High-throughput bioprospecting

Automatic colony picking of non-model fungal and bacterial species

Aim

In 2019, Singer Instruments teamed up with Isomerase, a Cambridge UK-based biological engineering company, to test the effectiveness of PIXL at picking and plating a range of non-model organisms.

This included a filamentous fungus and a range of actinobacteria, selected from among Isomerase’s extensive proprietary collection of more than 20,000 strains.

Figure 1. Collection of Isomerase source plates picked using PIXL.

Introduction

Microorganisms represent a major source of chemical diversity for bioprospecting. The rate at which this huge resource can be screened is a limiting factor to the discovery of new compounds, including chemical feedstocks, antibiotics, and other pharmaceuticals. 

The development of high-throughput screening techniques that support innovators to efficiently exploit a wide variety of microbial resources is therefore a global priority.

PIXL can potentially help to address this bioprospecting challenge by automating some of the culturing and downstream processing necessary for high-throughput experimentation.

One of PIXL’s core functions is to automatically detect colonies and then pick these to new plates for culturing or downstream analysis. For a colony-picking robot, colonies that have unusual colours or morphologies can pose a significant challenge for colony detection algorithms.

Furthermore, if the physical properties of the cells prohibit adherence to the picking device, or the cells do not survive being picked, then it will prove difficult to effectively automate cell transfer.

To understand PIXL’s full capability the team at Isomerase tried to ‘beat’ PIXL with a range of organisms, some of which they were confident would trip PIXL up.

Method

Isomerase were particularly interested to understand whether PIXL could pick colonies that exhibited atypical phenotypes.

This included the dark brown filamentous fungus Glarea lozoyensis and a wide range of filamentous bacteria from around the world, including Kitasatospora putterlickiae, Streptomyces avermitilis and Streptomyces venezuelae.

The organisms chosen were not only different colours but also exhibited different colony morphology, from the dry and powdery, to the extremely tenacious.

PIXL has several unique features that can help optimise for transfer efficiency when picking non-model organisms.

This includes a choice of detection algorithms and various mixing profiles that can be adapted to carefully ‘scrape’ the agar in repeat circular movements within a defined radius.

PIXL can also pick a variety of organisms continuously without stopping for wash cycles or to change tips, thanks to its proprietary polymer Pickupline, which is cleaved after every pick (see ‘How to pick a Picker’).

Results

Glarea lozoyensis

Kitasatospora putterlickiae

Streptomyces avermitilis & streptomyces venezuelae

Figure 2. PIXL successfully picked colonies of different species chosen by Isomerase. The species chosen exhibited a range of morphologies that PIXL was able to detect, pick and re-plate.

PIXL has already been shown to detect and pick model organisms such as S. cerevisiae (yeast), E. coli (gram-negative bacteria) and C. reinhardtii (algae).

Thanks to Isomerase, these latest findings demonstrate that PIXL is also capable of working with non-model organisms that exhibit atypical and challenging phenotypes.

Dr Martin Sim, senior scientist at Isomerase, had this to say about PIXL’s performance:

“I’m happy to say that every strain we picked and replica plated from the solid agar into the 96 well plates grew, and after three weeks in the incubator no plate has shown evidence of contamination.”

This advocates that PIXL is both versatile and reliable when it comes to picking different organisms of varying morphologies in parallel.

But what is it like ‘in the field’? Can it handle uneven agar surfaces? Sophisticated can sometimes mean complicated, so is PIXL difficult to work with? 

Here’s how Martin and his team found working with PIXL:

“Everyone was very impressed with the machine, especially its ease of use and the friendly software user interface, the polymer picking system. And of course how it was accurately handling uneven agar surfaces and working with our unusual colony morphologies.”

Conclusion

Non-model organisms are expanding the repertoire of synthetic biology, according to Synbiobeta, while the World Economic Forum continues to spotlight how countries around the world are adopting unique bioeconomy strategies tailored to their natural resources.

This case study provides further evidence for the effectiveness of PIXL at picking and plating non-model organisms. It highlights the role of lab automation in meeting growing global demand for high throughput bioprospecting, towards the development of sustainable, bio-based products and innovations.