Microbiome Lab
The Microbiome Labs are equipped with modern facilities to address scientific questions related to microbial diversity in bioeconomic production systems. Research in the laboratories focuses on understanding how agricultural management practices, food technology, and bioprocess engineering influence microbial communities.
The overall aim is to assess the impact of existing and innovative agronomic and technological processes on microbial diversity in order to develop optimized strategies for sustainable biomass production, safe and healthy food systems, and bioenergy generation, while minimizing undesired microbial effects.
The laboratories support interdisciplinary research on microbial communities in agricultural, environmental, and food-related systems, combining cultivation-based microbiology with modern molecular and sequencing approaches.
The laboratory facilities cover more than 900 m² across two floors and include over 20 specialized laboratories equipped for microbiological and molecular analyses.
The laboratories comply with German biosafety regulations and are equipped for work with microorganisms up to risk group 2, including genetic engineering work at biosafety level S1 (GenTG).
Research Focus
A central research focus of the laboratories is the study of soil, water, insect, and plant-associated microbiomes, including microbial inheritance across plant generations. The laboratories investigate how microorganisms colonize plant tissues, persist through developmental stages, and are transmitted from plants to seeds and subsequently to the next plant generation. These systems provide tractable models to study microbiome assembly, transmission routes, and host–microbe interactions in agricultural and natural ecosystems.
Methods and Analytical Capabilities
The laboratories integrate cultivation-based microbiology with modern molecular and sequencing approaches to investigate microbial diversity and function in complex biological systems. Methods include the isolation, cultivation, and characterization of aerobic and anaerobic microorganisms (archaea, bacteria, and fungi) as well as the analysis of complex microbial communities using molecular and sequencing-based approaches.
Key analytical capabilities include:
- Microbiome profiling using 16S and ITS rRNA gene amplicon sequencing and shotgun metagenomics
- Genome sequencing, RNA-seq, and metatranscriptomics through institutional and external sequencing facilities
- Analysis of antimicrobial resistance (AMR) in microbial communities
- Identification and characterization of microbial isolates using MALDI-ToF mass spectrometry
- Chromosomal tagging and strain tracking approaches for studying microbial colonization and transmission
- Physiological profiling of microbial isolates using phenotypic microarrays (OmniLog system)
- Experimental workflows for low-biomass and low-diversity microbiome systems, including contamination-aware approaches
- Gnotobiotic microcosm systems for controlled plant–microbiome interaction studies
- Root phenotyping in plant–microbiome experiments
Sequencing-based analyses and large-scale microbiome datasets are supported through institutional sequencing platforms and dedicated bioinformatics infrastructure.
