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Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics.

Nelkner J, Tejerizo GT, Hassa J, Lin TW, Witte J, Verwaaijen B, Winkler A, Bunk B, Spröer C, Overmann J, Grosch R, Pühler A, Schlüter AA.

Genes (Basel). 2019 Aug 9;10(8). pii: E601. doi: 10.3390/genes10080601.


de.NBI Cloud federation through ELIXIR AAI.

Belmann P, Fischer B, Krüger J, Procházka M, Rasche H, Prinz M, Hanussek M, Lang M, Bartusch F, Gläßle B, Krüger J, Pühler A, Sczyrba A.

F1000Res. 2019 Jun 10;8:842. doi: 10.12688/f1000research.19013.1. eCollection 2019.


Evaluation of vector systems and promoters for overexpression of the acarbose biosynthesis gene acbC in Actinoplanes sp. SE50/110.

Schaffert L, März C, Burkhardt L, Droste J, Brandt D, Busche T, Rosen W, Schneiker-Bekel S, Persicke M, Pühler A, Kalinowski J.

Microb Cell Fact. 2019 Jun 28;18(1):114. doi: 10.1186/s12934-019-1162-5.


Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes.

Nelkner J, Henke C, Lin TW, Pätzold W, Hassa J, Jaenicke S, Grosch R, Pühler A, Sczyrba A, Schlüter A.

Genes (Basel). 2019 Jun 3;10(6). pii: E424. doi: 10.3390/genes10060424.


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

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

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


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

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

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


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

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

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


Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors.

Maus I, Rumming M, Bergmann I, Heeg K, Pohl M, Nettmann E, Jaenicke S, Blom J, Pühler A, Schlüter A, Sczyrba A, Klocke M.

Biotechnol Biofuels. 2018 Jun 19;11:167. doi: 10.1186/s13068-018-1162-4. eCollection 2018.


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

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

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


Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase.

Alkhateeb RS, Vorhölter FJ, Steffens T, Rückert C, Ortseifen V, Hublik G, Niehaus K, Pühler A.

Appl Microbiol Biotechnol. 2018 Aug;102(15):6613-6625. doi: 10.1007/s00253-018-9106-2. Epub 2018 Jun 1.


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

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

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


Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants.

Hassa J, Maus I, Off S, Pühler A, Scherer P, Klocke M, Schlüter A.

Appl Microbiol Biotechnol. 2018 Jun;102(12):5045-5063. doi: 10.1007/s00253-018-8976-7. Epub 2018 Apr 30. Review.


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

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

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


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

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

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


Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants.

Stolze Y, Bremges A, Maus I, Pühler A, Sczyrba A, Schlüter A.

Microb Biotechnol. 2018 Jul;11(4):667-679. doi: 10.1111/1751-7915.12982. Epub 2017 Dec 4.


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

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

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


A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

Mayer G, Quast C, Felden J, Lange M, Prinz M, Pühler A, Lawerenz C, Scholz U, Glöckner FO, Müller W, Marcus K, Eisenacher M.

Brief Bioinform. 2017 Oct 30. doi: 10.1093/bib/bbx140. [Epub ahead of print]


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

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

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


The complete genome sequence of the actinobacterium Streptomyces glaucescens GLA.O (DSM 40922) carrying gene clusters for the biosynthesis of tetracenomycin C, 5`-hydroxy streptomycin, and acarbose.

Ortseifen V, Kalinowski J, Pühler A, Rückert C.

J Biotechnol. 2017 Nov 20;262:84-88. doi: 10.1016/j.jbiotec.2017.09.008. Epub 2017 Sep 14.


Bioinformatics solutions for big data analysis in life sciences presented by the German network for bioinformatics infrastructure.

Pühler A.

J Biotechnol. 2017 Nov 10;261:1. doi: 10.1016/j.jbiotec.2017.08.025. Epub 2017 Sep 1. No abstract available.


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

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

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


The MalR type regulator AcrC is a transcriptional repressor of acarbose biosynthetic genes in Actinoplanes sp. SE50/110.

Wolf T, Droste J, Gren T, Ortseifen V, Schneiker-Bekel S, Zemke T, Pühler A, Kalinowski J.

BMC Genomics. 2017 Jul 25;18(1):562. doi: 10.1186/s12864-017-3941-x.


A community proposal to integrate proteomics activities in ELIXIR.

Vizcaíno JA, Walzer M, Jiménez RC, Bittremieux W, Bouyssié D, Carapito C, Corrales F, Ferro M, Heck AJR, Horvatovich P, Hubalek M, Lane L, Laukens K, Levander F, Lisacek F, Novak P, Palmblad M, Piovesan D, Pühler A, Schwämmle V, Valkenborg D, van Rijswijk M, Vondrasek J, Eisenacher M, Martens L, Kohlbacher O.

F1000Res. 2017 Jun 13;6. pii: ELIXIR-875. doi: 10.12688/f1000research.11751.1. eCollection 2017.


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T.

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

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


Complete Genome Sequence of the Barley Pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T).

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.

Genome Announc. 2016 Dec 1;4(6). pii: e01334-16. doi: 10.1128/genomeA.01334-16.


Deep Sequencing Analysis Reveals the Mycoviral Diversity of the Virome of an Avirulent Isolate of Rhizoctonia solani AG-2-2 IV.

Bartholomäus A, Wibberg D, Winkler A, Pühler A, Schlüter A, Varrelmann M.

PLoS One. 2016 Nov 4;11(11):e0165965. doi: 10.1371/journal.pone.0165965. eCollection 2016.


Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis.

Maus I, Kim YS, Wibberg D, Stolze Y, Off S, Antonczyk S, Pühler A, Scherer P, Schlüter A.

J Microbiol Biotechnol. 2017 Feb 28;27(2):321-334. doi: 10.4014/jmb.1605.05083.


Identification of a novel mycovirus isolated from Rhizoctonia solani (AG 2-2 IV) provides further information about genome plasticity within the order Tymovirales.

Bartholomäus A, Wibberg D, Winkler A, Pühler A, Schlüter A, Varrelmann M.

Arch Virol. 2017 Feb;162(2):555-559. doi: 10.1007/s00705-016-3085-3. Epub 2016 Oct 12.


Corrigendum to "Complete genome sequence of the cellulolytic thermophile Ruminoclostridium cellulosi wild-type strain DG5 isolated from a thermophilic biogas plant" [J. Biotechnol. 188 (2014) 136-137].

Koeck DE, Wibberg D, Maus I, Winkler A, Albersmeier A, Zverlov VV, Liebl W, Pühler A, Schwarz WH, Schlüter A.

J Biotechnol. 2016 Nov 10;237:35. doi: 10.1016/j.jbiotec.2016.08.020. Epub 2016 Sep 15. No abstract available.


Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates.

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.

Biotechnol Biofuels. 2016 Aug 11;9:171. doi: 10.1186/s13068-016-0581-3. eCollection 2016.


Rhizobium favelukesii sp. nov., isolated from the root nodules of alfalfa (Medicago sativa L).

Torres Tejerizo G, Rogel MA, Ormeño-Orrillo E, Althabegoiti MJ, Nilsson JF, Niehaus K, Schlüter A, Pühler A, Del Papa MF, Lagares A, Martínez-Romero E, Pistorio M.

Int J Syst Evol Microbiol. 2016 Nov;66(11):4451-4457. doi: 10.1099/ijsem.0.001373. Epub 2016 Aug 3.


Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants.

Stolze Y, Bremges A, Rumming M, Henke C, Maus I, Pühler A, Sczyrba A, Schlüter A.

Biotechnol Biofuels. 2016 Jul 26;9:156. doi: 10.1186/s13068-016-0565-3. eCollection 2016.


Complete Genome Sequence of Herbinix luporum SD1D, a New Cellulose-Degrading Bacterium Isolated from a Thermophilic Biogas Reactor.

Koeck DE, Maus I, Wibberg D, Winkler A, Zverlov VV, Liebl W, Pühler A, Schwarz WH, Schlüter A.

Genome Announc. 2016 Jul 21;4(4). pii: e00687-16. doi: 10.1128/genomeA.00687-16.


A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti.

Draghi WO, Del Papa MF, Hellweg C, Watt SA, Watt TF, Barsch A, Lozano MJ, Lagares A Jr, Salas ME, López JL, Albicoro FJ, Nilsson JF, Torres Tejerizo GA, Luna MF, Pistorio M, Boiardi JL, Pühler A, Weidner S, Niehaus K, Lagares A.

Sci Rep. 2016 Jul 11;6:29278. doi: 10.1038/srep29278.


Draft Genome Sequence of Propionispora sp. Strain 2/2-37, a New Xylan-Degrading Bacterium Isolated from a Mesophilic Biogas Reactor.

Koeck DE, Maus I, Wibberg D, Winkler A, Zverlov VV, Liebl W, Pühler A, Schwarz WH, Schlüter A.

Genome Announc. 2016 Jun 23;4(3). pii: e00609-16. doi: 10.1128/genomeA.00609-16.


Complete Genome Sequence of the Methanogen Methanoculleus bourgensis BA1 Isolated from a Biogas Reactor.

Maus I, Wibberg D, Winkler A, Pühler A, Schnürer A, Schlüter A.

Genome Announc. 2016 Jun 23;4(3). pii: e00568-16. doi: 10.1128/genomeA.00568-16.


Genomics of high molecular weight plasmids isolated from an on-farm biopurification system.

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.

Sci Rep. 2016 Jun 20;6:28284. doi: 10.1038/srep28284.


Comparative transcriptome analysis of the biocontrol strain Bacillus amyloliquefaciens FZB42 as response to biofilm formation analyzed by RNA sequencing.

Kröber M, Verwaaijen B, Wibberg D, Winkler A, Pühler A, Schlüter A.

J Biotechnol. 2016 Aug 10;231:212-223. doi: 10.1016/j.jbiotec.2016.06.013. Epub 2016 Jun 14.


An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.

Ortseifen V, Stolze Y, Maus I, Sczyrba A, Bremges A, Albaum SP, Jaenicke S, Fracowiak J, Pühler A, Schlüter A.

J Biotechnol. 2016 Aug 10;231:268-279. doi: 10.1016/j.jbiotec.2016.06.014. Epub 2016 Jun 14.


Targeted genome editing in the rare actinomycete Actinoplanes sp. SE50/110 by using the CRISPR/Cas9 System.

Wolf T, Gren T, Thieme E, Wibberg D, Zemke T, Pühler A, Kalinowski J.

J Biotechnol. 2016 Aug 10;231:122-128. doi: 10.1016/j.jbiotec.2016.05.039. Epub 2016 Jun 1.


The influence of a modified lipopolysaccharide O-antigen on the biosynthesis of xanthan in Xanthomonas campestris pv. campestris B100.

Steffens T, Vorhölter FJ, Giampà M, Hublik G, Pühler A, Niehaus K.

BMC Microbiol. 2016 May 23;16:93. doi: 10.1186/s12866-016-0710-y.


Genetic engineering in Actinoplanes sp. SE50/110 - development of an intergeneric conjugation system for the introduction of actinophage-based integrative vectors.

Gren T, Ortseifen V, Wibberg D, Schneiker-Bekel S, Bednarz H, Niehaus K, Zemke T, Persicke M, Pühler A, Kalinowski J.

J Biotechnol. 2016 Aug 20;232:79-88. doi: 10.1016/j.jbiotec.2016.05.012. Epub 2016 May 12.


Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment.

Maus I, Cibis KG, Bremges A, Stolze Y, Wibberg D, Tomazetto G, Blom J, Sczyrba A, König H, Pühler A, Schlüter A.

J Biotechnol. 2016 Aug 20;232:50-60. doi: 10.1016/j.jbiotec.2016.05.001. Epub 2016 May 7.


Finished genome sequence and methylome of the cyanide-degrading Pseudomonas pseudoalcaligenes strain CECT5344 as resolved by single-molecule real-time sequencing.

Wibberg D, Bremges A, Dammann-Kalinowski T, Maus I, Igeño MI, Vogelsang R, König C, Luque-Almagro VM, Roldán MD, Sczyrba A, Moreno-Vivián C, Blasco R, Pühler A, Schlüter A.

J Biotechnol. 2016 Aug 20;232:61-8. doi: 10.1016/j.jbiotec.2016.04.008. Epub 2016 Apr 6.


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