Building an Alliance of Biofoundries Q&A with Paul Freemont

What does the Global Biofoundry Alliance mean for synthetic biology?

Go to the profile of Ross Cloney
May 20, 2019
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Earlier this month the synthetic biology world woke up to the announcement of a global alliance of sixteen biofoundriesPaul Freemont, co-founder of the Imperial College Centre for Synthetic Biology and SynbiCITE was kind enough to take the time to answer a few of my questions regarding the alliance and the future of role of foundries in synthetic biology.

 

Ross: Let’s start with the basics.  What is a biofoundry - despite the differences between members, what core characteristics do they share that defines something as a ‘foundry’?

 

Paul: Biofoundries generally provide Integrated experimental and computational infrastructure for designing building and testing genetic constructs in living cells. They generally employ a variety of liquid handling robots and automated protocols for simple molecular biology procedures like DNA assembly and automated DNA transformation – some biofoundries specialize in these aspects. These protocols allow high-throughput (HTP) screening and assay development which enable multiple experimental conditions to be explored in parallel, thus accelerating the whole Design-Build-Test-Learn cycleof synthetic biology/engineering biology. A major part of biofoundries also focuses on integrating analytics and measurements which generally involves mass spectrometry methods, next gen sequencing or other spectroscopic measurements aimed at sampling the ‘omics’ space as well as directly measuring targeted metabolites or biosynthetic products. Another major aspect of biofoundries is software which not only includes Laboratory Information and Management Systems (LIMs) but also BioCAD software tools for designing genetic constructs. Data-driven machine learning tools for analyzing the large datasets fills the Learn party of the DBTL cycle. Another feature is that many Biofoundries can be accessed via the cloud. I see biofoundries as the place where the synthetic biologist designer can test their ideas at scale without having to lift a pipette!

 

Ross: What’s the role of a biofoundry in the field of synthetic biology?  Are they intended purely for academic research or commercial development, or in the transition between the two?

 

Paul: I think that biofoundries sit at the interface between industry and academia and have roles to play in both aspects of synthetic biology/engineering biology. As public-funded facilities they are also able to develop open source technologies to accelerate academic research in synthetic biology. They are also able to work with industry to explore the utility of biofoundries in more applied biotechnology/biomedical research areas. In fact, many are encouraged to do so by their public funders. I see this as a unique feature of biofoundries where they can be enablers for many small companies and start-ups to access infrastructure they cannot afford as well as allow academic groupings to explore experimental research space that hitherto would not be accessible in their own laboratories.

 

Ross: Why a global alliance of biofoundries?  What does this enable that a single foundry, or a grouping of foundries in one country, wouldn’t be able to achieve individually?

 

Paul: The global nature of the alliance is really important as it promotes international cooperation in synthetic biology/engineering biology and biotechnology through collaborative biofoundry activities – remember that the concept of a biofoundry is very new and as such nobody really knows how to fully implement them. By sharing expertise and cooperation across the globe, it will lead to the co-development of open source technologies, shared protocols and reference materials as well as measurement standards and as such it will accelerate the uptake of the whole field of synthetic biology/engineering biology globally towards different research areas and applications. By working together, the whole global community benefits and a vision of accelerated biotechnology solutions to some of the world’s most pressing problems like energy, water, health food and climate change might happen more quickly (which we desperately need).

 

Ross: The alliance spans the globe but members are concentrated in North America, Europe, East Asia and Australia, with no current members based in South America, Africa or India among other places.   Do you know if there are there plans to establish biofoundries in these locations and if so, what benefits do you think they bring to these areas?

 

Paul: This is a great question and unfortunately developments in synthetic biology/engineering biology in these continents is slow. However, many of us are working closely with colleagues in these regions mainly on the educational and training parts of synthetic biology although part of this is to introduce the concept of programmable biology and low-cost infrastructure. I am currently working the Kenyan government agency NACOSTI and my ultimate dream is to set up a fully-operational Biofoundry in East Africa although there is much to do on the ground first. The most advanced region is possibly India but there is still an uncertainty about what synthetic biology is and how it could be implemented. I know several synthetic biology colleagues are engaged with Indian institutions so maybe soon we will see some biofoundry activities in India – I really hope so - of course the global alliance will also play a major role in promoting biofoundries worldwide providing information and expertise which can be accessed by any country wanting to know more about biofoundries and their utility for synthetic biology/engineering biology and biotechnology.

 

Ross: Finally, where do you see this alliance in the future and the role of biofoundries? What would a wildly successful outcome look like to you?

 

Paul: Another great question – I truly hope that the alliance will quickly establish global capability in synthetic biology/engineering biology which will lead to international cooperation and development in key areas like standards, reproducibility and reliability of biological measurement, metrology, biosecurity and rules for safe biodesign. I would like to see every academic institution have a biofoundry and as many regions in the world have access. I would like to see all public-funded biofoundries cooperate in an open manner for the greater public benefit. A doubly massive and slightly dreamy outcome would be the role of biofoundries in accelerating a transition to bio-based process and products as part of a global transition to a bioecononmy from a petro-chemical based economy. Based on current climate change projections, the future of humanity will rely in part on a rapid transition to a future world where sustainability and circular economies are second nature. One technology that can enable this is biotechnology and to fully exploit this technology, we need an environment of open technologies provided by biofoundries to promote and create a new and dynamic global synthetic biology industry for public benefit. However, if we achieve even 10% of this I will be over the moon as the global crises we are facing needs global action and much international cooperation and I am hopeful that the alliance can play a role in this. On a lighter note, I would really like to set free the worlds 14 million molecular biology pipetters, so they can think more about their experimental designs and data interpretation rather than spend hours in a lab moving their thumb up and down- this could perhaps be the ultimate success of biofoundries!

 

 

(The thumbnail and banner image is taken without modification from https://www.nature.com/articles/s41467-019-10079-2 “Building a global alliance of biofoundries” published under a CC-BY license.)

Go to the profile of Ross Cloney

Ross Cloney

Senior Editor, Nature Research

I handle manuscripts in synthetic biology and genome engineering for Nature Communications, along with therapeutic biotechnology . My research background was DNA damage and repair.

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