Science Support

Next generation sequencing, proteomics, and metabolomics applications for studying metaorganisms

The primary task of the Z3 project is to provide a specialized platform for next generation sequencing (NGS), proteomics-, and metabolomics-based applications tailored to the needs of the individual CRC 1182 subprojects. As the CRC projects work with a broad set of organisms when studying the origin and function of metaorganisms, the Z3 project aims to meet the specific requirements (e.g., sample preparation, input material from various sources, protocol adaptation) from non-standard sample types.

The NGS-based applications include whole genome sequencing, including the de novo whole genome sequencing of non-model organisms, whole exome sequencing, epigenome analysis via reduced representation bisulfite sequencing, transcriptome analysis including single cell protocols, as well as bacterial profiling via 16S rRNA gene amplicon sequencing and functional shotgun metagenomics/metatranscriptomics. The infrastructure of the Competence Centre for Genome Analysis (CCGA) serves as the backbone while dedicated personnel adjusts the applications and processing workflows to the needs of the CRC. We will hence provide maximum flexibility and deliver the most recent technological developments to the CRC members, while maintaining standardization of the CCGA pipelines.

The proteomics applications of the Z3 project employ liquid chromatography-mass spectrometry (LC-MS)-based proteomics methods for the identification, quantification and molecular characterization (i.e., posttranslational modifications) of proteins, proteomes (cytosolic, supernatants) and peptides/peptidomes. Both bottom-up and top-down proteomics workflows will be applied to provide proteoform-centric insights into the molecular mechanisms driving and controlling the interaction between the organisms. Proteomics approaches will also be applied for the analysis of rare or difficult to isolate cells, such as stem cells or organ specific cells to decipher molecular mechanisms within metaorganisms down to the cellular/organ level.

The Z3 project specific metabolomics applications will include spatial metabolomics with mass spectrometry imaging (MSI) and LC-MS/MS based methods for untargeted and targeted metabolite analysis of extracts from cells, tissues and supernatants of cell cultures. Our analysis of the metabolome detects endogenous metabolites and those deriving from the microbiome and environmental factors (e.g., nutrition, drugs, and environmental metabolites). The localization of in-vivo metabolic fingerprints of single cells and/or tissues in direct contact with microbial partners using spatial metabolomics capabilities will be essential phenotypic information for the diverse model and non-model organisms. The infrastructure of the metabolomics platform at Kiel University is currently in development and will be equipped with newest state-of the art mass spectrometry devices delivering the most recent metabolomics technology with highest sensitivity. The platform consists at the moment (Q1/2023) of one LC-MS/MS system, one MALDI-MSI system and a GCMS for metabolite analysis (guaranteed access via Bridging group of PI Liebeke between Kiel University and MPIMM, Bremen) and will be equipped with another LC-MS/MS system in Q4/2023 to ensure access to state-of-the art methods for the CRC.



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