Annual Conference 2025 of the Association for General and Applied Microbiology - Jahrestagung 2025 der Vereinigung für Allgemeine und Angewandte Mikrobiologie

Prof.Dr

Chair

Prof. Dr.

Antibiotics that do not cause Shiga-toxin mediated disease in C. rodentium φstx2d-infected mice and their effect on the intestinal microbiota

Infection biology

Enterohaemorrhagic Escherichia coli (EHEC) is a food-borne pathogen that causes disease ranging from watery diarrhoea to acute renal failure. Disease progression is attributed to the production of Shiga toxins (Stx). Treatment of EHEC infections remains supportive, and the use of antibiotics is highly controversial as they can induce Shiga toxin expression and may, therefore, increase the risk of haemolytic-uraemic syndrome development. While Stx induction has been assessed in vitro, the in vivo confirmation was hampered by the lack of an adequate mouse model. Introduction of a lysogenic phage encoding stx2d into the mouse pathogen C. rodentium, however, created a strain that mimics a human EHEC infection in mice.Infecting mice with C. rodentium φstx2d, we investigated the effects of antibiotic treatment on host pathology. Using the fluoroquinolone enrofloxacin known to induce Shiga toxin production, we observed that the mice showed rapid weight loss after treatment onset even though the infection was cleared. Furthermore, the kidney damage in these mice was comparable to that observed for infected but untreated mice. Several tested antibiotics, however, could clear the infection without resulting in kidney damage. These included ampicillin, rifampicin, and tetracycline. Unfortunately, the antibiotics that most efficiently cleared the C. rodentium φstx2d infection also had the most detrimental effect on the faecal microbiota, causing a severe decrease in microbiota diversity.Our data suggest that while some antibiotics increase Stx production and release, others may well be used as treatment options, especially during outbreaks. However, great care needs to be taken when using these antibiotics, as one has to weigh the harmful effects of both the infection and the antibiosis.

Abstract author

Short lecture

Prof.

Potassium-dependent switching dynamics between persistence and antibiotic susceptibility in Mycobacterium

Mycobacterium tuberculosis, which causes tuberculosis, leads to over one million deaths annually. This bacterium can develop resistance to multiple antibiotics, making it essential to find more efficient treatment methods to protect human health. One way bacteria evade antibiotics is by entering an altered physiological, non-growing state that allows them to survive antibiotic exposure. Such cells are called persisters. Recent studies suggest that potassium may influence the switch between persistent and susceptible states. Understanding and quantifying the effect of potassium on switching is crucial, for example in the clinical treatment of Mycobacterium infections.Mycobacterium smegmatis is a bacterium used as a non-pathogenic proxy for studying the virulent M. tuberculosis, with which it shares a large part of genetic homology, physiology, and cellular structure. We grew M. smegmatis cells to stationary phase with nutrient depletion for both short (1 day) and long durations (3 days). Following this, the cells were transferred to fresh medium with varying potassium concentrations, and their growth dynamics were observed. We found that stationary growth conditions and altered potassium concentrations affect population growth dynamics.We developed a mathematical model that accounts for cells switching out of the persistent state, as well as for growing cells. This model allows us to quantify effects on the total population growth, such as altering cell growth, various initial amounts of persister cells, and different switching rates into active state. Using the experimental data, the model was used to predict the fraction of persister cells in the population over time, as well as to provide switching rates, lag times, and growth rates. Different scenarios were simulated with the model to estimate the time until all persisters switched to susceptible state.Our experiments quantify effects of various potassium concentrations on the switching from persistent to susceptible states in M. smegmatis and M. tuberculosis. By using mathematical modelling, we provide new insight into the contributions of persister cells and switching rates to the cell pool. These insights will refine our knowledge of Mycobacterium and pave the way for more detailed assays in the future, as well as streamline plausible strategies for effective antibiotic treatment.

Cross-Kingdom interactions: A commensal yeast promotes Salmonella typhimurium virulence

Enteric pathogens engage in complex interactions with the host and the resident microbiota to establish gut colonization. Although mechanistic interactions between enteric pathogens and bacterial commensals have been extensively studied, whether and how commensal fungi affect pathogenesis of enteric infections remains largely unknown. Here we show that colonization with the common human gut commensal fungus Candida albicans worsened infections with the enteric pathogen Salmonella enterica serovar Typhimurium. Presence of C. albicans in the mouse gut increased Salmonella cecum colonization and systemic dissemination. We investigated the underlying mechanism and found that Salmonella binds to C. albicans via Type 1 fimbriae and uses its Type 3 Secretion System (T3SS) to deliver effector proteins into C. albicans. A specific effector, SopB, was sufficient to manipulate C. albicans metabolism, triggering increased arginine biosynthesis in C. albicans and the release of millimolar amounts of arginine into the extracellular environment. The released arginine, in turn, induced T3SS expression in Salmonella, increasing its invasion of epithelial cells. C. albicans deficient in arginine production was unable to increase Salmonella virulence in vitro or in vivo. In addition to modulating pathogen invasion, arginine also directly influenced the host response to infection. Arginine-producing C. albicans dampened the inflammatory response during Salmonella infection, whereas C. albicans deficient in arginine production did not. Arginine supplementation in the absence of C. albicans increased the systemic spread of Salmonella and decreased the inflammatory response, phenocopying the presence of C. albicans. In summary, we identified C. albicans colonization as a susceptibility factor for disseminated Salmonella infection, and arginine as a central metabolite in the cross-kingdom interaction between fungi, bacteria, and host.

The Replication Cycle of ΦKZ depends on a Phage-encoded Nuclease

Phage biology

Bacteriophages with genomes larger than 200 kBp, known as jumbo phages, interact with their hosts in complex ways. The P. aeruginosa phage ΦKZ, for example, encodes more than 300 genes, most of which are of unknown function. Using a novel mRNA-based knockdown approach, we screened for essential genes, leading to the identification of ΦKZ155. Knockdown of this gene abrogated phage replication and further analysis revealed that ΦKZ155 encodes an RNase HI, which is crucial for the replication of the phage genome.

Prof

Impact of bacteriophages on plant-pathogen interactions in a tripartite system

With the world population on the rise, it is crucial to optimize the utilization of arable resources and minimize food loss. Plant pathogenic bacteria which are estimated to account for 10% of our annual yield losses are gaining resistance against classical control strategies like antibiotics, which are a major problem. Bacteriophages as very specialized bacterial viruses hold great potential to overcome this challenge. Therefore, we investigate phages as a sustainable and targeted solution for biocontrol in agriculture with the potential to shape the plant microbiome.Our research has led to the isolation and characterization of novel phages for the economically relevant plant pathogen Xanthomonas (Erdrich et al., 2022). Among those, we recently isolated the strictly virulent phage Seregon, which proved to be suitable for biocontrol of the plant pathogen Xanthomonas campestris. However, the influence of bacteriophages on plant physiology, particularly during interactions with pathogenic bacteria in planta, remains a significant knowledge gap. Understanding the phage's impact on bacterial infection dynamics and plant defence responses is pivotal for successful application strategies.Here, we present infection studies of Arabidopsis thaliana with the plant pathogen Xanthomonas campestris. The application of the Xanthomonas phage Seregon could successfully counteract the bacterial infection almost to the level of the uninfected control. A meta-transcriptome analysis provided unprecedented insights into expression dynamics in this tripartite system and showed decreased plant defence gene upregulation in the presence of the bacteriophage. While X. campestris infection led to the expression of several salicylic acid-responsive genes and activation of the glucosinolate biosynthetic pathway. Furthermore, we observed a significant reduction of virulence expression in the bacterial transcriptome in the presence of the phage.In conclusion, we show that natural phage diversity can be harnessed for phage-based plant biocontrol. Furthermore, our findings indicate that the application of phages effectively protects Arabidopsis thaliana against the pathogen Xanthomonas campestris. These results highlight the promising role of phages in plant protection strategies and pave the way for further exploration of their use in agricultural practices.References Erdrich et al. 2022. Viruses 14 (7): 1449Erdrich et al. 2024. Microbial Biotechnology 6 (17): e14507

Anthropogenic impacts on the global groundwater viral ecosystem

Urbanization profoundly impacts ecological systems, yet its effects on groundwater viral communities, particularly bacteriophages, remain poorly understood. Groundwater sustains Earth's ecosystems and human societies through drinking water, agriculture, and natural habitats. Bacteriophages play a crucial role by modulating bacterial communities through predation and gene transfer, influencing microbial processes that maintain groundwater quality. We investigated the relationship between anthropogenic land use and viral diversity in groundwater ecosystems, hypothesizing that urbanization and agriculture reduce viral diversity while enhancing stress-resistance metabolic gene diversity. We analyzed 373 groundwater metagenomes across five global biomes, reconstructing 30,046 high-confidence uncultivated viral genomes using a custom pipeline and MetaPhlAn for bacterial diversity estimation. We annotated 7,495 auxiliary metabolic genes using DRAM-v, analyzed viral lifestyle using PhaTYP, and integrated high-resolution land cover and urbanization datasets with machine learning models. Our initial findings supported our hypotheses: urbanization correlated with reduced viral diversity in groundwater systems through host depletion and altered environmental conditions. Metabolic gene analysis revealed distinct patterns across land uses, with specific signatures in built-up, semi-arid, forest land covers, suggesting unique viral adaptations. We found consistent associations between urbanization and stress-resistance genes, indicating shifts in host functional potential. Further analysis showed approximately 65% of identified viruses were virulent, suggesting frequent lytic interactions. To address sample autocorrelation, subsequent analyses will incorporate spatial sampling techniques. These findings contribute to our understanding of viral ecology in groundwater ecosystems and could inform approaches to water management, agriculture, and pollution control in urbanized landscapes. Our results indicate that anthropogenic land use substantially influences groundwater viral communities, providing insights relevant for urban development and ecosystem management strategies.

Infection biology & phage biology

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