My main research interest is cell-to-cell interactions in bacteria and the role of these interactions in assembly, maintenance and recovery of bacterial consortia. In particular, our work focuses on cell-to-cell interactions mediated by quorum sensing signal molecules that foster interspecies interactions. We want to understand the role of these signaling processes in regulating bacterial group behaviors in polyspecies communities and the consequences of these processes in the beneficial and hostile interactions that these communities establish with their hosts. In the past, we demonstrated that bacteria can use quorum sensing signals to foster interspecies quorum sensing and we have discovered mechanisms that exists in some bacteria which enables them to interfere with quorum sensing signaling of other species. Our recent work enhances our understanding of how bacterial chemical interactions shape polyspecies bacterial communities and highlights the importance of interspecies interactions in modulating metabolic networks in bacterial communities such as the gut microbiota. Our findings reveal novel approaches that take advantage of these interactions to ameliorate host physiology.
Microbes live mostly in communities with other microbes in nature, including host-associated microbes, forming the different microbiota. In nature, most microbes are found living in microbial biofilms, rather than as free-living organisms. However, biofilms of human-associated microbes are usually linked to pathologies. I am focused on the study of commensal and/or host-health beneficial microbes' capacity to form biofilms within the host. Furthermore, I am interested in harnessing this capacity to impact host health and disease states, using microbial genetics and synthetic biology approaches.
I am currently a postdoc in the Bacterial Signalling group at the IGC (since 2017). After graduating in Microbiology at the University of Ljubljana (Slovenia, 2010) I did a joint-PhD between GSK Vaccines (at the time Novartis Vaccines) in Siena (Italy), and the University of Nottingham (UK), studying biofilms formation by an anaerobic pathogen Clostridioides difficile (2014). My first postdoctoral fellowship was with Dr. Ivan Matic (Paris, France), where I studied regulatory cross-talk between different stress responses in Escherichia coli (2014-2016). My research interest lies in the overlapping area between microbial interactions, stress responses and evolution. In Karina`s lab I am trying to find novel signaling systems in gut bacteria, and in a parallel project to understand mechanisms underlying the maintenance of the functional diversity in the gut microbiota. For these goals I am studying evolution of a predominant gut bacterium, Bacteroides thetaiotaomicron, under different nutritional diets, by using experimental evolution, next generation sequencing, phenotyping, metagenomics and metabolomics techniques. I am a lucky person, my job IS my hobby. Apart from science, I love travelling, sea, and I enjoy eating (there’s no denying) :)
In order to thrive in multispecies environments, such as the gut microbiota, many bacteria engage in collective behaviours that include, for example, virulence factor production or biofilm formation, that are often regulated by cell-cell signalling. As a PhD student in Karina's lab, my research focuses on the identification of the signalling mechanisms involved in regulating group behaviours in Bacteroides thetaiotaomicron, a prominent member of the gut microbiota. Moreover, I study the role of these mechanisms both in successful colonization of B. thetaiotaomicron and in host physiology.
I have long been interested in Metabolic, Nutritional and Feeding processes as underpinnings of many living systems; the relative simplicity and malleability of Microbes but fundamental role, stand as insightful organisms to study such systems. Within Karina’s lab I study life of specific microbes in the mammalian intestinal tract from an Ecological and Evolutionary framework.
I started in the Bacterial Signalling lab in November 2013. Before, I did my master thesis in developmental biology, but I dedicated a lot of time to molecular cloning and trobleshooting during my project. For that reason I decided that I would like to become a lab manager and give technical support to research. In Karina's group I learned some bases of microbiology and started helping people in their different projects. Besides that, I also ensure workflow in the lab on a daily basis, processing the orders and requesting assistence for equipments whenever is needed.
I first came across quorum sensing in one of my degree’s classes. Learning that bacteria can communicate with each other through a chemical language left me fascinated and curious. So, when the time came to choose my master thesis, I figured that Karina’s Lab would be the perfect fit for my interests and I knew it would be a great environment for me to learn and feed my curiosity. Currently, I’m working on my MSc thesis, identifying quorum sensing regulated mechanisms in Barnesiella intestinihominis and Barnesiella viscericola. Besides, I’m also interested in understanding the roles that those mechanisms play in gut colonization.
Biofilms are considered the predominant lifestyle form of bacteria, can be found in all sorts of environments, confer numerous advantages to bacteria and allow them to live as a community. They are often linked to disease and as such most research focus has been towards the elimination of bacterial biofilms. I am interested, however, in the biofilms that are produced by gut symbionts. In particular, my aim is to reveal which members of a defined microbial community are essential for biofilm formation and how they interact with each other.
I am studying quorum sensing manipulation as an approach to understanding the molecular mechanisms regulating the crosstalk between the host and gut microbiota in the context of diet-induced dysbiosis. This project will enable to determine if the negative effects of diet, at the host and at the microbiota level, can be counteracted by the intervention of bacterial chemical communication.
Former Recent PhD students
Filipe Vieira - PhD student Date of graduation: February 2021 Current Position: Postdoc at University of Munich E-mail: [email protected]
Insect-borne bacterial pathogens have to rapidly adapt to drastic environmental changes in order to cycle between infection and transmission to a new host. To do that, bacteria rely on fine integration of multiple environmental and self-produce (quorum sensing) signals to regulate the expression of virulence. In my PhD project using the plant pathogen Erwinia carotovora as a model organism, I studied how the molecular mechanisms that regulate expression of multiple virulence factors, specific or not for the interaction of Erwinia with each of its hosts, are hierarchically organized. The long term goal of this project is understanding the chain of reactions that leads to the bacterial “decision” of expressing virulence, to comprehend how we can manipulate the environment so that bacteria are mostly avirulent.
Ana Rita Oliveira - PhD student Date of graduation: January 2020 Current position: Postdoc at University of Chicago E-mail:[email protected]
Antibiotic treatments disturb gut resident bacteria (microbiota) and compromise its resilience to pathogens’ invasion or pathobionts’ expansion, exposing the host to their harmful effects. I am particularly interested in the role of bacteria-bacteria interactions taking place in the gut microbiota that enable colonization by a resilient, robust, and host-beneficial microbiota. I am focusing on quorum sensing-regulated bacterial behaviors and environmental conditions that are important in recovery of the gut microbiota from antibiotic-induced dysbiosis, to better understand the players in the balance between health and disease states.
Inês Torcato - PhD student Date of graduation: October 2019 Current Position: Scientific Consultant at X2 Science Solutions E-mail: [email protected]
I joined the Bacterial Signalling Lab in March 2015 as a PhD student. In the beginning of my scientific journey, I became interested in studying proteins involved in infectious processes. In the BAS lab, I followed that interest by identifying protein receptors involved in interspecies quorum sensing, i.e., in the communication between bacteria from different species. The discovery of these receptors through bioinformatics, structural biology and biochemical/microbiological approaches leads to the understanding of the molecular mechanisms that underlie bacterial communication. This knowledge will allow the modulation of interspecies quorum sensing and, consequently, of the processes regulated by this communication mechanism in highly populated communities such as the mammalian gut microbiota.
Özhan Özkaya - PhD student Date of graduation: May 2017 Current Position: Associate Relationship Manager at LifeSci Advisors E-mail: [email protected]
I did my PhD in the Bacterial Signalling and Evolutionary Biology laboratories at IGC. I combined the expertise of these two labs to investigate the evolution of social behaviors in Pseudomonas aeruginosa. This bacterium is a an opportunistic pathogen, which infects the lungs of Cystic Fibrosis patients. Bacteria are very social organisms that use various cooperative traits to adapt and survive in their environments. I studied the interactions between cooperator bacteria that secrete molecules at a high cost, which can be shared by the community as public gods. Other bacteria, the cheaters, are able to use these public gods without paying the cost of producing it and invade the community, promoting the elimination of the cooperants and eventually can lead to the collapse of the whole community. Previous studies have focused on single trait-single constraint scenarios, demonstrating that bacterial mutants can act as cheaters and identified various mechanisms to avoid cheating and maintaining cooperation. In my work I focused on the characterization of the cheating phenomenon by quantifying the magnitude of the relative fitness of the cheaters under various biotic and abiotic conditions. I compared the fitness advantages and costs of two different and independent social traits, production of iron-siderophore pyoverdine and quorum-sensing regulated elastase. I have shown that under conditions that these two social-traits are beneficial (a multiple traits-multiple constrains scenario) there is cheating among cheater bacteria. This competition between cheaters for different traits prevents the collapse of the population allowing the population to survive. Moreover, I demonstrated how quorum-sensing regulation can avoid the full loss of cooperation. With these studies I also showed that by manipulating the abiotic environment or the composition of the population, we can avoid or cause collapse of the population. These findings may help create new therapies for bacterial infections such as in the case of Cystic Fibrosis.