Periodic Reporting for period 1 - SECRETed (Sustainable Exploitation of bio-based Compounds Revealed and Engineered from naTural sources.)
Periodo di rendicontazione: 2021-06-01 al 2022-05-31
Surfactants are a very diverse group of lipids with a common amphiphilic nature (both hydrophilic and hydrophobic domains within the same molecule). This ultimately favors the solubilisation of hydrophobic substances in water. Thus, they are applied especially in household and industrial cleaning. Additionally, they can form complex structures, such as micelles, being employed also as carriers for active ingredients in the cosmetic, nutritional, and pharmaceutical industries. Those biosurfactants with the ability to chelate and transport Fe3+ ions are called marine (amphiphilic) siderophores. This special ability makes them useful in other interesting fields. Surfactants usually come from the petrochemical sectors. However, there is an increasing interest in obtaining them from renewable sources. Moreover, biosurfactants exhibit a higher activity, lower toxicity, and higher biodegradability. Despite their significant advantages, higher production costs and lower chemical diversity keep the biosurfactants market only at 10% of the global surfactant market. This emphasizes the need for better-producing strains and tailor-made biomolecules to satisfy the industry requirements.
The overarching goal of SECRETed is to unlock the potential of marine and extremophilic bacteria as sources of tailormade amphiphilic molecules by means of:
To screen SECRETed microbial collections for biosurfactants and siderophores to infer novel Biosynthetic Gene Clusters (BGCs) in charge of their synthesis.
To construct an integrated genomic and chemical database containing described siderophore and biosurfactant pathways and specific subclusters, their chemical structures, and physiochemical properties.
To produce and iteratively refine a ‘mix and match’ modelling pipeline.
To validate and optimize designed new-to-nature BGCs and metabolic engineering of selected chassis.
To characterize compounds and optimize production and purification methods.
To develop and validate an integrated mathematical model of the production process.
To demonstrate the proposed solution at TRL-6 with the application of developed microbial strains in pilot-plant scale bioprocesses.
To assess the environmental, economic, and social perspectives of the process and products.
To exploit project results.
The overarching goal of SECRETed is to unlock the potential of marine and extremophilic bacteria as sources of tailormade amphiphilic molecules by means of:
To screen SECRETed microbial collections for biosurfactants and siderophores to infer novel Biosynthetic Gene Clusters (BGCs) in charge of their synthesis.
To construct an integrated genomic and chemical database containing described siderophore and biosurfactant pathways and specific subclusters, their chemical structures, and physiochemical properties.
To produce and iteratively refine a ‘mix and match’ modelling pipeline.
To validate and optimize designed new-to-nature BGCs and metabolic engineering of selected chassis.
To characterize compounds and optimize production and purification methods.
To develop and validate an integrated mathematical model of the production process.
To demonstrate the proposed solution at TRL-6 with the application of developed microbial strains in pilot-plant scale bioprocesses.
To assess the environmental, economic, and social perspectives of the process and products.
To exploit project results.
Guides on standards and organization of protocols used for preparation and processing of samples, together with a joint effort in knowledge sharing and refinement of screening procedures have been performed.
More than 60 thermophiles, 300 psychrophiles and piezophiles, have been successfully screened to date. Moreover, more than 400 halophilic genomes have been inspected for their further selection into the screening procedure. In addition to the microbial sources, a library of 5.000 crude extracts (in organic solvents) was generated from their cultures. Those extracts have started to be tested to detect siderophores and biosurfactants.
Screening efforts over SECRETed microbial collections have provided to date more than 30 compounds whose promising properties and applications are starting to be validated.
Natural Language Process algorithms and their application in public databases and scientific publications have organized the biggest and most comprehensive biosurfactant and siderophore molecular database to date (2139 unique compounds, 1606 biosurfactants, 572 siderophores, and all available associated data).
A bottom-up approach has been dedicated to collecting refined and curated Biosynthetic Gene Clusters (BGCs) for Siderophores and Biosurfactants. Those are being employed as “anchoring points” to validate the action of phylogenetically related genes. Then, genomic information from more than 900 microbial producers will be inspected to explain the role of the genes in charge of SECRETed molecular diversity.
SECRETed has also collected information about protocols of DNA transfer, and genetic tools (including CRISPR-cas systems) that can be employed in SECRETed microbial physiologies. That also includes the characterization of suggested microbial chassis for their further usage.
Joint efforts into the refinement of already existing chemical procedures for the extraction, purification, and quantification of biosurfactants and siderophores have started to take place.
SECRETed end-users have also defined their experimental strategies to validate the industrial nature of selected compounds. Moreover, their industrial parameters are being calculated from SECRETed internal database of compounds (more than 1500 industrial parameters along 1200 biosurfactants).
Finally, twenty results are identified and reflect a range of services, knowhow, intermediate and end compound formulations. Several means IPRs protection have been considered. A draft exploitation roadmap of both market-oriented and scientific exploitation of the SECRETed results has been prepared for strategic planning.
SECRETed follows an intensive dissemination strategy to drive various messages through parallel channels to the general public and specific audiences. SECRETed holds more than 500 followers on its social media pages, 9 participations in events/conferences, 3 scientific articles, and took the initiative to launch the AIMS Cluster of projects (more information at: https://www.secreted.eu/).
More than 60 thermophiles, 300 psychrophiles and piezophiles, have been successfully screened to date. Moreover, more than 400 halophilic genomes have been inspected for their further selection into the screening procedure. In addition to the microbial sources, a library of 5.000 crude extracts (in organic solvents) was generated from their cultures. Those extracts have started to be tested to detect siderophores and biosurfactants.
Screening efforts over SECRETed microbial collections have provided to date more than 30 compounds whose promising properties and applications are starting to be validated.
Natural Language Process algorithms and their application in public databases and scientific publications have organized the biggest and most comprehensive biosurfactant and siderophore molecular database to date (2139 unique compounds, 1606 biosurfactants, 572 siderophores, and all available associated data).
A bottom-up approach has been dedicated to collecting refined and curated Biosynthetic Gene Clusters (BGCs) for Siderophores and Biosurfactants. Those are being employed as “anchoring points” to validate the action of phylogenetically related genes. Then, genomic information from more than 900 microbial producers will be inspected to explain the role of the genes in charge of SECRETed molecular diversity.
SECRETed has also collected information about protocols of DNA transfer, and genetic tools (including CRISPR-cas systems) that can be employed in SECRETed microbial physiologies. That also includes the characterization of suggested microbial chassis for their further usage.
Joint efforts into the refinement of already existing chemical procedures for the extraction, purification, and quantification of biosurfactants and siderophores have started to take place.
SECRETed end-users have also defined their experimental strategies to validate the industrial nature of selected compounds. Moreover, their industrial parameters are being calculated from SECRETed internal database of compounds (more than 1500 industrial parameters along 1200 biosurfactants).
Finally, twenty results are identified and reflect a range of services, knowhow, intermediate and end compound formulations. Several means IPRs protection have been considered. A draft exploitation roadmap of both market-oriented and scientific exploitation of the SECRETed results has been prepared for strategic planning.
SECRETed follows an intensive dissemination strategy to drive various messages through parallel channels to the general public and specific audiences. SECRETed holds more than 500 followers on its social media pages, 9 participations in events/conferences, 3 scientific articles, and took the initiative to launch the AIMS Cluster of projects (more information at: https://www.secreted.eu/).
SECRETed’s ambition is the generation of pioneer workflows integrating molecule design, strain design, and process optimization to produce new products and processes that will revolutionise the biosurfactants and siderophore-related industry.
First, SECRETed’s core expertise in biosurfactants and siderophores will accelerate the screening phase to be in line with defined overall goals.
Then, SECRETed progress beyond the state-of-the-art concerns the obtention of information contained in the public databases to cover SECRETed end-users needs. Predicted chemical descriptors with such properties will guide an inverse QSAR/QSPR approach to propose new-to-nature chimeric amphiphilic molecules in a "mix and match" approach.
To do this, SECRETed envisions the obtention and integration of siderophore and biosurfactant gene clusters, their phylogenetic relationships, and their role in biosynthetic pathways.
Finally, hybrid approaches involving modelling gene expression machinery and Genome-scale metabolic models (GEMs) will be employed to look for optimized strain designs.
SECRETed will expand the microbial producers’ catalog by including other species among marine and extremophilic bacteria for which standardized genetic toolboxes are not available yet.
Obtained results will overall provide the following general impacts:
Supporting the EU in becoming the global leader in Biosurfactant industry through the synthesis of tailor-made compounds according to the industry and consumer needs.
Pushing forward to a European greener technological industry by combining powerful synthetic and systems biology tools with optimization approaches in the design of processes.
The development of highly efficient microbial platforms with the ability to consume raw feedstocks remarks the importance of protecting the oceans and aquatic environments as our richest source of biological diversity and highlights the concept of circularity.
Connecting blue and white biotechnology is the main axis of the project. Their usage in 5 different fields will be evaluated: cosmetics, household care, food industry/nutrition, agrochemical industry, and genetic material delivery.
First, SECRETed’s core expertise in biosurfactants and siderophores will accelerate the screening phase to be in line with defined overall goals.
Then, SECRETed progress beyond the state-of-the-art concerns the obtention of information contained in the public databases to cover SECRETed end-users needs. Predicted chemical descriptors with such properties will guide an inverse QSAR/QSPR approach to propose new-to-nature chimeric amphiphilic molecules in a "mix and match" approach.
To do this, SECRETed envisions the obtention and integration of siderophore and biosurfactant gene clusters, their phylogenetic relationships, and their role in biosynthetic pathways.
Finally, hybrid approaches involving modelling gene expression machinery and Genome-scale metabolic models (GEMs) will be employed to look for optimized strain designs.
SECRETed will expand the microbial producers’ catalog by including other species among marine and extremophilic bacteria for which standardized genetic toolboxes are not available yet.
Obtained results will overall provide the following general impacts:
Supporting the EU in becoming the global leader in Biosurfactant industry through the synthesis of tailor-made compounds according to the industry and consumer needs.
Pushing forward to a European greener technological industry by combining powerful synthetic and systems biology tools with optimization approaches in the design of processes.
The development of highly efficient microbial platforms with the ability to consume raw feedstocks remarks the importance of protecting the oceans and aquatic environments as our richest source of biological diversity and highlights the concept of circularity.
Connecting blue and white biotechnology is the main axis of the project. Their usage in 5 different fields will be evaluated: cosmetics, household care, food industry/nutrition, agrochemical industry, and genetic material delivery.