Personal Homepage of Dr. Oliver Schwengers

Publications

2024

Fenske, L., Jelonek, L., Goesmann, A., Schwengers, O.. (2024). BakRep - a searchable large-scale web repository for bacterial genomes, characterizations and metadata. Microbial genomics.Volume 10(10), DOI: 10.1099/mgen.0.001305.

Hahnfeld, J., Schwengers, O., Jelonek, L., Diedrich, S., Cemič, F., Goesmann, A.. (2024). sORFdb – A database for sORFs, small proteins, and small protein families in bacteria. bioRxiv. DOI: 10.1101/2024.06.19.599710

Zumkeller, C., Spohn, M., Mihajlovic, S., Schwengers, O., Goesmann, A., Riviani, R., Meinita, M., Hastuti, D., Prihatiningsih, I., Dewi, R., Schäberle, T.. (2024). Draft genome sequence of Galbibacter sp. PAP.153, isolated from a marine sponge in Papua, Indonesia. Microbiology resource announcements. Volume 13(6), DOI: 10.1128/mra.01297-23.

Castro, C., Schwengers, O., Stahl-Rommel, S., Nguyen, H., Dunbar, B., Wallace, W., Castro-Wallace, S.. (2024). Bacterial genome sequences of uncharacterized Chitinophaga species isolated from the International Space Station. Microbiology resource announcements.Volume 13(6), DOI: 10.1128/mra.00075-24.

Böhringer, N., Wuisan, Z., Marner, M., Kresna, I., Mettal, U., Schmitt, S., Reiter, S., Liu, Y., Brinkrolf, K., Rupp, O., Schwengers, O., Findeisen, J., Herold, S., Matt, U., Schäberle, T. (2024). Nanoliter-scale selection of optimized bioengineered peptide antibiotics that rescue mice with bacterial lung infection. bioRxiv. DOI: 10.1101/2024.05.30.596569.

Zumkeller, C., Bletz, M., Rakotoarison, A., Sabino-Pinto, J., Reiter, S., Spohn, M., Schwengers, O., Goesmann, A., Vences, M., Mihajlovic, S., Schäberle, T. (2024). Draft genome sequences of 21 Pedobacter strains isolated from amphibian specimens. Microbiology resource announcements. Volume 13(4), DOI: 10.1128/mra.01185-23.

2023

Siems, K., Runzheimer, K., Rebrosova, K., Etzbach, L., Auerhammer, A., Rehm, A., Schwengers, O., Šiler, M., Samek, O., Růžička, F., Moeller, R. (2023). Identification of staphyloxanthin and derivates in yellow-pigmented Staphylococcus capitis subsp. capitis. Frontiers in microbiology. Volume 14, DOI: 10.3389/fmicb.2023.1272734.

Neidhöfer, C., Sib, E., Neuenhoff, M., Schwengers, O., Dummin, T., Buechler, C., et al.,. (2023). Hospital sanitary facilities on wards with high antibiotic exposure play an important role in maintaining a reservoir of resistant pathogens, even over many years. Antimicrobial resistance and infection control. Volume 12(1), DOI: 10.1186/s13756-023-01236-w.

Pulami, D., Schwabe, L., Blom, J., Schwengers, O., Wilharm, G., Kämpfer, P., Glaeser, S.. (2023). Genomic plasticity and adaptive capacity of the quaternary alkyl-ammonium compound and copper tolerant Acinetobacter bohemicus strain QAC-21b isolated from pig manure. Antonie van Leeuwenhoek. Volume 116(4), DOI: 10.1007/s10482-022-01805-w.

Zumkeller, C., Spohn, M., Mihajlovic, S., Schwengers, O., Goesmann, A., Riviani, R., Meinita, M., Schäberle, T., Harwoko, H. (2023). Draft Genome Sequence of Sinomicrobium sp. Strain PAP.21, Isolated from a Coast Sample of Papua, Indonesia. Microbiology resource announcements. DOI: 10.1128/mra.01268-22

Zumkeller, C., Spohn, M., Mihajlovic, S., Schwengers, O., Goesmann, A., Choironi, N., Schäberle, T., Harwoko, H.. (2023). Draft Genome Sequences of Algoriphagus sp. Strain PAP.12 and Roseivirga sp. Strain PAP.19, Isolated from Marine Samples from Papua, Indonesia. Microbiology resource announcements. DOI: 10.1128/mra.01264-22.

Maechler, F., Weber, A., Schwengers, O., Schwab, F., Denkel, L., Behnke, M., Gastmeier, P., Kola, A.. (2023). Split k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospitals and hospitals networks in Berlin, Germany. Microbial genomics. Volume 9(1) DOI: 10.1099/mgen.0.000937.

2022

Ren, Y., Chakraborty, T., Doijad, S., Falgenhauer, L., Falgenhauer, J., Goesmann, A., Hauschild, A., Schwengers, O., Heider, D.. (2022). Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. Oxford University Press.Volume 38(2), 325--334. DOI: 10.1093/bioinformatics/btab681

Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Schwengers O, Heider D (2022) Multi-label classification for multi-drug resistance prediction of Escherichia coli. Computational and structural biotechnology journal: 1264-1270, DOI:10.1016/j.csbj.2022.03.007

Dardić D, Böhringer N, Plaza A, Zubeil F, Pohl J, Sommer S, Padva L, Becker J, Patras MA, Bill M, Kurz M, Toti L, Görgens SW, Schuler SMM, Billion A, Schwengers O, Wohlfart P, Goesmann A, Tennagels N, Vilcinskas A, Hammann PE, Schäberle TF, Bauer A (2022) Antidiabetic profiling of veramycins, polyketides accessible by biosynthesis, chemical synthesis and precursor-directed modification. Organic Chemistry Frontiers, DOI:10.1039/D1QO01652K

2021

Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A (2021) Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial genomics 7(11), DOI:10.1099/mgen.0.000685

Ren Y, Chakraborty T, Doijad S, Falgenhauer L, Falgenhauer J, Goesmann A, Hauschild A, Schwengers O, Heider D (2021) Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. Bioinformatics, DOI:10.1093/bioinformatics/btab681

Pulami D, Schauss T, Eisenberg T, Blom J, Schwengers O, Bender JK, Wilharm G, Kämpfer P, Glaeser SP (2021) Acinetobacter stercoris sp. nov. isolated from output source of a mesophilic german biogas plant with anaerobic operating conditions. Antonie van Leeuwenhoek 114(3): 235-251, DOI:10.1007/s10482-021-01517-7

2020

Ayeni FA, Falgenhauer J, Schmiedel J, Schwengers O, Chakraborty T, Falgenhauer L (2020) Detection of blaCTX-M-27-encoding Escherichia coli ST206 in Nigerian poultry stocks. The Journal of antimicrobial chemotherapy, DOI:10.1093/jac/dkaa293

Schwengers O, Barth P, Falgenhauer L, Hain T, Chakraborty T, Goesmann A (2020) Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microbial Genomics, DOI:10.1099/mgen.0.000398

Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A (2020) ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS computational biology 16(3): e1007134, DOI:10.1371/journal.pcbi.1007134

Schwengers O, Hain T, Chakraborty T, Goesmann A (2020) ReferenceSeeker: rapid determination of appropriate reference genomes. Journal of Open Source Software 5(46): 1994, DOI:10.21105/joss.01994

2019

Falgenhauer L, Schwengers O, Schmiedel J, Baars C, Lambrecht O, Heß S, Berendonk TU, Falgenhauer J, Chakraborty T, Imirzalioglu C (2019) Multidrug-Resistant and Clinically Relevant Gram-Negative Bacteria Are Present in German Surface Waters. Frontiers in microbiology: 2779, DOI:10.3389/fmicb.2019.02779

Falgenhauer J, Imirzalioglu C, Falgenhauer L, Yao Y, Hauri AM, Erath B, Schwengers O, Goesmann A, Seifert H, Chakraborty T, Doijad S (2019) Whole-Genome Sequences of Clinical Enterobacter bugandensis Isolates from Germany. Microbiology resource announcements 8(29), DOI:10.1128/MRA.00465-19

2018

Perniss A, Schmidt N, Gurtner C, Dietert K, Schwengers O, Weigel M, Hempe J, Ewers C, Pfeil U, Gärtner U, Gruber AD, Hain T, Kummer W (2018) Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice. Scientific reports 8(1): 5681, DOI:10.1038/s41598-018-23830-4

Falgenhauer L, Imirzalioglu C, Oppong K, Akenten CW, Hogan B, Krumkamp R, Poppert S, Levermann V, Schwengers O, Sarpong N, Owusu-Dabo E, May J, Eibach D (2018) Detection and Characterization of ESBL-Producing Escherichia coli From Humans and Poultry in Ghana. Frontiers in microbiology: 3358, DOI:10.3389/fmicb.2018.03358

2017

Yu J, Blom J, Glaeser SP, Jaenicke S, Juhre T, Rupp O, Schwengers O, Spänig S, Goesmann A (2017) A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies. Journal of biotechnology: 2-9, DOI:10.1016/j.jbiotec.2017.07.010

Pappesch R, Warnke P, Mikkat S, Normann J, Wisniewska-Kucper A, Huschka F, Wittmann M, Khani A, Schwengers O, Oehmcke-Hecht S, Hain T, Kreikemeyer B, Patenge N (2017) The Regulatory Small RNA MarS Supports Virulence of Streptococcus pyogenes. Scientific reports 7(1): 12241, DOI:10.1038/s41598-017-12507-z

2016

Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A (2016) ReadXplorer 2-detailed read mapping analysis and visualization from one single source. Bioinformatics 32(24): 3702-3708, DOI:10.1093/bioinformatics/btw541