2015) Genomic avenue to avian colisepticemia. MBio 6(1).

Zschüttig A, Auerbach C, Meltke S, Eichhorn C, Brandt M, Blom J, Goesmann A, Jarek M, Scharfe M, Zimmermann K, others (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).

Wibberg D, Tielen P, Narten M, Schobert M, Blom J, Schatschneider S, Meyer A, Neubauer R, Albersmeier A, Albaum S, others (2015) Genome sequence of the urethral isolate Pseudomonas aeruginosa RN21. Genome announcements 3(4).

Humphreys CM, McLean S, Schatschneider S, Millat T, Henstra AM, Annan FJ, Breitkopf R, Pander B, Piatek P, Rowe P, others (2015) Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. BMC genomics 16(1): 1085.

Smits TH, Rezzonico F, Blom J, Goesmann A, Abelli A, Morelli RK, Vanneste JL, Duffy B (2015) Draft genome sequence of the commercial biocontrol strain Pantoea agglomerans P10c. Genome announcements 3(6).

2014

Ismail E, Blom J, Bultreys A, Ivanović M, Obradovi\ ́A, van Doorn J, Bergsma-Vlami M, Maes M, Willems A, Duffy B, others (2014) A novel plasmid pEA68 of Erwinia amylovora and the description of a new family of plasmids. Archives of microbiology 196(12): 891-899.

Sangal V, Burkovski A, Hunt AC, Edwards B, Blom J, Hoskisson PA (2014) A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing. Infection, Genetics and Evolution: 54-57.

Smits TH, Guerrero-Prieto VM, Hernández-Escarcega G, Blom J, Goesmann A, Rezzonico F, Duffy B, Stockwell VO (2014) Whole-genome sequencing of Erwinia amylovora strains from Mexico detects SNPs in rpsL conferring streptomycin resistance and in the avrRpt2 effector altering host interactions. Genome Announcements 2(1).

Anastasiou R, Mavrogonatou E, Blom J, Papandreou NC, Hamodrakas SJ, Ferreira S, Renault P, Supply P, Pot B, Tsakalidou E (2014) Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex. BMC Genomics (15),.(2014).

Tielen P, Wibberg D, Blom J, Rosin N, Meyer A, Bunk B, Schobert M, Tüpker R, Schatschneider S, Rückert C, others (2014) Genome sequence of the small-colony variant Pseudomonas aeruginosa MH27, isolated from a chronic urethral catheter infection. Genome announcements 2(1).

Vorhölter F, Arnold M, Wibberg D, Blom J, Winkler A, Viehoever P, Albersmeier A, Goesmann A, Zange S, Heesemann J, others (2014) Draft genome sequence of Pseudomonas aeruginosa strain WS394, a multidrug-resistant and highly cytotoxic wound isolate from chronic ulcus cruris. Genome announcements 2(6).

Guan Y, Ngugi DK, Blom J, Ali S, Ferry JG, Stingl U (2014) Draft genome sequence of an obligately methylotrophic methanogen, Methanococcoides methylutens, isolated from marine sediment. Genome announcements 2(6).

Wibberg D, Tielen P, Blom J, Rosin N, Schobert M, Tüpker R, Schatschneider S, Spilker D, Albersmeier A, Goesmann A, others (2014) Genome sequence of the acute urethral catheter isolate Pseudomonas aeruginosa MH38. Genome announcements 2(2).

Liu Y, Chen X, Blom J, Yi Z, Wen J, Zeng R (2014) Draft genome of formaldehyde-degrading strain, Pseudomonas monteilii IOFA19. Marine genomics: 1-2.

2013

Smits TH, Rezzonico F, López MM, Blom J, Goesmann A, Frey JE, Duffy B (2013) Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics. Systematic and applied microbiology 36(7): 449-456.

Ruijter JM, Pfaffl MW, Zhao S, Spiess AN, Boggy G, Blom J, Rutledge RG, Sisti D, Lievens A, De Preter K, others (2013) Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications. Methods 59(1): 32-46.

Wichmann F, Vorhölter F, Hersemann L, Widmer F, Blom J, Niehaus K, Reinhard S, Conradin C, Kölliker R (2013) The noncanonical type III secretion system of X anthomonas translucens pv. graminis is essential for forage grass infection. Molecular plant pathology 14(6): 576-588.

Soares SC, Silva A, Trost E, Blom J, Ramos R, Carneiro A, Ali A, Santos AR, Pinto AC, Diniz C, others (2013) The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains. PLoS One 8(1): e53818.

Barbé S, Llop P, Blom J, Cabrefiga J, Goesmann A, Duffy B, Montesinos E, Smits TH, López MM (2013) Complete sequence of E rwinia piriflorinigrans plasmids p EPIR 37 and p EPIR 5 and role of p EPIR 37 in pathogen virulence. Plant pathology 62(4): 786-798.

Pereira U, Soares S, Blom J, Leal C, Ramos R, Guimarães L, Oliveira L, Almeida S, Hassan S, Santos A, others (2013) In silico prediction of conserved vaccine targets in Streptococcus agalactiae strains isolated from fish, cattle, and human samples. Genet Mol Res 12(3): 2902-2912.

Dam B, Dam S, Blom J, Liesack W (2013) Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2. PloS one 8(10): e74767.

Mann RA, Smits TH, Bühlmann A, Blom J, Goesmann A, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, others (2013) Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core. PloS one 8(2): e55644.

Wu H, Qiao J, Blom J, Rueckert C, Reva O, Gao X, Borriss R (2013) The rhizobacterium Bacillus amyloliquefaciens subsp. plantarum NAU-B3 contains a large inversion within the central portion of the genome. Genome announcements 1(6).

Vassen V, Eichhorn C, Goesmann A, Blom J, Strauch E, Gunzer F (2013) Characterization and curing of plasmid pVN0028 from the Vibrio parahaemolyticus patient isolate VN-0028.: 110-110.

Guimarães LC, Soares SC, Albersmeier A, Blom J, Jaenicke S, Azevedo V, Soriano F, Tauch A, Trost E (2013) Complete genome sequence of Corynebacterium urealyticum strain DSM 7111, isolated from a 9-year-old patient with alkaline-encrusted cystitis. Genome announcements 1(3).

Koeck DE, Wibberg D, Koellmeier T, Blom J, Jaenicke S, Winkler A, Albersmeier A, Zverlov VV, Pühler A, Schwarz WH, others (2013) Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation. Journal of biotechnology 168(1): 62-63.

Eichhorn C, Claudia Z, Auerbach C, Goesmann A, Blom J, Alter T, Huehn S, Strauch E, Gunzer F (2013) Genome sequencing, annotation and gap closure of four V. parahaemolyticus strains isolated in Germany.: 112-112.

He P, Hao K, Blom J, Rückert C, Vater J, Mao Z, Wu Y, Hou M, He P, He Y, others (2013) Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp. plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites. Journal of biotechnology 164(2): 281-291.

Blom J (2013) Comparative genomics on gene and single nucleotide level..

Niu B, Vater J, Rueckert C, Blom J, Lehmann M, Ru J, Chen X, Wang Q, Borriss R (2013) Polymyxin P is the active principle in suppressing phytopathogenic Erwinia spp. by the biocontrol rhizobacterium Paenibacillus polymyxa M-1. BMC microbiology 13(1): 137.

Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rüsch-Gerdes S, others (2013) Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study. PLoS Med 10(2): e1001387.

Wibberg D, Blom J, Rückert C, Winkler A, Albersmeier A, Pühler A, Schlüter A, Scharf BE (2013) Draft genome sequence of Sinorhizobium meliloti RU11/001, a model organism for flagellum structure, motility and chemotaxis. Journal of biotechnology 168(4): 731-733.

Luque-Almagro VM, Acera F, Igeño MI, Wibberg D, Roldán MD, Sáez LP, Hennig M, Quesada A, Huertas MJ, Blom J, others (2013) Draft whole genome sequence of the cyanide-degrading bacterium P seudomonas pseudoalcaligenes CECT 5344. Environmental microbiology 15(1): 253-270.

2012

Blom J, Rueckert C, Niu B, Wang Q, Borriss R (2012) The complete genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 contains a gene cluster for nonribosomal synthesis of iturin A..

Jankowitsch F, Schwarz J, Rückert C, Gust B, Szczepanowski R, Blom J, Pelzer S, Kalinowski J, Mack M (2012) Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. Journal of bacteriology 194(24): 6818-6827.

Strobel T, Al-Dilaimi A, Blom J, Gessner A, Kalinowski J, Luzhetska M, Pühler A, Szczepanowski R, Bechthold A, Rückert C (2012) Complete genome sequence of Saccharothrix espanaensis DSM 44229 T and comparison to the other completely sequenced Pseudonocardiaceae. BMC genomics 13(1): 1-13.

Hao K, He P, Blom J, Rueckert C, Mao Z, Wu Y, He Y, Borriss R (2012) The genome of plant growth-promoting Bacillus amyloliquefaciens subsp. plantarum strain YAU B9601-Y2 contains a gene cluster for mersacidin synthesis..

Zischka M, Kuenne C, Blom J, Dabrowski PW, Linke B, Hain T, Nitsche A, Goesmann A, Larsen J, Jensen LB, others (2012) Complete genome sequence of the porcine isolate Enterococcus faecalis D32..

Schneider J, Andrea H, Blom J, Jaenicke S, Rückert C, Schorsch C, Szczepanowski R, Farwick M, Goesmann A, Pühler A, others (2012) Draft genome sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10..

Maus I, Wibberg D, Stantscheff R, Eikmeyer F, Seffner A, Boelter J, Szczepanowski R, Blom J, Jaenicke S, König H, others (2012) Complete genome sequence of the hydrogenotrophic, methanogenic archaeon Methanoculleus bourgensis strain MS2T, isolated from a sewage sludge digester..

Trost E, Blom J, de Castro Soares S, Huang I, Al-Dilaimi A, Schröder J, Jaenicke S, Dorella FA, Rocha FS, Miyoshi A, others (2012) Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia. Journal of bacteriology 194(12): 3199-3215.

Brankatschk K, Blom J, Goesmann A, Smits T, Duffy B (2012) Comparative genomic analysis of Salmonella enterica subsp. enterica serovar Weltevreden foodborne strains with other serovars. International journal of food microbiology 155(3): 247-256.

Schröder J, Maus I, Meyer K, Wördemann S, Blom J, Jaenicke S, Schneider J, Trost E, Tauch A (2012) Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient. BMC genomics 13(1): 141.

Mann RA, Blom J, Bühlmann A, Plummer KM, Beer SV, Luck JE, Goesmann A, Frey JE, Rodoni BC, Duffy B, others (2012) Comparative analysis of the Hrp pathogenicity island of Rubus-and Spiraeoideae-infecting Erwinia amylovora strains identifies the IT region as a remnant of an integrative conjugative element. Gene 504(1): 6-12.

Schork S, Schlüter A, Blom J, Schneiker-Bekel S, Pühler A, Goesmann A, Frosch M, Schoen C (2012) Genome sequence of a Neisseria meningitidis capsule null locus strain from the clonal complex of sequence type 198..

Filippini M, Qi W, Blom J, Goesmann A, Smits TH, Bagheri HC (2012) Genome sequence of Fibrella aestuarina BUZ 2T, a filamentous marine bacterium..

Zschüttig A, Zimmermann K, Blom J, Goesmann A, Pöhlmann C, Gunzer F (2012) Identification and characterization of microcin S, a new antibacterial peptide produced by probiotic Escherichia coli G3/10. PloS one 7(3): e33351.

Heinl S, Wibberg D, Eikmeyer F, Szczepanowski R, Blom J, Linke B, Goesmann A, Grabherr R, Schwab H, Pühler A, others (2012) Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage. Journal of Biotechnology 161(2): 153-166.

De Maayer P, Chan WY, Rezzonico F, Bühlmann A, Venter SN, Blom J, Goesmann A, Frey JE, Smits TH, Duffy B, others (2012) Complete genome sequence of clinical isolate Pantoea ananatis LMG 5342..

Parreira VR, Costa M, Eikmeyer F, Blom J, Prescott JF (2012) Sequence of two plasmids from Clostridium perfringens chicken necrotic enteritis isolates and comparison with C. perfringens conjugative plasmids. PLoS One 7(11): e49753.

De Maayer P, Chan W, Blom J, Venter SN, Duffy B, Smits TH, Coutinho TA (2012) The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification. BMC genomics 13(1): 625.

2011

Zschuettig A, Eichhorn C, Meltke S, Zimmermann K, Wassenaar T, Blom J, Goesmann A, Jarek M, Scharfe M, Gunzer F (2011) Genome analysis of probiotic Symbioflor 2 Escherichia coli DSM17252.: 103-103.

Brankatschk K, Blom J, Goesmann A, Smits TH, Duffy B (2011) Genome of a European fresh-vegetable food safety outbreak strain of Salmonella enterica subsp. enterica serovar Weltevreden..

Smits TH, Rezzonico F, Kamber T, Blom J, Goesmann A, Ishimaru CA, Frey JE, Stockwell VO, Duffy B (2011) Metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist Pantoea vagans C9-1. PLoS One 6(7): e22247.

Schoen C, Weber-Lehmann J, Blom J, Joseph B, Goesmann A, Strittmatter A, Frosch M (2011) Whole-genome sequence of the transformable Neisseria meningitidis serogroup A strain WUE2594..

Borriss R, Chen X, Rueckert C, Blom J, Becker A, Baumgarth B, Fan B, Pukall R, Schumann P, Spröer C, others (2011) Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons. International journal of systematic and evolutionary microbiology 61(8): 1786-1801.

Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, zu Siederdissen CH, Bort JAH, Wieser M, others (2011) Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of biotechnology 153(1-2): 62-75.

Borriss R, Rueckert C, Blom J, Bezuidt O, Reva O, Klenk H (2011) Whole genome sequence comparisons in taxonomy.: 409-436.

Pothier JF, Vorhölter F, Blom J, Goesmann A, Pühler A, Smits TH, Duffy B (2011) The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis. FEMS microbiology letters 323(1): 52-60.

Llop P, Cabrefiga J, Smits TH, Dreo T, Barbe S, Pulawska J, Bultreys A, Blom J, Duffy B, Montesinos E, others (2011) Erwinia amylovora novel plasmid pEI70: complete sequence, biogeography, and role in aggressiveness in the fire blight phytopathogen. PLoS One 6(12): e28651.

Szczepanowski R, Eikmeyer F, Harfmann J, Blom J, Rogers LM, Top EM, Schlüter A (2011) Sequencing and comparative analysis of IncP-1$α$ antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions. Journal of biotechnology 155(1): 95-103.

Imperi F, Antunes LC, Blom J, Villa L, Iacono M, Visca P, Carattoli A (2011) The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity. IUBMB life 63(12): 1068-1074.

Schneider J, Blom J, Jaenicke S, Linke B, Brinkrolf K, Neuweger H, Tauch A, Goesmann A (2011) RAPYD—rapid annotation platform for yeast data. Journal of biotechnology 155(1): 118-126.

Wibberg D, Blom J, Jaenicke S, Kollin F, Rupp O, Scharf B, Schneiker-Bekel S, Sczcepanowski R, Goesmann A, Setubal JC, others (2011) Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. Journal of Biotechnology 155(1): 50-62.

Pothier J, Smits T, Blom J, Vorhoelter F, Goesmann A, Pühler A, Duffy B (2011) Complete genome sequence of the stone fruit pathogen Xanthomonas arboricola pv. pruni. 101(6): S144-S145.

Joseph B, Schwarz RF, Linke B, Blom J, Becker A, Claus H, Goesmann A, Frosch M, Müller T, Vogel U, others (2011) Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome. PloS one 6(4): e18441.

Kant R, Blom J, Palva A, Siezen RJ, de Vos WM (2011) Comparative genomics of Lactobacillus. Microbial biotechnology 4(3): 323-332.

Luetticken R, Bruellhoff K, van der Linden M, Peltroche-Llacsahunga H, Blom J, Weber-Lehmann J, Ferretti J, McShan W (2011) Complete genome sequence of a streptococcus dysgalactiae subsp. equisimilis possessing Lancefield's Group A antigen and its comparative genomics.: 67-67.

Niu B, Rueckert C, Blom J, Wang Q, Borriss R (2011) The genome of the plant growth-promoting rhizobacterium Paenibacillus polymyxa M-1 contains nine sites dedicated to nonribosomal synthesis of lipopeptides and polyketides..

Krol E, Blom J, Winnebald J, Berhörster A, Barnett MJ, Goesmann A, Baumbach J, Becker A (2011) RhizoRegNet—A database of rhizobial transcription factors and regulatory networks. Journal of biotechnology 155(1): 127-134.

Powney R, Smits TH, Sawbridge T, Frey B, Blom J, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, others (2011) Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to Rubus plants. Journal of bacteriology 193(3): 785-786.

Blom J, Jakobi T, Doppmeier D, Jaenicke S, Kalinowski J, Stoye J, Goesmann A (2011) Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics 27(10): 1351-1358.

Hinse D, Vollmer T, Rückert C, Blom J, Kalinowski J, Knabbe C, Dreier J (2011) Complete genome and comparative analysis of Streptococcus gallolyticus subsp. gallolyticus, an emerging pathogen of infective endocarditis. BMC genomics 12(1): 400.

Borriss R, Chen X, Rueckert C, Blom J, Becker A, Baumgarth B, Fan B, Pukall R, Schumann P, Sproer C, others (2011) New Taxa-Firmicutes and Related Organisms. International Journal of Systematic and Evolutionary Microbiology: 000-000.

Schneiker-Bekel S, Wibberg D, Bekel T, Blom J, Linke B, Neuweger H, Stiens M, Vorhölter F, Weidner S, Goesmann A, others (2011) The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. Journal of biotechnology 155(1): 20-33.

Margaret I, Becker A, Blom J, Bonilla I, Goesmann A, Göttfert M, Lloret J, Mittard-Runte V, Rückert C, Ruiz-Sainz JE, others (2011) Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean. Journal of biotechnology 155(1): 11-19.

Rückert C, Blom J, Chen X, Reva O, Borriss R (2011) Genome sequence of B. amyloliquefaciens type strain DSM7T reveals differences to plant-associated B. amyloliquefaciens FZB42. Journal of biotechnology 155(1): 78-85.

2010

Schneider J, Vorhölter F, Trost E, Blom J, Musa Y, Neuweger H, Niehaus K, Schatschneider S, Tauch A, Goesmann A, others (2010) CARMEN-Comparative analysis and in silico reconstruction of organism-specific metabolic networks. Genet Mol Res 9(3): 1660-1672.

Mittard-Runte V, Bekel T, Blom J, Dondrup M, Henckel K, Jaenicke S, Krause L, Linke B, Neuweger H, Schneiker-Bekel S, others (2010) Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions.: 315-378.

Trost E, Götker S, Schneider J, Schneiker-Bekel S, Szczepanowski R, Tilker A, Viehoever P, Arnold W, Bekel T, Blom J, others (2010) Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion. BMC genomics 11(1): 91.

Smits TH, Rezzonico F, Kamber T, Blom J, Goesmann A, Frey JE, Duffy B (2010) Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp. Molecular plant-microbe interactions 23(4): 384-393.

Joseph B, Schneiker-Bekel S, Schramm-Glück A, Blom J, Claus H, Linke B, Schwarz RF, Becker A, Goesmann A, Frosch M, others (2010) Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence. Journal of bacteriology 192(20): 5363-5377.

2009

Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter F, Zakrzewski M, Goesmann A (2009) EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC bioinformatics 10(1): 154.

2008

Schoen C, Blom J, Claus H, Schramm-Glück A, Brandt P, Müller T, Goesmann A, Joseph B, Konietzny S, Kurzai O, others (2008) Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis. Proceedings of the national academy of sciences 105(9): 3473-3478.

Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehoever P, Gartemann K, Arnold W, Blom J, Brinkrolf K, Brune I, others (2008) Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Journal of Biotechnology 136(1-2): 22-30.

Schoen C, Blom J, Schramm-Glueck A, Linke B, Schneiker-Bekel S, Joseph B, Goesmann A, Schwarz R, Claus H, Vogel U, others (2008) In search for the genetic basis of virulence in Neisseria meningitidis..