Rolf KümmerliI’m an evolutionary biologist, fascinated by the small world of bacteria. But this was not how it all started. I initially studied anthropology at the University of Zurich, and earned my PhD at the University of Lausanne, working on social conflicts in ant colonies. As my career progressed, my study organisms became smaller. During my post-doctoral time (at the University of Edinburgh and ETH Zurich), I transformed from a behavioural ecologists into an evolutionary microbiologist, studying social interactions in bacteria. Currently, I’m heading the Microbial Evolutionary Ecology research group, as a SNSF Professor and ERC Consolidator Grant awardee, at the University of Zurich.
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Lab Members
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During my academic studies, I studied ecology, microbiology and biochemistry. Combining these different disciplines made me aware of the incredible, but inaccessible to the human eye, versatility observed in the bacterial world, whether in terms of biodiversity, colonized habitat, adaptability, or interaction including social behaviors. Indeed, bacteria can be found everywhere on earth, including in extreme environments such as digestive tracts, polar ice floes, deserts, hydrothermal zones or oil wells. But how can they adapt and survive in such hostile biotopes? My main interest is to understand how bacteria interact with their environment and how they can adapt to changes in order to survive. During my PhD at Cadarache in France (Aix-Marseille University), I worked on an efficient metal acquisition system in bacteria allowing them to survive in metal scarce environments, for example in hosts or in soil. This scientific journey opened my mind to new concepts regarding the mechanisms involved in bacterial interactions, and strengthened my interest in this research field. To pursue my exploration, I joined the Kümmerli lab, specialized in the study of social behaviors in bacteria (or “sociomicrobiology”). Here, I focus on the interactions between bacteria, and more specifically on the ecological and molecular determinants of interspecies competitive relationships to experimentally test the “competition sensing” theory. The postulate is that bacteria can sense their competitors and mount adaptive responses in return. In a context of infections, studying competition sensing could lead to a better understanding of the interactions ongoing in polymicrobial infections and ultimately might contribute to the development of new therapeutic options.
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Antibiotic resistance is one of the biggest threats to global health. The misuse of antibiotics in medicine and veterinary has led to the increase of infections untreatable by common antibiotics and alternative treatments are therefore urgently needed. In my PhD I tackle this issue by focusing on a common bacterial social trait – the secretion of siderophores – to find ways to suppress and manage human pathogens. Siderophores are iron-chelating agents synthesized and secreted by bacteria to scavenge iron from the environment and once bound to it, bacteria require a specific receptor for uptake. I will take advantage of this siderophore-receptor specificity by screening natural Pseudomonas communities for novel siderophores which don’t match the receptors of opportunistic human pathogens and thereby induce iron starvation in infections. I want to elucidate if exogenously added natural siderophores are suitable for application against opportunistic pathogens, if the siderophore treatment is able to control bacterial infections and thereby increase host survival, and finally, if the treatment is evolutionarily robust.
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During my master studies I set my focus in ecology and evolution where I was particularly interested in microorganisms in general and in the context of infectious diseases. While scientists have been focused on single species experiments for a long time I have great interest in multispecies interactions and dynamics under specific environmental conditions. Multispecies interactions can occur in the environment as well as during an infection and at present, there is little known about how multispecies interactions influence coexistence, competition or disease outcome. In my PhD project I will be studying the evolution of interaction networks among pathogens isolated from the lungs of children suffering from cystic fibrosis. Although the evolution of key pathogens like Pseudomonas aeruginosa and Staphylococcus aureus and their adaptation to the lung environment have been extensively studied, we know little on the evolution of the entire pathogen consortia. In other words, we do not know how pathogen interaction networks change over time and how shifts in interaction networks are associated with disease progression. I will focus on three common pathogens associated with cystic fibrosis: P. aeruginosa, S. aureus and H. influenza and use a combination of genotypic and phenotypic assays to elucidate, the evolution of each of the three pathogens, ecological and co-evolutionary patterns, and changes in the network topologies over time.
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Bacterial communities are among the most versatile systems to study topics at the confluence of evolution, ecology, and social behavior. As a PhD candidate at the Kummerli lab, I aim to look at multi-species interactions in the context of polymicrobial infections as a proxy to study evolutionary trajectories of different pathogens over the course of an infection. Using the focal strains of Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus aureus (half of the ESKAPE pathogens), I want to understand the effect they have on each-other over evolutionary time and under different stressful conditions. Uncovering these trajectories and mapping phenotype-genotype changes to specific conditions will go a long way in sharpening treatment options for improved outcomes in patients. I aim to employ experimental evolution to track evolutionary histories and use these lines to model interactions between pathogens and then apply these models to real-world clinical isolates. Having studied molecular microbiology during my Master’s at Leiden University, the Netherlands and worked with experimental evolution as a research assistant at the Indian Institute of Science, India, I hope to use my knowledge and skills to answer the questions I have: 1) Can we use evolution to select against antibiotic resistance? 2) Can bacteria benefit from diversity in polymicrobial infections, or do they lose out? 3) Are bacterial interactions with each-other, ubiquitous across infections of the same type? I enjoy science and I am invested in improving my teaching abilities. I believe that the best way to encourage younger scientists to pursue their scientific passions is to make science and learning more accessible and enjoyable. Outside the lab, I enjoy walking around Zurich, the city I am lucky to call my home. I also like the weekend pub visits to watch football. And in the limited spare time I get, I play video games to de-stress and clear my mind. If you are interested in the science we do at the Kummerli lab, or if you think we have common interests, please feel free to reach out to me, I am more than happy to talk!
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I am a biotechnologist whose main interest has always been the complex and evolving dynamic between pathogens and their hosts. During the course of my Master's degree, I interned at the Department of Veterinary Sciences of Turin, Italy, where I studied the impact of the parasite Toxoplasma gondii on the neurocognitive impairment of HIV-infected patients. As a PhD student in the Kümmerli Lab, I am now focusing on the ESKAPE pathogens, a leading cause of nosocomial and multidrug-resistant infections. The main focus of my research is to exploit social interactions between bacteria to improve treatment outcomes for these difficult-to-treat infections. I aim to determine if a pathogen modifies its behavior in the presence of a competing pathogen, using both in-vivo (i.e. Danio Rerio) and in-vitro models. I am also trying to assess if these competing behaviors could be exploited as an evolutionarily stable treatment. Having extensively collaborated with biologists, veterinarians, and clinicians, I firmly believe in the importance of bridging the gaps between scientific disciplines to overcome one of the main public health issues of our time, such as antibiotic resistance.
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My name is Simon Maréchal and I did a Bachelor in Biology followed by a Master in Molecular Life Sciences at the University of Lausanne. I have always been passionate about ecology, and during my studies, my interest in exploring the interactions within microbial communities grew. In particular, I wanted to understand how bacteria evolve and interact with one another and how their interactions feedback on their surrounding environments. During my studies, I had the opportunity to investigate these open questions with multiple evolutionary and coculture experiments, from the small Eppendorf tube to Bioreactor fermentation.
I started my PhD in Kümmerli’s Lab in October 2022 to pursue my quest to understand microbial interactions. By using bacterial communities isolated from the environment, my goal is to explore the traits that dictate the assembly and the stability of those bacterial communities. Are competition and predation the major traits driving the assembly of bacterial communities or is it cooperation that could emerge through the secretion of public goods molecules or cross-feeding interactions? |
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I hold a Bachelor's degree in Food Science from China Agricultural University and pursued my Master's studies at ETH, specializing in Human Health, Nutrition, and Environment. Throughout my academic journey, I developed a profound fascination for the intricate world of microbiomes and infectious diseases. My passion lies in understanding the complexities of bacteria, intriguing microorganisms characterized by their temporal evolutionary trajectories and spatial social behaviors. While extensive research has well explored population-level interactions of pathogens, there remains a significant gap in our understanding of single-cell level gene expression and interaction heterogeneity. As a Ph.D. student at the Kümmerli lab, my research endeavors focus on unraveling the intricacies of bacterial interactions at the single-cell level temporally and spatially. Specifically, I will be focusing on Pseudomonas aeruginosa, employing state-of-the-art technologies such as time-lapse microscopy and advanced image analysis methods to quantitatively investigate heterogeneity in specific gene expression as well as underlying interactions. My ultimate curiosity lies in comprehending the pivotal pathogen-pathogen and pathogen-host interactions at the single-cell level. By shedding light on these mechanisms, I aspire to contribute to the development of novel treatment strategies.
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I graduated from Paris-Diderot University with a Masters in “IMVI” (Infectiology: Microbiology, Virology, Immunology). After my studies, I worked for 3.5 years as Technician in Enzymology-Structural Biology, at the CNRS (France) and then 6.5 years as Technician in Molecular Biology, at the IMBB (Institute of Molecular Biology and Biophysics, ETH Zürich). Now, I am happy to come back to my roots (microbiology) becoming the new Technician of the Kümmerli group. I’ve always been fascinated by bacteria and how much they can adapt to their environment; for example, by acquiring antibiotic resistances in a flash, or acclimatizing to very extreme conditions (some bacteria can grow in nuclear reactors, some others can live at temperatures higher than 100 °C at large depths in the sea). Bacteria show us that life can be everywhere and can adapt to anything. That’s what I find the most fascinating about them. On the other hand, they are also fundamental for our good health (commensal flora) and we wouldn’t survive without them. So little, yet so important. There are dozens of reasons to be interested in bacteria. In the Kümmerli lab, the focus is on the social behaviors of bacteria: quorum sensing, biofilm formation, secretion and sharing of beneficial metabolites, interactions in multi-species communities... We especially study some opportunistic pathogens that represent a threat for immuno-compromised people. Those pathogens have become so multi-resistant that it might soon be impossible to treat them. Here, we help addressing a potentially big public health crisis. As technician of this lab, I’m proud to contribute and to support several basic science projects that may have important ramifications in the quest to finding new treatments.
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I studied Biology at the University of Zürich and graduated with a Masters in systematics and evolution. During my Masters, I worked with agent-based models to investigate social behaviors in bacteria, such as the enforcement of cooperation through policing or division of labor during biofilm formation. I am interested in social interactions, in bacteria, as well as throughout the natural world. Especially fascinating to me are the parallels that can be found between seemingly very different life-forms. In my role as an assistant, I continue my work with agent-based models to elucidate social interactions in bacteria, and I help to facilitate microscopy image analyses to see those interactions play out in real life.
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I was born in the sunny Italian-speaking canton Ticino where I attended the scientific high school Liceo Lugano 2 (Savosa) in Biology and Chemistry. From the beginning, I’ve been fascinated by Cellular Biology and particularly how the smallest structural and functional units of life - the so called cells - work and adapt with respect to changing surrounding selective pressures. Especially during my diploma work on mesoporous silica nanoparticles as efficient drug carriers and an internship at the AO Research Institute (Davos), I discovered my interest in biomedical research. Fascinated by the human body as a complex biological system I crossed the Alps to study.
I recently graduated with a Biomedicine BSc degree from the University of Zurich and joined the Kümmerli lab as a Master student. The microscopic world of bacterial pathogens and their evolution caught my attention. I always find it incredible that about 2.5 billion years ago the first Cyanobacteria oxygenated the atmosphere making life on Earth possible, while nowadays the emergence of drug-resistant bacterial strains is one of the most serious public health problems. If prokaryotes, on the one hand, evolved to perform critical functions that sustain the biosphere, on the other hand, they constantly change over time affecting our planet. In my Master's thesis, I’m going to work on the evolution of antibiotic resistance in polymicrobial lung infections in children suffering from cystic fibrosis (CF). CF is a genetic disease resulting in a defect in transepithelial Cl- transport and abnormal production of mucous, which strongly predispose to lifelong polymicrobial lung infections. I will investigate the evolution of antibiotic resistance in Staphylococcus aureus (SA), Hemophilus influenzae (HI), and Pseudomonas aeruginosa (PA) longitudinally isolated from the lungs of twenty-two CF children across eight years. The aim is to improve our understanding of the antimicrobial susceptibility profiles of the respiratory microbiota in CF during the first stages of the disease and their link to disease progression. I will test (i) whether resistance evolved over time, especially after aggressive antibiotic treatment targeting PA, (ii) whether antibiotic profiles differ between PA-infected and not PA-infected children, and (iii) whether exists a correlation between resistance evolution and antibiotic treatment history of the CF children. |
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During the last year of my biomedicine bachelor, my interest in bacteria has been aroused. It is crazy how bacteria find everywhere a place in the world. Although they are very small, bacteria can differ greatly from species to species. While we benefit from some, others can be life-threatening for us. The interplay of bacteria and humans is an ongoing story and I find it really fascinating to watch this evolutionary arms race almost live today. While I find this exciting, it represents a major global problem. Therefore I joined the Kümmerli lab to gain further knowledge in this field.
Already weakened patients suffering from burn wounds are perfect victims for opportunistic bacteria. Samples of these wounds have been taken regularly during the hospital stay. As my master thesis, I am going to look at these clinical samples and focus on the antibiotic resistance or virulence factors of the bacteria strains that are present. I am very curious to see if we are successful in tracking the evolution of pathogens and where it will finally take us. |
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During my bachelor, I discovered the world of microbiology. In special courses, I was able to catch a glimpse of laboratory work with microbes. This showed me that I wanted to work with them and that's why I joined the Kümmerli lab. ESKAPE pathogens are an increasing problem, as they lead to nosocomial infections and their multiresistance makes conventional medical practices difficult. In my master's thesis, I try to understand how interactions within polymicrobial infections work. For this purpose, zebrafish are used as a model host. To show the bacterial interactions, the survival of the host and also the pathogenic effect, between single-species and polymicrobial infections are compared, evaluated and quantified. Thanks to fluorescent bacteria, the interactions at different time points can be shown over time. In the end, we will better understand pathogen interactions and, thus, polymicrobial infections, which could lead to the development of new therapies.
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I majored in Food Science for my undergraduate degree and Microbiology for my Master and PhD degrees at the East China University of Science and Technology. In terms of viruses, some of the most commonly mentioned are those that cause fevers, such as the influenza virus. Bacteriophages are bacterial viruses that specifically infect bacteria but cannot infect other cells. In my PhD project, I used phages to kill pathogens in order to treat infectious diseases. Various animal infection models such as mouse, zebrafish, turbot, etc. have been used to evaluate the efficacy of phage therapy. However, during treatment, bacteria develop resistance to the phage quickly, reducing the therapeutic effect. I subsequently used experimental evolution to explore how bacteria gradually become resistant to phages. Meanwhile, I'm trying to get the phage to evolve to re-infect resistant bacteria in order to improve the therapeutic effect.
I joined the Kümmerli’s Lab as an exchange PhD student in October 2023. Here, I focus on how prophages interact with Pseudomonas and affect cystic fibrosis disease over time scales. I will isolate various prophages from the pathogens, establish infection networks, sequence the phage genome, and determine antimicrobial activity. My goal is to explore patterns of prophage-bacteria interactions in cystic fibrosis patients, leading to a better understanding of the role of phages in disease development. |
Former Lab Members
Postdocs:
Adin Ross-Gillespie (Project Manager @ Merck Group)
Santosh Sathe (Postdoc @ University of Konstanz)
Özhan Özkaya (associate relationship manager @ LifeSci advisors)
Jos Kramer (Postdoc @ ETH Zürich)
Richard Allen
Ph.D. Students:
Elisa Granato (BBSRC Discovery Fellow @ University of Oxford)
Michael Weigert (Technical Trainer @ Weiss Technik)
Anne Leinweber (Manager of Quality Control @ Hain Lifescience GmbH)
Elena (Butaite) Baumgartner (Data Manager @ Universitätsspital Zürich)
Chiara Rezzoagli (Sterility Assurance Project Leader @ Sintetica SA)
Alex Figueiredo (Postdoc @ University of Oxford)
Selina Niggli (Scientific Officer @ Swiss National Science Foundation)
Priya Jayakumar (Scientist @ Cytometry Facility UZH)
Subham Mridha (Postdoctoral Research Associate @ University of Zurich)
Désirée Schmitz
M.Sc. Students:
David Wilson (Research Associate @ Redbiotec AG)
Martina Archetti (Intern in Affiliate Marketing Programs @ Roche)
Nadine Koch (Regulatory Affairs Specialist @ Smith & Nephew)
Lorenzo Alimonti (GMP Technological Development Department Operator @ Istituto Biochimico Italiano G. Lorenzini)
Johanna Giger (Laboratory Technician, Molecular Diagnostics @ Biolytix AG)
Flavie Roncoroni (Microbiologist technician @ Givaudan)
Ove Mattmann (Founder of Fungi4Future)
Maria Muscalu (Intern @ Roche)
Roger Kuratli (Lab technician @ Group Hale UZH)
