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Project Results

The ShikiFactory100 project will generate results in a range of formats. Navigate this page to find project deliverables, scientific publications and available communication material.





Project Deliverables

Public deliverables will be made available below as soon as they are complete:


WP1: Project Management - led by SilicoLife

  •  D1.4: Final project report to the European Commission - due MONTH 48


WP2: Retrosynthesis & Enumeration - led by SilicoLife

  •  D2.4: Pathway database with all ranking and analysis metrics - due MONTH 36


WP3: Chemical Synthesis of New Products - led by GalChimia

  •  No public deliverables


WP4: Gene Discovery & Protein Engineering - led by Universidade NOVA de Lisboa

  •  No public deliverable


WP5: In Silico Metabolic Engineering - led by EMBL

  • D.5.5: Public Final version of the updated models, due MONTH 42


WP6: Pathway Screening - led by University of Manchester

  •  No public deliverables


WP7: Cell Factory Construction - led by DTU

  •  No public deliverables

WP8: Product Validation & Sustainability Appraisal - led by DSM

  •  D8.5: Sustainability appraisal and risk assessment of 10 target molecules, due MONTH 48


WP9: Exploitation and Dissemination - led by NNFCC


Communication Material

Below is a collection of resources used to promote and disseminate information associated with the ShikiFactory100 project. 

Project video - a short video explaining the scope of the project in more detail. It can also be accompanied by English, Spanish and Portuguese subtitles.

Newsletter 01 - welcome to the first Shikifactory100 Newsletter!. Here, we aim to update you on all the progress made by our partners so far.

Project Leaflet  - contains general information about the project and describes its three major vectors (discovery, design & implementation, and validation).

Roll-up Banner - for project promotion at events such as conferences and trade fairs. 

Newsletter 02 - welcome to the final Shikifactory100 Newsletter! Here, we aim to update you on all the progress made by our partners.


Project Articles

Shikimate pathway - this article aims to provide background information about the research carried out by the project. It describes key metabolic pathways for living organisms, including the shikimate pathway, central to the Shikifactory100 project, and their applications at an industrial level.

Synthetic Biology for the Production of Biobased Molecules - this article aims to provide a background to the field of synthetic biology.  

Business plans for the Shikifactory100 project - this article gives more details about ShikiFactory100's business model and business plan.

Synthetic biology, sustainability and the circular bioeconomy - this article explores the process of transitioning towards a sustainable biobased bioeconomy.


Molecule Cards

As part of the ShikiFactory100 social media campaign, we have created molecule cards that introduce some of the 100 compounds the ShikiFactory project is working on. As these cards are posted on Twitter and LinkedIn, they will be made available on our website in the space below.



Scientific Publications

Synthetic biology can provide an alternative method for the production of bio-based industrial chemicals. But constructing the engineered microbial strains required for producing new chemicals can be time consuming. In this paper, the authors try to quantify the time requirements, on the basis of a state-of-the-art semi-automated strain engineering platform, using a collection of monomers for biomaterial production as their test case.


Psylocibin is a compound most famously found in “magic mushrooms”. It has potent psychotropic properties, which aside from its notorious recreational uses, is also thought to hold potential for the treatment of a range of psychological and neurological ailments. In their study, Milne et al demonstrate that psylocibin could be produced using engineered yeast Saccharomyces cerevisiae. Furthermore, the yeast could produce psilocybin derivatives that may have new useful pharmaceutical properties.


Aromatic amino acids are valuable chemicals and are precursors for a range of industrial compounds. This particular study looks at p-coumaric acid, which is a central precursor for many aromatic secondary metabolites, and aims to improve its production in yeast. Borja et al observed a significant effect that the carbon source had on the production, where xylose was a better substrate for p-coumaric acid production than glucose.


The comprehensive study of metabolites within cells, biofluids and tissues, referred to as metabolomics, often generates huge amounts of complex data generated by mass spectrometry. Identifying specific metabolites from such large amounts of data is a major challenge faced by researchers running metabolomics experiments. In this paper, Del Carratore et al. describe a new annotation method, explaining how the annotations are being applied and how to evaluate the confidence of the resulting annotations.


The need for efficient DNA construction methods is inherent to the field of Synthetic Biology. With this comes the need to verify the accuracy and quality of the engineered DNA through high-precision sequencing methods. In this paper, the researchers outline an innovative methodology that will enable newly constructed DNA samples to be sequenced and verified accurately and cheaply.


Rosmarinic acid is a compound found in several plants. It is widely used as a food and cosmetic ingredient and has various pharmaceutical applications. However the production of this compound remains limited as natural availability is low and chemical synthesis is too complex. This study, for the first time, shows recombinant production of rosmarinic acid in engineered yeast.


Resveratrol is a plant secondary metabolite with a range of medicinal properties. Its low availability from the plants has led researchers to develop microbial production of the compound, however commercially viable production levels are still proving difficult. In this study, the authors demonstrated that Yarrowia lipolytica is a promising host for the production of resveratrol along with several other valuable products.


Metabolic engineering involves the engineering and optimization of processes from single-cell to fermentation in order to increase production of valuable chemicals. Significant advances in strain engineering are leading metabolic engineering to become a truly manufacturing technology capable of producing goods on an industrial scale. This review article demonstrates that the success of metabolic engineering heavily relies on biodesign algorithms which identify promising production routes and regulation strategies.


The increasing demand for bio-based compounds is now allowing biofoundries to produce and deliver valuable goods on an industrial scale. Nowadays, entire portfolios of producer strains are being developed in record times thanks to the integration and automation of the design, build, test and learn (DBTL) steps of the production cycle. As new in silico design tools are being developed to improve the efficacy of DBTL pipelines, the ever-increasing data gathered by biofoundries can now be added to these in-silico tools, therefore rendering them even more powerful and reliable. This paper discusses the future of biomanufacturing in an environment where the process will not only be fully automated, but will also be able to learn and adapt quickly to produce optimal designs.



Scientific results from the ShikiFactory100 project will also be made available via CORDIS (Community Research and Development Information Service, the European Commission's public repository for the dissemination of information from all EU-funded research projects.

Results are to be stored and shared between partners via the ICE and GitLab platforms. 


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