Periodic Reporting for period 1 - BLUETOOLS (INNOVATIVE TOOLS FOR SUSTAINABLE EXPLORATION OF MARINE MICROBIOMINNOVATIVE TOOLS FOR SUSTAINABLE EXPLORATION OF MARINE MICROBIOMES: TOWARDS A CIRCULAR BLUE BIOECONOMY AND HEALTHIER MARINE ENVIRONMENTS)
Reporting period: 2022-12-01 to 2024-05-31
Marine microbiomes represent 90% of the total living marine biomass but only a small fraction of them can be cultivated. For this reason, they are an underexplored source of bioactive compounds, carbohydrate polymers and proteins, among others. Sampling the marine biodiversity, screening, identifying and isolating the relevant microbes is cumbersome, expensive and results in a heavy environmental burden, low yields, high costs and long times to market. BLUETOOLS will unravel the potential of marine microbiomes for healthier oceans and the Blue Bioeconomy through integration of different fields to develop cutting-edge tools that support fast, efficient AND sustainable exploration and exploitation of microbiomes, avoiding the drawbacks of conventional biodiscovery practices. This general objective comprises 6 goals:
• Reduce the environmental impact of bioprospecting by investigating alternative and sustainable sources of microbiomes.
• Establish innovative cultivation and enrichment procedures using minimal volumes to maximise the potential of marine microbiomes for environmental and industrial applications.
• Develop beyond the state-of-the-art bioinformatic tools to overcome the current limitations of metagenomic data processing pipelines for genome-resolved, high-quality data, portability and interoperability.
• Use a fast and versatile discovery approach to discover microbes, proteins and genes for several applications, among others pharma and medicine, materials, environmental applications, agriculture.
• Create the road for the generated solution products to reach the market through specialized training, exploitation, dissemination, communication, and engagement with key societal actors.
• Ensure the cost and environmental performance of BLUETOOLS's microbiome-based solutions are competitive through the integrated use of Life Cycle Assessment (LCA).
• Reduce the environmental impact of bioprospecting by investigating alternative and sustainable sources of microbiomes.
• Establish innovative cultivation and enrichment procedures using minimal volumes to maximise the potential of marine microbiomes for environmental and industrial applications.
• Develop beyond the state-of-the-art bioinformatic tools to overcome the current limitations of metagenomic data processing pipelines for genome-resolved, high-quality data, portability and interoperability.
• Use a fast and versatile discovery approach to discover microbes, proteins and genes for several applications, among others pharma and medicine, materials, environmental applications, agriculture.
• Create the road for the generated solution products to reach the market through specialized training, exploitation, dissemination, communication, and engagement with key societal actors.
• Ensure the cost and environmental performance of BLUETOOLS's microbiome-based solutions are competitive through the integrated use of Life Cycle Assessment (LCA).
The activities of BLUETOOLS since the beginning of the project have been directed mostly at procuring samples and establishing new metagenome mining strategies as well as using established methods to yield already the first candidate genes and enzymes, which has led to an early kick-off of their validation.
First, a methodological framework was established for sampling, DNA extraction and sequencing. New sampling has been carried out following ABS considerations, while promoting an extensive reuse of prior samples. As an example, we have acquired and reused several hundreds of samples from up to 25 different environments amounting to 68% of our envisioned sampling target.
We have also started the development of new tools to improve current bioinformatic pipelines, building on current databases and research infrastructure as well as minding and fostering interoperability in cooperation with relevant actors, such as ELIXIR, DoE-JGI and EMBL-EBI. The BLUETOOLS bioinformatic pipeline is already established and its functionality and interoperability will expand further in RP2.
In the meantime, sequence-based and activity-based discovery of new biomolecules and their associated functionalities has started. Several new high and (ultra)high-throughput screening assays have been developed and will be applied in the next reporting period. In the meantime, using bioinformatic approaches, we have uncovered several thousands of candidate BGCs of which 12 are being tested for confirmation, 246 novel enzymes ready to be commercialised, 51 candidate resistance genes, 1 enzyme with putative antifouling activity. This represents 60% of the enzyme target, 85% of the resistance genes, 100% of the BGC candidates, 33% of the biofouling solutions envisioned for BLUETOOLS.
In parallel, communication strategies aimed at promoting the existence of the project have been launched, and the first results have been disseminated in the form of 3 manuscripts and 5 communications in conferences. In addition, some training and outreach activities have taken place.
First, a methodological framework was established for sampling, DNA extraction and sequencing. New sampling has been carried out following ABS considerations, while promoting an extensive reuse of prior samples. As an example, we have acquired and reused several hundreds of samples from up to 25 different environments amounting to 68% of our envisioned sampling target.
We have also started the development of new tools to improve current bioinformatic pipelines, building on current databases and research infrastructure as well as minding and fostering interoperability in cooperation with relevant actors, such as ELIXIR, DoE-JGI and EMBL-EBI. The BLUETOOLS bioinformatic pipeline is already established and its functionality and interoperability will expand further in RP2.
In the meantime, sequence-based and activity-based discovery of new biomolecules and their associated functionalities has started. Several new high and (ultra)high-throughput screening assays have been developed and will be applied in the next reporting period. In the meantime, using bioinformatic approaches, we have uncovered several thousands of candidate BGCs of which 12 are being tested for confirmation, 246 novel enzymes ready to be commercialised, 51 candidate resistance genes, 1 enzyme with putative antifouling activity. This represents 60% of the enzyme target, 85% of the resistance genes, 100% of the BGC candidates, 33% of the biofouling solutions envisioned for BLUETOOLS.
In parallel, communication strategies aimed at promoting the existence of the project have been launched, and the first results have been disseminated in the form of 3 manuscripts and 5 communications in conferences. In addition, some training and outreach activities have taken place.
BLUETOOLS is developing tools beyond the state of the art to mine marine microbiomes for novel enzymes, genes, microbes and molecules. For instance, we have developed 3 new ultrahigh-throughput screening assays as well as a best-in-class bioinformatic pipeline. Novel biological concepts, such as specific gene modifications involved in bacterial pathogenesis and with wider implications and applications have been published with great impact among the scientific community.
The collaborative and intersectoral work developing and applying these tools has allowed BLUETOOLS to generate high-quality data, several panels of novel enzymes and hits for new antibacterial solutions expected to increase the innovation potential and economic prospects. AS the project moves from the sampling into the screening phase, we expect to uncover further novel enzymes and genes, as well as confirm these “front-runner” hits into leads.
Regarding wider societal impacts, BLUETOOLS promotes a culture of “econology” or combining economy and ecology in the sustainable exploration and exploitation of marine microbiomes. To this end, BLUETOOLS complies with the existing framework towards ABS, while explores complementary aspects and implications of the Nagoya Protocol, such as the tension between ABS on DSI and Open Science. The project has developed the required tools and channesl to convey awareness of this topic and the project itself through a strategy that lays out key messages, target groups and suitable communication channels to reach the target groups, such as a website that received 2100+ visits, social media channels with 350+ followers, a project video with 3200+ views, 14 articles and blog posts distributed to 80.000+ readers, 2 infographics, a roll-up, a brochure, and a factsheet. We have also, already reached over 50,000 people through our posts on our social media.
BLUETOOLS is promote transitions to a circular bioeconomy with our technological value proposition across different industrial sectors in Europe and beyond with a multi-actor approach across value chains focused on local resources, through the activities for partners PROZO (Northern Europe) and SERVIER (Eastern Europe), IIT in the Mediterranean area, valorising microbiomes for biomedicine application, or BASF valorising wastewater for polymer degrading microbiomes. Moreover, BLUETOOLS reaches out globally by collaborating with Blue Growth projects (e.g. AtlantECO) or Advisory Board institutions in North and South America,
Finally, although it is too early to estimate the approximate and much less the real impact of BLUETOOLS discoveries, some trends begin to emerge where the project is more advanced. For instance, preliminary scale-up experiments of pharmaceutical syntheses at SERVIER, indicate significant reduction (~40-60%) in use of chemicals, time and costs.
The collaborative and intersectoral work developing and applying these tools has allowed BLUETOOLS to generate high-quality data, several panels of novel enzymes and hits for new antibacterial solutions expected to increase the innovation potential and economic prospects. AS the project moves from the sampling into the screening phase, we expect to uncover further novel enzymes and genes, as well as confirm these “front-runner” hits into leads.
Regarding wider societal impacts, BLUETOOLS promotes a culture of “econology” or combining economy and ecology in the sustainable exploration and exploitation of marine microbiomes. To this end, BLUETOOLS complies with the existing framework towards ABS, while explores complementary aspects and implications of the Nagoya Protocol, such as the tension between ABS on DSI and Open Science. The project has developed the required tools and channesl to convey awareness of this topic and the project itself through a strategy that lays out key messages, target groups and suitable communication channels to reach the target groups, such as a website that received 2100+ visits, social media channels with 350+ followers, a project video with 3200+ views, 14 articles and blog posts distributed to 80.000+ readers, 2 infographics, a roll-up, a brochure, and a factsheet. We have also, already reached over 50,000 people through our posts on our social media.
BLUETOOLS is promote transitions to a circular bioeconomy with our technological value proposition across different industrial sectors in Europe and beyond with a multi-actor approach across value chains focused on local resources, through the activities for partners PROZO (Northern Europe) and SERVIER (Eastern Europe), IIT in the Mediterranean area, valorising microbiomes for biomedicine application, or BASF valorising wastewater for polymer degrading microbiomes. Moreover, BLUETOOLS reaches out globally by collaborating with Blue Growth projects (e.g. AtlantECO) or Advisory Board institutions in North and South America,
Finally, although it is too early to estimate the approximate and much less the real impact of BLUETOOLS discoveries, some trends begin to emerge where the project is more advanced. For instance, preliminary scale-up experiments of pharmaceutical syntheses at SERVIER, indicate significant reduction (~40-60%) in use of chemicals, time and costs.