Personal Homepage of Dr. Sebastian Jaenicke

Publications

2021

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) sigma factor family. Nucleic Acids Research, DOI:10.1093/nar/gkaa1229

2020

Lori, M., Piton, G., Symanczik, S., Legay, N., Brussaard, L., Jaenicke, S., Nascimento, E., Reis, F., Sousa, J.P., Mäder, P. and others, 2020. Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change-induced rain regimes. Scientific Reports, 10(1), pp.1-15.

2019

Nelkner, J., Henke, C., Lin, T.W., Pätzold, W., Hassa, J., Jaenicke, S., Grosch, R., Pühler, A., Sczyrba, A. and 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, 10(6), p.424.

2018

Lori, M., Symanczik, S., Maeder, P., Efosa, N., Jaenicke, S., Buegger, F., Tresch, S., Goesmann, A. and Gattinger, A., 2018. Distinct nitrogen provisioning from organic amendments in soil as influenced by farming system and water regime. Frontiers in Environmental Science, p.40.

Maus, I., Rumming, M., Bergmann, I., Heeg, K., Pohl, M., Nettmann, E., Jaenicke, S., Blom, J., Pühler, A., Schlüter, A., Sczyrba, A. and Klocke, M., 2018. Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. Biotechnology for Biofuels, 11(1), p.167, DOI:10.1186/s13068-018-1162-4.

Jaenicke, S., Albaum, S.P., Blumenkamp, P., Linke, B., Stoye, J. and Goesmann, A., 2018. Flexible metagenome analysis using the MGX framework. Microbiome, 6(1), p.76, DOI:10.1186/s40168-018-0460-1.

2017

Jünemann, S., Kleinbölting, N., Jaenicke, S., Henke, C., Hassa, J., Nelkner, J., Stolze, Y., Albaum, S.P., Schlüter, A., Goesmann, A., SWczyrba, A. and Stoye, J., 2017. Bioinformatics for NGS-based Metagenomics and the Application to Biogas Research. Journal of Biotechnology.

Yu, J., Blom, J., Glaeser, S., Jaenicke, S., Juhre, T., Rupp, O., Schwengers, O., Spänig, S. and 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.

Schmautz, Z., Graber, A., Jaenicke, S., Goesmann, A., Junge, R. and Smits, T.H.M., 2017. Microbial diversity in different compartments of an aquaponics system. Archives of Microbiology, pp.1-8, DOI:10.1007/s00203-016-1334-1.

2016

Jaenicke, S., Bunk, B., Wibberg, D., Spröer, C., Hersemann, L., Blom, J., Winkler, A., Schatschneider, S., Albaum, S.P., Kölliker, R. and others, 2016. Complete genome sequence of the barley pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T). Genome Announcements, 4(6), pp.e01334-16.

Hilker, R., Bernd Stadermann, K., Schwengers, O., Anisiforov, E., Jaenicke, S., Weisshaar, B., Zimmermann, T. and Goesmann, A., 2016. ReadXplorer 2 - detailed read mapping analysis and visualization from one single source. Bioinformatics, p.btw541, DOI:10.1093/bioinformatics/btw541.

Maus, I., Koeck, D.E., Cibis, K.G., Hahnke, S., Kim, Y.S., Langer, T., Kreubel, J., Erhard, M., Bremges, A., Off, S., Stolze, Y., Jaenicke, S., Goesmann, A., Sczyrba, A., Scherer, P., König, H., Schwarz, W.H., Zverlov, V.V., Liebl, W., Pühler, A., Schlüter, A. and 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(1), pp.1-28, DOI:10.1186/s13068-016-0581-3.

Martini, M.C., Wibberg, D., Lozano, M., Tejerizo, G.T., Albicoro, F.J., Jaenicke, S., Van Elsas, J.D., Petroni, A., Garcillán-Barcia, M.P., De La Cruz, F. and others, 2016. Genomics of high molecular weight plasmids isolated from an on-farm biopurification system. Scientific Reports, DOI:10.1038/srep28284.

Ortseifen, V., Stolze, Y., Maus, I., Sczyrba, A., Bremges, A., Albaum, S.P., Jaenicke, S., Fracowiak, J., Pühler, A. and Schlüter, A., 2016. An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. Journal of Biotechnology, pp.268-279, DOI:10.1016/j.jbiotec.2016.06.014.

Gómez-Consarnau, L., González, J.M., Riedel, T., Jaenicke, S., Wagner-Döbler, I., Sañudo-Wilhelmy, S.A. and Fuhrman, J.A., 2016. Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. The ISME Journal, 10(5), pp.1102-1112, DOI:10.1038/ismej.2015.196.

2015

Rückert, C., Kriete, M., Jaenicke, S., Winkler, A. and 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. and 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.

Rupp, O., Brinkrolf, K., Buerth, C., Kunigo, M., Schneider, J., Jaenicke, S., Goesmann, A., Pühler, A., Jaeger, K. and Ernst, J.F., 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, DOI:10.1016/j.jbiotec.2015.06.423.

Stolze, Y., Zakrzewski, M., Maus, I., Eikmeyer, F.G., Jaenicke, S., Rottmann, N., Siebner, C., Pühler, A. and 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(1), DOI:10.1186/s13068-014-0193-8.

Rückert, C., Albersmeier, A., Busche, T., Jaenicke, S., Winkler, A., Friðjónsson, Ó.H., Hreggviðsson, G.Ó., Lambert, C., Badcock, D., Bernaerts, K., Anne, J., Economou, A. and Kalinowski, J., 2015. Complete genome sequence of Streptomyces lividans TK24. Journal of Biotechnology, pp.21-22, DOI:10.1016/j.jbiotec.2015.02.004.

Vinardell, J., Acosta-Jurado, S., Göttfert, M., Zehner, S., Becker, A., Baena-Ropero, I., Blom, J., Crespo-Rivas, J., Goesmann, A., Jaenicke, S., Krol, E., McIntosh, M., Margaret, I., Pérez-Montaño, F., Schneiker-Bekel, S., Serrania, J., Szczepanowski, R., Buendia-Claveria, A., Lloret, J., Bonilla, I., Pühler, A., Ruiz-Sainz, J. and Weidner, S., 2015. The Sinorhizobium fredii HH103 genome: a comparative analysis with S. fredii strains differing in their symbiotic behaviour with soybean. Molecular Plant-Microbe Interactions, DOI:10.1094/mpmi-12-14-0397-fi.

2014

Klippel, B., Sahm, K., Basner, A., Wiebusch, S., John, P., Lorenz, U., Peters, A., Abe, F., Takahashi, K., Kaiser, O., Goesmann, A., Jaenicke, S., Grote, R., Horikoshi, K. and Antranikian, G., 2014. Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles, 18(5), pp.853-863, DOI:10.1007/s00792-014-0676-3.

Tippelt, A., Möllmann, S., Albersmeier, A., Jaenicke, S., Rückert, C. and Tauch, A., 2014. Mycolic Acid Biosynthesis Genes in the Genome Sequence of Corynebacterium atypicum DSM 44849. Genome Announcements, 2(4), DOI:10.1128/genomeA.00845-14.

2013

Bolzan de Campos, S., Youn, J., Farina, R., Jaenicke, S., Jünemann, S., Szczepanowski, R., Beneduzi, A., Vargas, L.K., Wendisch, V.F. and Passaglia, L., 2013. Changes in Root Bacterial Communities associated to two different development stages of Canola (Brassica napus L. var oleifera) evaluated through Next-Generation Sequencing. Microbial Ecology, 65(3), pp.593-601, DOI:10.1007/s00248-012-0132-9.

Roetzer, A., Diel, R., Kohl, T.A., Rückert, C., Nübel, U., Blom, J., Wirth, T., Jaenicke, S., Schuback, S., Rüsch-Gerdes, S., Supply, P., Kalinowski, J. and Niemann, S., 2013. Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study. PLoS Medicine, 10(2), DOI:10.1371/journal.pmed.1001387.

Koeck, D.E., Wibberg, D., Koellmeier, T., Blom, J., Jaenicke, S., Winkler, A., Albersmeier, A., Zverlov, V.V., Pühler, A., Schwarz, W.H. and Schlüter, A., 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), pp.62-63, DOI:10.1016/j.jbiotec.2013.08.011.

Toepel, J., Illmer-Kephalides, M., Jaenicke, S., Straube, J., May, P., Goesmann, A. and Kruse, O., 2013. New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics. Plant Biotechnology Journal, 11(6), pp.717-733, DOI:10.1111/pbi.12062.

Luque-Almagro, V.M., Acera, F., Igeño, M.I., Wibberg, D., Roldán, M.D., Sáez, L.P., Hennig, M., Quesada, A., Huertas, M.J., Blom, J., Merchán, F., Escribano, M.P., Jaenicke, S., Estepa, J., Guijo, M.I., Mart\ńez-Luque, M., Mac\'ś, D., Szczepanowski, R., Becerra, G., Ramirez, S., Carmona, M.I., Gutiérrez, O., Manso, I., Pühler, A., Castillo, F., Moreno-Vivián, C., Schlüter, A. and Blasco, R., 2013. Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344. Environmental Microbiology, 15(1), pp.253-270, DOI:10.1111/j.1462-2920.2012.02875.x.

Weidner, S., Baumgarth, B., Göttfert, M., Jaenicke, S., Pühler, A., Schneiker-Bekel, S., Serrania, J., Szczepanowski, R. and Becker, A., 2013. Genome Sequence of Sinorhizobium meliloti Rm41. Genome Announcements, 1(1), DOI:10.1128/genomeA.00013-12.

Eikmeyer, F.G., Rademacher, A., Hanreich, A., Hennig, M., Jaenicke, S., Maus, I., Wibberg, D., Zakrzewski, M., Pühler, A., Klocke, M. and Schlüter, A., 2013. Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms. Biotechnology for Biofuels, 6(1), DOI:10.1186/1754-6834-6-49.

Guimarães, L.C., Soares, S.C., Albersmeier, A., Blom, J., Jaenicke, S., Azevedo, V., Soriano, F., Tauch, A. and 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), DOI:10.1128/genomeA.00264-13.

2012

Zakrzewski, M., Goesmann, A., Jaenicke, S., Jünemann, S., Eikmeyer, F.G., Szczepanowski, R., Al-Soud, W.A., Sørensen, S., Pühler, A. and Schlüter, A., 2012. Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. Journal of Biotechnology, 158(4), pp.248-258, DOI:10.1016/j.jbiotec.2012.01.020.

Schröder, J., Maus, I., Meyer, K., Wördemann, S., Blom, J., Jaenicke, S., Schneider, J., Trost, E. and 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), DOI:10.1186/1471-2164-13-141.

Dohrmann, A.B., Küting, M., Jünemann, S., Jaenicke, S., Schlüter, A. and Tebbe, C.C., 2012. Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties. The ISME Journal, 7(1), pp.37-49, DOI:10.1038/ismej.2012.77.

Trost, E., Blom, J., de Castro Soares, S., Huang, I., Al-Dilaimi, A., Schröder, J., Jaenicke, S., Dorella, F.A., Rocha, F.S., Miyoshi, A., Azevedo, V., Schneider, M.P., Silva, A., Camello, T.C., Sabbadini, P.S., Santos, C.S., Santos, L.S., Hirata, R.J., Mattos-Guaraldi, A.L., Efstratiou, A., Schmitt, M.P., Ton-That, H. and Tauch, A., 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), pp.3199-3215, DOI:10.1128/JB.00183-12.

Schneider, J., Andrea, H., Blom, J., Jaenicke, S., Rückert, C., Schorsch, C., Szczepanowski, R., Farwick, M., Goesmann, A., Pühler, A., Schaffer, S., Tauch, A., Köhler, T. and Brinkrolf, K., 2012. Draft Genome Sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10. Eukaryotic Cell, 11(12), pp.1582-1583, DOI:10.1128/EC.00258-12.

Maus, I., Wibberg, D., Stantscheff, R., Eikmeyer, F.G., Seffner, A., Boelter, J., Szczepanowski, R., Blom, J., Jaenicke, S., Konig, H., Pühler, A. and Schlüter, A., 2012. Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester. Journal of Bacteriology, 194(19), pp.5487-5488, DOI:10.1128/JB.01292-12.

Weidner, S., Becker, A., Bonilla, I., Jaenicke, S., Lloret, J., Margaret, I., Pühler, A., Ruiz-Sainz, J.E., Schneiker-Bekel, S., Szczepanowski, R., Vinardell, J.M., Zehner, S. and Göttfert, M., 2012. Genome Sequence of the Soybean Symbiont Sinorhizobium fredii HH103. Journal of Bacteriology, 194(6), pp.1617-1618, DOI:10.1128/JB.06729-11.

Schneider, J., Rupp, O., Trost, E., Jaenicke, S., Passoth, V., Goesmann, A., Tauch, A. and Brinkrolf, K., 2012. Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities. FEMS Yeast Research, 12(3), pp.382-386, DOI:10.1111/j.1567-1364.2012.00791.x.

Filippini, M., Qi, W., Jaenicke, S., Goesmann, A., Smits, T.H.M. and Bagheri, H.C., 2012. Genome Sequence of the filamentous Bacterium Fibrisoma limi BUZ 3(T). Journal of Bacteriology, 194(16), DOI:10.1128/JB.00869-12.

2011

Jaenicke, S., Zakrzewski, M., Jünemann, S., Pühler, A., Goesmann, A. and Schlüter, A., 2011. Analysis of the Metagenome from a Biogas-Producing Microbial Community by Means of Bioinformatics Methods., pp.403-414, DOI:10.1002/9781118010549.

Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B., Schneiker-Bekel, S., Szczepanowski, R., Goesmann, A., Setubal, J.C., Schmitt, R., Pühler, A. and Schlüter, A., 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), pp.50-62, DOI:10.1016/j.jbiotec.2011.01.010.

Schneider, J., Blom, J., Jaenicke, S., Linke, B., Brinkrolf, K., Neuweger, H., Tauch, A. and Goesmann, A., 2011. RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology, 155(1), pp.118-126, DOI:10.1016/j.jbiotec.2010.10.076.

Blom, J., Jakobi, T., Doppmeier, D., Jaenicke, S., Kalinowski, J., Stoye, J. and Goesmann, A., 2011. Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics, 27(10), pp.1351-1358, DOI:10.1093/bioinformatics/btr151.

Kueberl, A., Schneider, J., Thallinger, G.G., Anderl, I., Wibberg, D., Hajek, T., Jaenicke, S., Brinkrolf, K., Goesmann, A., Szczepanowski, R., Pühler, A., Schwab, H., Glieder, A. and Pichler, H., 2011. High-quality genome sequence of Pichia pastoris CBS7435. Journal of Biotechnology, 154(4), pp.312-320, DOI:10.1016/j.jbiotec.2011.04.014.

Gonzalez, J.M., Pinhassi, J., Fernández-Gómez, B., Coll-Llado, M., Gonzalez-Velazquez, M., Puigbo, P., Jaenicke, S., Gomez-Consarnau, L., Fernandez-Guerra, A., Goesmann, A. and Pedros-Alio, C., 2011. Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. MED134. Applied and Environmental Microbiology, 77(24), pp.8676-8686, DOI:10.1128/aem.06152-11.

Jaenicke, S., Ander, C., Bekel, T., Bisdorf, R., Dröge, M., Gartemann, K., Jünemann, S., Kaiser, O., Krause, L., Tille, F., Zakrzewski, M., Pühler, A., Schlüter, A. and Goesmann, A., 2011. Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing. PLoS ONE, 6(1), DOI:10.1371/journal.pone.0014519.

2010

Mittard-Runte, V., Bekel, T., Blom, J., Dondrup, M., Henckel, K., Jaenicke, S., Krause, L., Linke, B., Neuweger, H., Schneiker-Bekel, S. and Goesmann, A., 2010. Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions., pp.315-396, DOI:10.1007/978-90-481-8639-6.

Trost, E., Ott, L., Schneider, J., Schröder, J., Jaenicke, S., Goesmann, A., Husemann, P., Stoye, J., Alves Dorella, F., Souza Rocha, F., de Castro Soares, S., D'Afonseca, V., Miyoshi, A., Ruiz, J., Silva, A., Azevedo, V., Burkovski, A., Guiso, N., Join-Lambert, O.F., Kayal, S. and Tauch, A., 2010. The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. BMC Genomics, 11(1), DOI:10.1186/1471-2164-11-728.

Smits, T.H.M., Jaenicke, S., Rezzonico, F., Kamber, T., Goesmann, A., Frey, J.E. and Duffy, B., 2010. Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity. BMC Genomics, 11(1), DOI:10.1186/1471-2164-11-2.

Schlüter, J., Reinkensmeier, J., Daschkey, S., Evguenieva-Hackenberg, E., Janssen, S., Jaenicke, S., Becker, J.D., Giegerich, R. and Becker, A., 2010. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics, 11(1), DOI:10.1186/1471-2164-11-245.

2009

Kröber, M., Bekel, T., Diaz, N.N., Goesmann, A., Jaenicke, S., Krause, L., Miller, D., Runte, K.J., Viehöver, P., Pühler, A. and others, 2009. Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. Journal of Biotechnology, 142(1), pp.38-49, DOI:10.1016/j.jbiotec.2009.02.010.

2001

Balke, M., Dettbarn, T., Homann, R., Jaenicke, S., Köhler, T., Mersch, H. and Weiss, H., 2001. Eine asynchrone Implementierung eines Microprozessors auf einem FPGA..