News

About the Cluster of Excellence CMFI

The surfaces of the human body host colonies of microorganisms, known as microbiomes. Along with bacteria which have a positive effect on human health, microbiomes contain potentially life-threatening pathogens. In the past, broad-spectrum antibiotics have often been used to tackle them. Nowadays it is known that this not only promotes resistance to antibiotics – in many cases it also damages the microbiome as a whole. Researchers in the Cluster of Excellence "Controlling Microbes to Fight Infections" aim to develop a new strategy to control infections.

Their goal is to find new, targeted agents which will have a positive effect on the microbiome. We know that useful bacteria help to keep down the harmful ones. In order to understand and exploit the underlying mechanisms, the Cluster of Excellence will bring together researchers from the fields of molecular, bioinformatics and clinical disciplines. The speakers of the Cluster are professor Andreas Peschel and professor Heike Brötz-Oesterhelt of the Interfaculty Institute of Microbiology and Infection Medicine at the University of Tübingen, along with professor Ruth Ley, Director of the Max Planck Institute for Developmental Biology. The University Hospital Tübingen and the German Center for Infection Research (DZIF) are also partners in the Cluster.

Events

16.12.2021

Michael Zimmermann, tba

Joint Microbiological Colloquium, 16.12.2021 | 12:30 pm

Read more

12.01.2022

Ruth Ley, Twin research and microbiota

Studium Generale, 12.01.2022 | 08:15 pm

Read more

Open Positions

Postdoctoral Researcher

Postdoctoral position (f/m/d) in host-microbial interactions and organoids


One position for a talented and highly motivated post-doctoral researcher is available within the scientific team “Mitochondria and Inflammation in Neurodegeneration” led by Michela Deleidi at the DZNE Tübingen. We are interested in the immunological basis of neurodegenerative diseases, particularly focusing on Parkinson's disease. The position is funded within an ERC funded project. This will be a project aimed at clarifying the role of the microbiome in Parkinson’s disease and providing insight into a potential treatment window. This is an exciting opportunity to join a project that will establish normal and disease matched intestinal organoids, co-cultured with host microbial community, as a novel platform to understand host-microbe interactions. The successful applicant will work in a highly stimulating environment to pursue an exciting visionary cross-disciplinary project aimed at unraveling neuro-immune interactions in Parkinson's disease by means of patient primary cells and stem cell-derived organoids. The study at our site will involve wide range of techniques in the fields of microbiology and cell biology including induced pluripotent stem cell culture, organoid generation, and single-cell-RNA sequencing.

In line with the CMFI research, this project aims at identifying the role of the human microbiome in disease that could help design targeted therapeutic interventions.


Please see the Deleidi lab website for more about the research

https://www.deleidilab.org


Your profile:

The ideal candidate should have:
 

- Ph.D. and/or M.D. or equivalent degree in a relevant discipline area, such as microbiology or
cellular and molecular biology.
- Demonstrated knowledge of human intestinal biology and/or human gut microbiome
- Demonstrated experience in tissue and organoid culture
- Experience with culturing gut microbes
- Demonstrated skills in molecular biology, including PCR, western blot and ELISA
- Demonstrated skills in advanced microscopy techniques including immunofluorescence and IHC
- Outstanding record of achievements from prior training
- High level written and oral communication skills with the ability to represent the research team
(presentation of research outcomes at national and international conferences).
- Excellent communication and interpersonal skills.

We offer
• Excellent scientific infrastructure and state-of-the-art methodologies
• An international environment characterized by a strong focus on science and research
• Research training via strategic research and development projects with a clear focus that will
deliver real impact through science
• A high potential for individual career development of our employees (including targeted
personnel development through our young scientist career development program)
• An innovative culture supporting the development and demonstration of original thinking and
expertise leading to peer-recognition; and
• Opportunities to develop skills and experience in collaborative research teams to effectively
work within national and international multi/transdisciplinary and multi-stakeholder
environments.

Employment, payment and social benefits are determined by the Public Sector Collective Agreement
(Tarifvertrag für den öffentlichen Dienst – TVöD Bund). The position is open immediately and review of
applications will continue until a suitable candidate is found. A full-time appointment of initially 2 years
with the possibility of an extension.


The DZNE is an equal opportunity employer. It especially welcomes and encourages disabled individuals
to apply.


Application
To apply, please email your CV and a cover letter summarizing your research experience and interest
along with the contact information of three references to: michela.deleidispam prevention@dzne.de

The review of applications will begin on December 5, 2021 and will continue until the position is filled.

Postdoctoral Researcher

Postdoc position (E13 TV-L, 100%) – Interactions between infected macrophages and endothelial cells under shear fluid flow on an endothelium-on-chip device

to be filled assoon as possible. The position is initially limited to three years.


The Bastounis lab at the Interfaculty Institute of Microbiology & Infection Medicine and the Loskill lab at the Institute of Biomedical Engineering at the University of Tübingen are looking to fill one Postdoctoral position (E13 TV-L, 100%) as part of a collaborative research project funded by the Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI).
The earliest starting date for this position will be on 01.02.2022. The position is funded for a period of three years. The available position focuses on deciphering the interactions between endothelia and bacterially-infected macrophages in an endothelium-on-chip device.

Specific research project
One way that intracellular bacterial pathogens like L. monocytogenes spread systemically in vivo is by being carried from tissue to tissue within immune cells. Thus, it is critical to understand how infected immune cells transfer pathogens into endothelial cells or transmigrate
through them. By co-culturing endothelial cells with infected macrophages in an endothelium-on-chip device that allows exposing cells to (patho)physiological shear fluid flow, we aim to explore the roles (1) of the mechanics of “donor macrophage” versus “recipient endothelial
cell” during heterotypic bacterial transfer and (2) of the tensional forces of endothelial cells (that can be thought of as a proxy of the endothelial cell barrier integrity) in regulating infected-macrophage transmigration though the endothelium.

Candidate profile
The ideal candidate preferably brings along a degree that demonstrates an interdisciplinary background in both life and engineering sciences. While a background in host-pathogen interactions, cell biology, microscopy is a plus, a solid background in basic computer programming (e.g., MATLAB, Python etc.), image processing as well as microfluidics and microfabrication is also important to carry out the planned studies and analysis. We are looking for a highly motivated candidate with excellent communication and initiative skills, who is excited to conduct interdisciplinary studies and can team up with the various scientists in the Bastounis lab (https://www.bastounislab.org) and in the Loskill lab (http://www.loskill-lab.com).

We offer work environment that is strongly stimulating with state-of-the-art infrastructure and various facilities (check the IMIT, CMFI and NMI websites) which will provide the successful applicant with unique opportunities to develop a strong interdisciplinary portfolio in microbiology,
microscopy, cell biology, biomechanics and bioengineering.

For further information about the position, please contact Dr Peter Loskill and Dr Effie Bastounis by e-mail at peter.loskillspam prevention@uni-tuebingen.de and effie.bastounisspam prevention@uni-tuebingen.de.

Applications with a short cover/motivation letter, CV/biosketch, diploma(s) and two contacts for references should be sent via email to both principal investigators.

The University aims to increase the proportion of women in research and teaching and urges suitably qualified women scientists to apply. Qualified international researchers are expressly invited to apply. Disabled persons with equal aptitude will be given preferential consideration.

 

PhD Student

PhD position (E13 TV-L, 65%) – Host-pathogen interactions and cell biomechanics


to be filled as soon as possible. The position is initially limited to three years.

The Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI) and the Interfaculty Institute of Microbiology & Infection Medicine (IMIT) at the University of Tübingen are looking to fill one PhD position (E13 TV-L, 65%) as part of Junior Group Leader Dr. Effie Bastounis’ research group. The earliest starting date for this position will be on 01.02.2022. The position is funded for a period of 3 years at least. The available position focuses on exploring the role of intra- and extra-cellular physical forces in driving intracellular bacterial spread through infected epithelia.


Specific research project
During infection with the food-borne intracellular bacterial pathogen L. monocytogenes, large infected domains in epithelial cell monolayers are forced to extrude to form 3D mounds due to the collective and cooperative onslaught triggered by their uninfected neighbors. This mechanical competition between uninfected and bacterially-infected cells is driven by innate immunity signals and appears to limit pathogen dissemination through the epithelium (Bastounis et al 2021). The project seeks to investigate how signaling and cytoskeletal dynamics correlate with changes in host cell mechanics during intracellular bacterial spread through epithelial monolayers. We also want to understand the contribution of extracellular mechanical cues (extracellular matrix stiffness) in promoting or obstructing this biomechanical battle in favor of the host.


Candidate profile
The ideal candidate preferably brings along a degree that demonstrates an interdisciplinary background in both life and engineering sciences. While a background in host-pathogen interactions, cell biology, microscopy is a plus, a solid background in basic computer programming (e.g. MATLAB, Python etc.) and/or image processing is also important to carry out the planned studies and analysis. We are looking for a highly motivated candidate with excellent communication and initiative skills, who is excited to conduct interdisciplinary studies and can team up with the various scientists with whom we are collaborating. We offer work environment that is strongly stimulating with state-of-the-art infrastructure and various facilities (check the IMIT and CMFI websites) which will provide the successful applicant with unique
opportunities to develop a strong interdisciplinary portfolio in microbiology, microscopy, cell biology and biomechanics.

For further information about the position, please contact Effie Bastounis by e-mail at effie.bastounisspam prevention@uni-tuebingen.de, and visit our website https://www.bastounislab.org.

Applications with a short cover/motivation letter, CV/biosketch, diploma(s) and two contacts for references should be sent via email to effie.bastounisspam prevention@uni-tuebingen.de.

The University aims to increase the proportion of women in research and teaching and urges suitably qualified women scientists to apply. Qualified international researchers are expressly invited to apply. Disabled persons with equal aptitude will be given preferential consideration.

 

PhD Student

PhD position (E13 TV-L, 65%) – Intestinal cell biomechanics during bacterial infection


to be filled as soon as possible. The position is initially limited to three years.

The Bastounis lab in the Interfaculty Institute of Microbiology & Infection Medicine/Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI) at the University of Tübingen is looking to fill one PhD position (E13 TV-L, 65%) as part of a DFG funded project in collaboration with the Constantinou lab at TU Braunschweig. The earliest starting date for this position will be on 01.03.2022. The position is funded for a period of three years. The available position focuses on deciphering host-pathogen interactions using an organotypic stretching device and biomechanical approaches.

Specific research project
During infection with the food-borne intracellular bacterial pathogen L. monocytogenes, large infected domains in epithelial cell monolayers are forced to extrude to form 3D mounds due to the collective and cooperative onslaught triggered by their uninfected neighbors. This mechanical competition between uninfected and bacterially-infected cells is driven by innate immunity signals and appears to limit pathogen dissemination through the epithelium (Bastounis et al 2021). The project seeks to investigate how biochemical and physical cues in concert orchestrate intracellular bacterial dissemination in epithelial cells in monolayer in a multifunctional cell stretching platform, that will allow us to mimic peristalsis-like cellular stretching, similar to what epithelial cells are experiencing in the intestine.

Candidate profile
The ideal candidate preferably brings along a degree that demonstrates an interdisciplinary background in both life and engineering sciences. While a background in host-pathogen interactions,
cell biology, microscopy is a plus, a solid background in basic computer programming (e.g. MATLAB, Python etc.) and/or image processing is also important to carry out the planned studies and analysis. We are looking for a highly motivated candidate with excellent communication and initiative skills, who is excited to conduct interdisciplinary studies and can team up with the various scientists with whom we are collaborating and particularly with the Constantinou lab at TU Braunschweig who will develop the multifunctional cell stretching platform (https://www.tu-braunschweig.de/imt/institut/team/iordania-constantinou).
We offer work environment that is strongly stimulating with state-of-the-art infrastructure and various facilities (check the IMIT and CMFI websites) which will provide the successful applicant with unique opportunities to develop a strong interdisciplinary portfolio in microbiology, microscopy, cell biology and biomechanics.

For further information about the position, please contact Effie Bastounis by e-mail at effie.bastounisspam prevention@uni-tuebingen.de, and visit our website https://www.bastounislab.org.

Applications with a short cover/motivation letter, CV/biosketch, diploma(s) and two contacts for references should be sent via email to effie.bastounisspam prevention@uni-tuebingen.de.

The University of Tübingen aims to increase the proportion of women in research and teaching and urges suitably qualified women scientists to apply. Qualified international researchers are expressly invited to apply. Disabled persons with equal aptitude will be given preferential consideration.

 

Postdoctoral Researcher

The Functional Metabolomics Lab, part of the Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI) at the University of Tübingen, aims to understand and control microbial communities in order to contribute to the fight against infections. The group uses a multidisciplinary approach at the interface of natural product research, mass spectrometry-based metabolomics, and proteomics as well as chemical biology (www.functional-metabolomics.com).

For a project in the Collaborative Research Center CellMap (https://trr261.de), we are looking for a:

Postdoctoral Researcher (f/m/d)

to work on the application of native mass spectrometry and metabolomics approaches to study ClpP protease regulation mechanisms and the screening for new inhibitors.

For the position, we offer salary according to TV-L, E13 (100%). Besides inclusive environment, supportive mentoring and guidance for your individual career development, we provide detailed scientific training and access to state-of- the-art equipment and open science communication. Beyond scientific publications, this will include conference visits, organization and attendance of workshops and close collaborations with other research groups, including possible research visits at other universities.

As part of the CMFI Cluster of Excellence in Tübingen, you will be working in an excellent research environment with plenty of potential collaboration partners, a high amount of autonomy, and possibilities to develop and apply for funding for your own research ideas. The main focus of the position will be on research (no formal teaching duties); however, there will be the possibility to participate in college level teaching and mentoring of bachelor and master students.

At the time of employment, the candidate should have a PhD degree in analytical chemistry, biochemistry, biotechnology, or a related field. We expect that the candidate will be interested in highly interdisciplinary research; has an independent, responsible, and committed work attitude and is fluent in (scientific) English.

We expect strong knowledge of and interest to further develop bioanalytical techniques, in particular high-resolution mass spectrometry-based approaches.

Ideally, the candidate will bring experience in native mass spectrometry and protein biochemistry methods, such as heterologous protein expression and protein purification

Applications and inquiries should be sent to daniel.petrasspam prevention@uni-tuebingen.de.

Please send your application as a single PDF file that includes: a brief statement on your research interests and experience; your CV (including a list of publications); contact information for two academic references; and university transcripts.

The University of Tübingen is an Equal Opportunity Employer with a strong institutional commitment to excellence through diversity. All qualified applicants will be considered for employment without regards to gender, race, color, national origin, sexual orientation, religion, disability, or age.

 

PhD Student

 

 

The Functional Metabolomics Lab, part of the Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI) at the University of Tübingen, aims to understand and control microbial communities in order to contribute to the fight against infections. The group uses a multidisciplinary approach at the interface of natural product research, mass spectrometry-based metabolomics, and proteomics as well as chemical biology (www.functional-metabolomics.com).

The lab's science mission is to develop and apply mass spectrometry-based tools to systematically determine the role of small molecules in complex microbial communities and to mine them for novel bioactive compounds. For the development and application of native mass spectrometry and bioactivity guided metabolomics methods we are looking for a:

PhD Student (f/m/d)

The project will focus on the method development and application of native MS, HPLC fractionation, and bioactivity-guided approaches in combination with non-targeted metabolomics for the screening of culture extracts and environmental samples.

For the position, we offer salary according to TV-L, E13 (65%). Besides supportive mentoring and guidance for your individual career development, we provide detailed scientific training on state-of-the-art equipment and open, community-focused science communication. Beyond scientific publications, this will include conference visits, organization and attendance of workshops and possible research visits to other universities and field sites.

As part of the Cluster of Excellence CMFI in Tübingen you will be located in an excellent research environment with plenty of potential collaboration partners, a high amount of autonomy, and possibilities to develop your own research ideas.

At the time of employment, the candidate should have a masters or equivalent degree in chemistry, biochemistry, biotechnology, or a related field. We expect that the candidate is interested in highly interdisciplinary research, has an independent, responsible and committed work attitude, and is fluent in (scientific) English.

We expect good knowledge of bioanalytical techniques, in particular mass spectrometry as well as biochemistry and/or microbiology.

Ideally, the candidate will bring basic statistical and computational skills (e.g., scripting in Python, R, or MATLAB) and an interest to learn computational methods for mass spectrometry data analysis.

Applications or questions about the position should be sent to daniel.petrasspam prevention@uni-tuebingen.de.

Please send your application as a single PDF file that includes: a brief statement on your interests and experience; your CV; contact information for two academic references; and university transcripts.

The University of Tübingen is an Equal Opportunity Employer with a strong institutional commitment to excellence through diversity. All qualified applicants will be considered for employment without regard to gender, race, color, national origin, sexual orientation, religion, disability, or age.

The review of applications will begin in August 2021 and will continue until the position is filled.

 

Postdoctoral Researcher

 

The Functional Metabolomics Lab, part of the Cluster of Excellence “Controlling Microbes to Fight Infections” (CMFI) at the University of Tübingen, aims to understand and control microbial communities in order to contribute to the fight against infections. The group uses a multidisciplinary approach at the interface of natural product research, mass spectrometry-based metabolomics, and proteomics as well as chemical biology (www.functional-metabolomics.com).

The lab's science mission is to develop and apply mass spectrometry-based tools to systematically determine the role of small molecules in complex microbial communities and to mine them for novel bioactive compounds. To build up the mass spectrometry pipeline, we are looking for a:

Postdoctoral Researcher (f/m/d)

to work on method development and application of tandem MS and native MS approaches for the analysis of culture extracts and environmental samples, as well as the bioinformatic data analysis.

For the position, we offer salary according to TV-L, E13 (100%). Besides supportive mentoring and guidance for your individual career development, we provide detailed training and access to state-of- the-art equipment and open, community-focused science communication. Beyond scientific publications, this will include conference visits, organization and attendance of workshops and possible research visits to other universities and field sites.

As part of the Cluster of Excellence CMFI in Tübingen, you will be working in an excellent research environment with plenty of potential collaboration partners, a high amount of autonomy, and possibilities to develop and apply for funding for your own research ideas. The main focus of the position will be on research (no formal teaching duties); however, there will be the possibility to participate in college level teaching and mentoring of bachelor and master students.

At the time of employment, the candidate should have a PhD degree in analytical chemistry, biochemistry, biotechnology, or a related field. We expect that the candidate will be interested in highly interdisciplinary research; has an independent, responsible, and committed work attitude and is  fluent in (scientific) English.

We expect strong knowledge of and interest to develop bioanalytical techniques, in particular high- resolution mass spectrometry-based approaches (such as metabolomics, proteomics, or structure elucidation).

Ideally, the candidate will bring fundamental statistical and computational skills (e.g., scripting in Python, R, or MATLAB) and an interest to broaden their use of computational methods for mass spectrometry data analysis.

Applications and inquiries should be sent to daniel.petrasspam prevention@uni-tuebingen.de.

Please send your application as a single PDF file that includes: a brief statement on your interests and experience; your CV (including a list of publications); contact information for two academic references; and university transcripts.

The University of Tübingen is an Equal Opportunity Employer with a strong institutional commitment to excellence through diversity. All qualified applicants will be considered for employment without regard to gender, race, color, national origin, sexual orientation, religion, disability, or age.

The review of applications will begin in August 2021 and will continue until the position is filled.

Postdoctoral researchers in Mathematical and Computational Population Genetics

 

The newly founded independent junior research group „Mathematical and Computational Population Genetics“, headed by Franz Baumdicker at the University of Tübingen has an opening for

Postdoctoral researchers (f/m/d)

The group develops and applies mathematical models and bioinformatic tools with a special focus on microbial evolution. We are interested in a variety of evolutionary scenarios including CRISPR Cas Evolution, Pan-Genome Evolution, Horizontal Gene Transfer, Fluctuationg Selection, and Cooperation in Bacteria.

The postdoc should be interested to operate at the intersection of Mathematical Population Genetics / Computational Biology / Bioinformatics using mathematical population genetics, phylogenetics, statistical analysis, machine learning algorithms, and large scale simulations to derive new mathematical results, develop open source software and apply them to (microbial) genome data.

For scientific questions please contact: franz.baumdicker@uni-tuebingen.de.

 

Candidate profiles we would love to see:

  • PhD degree in (Bio-)Mathematics, Statistics, Bioinformatics, Computational Biology or a related field
  • Interest in interdisciplinary research
  • Strong mathematical preparation and interest and/or good computational skills (e.g. in Python, R)
  • Independent, responsible and committed work
  • Fluency in (scientific) English

 

What we offer:

  • Salary according to TV-L, E13 (100%)
  • The group is part of two Excellence Clusters (Controlling Microbes to Fight Infections & Machine Learning) in Tübingen, which offers an excellent research environment with plenty of potential collaboration partners.
  • Flexible starting date and the possibility to start the project remotely in the initial phase
  • Focus on research (no formal teaching duties)
  • Intense personal and scientific mentoring in an open and supportive environment
  • Integration into a young and agile research group
  • Responsibility to conduct your own research projects with a high amount of autonomy
  • The opportunity to visit and organize conferences, workshops and research visits to other universities and summer schools.
  • Possibilities to develop your own research ideas and mentor Ph.D. students

 

The University of Tübingen is an Equal Opportunity Employer with a strong institutional commitment to excellence through diversity. All qualified applicants will be considered for employment without regard to gender, race, color, national origin, sexual orientation, religion, disability, or age. Researchers from outside Germany are particularly encouraged to apply.

Applications and inquiries should be sent to franz.baumdickerspam prevention@uni-tuebingen.de.

Please send your application as a single PDF file and include a brief statement on your interests and experience, CV (including a possible list of publications and the contact info of two academic references), and university transcripts.

The review of applications will begin in July 2021 and continue until the positions are filled.

PhD students in Mathematical and Computational Population Genetics

 

The newly founded independent junior research group „Mathematical and Computational Population Genetics“ headed by Franz Baumdicker at the University of Tübingen has an opening for

PhD students (f/m/d)

The group develops and applies mathematical models and bioinformatic tools with a special focus on microbial evolution.

The PhD students will work at the intersection of Mathematical Population Genetics / Computational Biology / Bioinformatics using population genetics, phylogenetics, statistical analysis, machine learning algorithms, and large scale simulations to derive new theoretical results, develop open source software and apply them to (microbial) genome data.

We are interested in a variety of evolutionary scenarios including CRISPR-Cas Evolution and Dynamics, Pan-Genome Evolution, Horizontal Gene Transfer, Fluctuationg Selection, and Cooperation in Bacteria.

For scientific questions please contact: franz.baumdicker@uni-tuebingen.de.


Candidate profiles we would love to see:

  • Master's degree in (Bio-)Mathematics, Statistics, Bioinformatics, Computational Biology or a related field
  • Interest in interdisciplinary research
  • Strong mathematical preparation and interest and/or good computational skills (e.g. in Python, R)
  • Independent, responsible and committed work
  • Fluency in (scientific) English


What we offer:

  • Salary according to TV-L, E13 (65%)
  • Dissertation at the Faculty of Natural Sciences working with two advisors
  • The group is part of two Excellence Clusters (Controlling Microbes to Fight Infections & Machine Learning) in Tübingen, which offers an excellent research environment with plenty of potential collaboration partners.
  • Possibly integration into the DFG priority programme SPP2141, where appropriate
  • Focus on research (no formal teaching duties)
  • Intense personal and scientific mentoring in an open and supportive environment
  • Integration into a young and agile research group
  • The opportunity to visit conferences, workshops, other research groups and summer schools.
  • Responsibility to conduct your own research projects with a high amount of autonomy
  • Possibilities to develop your own research ideas in a young and agile team


The University of Tübingen is an Equal Opportunity Employer with a strong institutional commitment to excellence through diversity. All qualified applicants will be considered for employment without regard to gender, race, color, national origin, sexual orientation, religion, disability, or age. Researchers from outside Germany are particularly encouraged to apply.

Applications and inquiries should be sent to franz.baumdickerspam prevention@uni-tuebingen.de.

Please send your application as a single PDF file and include- brief statement on the applicant's interests and experience, CV (including a possible list of publications and the contact info of two academic references), and university transcripts.

The review of applications will begin in July 2021 and continue until the positions are filled.