PhD position at MoKi Analytics for molecular imaging of the microbiome in different non-communicable inflammation-driven diseases

We are looking for an Early Stage Researcher (ESR) with a focus on using the molecular imaging technique fluorescence in situ hybridization (FISH) to elucidate the role of the microbiome in different non-communicable inflammation-driven diseases. This ESR project is part of the GROWTH consortium, a Marie-Sklodowska Curie Innovative Training Network (European Industrial Doctorates).

About MoKi Analytics

MoKi Analytics GmbH is a young and innovative company, started from the Charité – University Hospital Berlin in 2017. We offer high-end products and expert services for the detection of microorganisms in clinical samples. Our focus are innovative imaging methods at the interface of molecular biology, histology and pathology. Among other services dedicated to cutting-edge microbiome research, MoKi Analytics delivers a unique combination of the microscopic technique fluorescence in situ hybridization (FISH) with Next Generation Sequencing (NGS). MoKi Analytics premises are affiliated closely to the Charité- University Hospital (Berlin) emphasizing the open and collaborative atmosphere in our company. The MoKi Analytics team consists of medical and biological scientists and technicians.

About GROWTH

The GROWTH consortium, funded by the European Commission (2019-2023), is made up to train a new generation of researchers working on new pathological insights, biomarker diagnostics and personalized nutritional interventions for intestinal failure in neonates and preterm infants. Academic and industry partners, covering various disciplines ranging from fundamental research to clinical paediatrics and analytical chemistry to organoid and gut-on-chip applications, have teamed up in the EU:

– DSCN Research BV (The Netherlands)

– University Hospital Bonn (Germany)

– Imperial College London (United Kingdom)

– Academic Medical Center (The Netherlands)

– Cherry Biotech (France)

– VU Medical Center (The Netherlands)

– MoKi Analytics (Germany)

GROWTH is a European Industrial Doctorate programme that requires PhD students to spend at least 50% of their time (18 months) in the non-academic sector.

GROWTH website url: http://www.growth-horizon2020.eu/

About the ESR Project

The PhD student will be enrolled in the Charité – University Hospital Graduate School and supervised by an academic and non-academic supervisor, equally exposing the candidate to the academic and non-academic sector. Academic supervisor will be PD Dr. Annette Moter.

The ESR will perform molecular microscopic studies to understand the role of microbial and mycobiota communities in a spatial context. FISH in combination with 16S rRNA amplification and sequence analysis (Sanger and NGS) will be employed to analyze microbial communities in in vitro samples, samples from in vivo models and ex vivo clinical samples with focus on the gastro-intestinal tract. Preliminary data suggest: 1) gut anastomoses are associated with specific microbial communities, 2) visualization of microbiota and mycobiota might play a key role in the interpretation of NGS results. Therefore, imaging by FISH in combination with sequencing needs to be established for the gastro-intestinal tract.

COLLABORATORS IN THIS ESR PROJECT:

– Academic Medical Center (Amsterdam, The Netherlands)

– University Hospital Bonn (Bonn, Germany)

Secondments

During the 36 months of the ESR project, the candidate will have the opportunity to spend:

– 7 months at the University Hospital Bonn (Bonn, Germany) to generate data on micro- and mycobiota by microscopy and NGS sequencing in human and mouse anastomotic tissue in different stages of healing. – 11 months at Academic Medical Center (AMC, Amsterdam, The Netherlands) to acquire skills in and use of analytical pipelines of 16S and ITS data bioinformatics and computing as well as correlation analyes of all results generated during the project.