RESEARCH FOCI

Wellen

“The greatest obstacle to discovery is not ignorance - it is the illusion of knowledge.”

In nature, diverse and numerous microbial interactions exist that have far-reaching influences on nature and multicellular organisms. Under the umbrella of "microbial interactions", I study fundamental microbial interactions to ultimately identify and characterize novel naturally occurring biomolecules for their application in biotechnology. Thereby, my research topics deal with interactions among bacteria, between bacteria and bacteriophages, and with host-microbe interactions.
 

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Bacteriophages - key players in microbiomes and an alternative to antibiotics

Bacteriophages are probably the most abundant and diverse units in the biosphere. Phages are essential drivers for the dynamics of microbial communities since they influence the presence, abundance, and activity of bacteria both as lysogenic and as lytic phages. However, little is known about their impact, especially in areas that have been underexplored such as soils. With a combination of metagenomic analyses and cultivation-dependent approaches, my co-workers and I aim to gain insights into the genetic diversity and functions of phages to investigate their impact on bacterial diversity, virulence, bacterial evolution, and the stability of ecosystems. In collaboration with bioinformaticians, we analyze massive sequence data sets to resolve the "viral dark matter" and elucidate the ecological function of phages in the regulation of microbial abundances and diversity. The natural ability of phages to ultimately lyse their bacterial hosts also holds great potential for using phages biotechnologically or medicinally to eliminate harmful bacteria. In those days, antibiotics can no longer be the sole strategy for combating bacterial infections due to the steadily growing antibiotic resistance. Novel alternative strategies have to be developed, which might be synergistically applied in the future. Unexplored soil habitats represent a vast source for identifying new antimicrobials, i. a. phages against pathogenic bacteria in aqua- and agriculture and human pathogens. We frequently improve traditional cultivation techniques to enrich and isolate phages against pathogenic selection strains, e.g., Salmonella, Shigella, Vibrio, Klebsiella, Pseudomonas, Bacillus. These isolated phages are characterized concerning their structure, morphology, genome, host spectrum, stability, and resistance level for possible application. We further analyze the effectiveness and efficiency of phages on both planktonic and biofilm cells in vitro and in vivo. Moreover, we aim to improve the therapeutic potential of phages due to targeted genetic engineering of selected phages using modern molecular and synthetic biology methods. In one project, we combine two promising anti-biofilm strategies (Quorum sensing interference and phages) to attack pathogenic bacteria with genetically modified phages.

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Impact of phages on Escherichia coli K12 MG1655. (A) The impact of phages on planktonic cells of E. coli K12 was elucidated by optical density measurements at 600 nm over time; (B) Impact of phages on biofilm cells was elucidated using 96 well MBEC plates. Biofilms were detected using the crystal violet assay.

Host-microbe interactions

Interactions between multicellular organisms and microbes are not the exception but the rule. Thus, this tight relationship between a host and its associated microbiota is considered in the metaorganism concept. Within a metaorganism, immune, metabolic, neurological, and various other processes affect the microbiome but are vice versa also influenced by it. How metaorganisms develop and maintain their specific microbiome and their impact and function on the host are mainly researched on a few model organisms. I investigated host-microbe interactions of the moon jellyfish Aurelia aurita, a basal metazoan, which harbors species-, population-, compartment-, and life stage-specific microbial communities. Here, I observed a crucial impact of the microbiota on the host's health, particularly on the offspring generation of the jelly.

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In the meantime, I intend to study the impact of microbes on a novel metaorganismal system by applying my expertise in fungal biology. Within the last decades, it has become clear that bacteria-fungi interactions are crucial to the functions in both natural and anthropogenic ecosystems, including human health. However, there are currently only a few model systems to analyze those complex interactions to the best of my knowledge. The bacteria-fungi metaorganism provides an exciting and relatively simple model for the study of eukaryote–bacterial interactions. One advantage is that many fungi are haploid, easy to transform, and maybe grown both in the absence or presence of bacterial partners. In this way, fungal metaorganisms can become a model system for assessing evolutionarily conserved molecular interactions between eukaryotic cells and bacteria. We aim to elucidate how symbiotic bacteria–eukaryote interactions remain stable under different environmental conditions and over time by conducting in vitro and in vivo experiments with Ascomycota (Candida and Aspergillus). A long-term goal is to harness the great potential of the bacteria-fungi metaorganism in sustainable agriculture. On the other hand, to untangle their harmful properties, for instance, in human health, ultimately leading to improved therapeutics.

Inhibition of biofilms with quorum quenching molecules

Increased resistance to antibiotics requires new strategies to combat bacterial infections. Such serious infections are often caused by biofilms, where bacteria live in close proximity to each other embedded in a self-produced protecting matrix. Biofilm formation relies on the communication of bacteria, called quorum sensing. Besides bacteriophages, the interference of quorum sensing (QS) is a promising approach to fight infectious biofilms by inhibiting the  bacterial cell-cell communication (quorum quenching, QQ). During my Ph.D., I constructed reporter strains that enable the identification of QS-interfering molecules in a high throughput screen. Consequently, I identified and characterized numerous QQ-conferring bacterial isolates and metagenomic clones from various environmental samples throughout my Ph.D. and PostDoc. The QQ protein QQ-2 was identified as most potent quenching enzyme which prevents even clinical Klebsiella biofilms.

 

 

 

 

We constantly analyzes promising QQ molecules from aquatic and terrestrial habitats (soil), the medical and industrial sectors, and various host-microbe partnerships. The main focus is on inhibiting biotechnologically relevant biofilms of Bacillus spp., Escherichia spp., Klebsiella spp., Salmonella spp., Staphylococcus spp., Pseudomonas spp., and the yeast Candida albicans. I now aim to step from the mere identification of QQ activities to the molecular characterization of the molecules to gain insights into the underlying reaction mechanism. 

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Inhibition of Klebsiella oxytoca biofilms due to concentration

dependent immobilization of QQ-2.