PhD Project 5
Extremophilic microorganisms against human, agricultural and aquacultural infections
Nerea Miro Garcia
I am a PhD fellow in Marine Natural Products Chemistry at GEOMAR Helmholtz Centre for Ocean Research Kiel (Germany). My role in the HOTBIO project is the bioactivity-guided isolation and structure elucidation of new antibiotic secondary metabolites from extreme marine microorganisms that can be later applied as medicines, agrochemicals or aquaculture drugs. More specifically, my research focuses on the optimized cultivation of extremophilic microorganisms by e.g., OSMAC approach; extraction and screening of microbial extracts against a panel of pathogens associated with human, agriculture and aquaculture infections; deep UPLC-MS and MS/MS based untargeted metabolomics using molecular networking/GNPS platform and open-source software for mass spectrometry data processing (MZmine3, SIRIUS, etc.); and genome mining/screening of the most promising microorganisms to inform the isolation of the secondary metabolites. I hold a master’s degree in Applied Blue Biotechnology and two bachelor’s degrees in Oceanography and Biotechnology from Catholic University of Valencia (Spain).
Extremophilic microorganisms against human, agricultural and aquacultural infections
Objectives: Microorganisms thriving in previously unexplored extreme marine environments represent a golden opportunity for discovery of novel and potent anti-infectives. Antibiotic discovery efforts have so far focused on Gram-positive marine bacteria (e.g., actinobacteria). This PhD project will aim to focus on less studied marine microbes, such as Gram-negative bacteria that are predominant in ocean bacterioplankton as well as in various extreme marine environments (a large collection available at GEOMAR).
The specific objectives are:
1) Optimized cultivation of microorganisms (WP2) by e.g., OSMAC approach to activate biosynthetic gene clusters (BGCs).
2) Extraction and screening of microbial cultures against a large panel of pathogens associated with human infections (ESKAPE and others), crop diseases (agriculture) and aquaculture diseases (fish and seaweed pathogens).
3) Deep UPLC-MS and MS/MS based metabolomics for dereplication of microbial extracts using molecular networks/GNPS platform.
4) Genomic mining/screening of the most promising microorganisms (with the highest bioactivity and chemical novelty) to inform the isolation of the secondary metabolites.
5) Purification of bioactive molecules (guided by bioactivity & bioactive molecular networks) and structure elucidation by spectroscopic methods.
6) Analysis of the key components of the biosynthetic pathway (BGCs) leading to hit bioactive molecules.
7)Preclinical studies on compounds, including mechanism of bioactivity and ADMET profiling.
