PhD Students

INM

Colloidosomes as a mechanically robust microencapsulation format for therapeutic bacteria

This project aims to develop colloidosomes as a novel approach for encapsulating genetically engineered bacteria functioning as Living Therapeutic Materials (LTMs). The bacteria are designed to sense inflammatory stimuli involved in skin inflammation or inflammatory bowel diseases and release anti-inflammatory agents, modulating the immune response. The material used for the LTM must exhibit mechanical properties that enable it to resist fracture and ensure structural integrity. Colloidosomes are formed from a water-in-oil Pickering emulsion, stabilized by amphiphilic silica nanoparticles. The resulting colloidosomes have hydrophilic lumen, that allows bacterial encapsulation and the silica shell provides mechanical properties that enable it to resist fracture and ensure structural integrity while maintaining selective permeability, allowing the diffusion of therapeutic molecules.

TU Berlin

Life Cycle Assessment of Living Materials

Life Cycle Assessment (LCA) is a tool used to analyze and quantify the environmental impact of products and systems across various impact categories, such as climate change. As living materials are an emerging field with many promising new developments, it is important to assess their potential environmental impact. Conducting LCA during the development phase allows for early adjustments toward more sustainable material solutions in the future. In my work, I assess the potential future impacts of newly developed living materials using prospective LCA.

University of Saarland

Influence of bacterial secretome on the innate immune defense of humans

INM

Developing inflammation-responsive bacteria for living therapeutic materials

HIPS

HIPS

A Novel Sesterterpenoid for Targeted Antifungal Therapy: Total Synthesis and Preclinical Evaluation

Antimicrobial resistance (AMR) is a global health issue that has emerged over recent decades and calls for special attention and innovative approaches to combat it. Recognizing this threat, the World Health Organization (WHO) published its first Fungal Priority Pathogens List in 2022, designating Candida albicans, Candida auris, and Aspergillus fumigatus as Critical Priority pathogens of greatest public health concern. This situation underscores the urgent need for new, safe, and effective antifungal therapeutics – novel treatments that are also affordable and accessible. Thus, my research focuses on the total synthesis of a sesterterpenoid compound showing potent sub-micromolar activity against C. albicans and Aspergillus, and also lower micromolar activity against other pathogenic fungi (e.g. Fusarium spp.), with moderate cytotoxicity in human cells, underscoring its potential for selective and safe antifungal therapy.

University of Saarland & INM

Epigenetic and Transcriptomic Regulation of Engineered Bacteria in Hydrogel-Based Living Materials

The rising prevalence of inflammatory, infectious, oncological, and metabolic diseases highlights the need for innovative therapeutic approaches. Traditional drugs derived from natural products face limitations in cost, scalability, and environmental impact. Genetically engineered bacteria such as E. coli, Lactobacillus, and Salmonella offer sustainable alternatives, capable of producing therapeutic molecules and acting as smart drug delivery systems within the gut microbiota. To improve biosafety and therapeutic efficacy, these microbes are increasingly embedded in hydrogels, forming ‘living materials’ that protect against immune responses and environmental stress. However, the hydrogel environment can itself affect bacterial gene regulation and stability. As environmental stressors are known to trigger epigenetic changes, a deeper understanding of bacterial adaptation at the molecular level is essential. I therefore propose a comprehensive analysis of the epigenome, transcriptome, and epitranscriptome of engineered bacteria in hydrogels using Oxford Nanopore and RNA sequencing. This will provide crucial insights into their regulatory mechanisms, enabling the optimization of living materials for future biomedical applications.

University of Saarland

Intelligent microbiome manipulation to treat lung infections

My project focuses on developing a microfluidic platform that encapsulates lung-resident bacteria, including both commensals and COPD-associated pathogens, within defined alginate microenvironments for controlled co-culture with human lung epithelial cells. This system enables modelling of key COPD-relevant processes; including epithelial barrier dysfunction, chronic inflammation, and dysregulated host–microbe interactions driven by altered airway microbiota. By examining how disease-associated microbial communities modulate epithelial integrity and inflammatory signaling, the platform provides mechanistic insight into microbiome-driven pathways that contribute to COPD pathogenesis and susceptibility to infection. Ultimately, this approach supports the rational manipulation of the lung microbiome as a therapeutic strategy to prevent exacerbations and improve lung health in COPD.

INM

HYPER

INM

University of Saarland

INM

Engineering biosensors in probiotic bacteria for developing disease-responsive living therapeutic material

HIPS

Multi-scale approaches to understanding aging across biological scales: molecular mediators and therapeutic targeting strategies

Amila investigates molecular mechanisms of aging across multiple
biological scales, from cellular models to mouse and human tissues. Her
work focuses on understanding how extracellular vesicles, microRNAs, and
protein-level changes contribute to aging processes, with special
emphasis on brain aging and microglial function. Using integrated
multi-omics approaches combining transcriptomics and proteomics, her
research characterizes temporal dynamics and spatial patterns of
aging-related molecular changes across different brain regions. The
therapeutic component explores locked nucleic acid (LNA)-based
interventions to modulate microRNA activity, bridging fundamental aging
mechanisms with potential therapeutic applications

University of Saarland

HIPS

δ-Lactone Sesterterpenoids from Fungal Sources for Antifungal Therapy

HIPS

Heterologous expression and genetic engineering of natural product biosynthetic pathways

Selina Deckarm works as a doctoral researcher in the field of microbial natural products in the research group of Prof. Dr. Rolf Müller at HIPS. She focuses on heterologous expression and genetic modification of bacterial natural product biosynthetic pathways including the goals: to improve production yields, to elucidate the biosynthesis and to develop new promising myxobacterial antibiotics.

INM

Living capsules for bio-therapeutics

My research focuses on using  suitable  polymers to develop double emulsions, Core- Shell structured hydrogels (microcapsules)  with microfluidics to encapsulate Bacteria and enabling  the fabrication of functional living capsules.  The main activities will involve characterization of mechanical, swelling and degradation properties of these microcapsules. Then characterize the metabolic activity of the encapsulated microbes, and study the changes in the metabolism as a consequence of confinement and material properties. Thus optimize the microcapsules structure & properties for functional and high productivity of  encapsulated bacteria to produce therapeutic molecules.

University of Saarland

New natural compounds from Streptomyces through heterologous expression of biosynthetic gene cluster

The aim is to utilize the heterologous host Streptomyces albus del 14 for the expression of interesting biosynthetic gene cluster of secondary metabolites to access the chemical potential of close related streptomyces species for natural product discovery, covered by genomic libraries. Potentially new natural products with interesting properties are to be isolated, the structure elucidated and the underlying biosynthetic pathway unravelled. Some of those strains producing natural products are aimed to be incorporated into living materials.

INM

Microbiome bacteria engineering for living therapeutic materials

As part of the development of living therapeutic materials this work aims for the design of genetic circuits in Corynebacterium spp. These circuits are controlled by external triggers such as heat or light and shall regulate the production of drugs by the bacteria eventually.

University of Saarland

Impact of extracellular matrix components on killing efficiency of natural killer cells

Natural killer (NK) cells are critical players in the elimination of infected and tumor cells. As they patrol tissues to locate their target cells, NK cells encounter complex 3D environments primarily composed of extracellular matrix (ECM), with collagen being the most abundant ECM component. Hyaluronic acid (HA), another essential ECM component, is particularly enriched in some organs and tissues, such as the skin, respiratory tract, and blood vessels. In my work, I investigate how the presence of HA in 3D collagen matrices affects the killing functions of NK cells, such as cytotoxicity, infiltration, migration, and viability. To achieve this goal, I employ various approaches, including live cell imaging, real-time killing assay and flow cytometry.

University of Saarland

Systems metabolic engineering of Corynebacterium glutamicum for the valorization of lignin-derived aromatics

Corynebacterium glutamicum is an established workhorse of industrial biotechnology. The microbe possesses a vast metabolism for the degradation and assimilation of aromatic compounds providing a huge opportunity to valorize the massive amounts of aromatics in lignin waste streams that are annually generated as an unfavorable by-product in biomass-fractionation facilities. In my work, I am using different tools of systems biotechnology and metabolic engineering to characterize the cellular network underlying aromatics metabolism as a knowledge base to tailor C. glutamicum for the production of aromatic-based sustainable polymer precursors and bioactive compounds.

University of Saarland & INM

Evaluation of bacterial behavior in Pluronic-based living therapeutic materials and biocompatibility assessment in vitro and in vivo

Living Therapeutic Materials (LTMs) enclose living biofactories within nonliving matrices, such as natural and synthetic polymers, and can produce and release drugs in situ and on demand. For therapeutic applications, LTMs are in direct contact with the host and thus their safety is to be guaranteed throughout the entire exposure time. We aimed to establish a practical workflow for assessing the cytocompatibility of LTMs in vitro that allows the parallel investigation of a higher number of application conditions. Further, we intended to investigate the safety of these LTMs using a mouse model in vivo. This marks a step towards establishing a roadmap for the biocompatibility assessment of LTMs in a standardized way.

HIPS

Comparative Metagenomic analysis on COPD and health control samples

His research aims to develop a novel therapeutic approach for the treatment of lung infections by using therapeutic microorganisms as living materials. Bioinformatic analysis of metagenomic data from patients with lung diseases and healthy individuals is used to identify beneficial commensal bacteria and resistance mechanisms of pathogens. His areas of interest include metagenomic data analysis and sequence algorithms.

INM

HIPS

Investigation of the biosynthesis of myxobacterial second metabolites

INM

University of Saarland

Keeping living therapeutic materials (LTMs) under the radar of neutrophils

INM

Fabrication of Living Therapeutic Materials by Extrusion Printing

INM

Graduation May 2025

Thermoplasmonic stimulation of gold nanorods for engineered living materials

We design Engineered Living Materials with core-shell structures that are NIR light responsive and can rapidly reach 39°C-44°C to induce protein (mCherry) or antibiotic (Darobactin) production. The protein and drug production is quantified as a function of plasmonic stimulation by gold nanorods via ex situ fluorescence microscopy and ESI-MS.

HIPS

Graduation: February 2025

Bioanalytical investigations of natural products and their derivatives: Mode of resistance, pharmacological properties and off-target characterization of cystobactamids

University of Saarland

Graduation: January 2025

Metabolically engineered Corynebacterium glutamicum with biosensing and drug delivering properties for living therapeutic material applications

The human ocular surface is a complex environment influenced by various intrinsic and extrinsic stressors causing homeostasis disruption and eventually the development of eye diseases. Promising new directions for its treatment are the use of remarkable protective properties of ectoine, a widely distributed compatible solute originating from extreme environments. A cluster of genes involved in ectoine production serves as a starting point to upgrade Corynebacterium glutamicum to a versatile cell factory with therapeutic capabilities and afterward encapsulation into sophisticated polymeric matrices for a better efficacy and safety.

INM

Graduation: December 2024

Engineering temperature-responsive gene circuits in bacteria to regulate therapeutic production

Thermo-responsive genetic circuits are being designed in beneficial microbes to allow the thermally activated release of antimicrobial compounds to inhibit the growth of pathogenic bacteria.

University of Saarland

Graduation: April 2024

Response of immune killer cells to mechanical cues and living therapeutic materials

I worked on characterizing the immune response of human peripheral mononuclear cells to bacteria encapsulated in pluronic based hydrogels (AG Sankaran) in vitro. We examined the subsets of NK and T cells, release of cytokines and cytotoxic proteins.

INM

Graduation: February 2024

Light-regulated Pro-angiogenic Engineered Living
Materials

HIPS

Graduation: March 2024

Structure-and activity-guided biotechnological engineering to produce improved anti-Gram-negative darobactins

Carsten Seyfert works in the group of Prof. Dr. R. Müller at HIPS as a PhD student. His focus is on bioengineering of biosynthetic pathways for heterologous expression, production and purifcation of optimized novel naturally derived derivatives of antibacterial compounds using a structure-and activity-driven approach to characterize their biophysical and antibacterial properties.

University of Saarland

Graduation: January 2024

Production of the polyketide-based nutraceuticals and pharmaceuticals
using metabolically engineered Actinobacteria

Curcuminoids are secondary metabolites extracted from turmeric (Curcuma longa, L.). These compounds exhibit myriad of biological activities. A property of curcuminoids that draws special attention is its anti-HPV (human papilloma virus) activity. More than 99% cases of cervical cancer are caused by chronic HPV infections. In this work, we aim to metabolically engineer C. glutamicum, a bacterium with GRAS status widely used in white biotechnology, into curcuminoid producing living therapeutic microbe. This approach offers a promising solution in overcoming the challenge of drug delivery in the treatment of cervical cancerous lesions.

HIPS

Graduation: November 2023

Expanding the scope of bioactive natural products from myxobacteria through alteration of cultivation conditions

Sebastian cultivates myxobacteria using different approaches to improve production of bioactive natural products. He then isolates, purifies and investigates those secondary metabolites for their structure, physico-chemical properties, bioactivities, and biosynthesis.

INM

Graduation: March 2023

Functional and safe encapsulation of Escherichia coli in Pluronic hydrogels for engineered living materials

My research focuses on using pluronic-based hydrogels to encapsulate microorganisms and enabling the precise control of their function for the fabrication of functional ELMs. My work ranges from studying the fundamental properties of genetically modified bacteria within pluronic hydrogels (such as shape, morphology, and metabolic activity) and mechanical characterization of pluronic matrices using rheology to developing efficient biosensors and ELM designs (including 3D printing) for in vitro immune response characterization and drug delivery applications.

University of Saarland

Graduation: November 2022

Analysis of the epithelial cell fate in organoid- and 3D-cultures of the human cervix uteri in the context of human papillomavirus infection

I have studied the cell fate of human primary cells of the cervix uteri using organoid culture, which allows cultivation of adult stem cells according to their tissue origin. This work and culture method could provide a basis for therapeutic testing and applications in a three-dimensional context with regard to human papillomavirus infection and cervical cancer progression.

University of Saarland

Graduation: April 2021

Discovery of new natural products and biosynthetic gene clusters encoded in the genome of Streptomyces albus subsp. Chlorinus

University of Saarland

Establishing of an Organ-on-a-Chip-System as a new possibility to analyze bacterial inflammation in different organ systems

To simulate an infectious event in the lung and the effects on other parts of the human body, bacterial stimulated lung cells and liver cells are connected in a circulation system. After the experiment the output from the system is used to measure specific cytokines and the gene expression of involved acute phase proteins.

INM

University of Saarland