Ultra High Throughput Screening to Push Protein Production Titers to the Max


Rapid, ultra high throughput screening at Ginkgo: Find the needle in the haystack, fast.

Ginkgo’s plate-free, screening technology, Encaps, can unlock your strain’s commercial value 

Introducing Ginkgo’s EncapS Foundry

The power of massive screening can be applied to a wide range of biotech R&D challenges, from optimizing the activity and specificity of particular enzymes to optimizing titers of target molecules in production strains. Generating large libraries of mutant enzymes or whole cells is easy; screening the massive libraries (>106 colonies) needed to find your optimal clone is time-consuming and labor-intensive. In traditional screening, strains have to be individually cultivated and tested for your desired activity. Depending on the assay and culturing conditions, screening large libraries could take the better part of a year, if not more, and often represents a bottleneck in biological engineering. 

What if you could screen 1 million variants of your strain for improved phenotypes in just weeks? Once we’ve developed a nano-liter scale assay and generated the strain or protein library, Ginkgo’s proprietary encapsulation and screening technology (EncapS) can efficiently pick out that rare variant from a massive library. Whether it’s applied to the beginning of a strain development project to show proof of concept, or used at the end of a campaign to squeeze out the final bit of activity from your strains, EncapS is a fast way to screen through millions of variants quickly.  

This screening technology is compatible with a wide range of production hosts, including gram-positive and gram-negative bacteria, yeast, filamentous fungi (e.g., Aspergillus, Trichoderma), and mammalian cell lines. Assays can be tailored to measure a variety of desired phenotypic outcomes — from secretion, to activity, to specificity.  With your strain as a starting point, a mutagenesis-driven screening campaign or a large, combinatorial library can deliver top hits in a fraction of the time compared to other high throughput methods. 

Partners can leverage this type of screening for many different R&D targets and commercial goals. In the following detailed case study, our partner leveraged EncapS to achieve a 50% titer improvement for a protein ingredient they were producing through fermentation. To start with, our partner’s R&D team had spent years engineering their Pichia production strain to produce and secrete more of the protein of interest. When their R&D efforts plateaued, they sought out our platform capabilities to improve their strain’s performance and reach a competitive price point.

When rational engineering stalls

A company supplying ingredients for the nutrition and wellness sector was developing a low molecular weight protein. They needed to produce more of the protein per fermentation batch to achieve a competitive price point. Their R&D strategy was to rationally engineer yeast cells to secrete more of the protein during fermentation. 

When their rational strain engineering efforts plateaued, they partnered with Ginkgo to leverage ultra high throughput encapsulated screening approaches to explore the impact of mutations spanning the whole genome on protein production.

Working with Ginkgo’s EncapS Foundry

Since rational engineering wasn’t improving titers, the EncapS team applied an unbiased approach to our partner’s starting strain. We reasoned that random mutagenesis could develop traits in the strain that rational engineering couldn’t access. 

Traditional screening requires culturing each strain individually, then testing them for production using plate-based assays: a daunting task for the number of strains that would need to be screened in a random-mutagenesis campaign. Even pooled screening methods that sort variants grown in the same culture fall short if the target product is secreted by the strain into the media. 

Encapsulating single cells in nanoliter reactors enables screening for secreted products trapped in the capsule under cultivation conditions that are later used in the production process.. Ginkgo’s EncapS Foundry is designed for exactly this purpose: generating large libraries and screening them for the top producers quickly.

After onboarding the partner’s starting strain, the EncapS team developed a nanoliter-scale assay for our partner’s peptide – a fluorescence-based marker to signal protein production. By converting protein production to a fluorescent signal, the team could sort through thousands of encapsulated cells in a matter of minutes and screen 100x more strains than traditional plate-based fluorescent cells or HPLC-based screening methods.

With this nanoliter-scale assay in hand, we generated a library of 200,000 genetic variants of our partner’s production strain using physical and chemical mutagenesis. These variants were encapsulated, and protein production was measured using the custom-designed nanoliter assay. We selected the top-producing strain from this mutant library and repeated this design and test loop two more times, each time generating an unbiased library of >200,000 strains using mutagenesis of the top hit from the previous round of screening. Within four months, our screening had pushed past our partner’s plateau, identifying a strain that yielded 50% more protein than the original, rationally-engineered base strain.

Our Capabilities

Custom nanoliter-scale fluorescence-based assay development
Our team develops these assays for a wide range of secreted products to facilitate plate-free screening in ultra high throughput.

Large-scale screening of strain variants
Where rational strain engineering fails screening large-scale  unbiased libraries may access traits that may not have been accessible through traditional engineering campaigns.

Ultra high throughput plate-free screening technology
Leveraging EncapS technology allows efficient screening of large libraries at a fraction of the time of traditional screening techniques.

Efficient strain development
Our team efficiently identified strains with optimized production capabilities through multiple rounds of screening within 4 months.

EncapS can unlock commercial value across industries

This case study demonstrates how EncapS can quickly and effectively screen through massive microbial libraries. This partnership was able to break through the plateaus reached after years of rational engineering by taking an unbiased approach to strain development. Whereas traditional screening of libraries of >700,000 colonies may take a considerable amount of time, infrastructure, and effort that may not result in promising outcomes in a fermenter, our screening took 4 months and resulted in a 50% increase in our partner’s titers.

This technology is a boon to other challenging problems in strain development or optimization. For example, microbes isolated from soil have significant potential as biological crop protection agents but may be unstable in formulation. While gene editing can improve the performance and stability of these isolates, developing the strain engineering tools and protocols may require significant R&D investment. Mutagenesis, paired with EncapS provides an efficient route to unlocking a strain’s full potential.

In Summary


Genetic variants screened us three iterations of the EncapS technology


Improvement of target protein production on customer’s base strain


Months dedicated to three successive rounds of screening

< 1

Year from tech transfer to delivery of an improved strain