{"id":128999,"date":"2026-09-09T11:27:14","date_gmt":"2026-09-09T11:27:14","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/?page_id=128999"},"modified":"2026-09-09T15:09:28","modified_gmt":"2026-09-09T15:09:28","slug":"blueprint","status":"publish","type":"page","link":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/projects\/blueprint\/","title":{"rendered":"BLUEPRINT"},"content":{"rendered":"\n
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Computationally-guided design of marine microbial consortia for biotech applications<\/p>\n\n\n\n\n

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Marine microbial communities underpin ocean ecosystem functioning and represent a largely unexplored resource for the blue bioeconomy. Advances in high-throughput sequencing have dramatically expanded access to marine genomic and metagenomic data, revealing immense microbial diversity and metabolic potential. However, much of this information is derived from metagenome-assembled genomes (MAGs), that are reconstructed from complex community samples in contrast to genomes of isolated species, which hampers further experimental investigation. As a result, translating predicted metabolic functions into rational experimental design with culturable organisms remains a major bottleneck.<\/p>\n\n\n\n

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Figure 1. BLUEPRINT project iterative design. Image generated by ChatGPT.<\/em><\/figcaption><\/figure>\n\n\n\n

To address this gap, we have developed a computational pipeline to design synthetic marine communities based on the following rationale. We suggest that culturable species which are metabolically similar to MAGs predicted to have a specific function and interact in the wild are likely to enhance each other’s function if co-cultured in vitro. Therefore, our pipeline consists of three modules: <\/p>\n\n\n\n

1) Metabolic function search in isolated genomes and MAGs<\/p>\n\n\n\n

2) Propagation of species interactions from the MAGs co-occurrence network to isolated genomes<\/p>\n\n\n\n

3) Metabolic modelling to predict interacting potential of pairs of species with functions based on exchanged metabolites.<\/p>\n\n\n\n

Computationally predicted pairs of species are experimentally tested for relevant biotechnological applications: degradation of pollutants, production of polyhydroxyalkanoates, and production of carotenoids. The abundance of compounds of interest and relative species abundance in co-cultures are being validated using targeted analytical techniques and genomic approaches.<\/p>\n\n\n\n

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Figure 2. Schematic representation of the computational pipeline developed to identify synthetic microbial communities with biotechnological potential from ocean metagenomes, followed by experimental validation. Image generated by ChatGPT.<\/em><\/figcaption><\/figure>\n\n\n\n

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Project lead<\/h3>\n\n\n
\n \n \n
\n \"image\n \n

\n Maria Zimmermann<\/a>\n <\/h3>\n \n

\n Group Leader\n <\/p>\n \n \n \n \n

<\/p>\n\n\n\n

Lead scientist<\/h3>\n\n\n
\n \n \n
\n \"image\n \n

\n Sara Benito Vaquerizo<\/a>\n <\/h3>\n \n

\n Postdoctoral Fellow\n <\/p>\n \n \n \n \n

<\/div>\n\n\n\n

Collaborators<\/h3>\n\n\n
\n \n \n
\n \"image\n \n

\n Dragana Despotovic<\/a>\n <\/h3>\n \n

\n Postdoctoral Fellow (EIPOD)\n <\/p>\n \n \n \n \n \n \n \n Edit\n <\/a>\n <\/article>\n <\/div>\n\n\n\n

<\/p>\n\n\n

\n \n \n
\n \"image\n \n

\n Michael Zimmermann<\/a>\n <\/h3>\n \n

\n Group Leader\n <\/p>\n \n \n \n \n \n \n \n Edit\n <\/a>\n <\/article>\n <\/div>\n\n\n\n

<\/p>\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":5,"featured_media":0,"parent":714,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-128999","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/pages\/128999","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/comments?post=128999"}],"version-history":[{"count":9,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/pages\/128999\/revisions"}],"predecessor-version":[{"id":129205,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/pages\/128999\/revisions\/129205"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/pages\/714"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/media?parent=128999"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/planetary-biology\/wp-json\/wp\/v2\/embl_taxonomy?post=128999"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}