My project DEFCOMANT funded from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101020356, is approaching its final stage.

My hunch about Antarctic microorganisms being a hotbed of novel natural products proved true! For two years, I wooed these chilly microbes, using genomics, metabolomics, and bioactivity analyses to unlock their secrets. We unearthed a treasure trove of unexpected biosynthetic clusters encoding novel natural products, many silent in the lab - just as we anticipated. This wasn't a walk in the park, but by wielding a diverse toolkit and especially integrating genetics with metabolomics, we're close to uncovering compounds that could potentially tackle multidrug-resistant pathogens.

The challenge isn't finding new natural products in Antarctic bacteria, it's unlocking their potential. We must get creative and crack the code!

This is a public summary of my DEFCOMANT project as requested by the EU Commision. If you find anything interesting, please don't hesitate to contact me. I'm happy to discuss it further.

My project DEFCOMANT was be carried out at the University of Vienna, Department of Microbial Ecology of the Centre for Microbiology and Environmental Systems Science (CMESS), with support of the Czech Antarctic Infrastructure (Masaryk University, Brno, ID: LM2015078).

Summary of the context and overall objectives of the project:

The Action ""Establishing defined communities of Antarctic soil bacteria as potential sources of antimicrobials" delves into the untapped Antarctic soil bacteria as a rich and unexplored source of antimicrobial compounds. With its vast and unexplored bacterial diversity, this frozen continent represents a potential treasure trove of novel antimicrobial compounds. Importantly, this project goes beyond mere discovery; it also investigates our ability to unlock these hidden antimicrobials through innovative cultivation approaches and tailored microbial consortia design.

Our reliance on microbes as a source of life-saving antibiotics is undeniable. The majority of antibiotics used in human medicine today stem from bacterial and fungal sources. However, the "golden antibiotic era" of compound-by-compound discovery has unfortunately slowed down dramatically. Despite extensive screening of microbial cultures and chemical libraries, the desired results have been elusive. This is where the focus shifts back to nature's untapped potential. By exploring unexplored and highly adapted microbes from extreme environments like Antarctica, and by developing novel methods to stimulate antimicrobial production in the lab, we can reignite the search for effective antimicrobials.

The escalating threat of resistant pathogens demands innovative solutions. The antibiotic revolution saved countless lives, but its very success has fuelled the rise of "superbugs" armed with multiple resistance mechanisms. To combat this growing crisis, we must explore new possibilities how to find novel antimicrobial compounds, or novel approaches how to combat resistant pathogens. This Marie Skłodowska Curie Action (MSCA) was designed to unlock the antimicrobial potential of extremophiles in Antarctica. These hardy bacteria face a brutal environment – freezing temperatures, intense UV radiation, and limited resources. But such harshness fosters resilience, driving these microbes to produce unique and potentially powerful chemical compounds. What makes Antarctic extremophiles so promising? Unlike their counterparts in milder environments, these bacteria have evolved under intense pressure, leading to the development of specialized adaptations and novel secondary metabolites. By studying these "extremophile cocktails," we hope to discover antimicrobial compounds with unique modes of action, potentially bypassing existing resistance mechanisms.

Objectives of this MSCA have been to:

(a) to recover (near) complete genomes from unique Antarctic isolates and then to predict their biosynthetic potential and other phenotypic traits from the genomes

(b) to establish microbial consortia and improve co-cultivation conditions to stimulate production of antimicrobial compounds

(c) to test antimicrobial activity of designed consortia against the most critical MDR human pathogens and against a set of human gut commensal strains.

Another goal of the MSCA Fellowship was to foster the development of the individual researcher, which I believe was successful 😊.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far:

Work performed during this fellowship was ascribed to three work packages (WPs). WP1 was designed to screen and classify bacterial strains isolated from Antarctic soils and select several representants for whole-genome sequencing to access biosynthetic potential encoded in their genomes. This WP led to two conference contributions and one forthcoming publication. WP2 was designed to directly access this biosynthetic potential and stimulate production of novel antimicrobial compounds via rational design of microbial consortia (mini microbial communities) and stimulation of monocultures. This WP resulted in two conference contributions, with one of these contributions being invited keynote speaker. Results of this WP are composed into two forthcoming papers currently being finalised. WP3 was aimed to test the antimicrobial effect of compounds produced by Antarctic bacteria against a set of the most clinically relevant and critical multidrug resistant human pathogens and human gut microbiota members. Results of WP3 are part of the two forthcoming publications described in WP2 and will be communicated with scientific audience at upcoming conferences. In general, the extensive datasets acquired during the MSCA fellowship are anticipated to significantly extend the project's reach and impact by influencing numerous future publications beyond the initial works produced and published during the fellowship itself.

During the Action, I actively communicated the action to the broader public, participated in a public discussion panel, delivered 5 online and 3 print interviews, contributed to a book entry in the "Hundred Times Antarctica" popularizing Antarctic science, was invited into a radio interview on antimicrobial resistance and Antarctic research, and twice pitched the project at Falling Walls Lab competition. This research was also presented at the Austrian Polar Research Institute annual meeting facilitating networking between Austrian and Czech polar initiatives. I engaged with the young generation through a poster in the poster gallery on Antarctic Research, 2 printed interviews encouraging young women in science and a presentation at gymnasium engaging students. I alo maintained a vibrant social media presence on LinkedIn, Facebook, X and a this research website.

Progress beyond the state of the art, expected results until the end of the project and potential impacts :

This MSCA has significantly influenced the field of polar microbiology and the search for novel compounds in extreme environments. Notably, the project's systematic focus on a broader spectrum of Antarctic isolates has illuminated previously hidden aspects of their biosynthetic potential. This groundbreaking knowledge is accompanied by high-quality sequencing and metabolomics data, all of which will be freely accessible in open databases. This open-access approach unlocks new frontiers for targeted research and comparative analysis within the scientific community. Furthermore, the methods used during this research, combined with the obtained data and open culture collection readily available through the Czech Antarctic Research Programme, create a solid foundation for future research efforts. This paves the way for innovative explorations and discoveries using the unique potential of psychrophilic and psychrotrophic microorganisms from Antarctica or other polar regions.

Impact of this Action extends far beyond academia, holding the potential to shape the future in several exciting ways. By shedding light on the biosynthetic potential of Antarctic microbes, this project lays the groundwork for the development of new antibiotics and antifungal compounds. The open-access data and resources generated by this project can motivate and empower future generations of scientists to explore the hidden potential of extremophiles and contribute to solutions for global challenges. This includes not only exploration of novel antimicrobials but also unique adaptations of Antarctic psychrophiles that could lead to the development of cold-adapted enzymes and biocatalysts fuelling sustainable solutions. And finally, results of this Action highlight the critical need to protect these vulnerable resources, safeguarding tools for addressing humanity's biggest challenges. This goes beyond biodiversity preservation; it's about securing a future rich with possibilities in medicine, sustainability, and beyond.

Useful links for more details:

EU: https://cordis.europa.eu/project/id/101020356

DOME (CMESS): https://www.microbial-ecology.net/ 

Czech Antarctic Research Programme: https://carp.sci.muni.cz/

Austrian Polar Institute: https://www.polarresearch.at/