Group members

Philipp

Philipp Engel, Principal investigator

philipp.engel@unil.ch

Philipp Engel carried out his doctoral research at the Biozentrum in Basel, Switzerland, in the laboratory of Christoph Dehio. In Basel, he studied the bacterial pathogen Bartonella with a focus on Type IV secretion systems, host adaptation and bacterial genomics. He then moved to the USA to join the laboratory of Prof. Nancy Moran as a postdoctoral fellow at Yale University. He worked on various aspects of the gut microbiota of honey bees, which included genomic and functional aspects aiming at the understanding of the symbiotic roles of the bee gut symbionts. During his time at Yale, Philipp also worked for four months in the Department of Chemistry with Prof. J. Crawford, to establish a collaboration on the studies of small molecules produced by the bee gut microbiota. In January 2014, Philipp moved back to Switzerland where he started his independent research at the University of Lausanne, continuing his work on the bee gut microbiota.

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Kirsten

Kirsten Ellegaard, Post-doctoral researcher

Kirsten.Ellegaard@unil.ch

Kirsten Ellegaard carried out her doctoral research at Uppsala University, Sweden, in the laboratory of Siv Andersson. Her major research interests include speciation processes, evolution and interactions within microbial communities. During her PhD, she studied the obligate bacterial endosymbiont Wolbachia, particularly in terms of gene flow, recombination and speciation. Furthermore, since Wolbachia cannot be cultured, she also developed a protocol for isolation and genome sequencing of these bacteria from fruit flies, based on whole-genome amplification. Towards the end of her PhD, she shifted her research towards comparative genome analyses of lactic acid bacteria colonizing the honeybee gut. Kirsten joined the Engel lab in June 2015. Here, she will combine bioinformatic tools with laboratory experiments, in order to gain a better understanding of the evolution and function of the bacterial communities in the honeybee gut.

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Germán Bonilla-Rosso, Post-doctoral researcher

german.bonillarosso@unil.ch

Understanding the relationship between diversity and community functioning is a fundamental problem for modern biology, and lies at Germán Bonilla-Rosso’s main interest. Because biological variation exists at many different levels, its study requires approaches at different scales. During his PhD in Valeria Souza’s group in México, Germán analysed functional diversity in metagenomes from both oligotrophic microbial mats and marine surface waters. He then moved to Sara Hallin’s group in Uppsala, Sweden, where he focused on diversity within the denitrifier guild, specifically working with the phylogenies of nitrite reductases. There he also participated in projects studying microbial communities from tundra soils and nitrate-removing sediments in the arctic. In 2017, he joined the Engel lab where he will try to better understand the evolutionary processes affecting the relationship between genome diversity and function of the honeybee gut microbiome.

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Sudip Das, Post-doctoral researcher

sudip.das@unil.ch

Host-microbe interactions are one of the most remarkable natural phenomenon and by which, Sudip has always been intrigued. Trained as an infection biologist he likes to bridge classical microbiology, immunology and molecular biology. He studied interdisciplinary biotechnology at KIIT University in India. Then, he worked in the group of Prof. Dr. Wolf- Dietrich Hardt at ETH Zürich, Switzerland for his Master’s thesis research, where he investigated Salmonella Typhimurium and host gut interactions in immune-compromised mice. Sudip received his doctoral degree from the University of Würzburg, Germany where he studied bacterial intracellular infections in the group of Prof. Dr. Thomas Rudel. His major interest was Staphylococcus aureus virulence factors, which he investigated by using Transposon Insertion deep sequencing (Tn-seq) and RNA deep sequencing (RNA-seq) in both in human cells and mice models. He also investigated the manipulation of host inflammatory responses during infections with Chlamydia trachomatis. Along with genome-wide high throughput sequencing methods, Sudip is continuously interested in host immune responses to bacteria. Sudip joined the Engel lab in May 2017 as a Postdoctoral researcher and together with the Marsland lab at the University Hospital (CHUV), he will investigate human lung microbiota and its influence on the immune system.

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Diego Gonzalez, Visiting post-doctoral researcher

diego.gonzalez@unil.ch

Microbiology gives us unrivalled opportunities to understand how natural selection generates complex physiological or behavioral patterns through very simple decision-making and information transduction molecular systems. During his PhD at the University of Lausanne, Diego Gonzalez studied, under the supervision of Justine Collier, how DNA methylation helps timing and coordinating the complex succession of intracellular events leading to cell division in the model bacterium Caulobacter crescentus. He then moved to the University of Oxford (UK) where he worked on the behavioral ecology of bacterial competition in the group of Prof. Kevin Foster. There, he studied coordinated and indirect aggressive behaviors which naturally emerge in bacterial populations based on cell-cell interactions and a simple form of stress-response regulation. During his visiting year in the group of Prof. Philipp Engel, he will help elucidating how stochastic regulatory switches might be key to the balance of the bacterial communities inhabiting the bee gut.

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Olivier_Emery_crop

Olivier Emery, PhD student

Olivier.Emery@unil.ch

Olivier Emery accomplished his Master in genomics and experimental biology at the University of Lausanne, Switzerland, in the group of Prof. Yves Poirier at the Departement of Plant Molecular Biology (DBMV). His project focused on the identification of Arabidopsis thaliana mutants deficient in phosphate acquisition. Subsequently, he did an internship at the Laboratory for Environmental Biotechnology of the Swiss Federal Institute of Technology of Lausanne (EPFL) in the group of Prof. Jean-Paul Schwitzguébel to study microalgae as a potential source for biodiesel and high-value compounds. Afterwards, he started a second Master in biology, at the University of Geneva, oriented towards bioinformatics and data analysis in biology. For his Master project, he chose to study sexual dimorphism in gene expression in the dioecious plant Mercurialis annua using RNA-sequencing in the group of Prof. John Pannell at the Departement of Ecology and Evolution (DEE, University of Lausanne). He joined the Engel group in June 2014 as a PhD student to study various aspects of the symbiosis between a gut symbiont and its host, the honey bee.

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Lucie_crop

Lucie Kešnerová, PhD student

Lucie.Kesnerova@unil.ch

Lucie obtained her Master in cell and molecular biology of plants at Charles University in Prague, Czech Republic. She was a member of the Laboratory of Plant Virology (IEB, AS CR) where she worked under the supervision of Dr. Tomas Moravec. During her Master project she studies tobacco mosaic virus (TMV) and used molecular methods to produce rod TMV particles of adjusted length in Nicotiana benthamiana plants. Her research on this topic skilled her in molecular biology, agroinfiltration and transmission electron microscopy.
She moved to Lausanne in October 2014 to start her PhD. She will study the influence of different members of microbial gut community on honey bee health and the interactions between them and the host.
While she has satisfied her keen interest in botany in Prague botanical garden as a guide, she is now blissful in working on bacterial symbionts and being surrounding by mountains during summer (and winter) months.

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Konstantin

Konstantin Schmidt, PhD student

Konstantin.Schmidt@unil.ch

Konstantin obtained his Master´s degree in Biochemistry at the Martin-Luther-University Halle-Wittenberg under the supervision of Dr. T. Pfirrmann where he analysed the involvement of a protein complex into ciliogenesis of mammalian cells and developing Xenopus laevis embryos. He is interested in analysing and understanding the bases of host microbe interactions on a molecular level. He wants to elucidate which mechanisms determine and are involved in an interaction between two organisms and how certain organisms either pathogenic or symbiotic may overcome or withstand the host immune system and responses. So far his studies were focused pathogenic host microbe interactions in plants. He carried out his Bachelor´s thesis as well as a job as a student´s research assistant in the lab of Prof. Dr. U. Bonas under the supervision of Dr. J. Stuttmann where he analysed an immune-regulatory protein of Arabidopsis thaliana important for the defence against the oomycete pathogen Hyaloperonospora arabidopsidis. During his Master studies he did an internship in the Lab of Dr. N. Dissmeyer where he studied pathogenic mechanisms to overcome A. thaliana immune responses. Konstantin joined the Engel group in December 2015 as a PhD student. Here he will work on bacterial genetics of microbial symbiosis in the honey bee gut

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Silvia Brochet, PhD student

Silvia.Brochet@unil.ch

Silvia completed her Bachelor studies in Molecular Cell Biology at the University of Turin (Italy). Then, she joined the Master program in Molecular Life Sciences of the University of Lausanne in September 2015, where she carried out her Master project in the lab of Christoph Keel at the Department of Fundamental Microbiology. She studied the role of the Type VI secretion system of the plant beneficial bacterium Pseudomonas protegens CHA0 in insect pathogenesis and inter-bacterial competition. During her master thesis, Silvia also joined the lab of Philipp Engel for a short six-months project focusing on the possible influence of a pathogen on the honey bee gut microbiome. During this time, Silvia developed a passion for studying the honey bee gut microbiota. She is in particular interested in the multitude of inter-bacterial interactions that must exist in this system. Thus, Silvia decided to start PhD project on this topic and joined the lab in March 2017.

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Michaël Troilo, technician

 

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Théodora Steiner, technician

 

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Previous lab members:

  • Roxane Moritz, First-step student
  • Francisca Segers, Master student
  • Loic Mermoud, First-step student
  • Mathieu Clement, Master student
  • Kathrine Lane, Visiting researcher