Jochen Klumpp

Last Name

Klumpp

First Name

Jochen

ORCID

0000-0003-3410-2702

Organisational unit

02078 - IT Services Gruppe (ISG) D-HEST / IT Services Group (ISG) D-HEST

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Publications1 - 10 of 96

Biocontrol of Salmonella Typhimurium in RTE foods with the virulent bacteriophage FO1-E2
Guenther, Susanne; Herzig, Oliver; Fieseler, Lars; et al. (2012)
International Journal of Food Microbiology
Next generation sequencing technologies and the changing landscape of phage genomics
Klumpp, Jochen; Fouts, Derrick E.; Sozhamannan, Shanmuga (2012)
Bacteriophage
The dawn of next generation sequencing technologies has opened up exciting possibilities for whole genome sequencing of a plethora of organisms. The 2nd and 3rd generation sequencing technologies, based on cloning-free, massively parallel sequencing, have enabled the generation of a deluge of genomic sequences of both prokaryotic and eukaryotic origin in the last seven years. However, whole genome sequencing of bacterial viruses has not kept pace with this revolution, despite the fact that their genomes are orders of magnitude smaller in size compared with bacteria and other organisms. Sequencing phage genomes poses several challenges; (1) obtaining pure phage genomic material, (2) PCR amplification biases and (3) complex nature of their genetic material due to features such as methylated bases and repeats that are inherently difficult to sequence and assemble. Here we describe conclusions drawn from our efforts in sequencing hundreds of bacteriophage genomes from a variety of Gram-positive and Gram-negative bacteria using Sanger, 454, Illumina and PacBio technologies. Based on our experience we propose several general considerations regarding sample quality, the choice of technology and a “blended approach” for generating reliable whole genome sequences of phages.
A cocktail of in vitro efficient phages is not a guarantee for in vivo therapeutic results against avian colibacillosis
Tsonos, Jessica; Oosterik, Leon H.; Tuntufye, Huruma N.; et al. (2014)
Veterinary microbiology
Listeria phage A511, a model for the contractile tail machineries of SPO1-related bacteriophages
Habann, M.; Leiman, Petr G.; Vandersteegen, Katrien; et al. (2014)
Molecular Microbiology
A perfect fit: Bacteriophage receptor-binding proteins for diagnostic and therapeutic applications
Klumpp, Jochen; Dunne, Matthew; Loessner, Martin (2023)
Current Opinion in Microbiology
Bacteriophages are the most abundant biological entity on earth, acting as the predators and evolutionary drivers of bacteria. Owing to their inherent ability to specifically infect and kill bacteria, phages and their encoded endolysins and receptor-binding proteins (RBPs) have enormous potential for development into precision antimicrobials for treatment of bacterial infections and microbial disbalances; or as biocontrol agents to tackle bacterial contaminations during various biotechnological processes. The extraordinary binding specificity of phages and RBPs can be exploited in various areas of bacterial diagnostics and monitoring, from food production to health care. We review and describe the distinctive features of phage RBPs, explain why they are attractive candidates for use as therapeutics and in diagnostics, discuss recent applications using RBPs, and finally provide our perspective on how synthetic technology and artificial intelligence-driven approaches will revolutionize how we use these tools in the future.
Comparative Genome Analysis of Listeria Bacteriophages Reveals Extensive Mosaicism, Programmed Translational Frameshifting, and a Novel Prophage Insertion Site
Dorscht, Julia; Klumpp, Jochen; Bielmann, Regula; et al. (2009)
Journal of Bacteriology
A Novel Tn3-Like Composite Transposon Harboring bla(VIM-1) in Klebsiella pneumoniae spp. pneumoniae Isolated from River Water
Zurfluh, Katrin; Power, Karen A.; Klumpp, Jochen; et al. (2015)
Microbial Drug Resistance
Feasibility of spray drying bacteriophages into respirable powders to combat pulmonary bacterial infections
Vandenheuvel, Dieter; Singh, Abhishek; Vandersteegen, Katrien; et al. (2013)
European Journal of Pharmaceutics and Biopharmaceutics
Complete Genome Sequence of Listeria monocytogenes Lm60, a Strain with an Enhanced Cold Adaptation Capacity
Tasara, Taurai; Weinmaier, Thomas; Klumpp, Jochen; et al. (2014)
Genome Announcements
The complete genome sequence of Listeria monocytogenes Lm60, a fast cold-adapting serotype 1/2a human isolate, is presented.
Genome Sequences of the Listeria ivanovii subsp. Ivanovii Type Strain and Two Listeria ivanovii subsp. Londoniensis Strains
Hupfeld, Mario; Fouts, Derrick E.; Loessner, Martin J.; et al. (2015)
Genome Announcements
We present the complete genomes of Listeria ivanovii subsp. ivanovii WSLC 3010 (ATCC 19119T), Listeria ivanovii subsp. londoniensis WSLC 30151 (SLCC 8854), and Listeria ivanovii subsp. londoniensis WSLC 30167 (SLCC 6032), representing the type strain of the species and two strains of the same serovar but different properties, respectively.

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Jochen Klumpp

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