Pioneering Strategies Against Bacterial Infections - PEST-BIN


1. Technical University of Denmark, Kongens Lyngby, Denmark

Host for: ESR5, ESR7, ESR13

Recruiting PI: Prof. Ivan Mijakovic - Project Coordinator

Ivan Mijakovic

Professor Ivan Mijakovic leads an interdisciplinary research team implanted at two sites: DTU Biosustain in Denmark and Chalmers University of Technology in Sweden. Our core competence is bacteriology and our research interests range from very basic to applied ones. On the basic research side, we are interested in bacterial signaling and cellular regulation based on protein phosphorylation and we also explore biochemistry of early cells in relation to the genetic code and establishment of early genomes. On the applied side, we are pioneering new approaches to curb bacterial infections, based on advanced 2D materials, nanoparticles and genome mining for discovery of new antibiotics and their targets. We are a gender-balanced and very international team (20 group members from 11 different countries), and we provide a stimulating and supportive research environment for young scientists.

Lab websites:
Mijakovic lab

Bacterial Signal Transduction group

2. Chalmers University of Technology, Gothenburg, Sweden

Host for: ESR2, ESR3, ESR14

Recruiting PI: Prof. August Yurgens, Associate Prof. Roland Kádár, Prof. Nina Kann

Prof. Nina Kann

Nina Kann

Nina Kann is professor in organic chemistry, heading a research group involved in areas such as organometallic chemistry, asymmetric synthesis and green chemistry. Research focus includes method development using reactions catalysed by ruthenium, iron, palladium and enzymes, with applications in the synthesis of foldamers and antivirals. A recent project also looks at the use of biobased precursors for organic synthesis.

Prof. August Yurgens

August Yurgens

August Yurgens is a Professor of Solid State Physics at the Department of Microtechnology and Nanoscience (MC2) of Chalmers University of Technology. His research interest is graphene physics and its bio- and high-frequency sensor applications. The technological platform is scalable chemical vapor deposition method giving either in-plane- or out-of-plane-aligned graphene sheets. Combined with micro/nano patterning, the technology allows for versatile graphene structures and devices.

Associate Prof. Roland Kádár

Roland Kádár

Kádár’s group is focused on the Rheology and processing of soft matter. Understanding flow-field-matter/compositional interactions in relation to fundamental rheological properties is essential for obtaining products with favorable performance. General research activities of interest are: (i) Advanced characterization methods, method development, (ii) Tailoring multifunctional properties in nanostructured materials and (iii) Dynamics of simple and complex fluids for processing applications.

3. Rudjer Boskovic Institute, Zagreb, Croatia

Host for: ESR12

Recruiting PI: Tomislav Domazet-Lošo

Tomislav Domazet-Lošo

Our lab focuses on macroevolutionary patterns across the tree of life. We combine experimental and computational approaches to understand macroevolutionary dynamics in different clades including animals, plants, fungi and bacteria. Recently, we are trying to bring phylostratigraphic technology to the evolutionary and functional questions in bacteria, especially focusing on the bacterial multicellular behavior and its links to the multicellularity in animals. Our latest results show that developing Bacillus biofilms have embryo-like features.

Institute website: Ruđer Bošković Institute

4. Gothenburg University/Sahlgrenska University Hospital, Gothenburg, Sweden

Host for: ESR1

Recruiting PI: Roger Karlsson

Roger Karlsson

We are interested in using genomics and proteomics for the identification and characterization of microorganisms. More specifically, we are interested in developing rapid diagnostic tools for infectious diseases, identifying and characterizing pathogens directly in clinical patient samples, by the discovery of unique peptide biomarkers. Benefits of using proteomics-based identification of pathogens, also known as proteotyping, is that not only can the species or even the strain of the pathogen be identified, by direct analysis of a clinical sample, but also traits such as expressed antibiotic resistance and virulence may be identified, without time-consuming culturing steps or multiple analyses steps.

Department of infectious diseases, Institute of Biomedicine, University of Gothenburg

Clinical microbiology, Sahlgrenska University Hospital, Västra Götaland Region, Gothenburg

Culture collection of the University of Gothenburg (CCUG)

5. University of the Balearic Islands, Palma, Spain

Host for: ESR11

Recruiting PI: Professor Margarita Gomila

Margarita Gomila

My training as a researcher and my participation in several research projects have consolidated my professional experience in the field of molecular microbial ecology, particularly in the study of the microbiota present in aquatic habitats. In our lab we opened a pioneering research line in the analysis of pure hospital waters, applying molecular techniques to the study of haemodialysis water and considering the hospital as another “environment”, available for bacterial growth. We have strong experience working on ecology, epidemiology, taxonomy and identification of microorganisms from environmental and clinically interest, as i.e. Achromobacter, Corynebacterium, Pseudomonas, Streptococcus, Mycobacterium or Xylella. My currently research interests involve (meta)genomics and computational biology in the context of microbial ecology with the goal to broaden understanding of the genetic and metabolic potential of the microorganisms. We are working in the analysis of whole genomes of microorganisms of interest, mainly Pseudomonas, Mycobacterium and Xylella, in order to characterize the mobile genetic elements (phages, plasmids) and their associated virulence and antibiotic resistance genes, detection of new antibiotic resistances. Finally, we have experienced in metagenomics, using NGS methodologies in hospital haemodialysis waters and plants, with the aim to address the complexity of these samples, characterizing the organisms present in these systems and identifying their role in the microbial community.

MICROBIO website

6. NAICONS, Milano, Italy

Host for: ESR15

Recruiting PI: Stefano Donadio, PhD, Founder, CEO, & President of the Board

Stefano Donadio

NAICONS owns a large and diversified collection of 45,000 actinomycetes, soil-dwelling bacteria with a remarkable capacity to produce antibiotics and other bioactive metabolites. The research team consists of scientists with experience in microbiology and natural products, with a strong track record in the discovery, purification and structural determination of microbial metabolites. Our own research programs are supported by regional, national and European grants.

NAICONS website

7. AltraBio, Lyon, France

Host for: ESR6

Recruiting PI: Simon de Bernard

Simon de Bernard

Dr. Simon de Bernard, Ph.D. (Biochemistry and Molecular Biology) and graduate of the “École Polytechnique”, started his career as Project Manager at ValiGen (Paris, France) and Senior Project Manager at IT.Omics (Lille, France). In 2006, he co-founded AltraBio, a biotechnology SME in Lyon, France. AltraBio’s main focus is the development and implementation of innovative approaches for the analysis, mining and interpretation of life science data, especially resulting from omics technologies.

AltraBio website

8. CNRS - French National Centre for Scientific Research, Lyon, France

Host for: ESR8

Recruiting PI: Christophe Grangeasse

Christophe Grangeasse

The team’s work focuses on the biology of the human bacterial pathogen Streptococcus pneumoniae (pneumococcus). We study not only the processes governing the cell cycle (cell division, morphogenesis and genome duplication), but also the assembly and export processes of the polysaccharide capsule, which is the main factor of virulence of the pneumococcus. Using an integrated and multidisciplinary approach involving molecular biology, biochemistry, bacterial genetics, structural biology and cell imaging, we also study the regulatory mechanisms coordinating these processes. Among these, a particular attention is dedicated to protein phosphorylation and especially to the role of the serine-, threonine- or tyrosine-kinases.

Lab website:

Bacterial Pathogens and Protein Phosphorylation (C. Grangeasse)

9. University of Tübingen, Tübingen, Germany

Host for: ESR9

Recruiting PI: Prof. Dr. Boris Macek

Boris Macek

The Chair of Quantitative Proteomics at the University of Tuebingen performs research in areas of proteogenomics, phosphoproteomics, biological signal transduction and quantitative analysis of protein modifications. It is held by Prof. Boris Macek, who moved to Tuebingen in 2008 after completing his education at Universities of Zagreb, Muenster and Odense, as well as at the Max Planck Institute of Biochemistry in Martinsried. We gather an international team of researchers with core expertise in shotgun mass spectrometry-based proteomics. Quantitative workflows are mainly based on stable isotope labeling of cells and tissues and measurements of resulting protein digests using high resolution mass spectrometry. In addition, we possess considerable infrastructure and expertise in protein/peptide separation technologies based on various analytical HPLC methods, as well as bioinformatic analysis of shotgun proteomics data. We apply this technology to a range of biomedical topics such as the influence of point mutations on signal transduction in cancer, influence of the gut microbiome on neuroinflammation in autism-spectrum disorders, and role of bacterial S/T/Y kinases in persistence.

Quantitative Proteomics & Proteome Center Tuebingen website

10. Clinical Microbiomics A/S, Copenhagen, Denmark

Host for: ESR10

Recruiting PI: H. Bjørn Nielsen, PhD, Chief Scientific Officer

Bjørn Nielsen

H. Bjørn Nielsen and Clinical Microbiomics focus on delivering world leading microbiome research to our academic and industrial clients. To that end we develop rigorous and powerfull laboratory, business and computational frameworks. Using machine learning for linking within-specie phylogenetic diversity to host health is one such framework. Importantly, our research is directed by marked pull and our visions for the future, ensuring its utility and relevance. At Clinical Microbiomics we work as a cross-disciplinary team (science, sales and management) and we strive to have a healthy life/work balance. We have backgrounds in microbiome research, lifescience, physics, data science, communication and management.

Clinical Microbiomics website

11. INRAE: National Research Institute for Agriculture, Food and Environment, Paris, France

Host for: ESR4

Recruiting PI: Céline Henry, Hélène Bierne

Céline Henry

Céline Henry

The Plateforme d’Analyse Protéomique de Paris Sud-Ouest (PAPPSO facility) provides research teams with equipments, skills and expertises in the field of proteomics, to allow them to respond to the most simple questions (identification of proteins from an organism the genome of which is entirely sequenced) as well as to complex questions (protein quantification in complex samples, dynamics of post-translational modifications,…) in the framework of collaborative projects and contracts. PAPPSO is specialized in high throughput proteomics (quantitative analysis of large cohorts of samples) and in the analysis of highly complex samples (métaprotéomics). The platform develops bioinformatics tools that allow the processing of these experiments and provides asistance to users for data interpretation.

Lab website:
Plateforme d’Analyse Protéomique de Paris Sud Ouest (PAPPSO)

Institute website:
Micalis Institute


Hélène Bierne

Hélène Bierne

Our team is exploring the long-term effects of the bacterial pathogen Listeria monocytogenes on mammalian hosts. Using microbiology, cellular and molecular biology, genetics and biochemistry techniques, we study how bacteria and host cells reprogram themselves phenotypically, genetically and epigenetically, to allow Listeria to infect and persist in the host over the long term. This research aims to find new ways to detect asymptomatic infections and treat acute infections.

Lab website:
Epigenetics and Cellular Microbiology / Helene Bierne

Institute website:
Micalis Institute