With wide-ranging therapeutic applications, probiotic research has the potential to significantly impact how we develop medications. Nevertheless, probiotic microorganisms can be difficult to work with as they are anaerobic, have strict contamination protocols, and can form tenacious colonies. Automated colony picking helps to overcome these challenges by reducing contamination risks, facilitating environmental maintenance and promoting consistent, reproducible results by removing opportunities for human error. As a versatile and scalable tool, the colony picker can significantly contribute to the quality and pace of research into the development of precision probiotics.

What are precision probiotics?

Probiotics are live microorganisms that provide a health benefit, typically known for supporting gut and immune health. Precision probiotics move away from a conventional ‘one size fits all’ approach, where personalised treatments can be used to improve health in the general population [1].

What are the therapeutic uses of probiotics?

Emerging targets for precision probiotic therapies include:

  • Obesity and associated health problems [2]
  • Central nervous system disorders such as Alzheimer’s, where treatments with probiotics have been successful in mice [3]
  • Reducing osteoporosis in postmenopausal women [4]
  • Cancers via immunotherapies to improve adaptive immune response against cancer development [5]
  • Many other conditions [2]


Effective probiotics must be free from pathogens and should not contain any toxic products to be safe for consumption [6]. Next-generation probiotics are considered to be genetically modified organisms so there are strict production regulations to avoid contamination [6]. 

One of the biggest concerns with probiotic use is the introduction of antibiotic-resistance genes to other microorganisms in the digestive tract [2], as probiotic use becomes increasingly common, stronger regulation is more likely to be implemented to reduce the risk of contamination. 

Selecting production colonies with a colony picker reduces the risk of disrupting a sterile environment. PIXL uses sterile PickupLine to transfer colonies with a <0.03% contamination rate and UV disinfection can be used to sterilise PIXL between cycles. This ensures a contamination-free environment suited towards working with probiotic microorganisms.


The anaerobic nature of probiotic microorganisms proves to be a challenge when developing strains. Taking these microorganisms out of an anaerobic environment will limit their lifespan, putting pressure on scientists for solutions that limit oxygen exposure [7]. Environmental maintenance is a significant problem in production as it can be costly and time-consuming [8].

PIXL has a small footprint that fits easily into an anaerobic chamber and is compatible with changes in humidity and temperature. Mari Rodriguez at SNIPR Biome uses PIXL in an anaerobic chamber to make targeted microbiome precision medicines. 

Listen to Mari’s interview to learn more about how PIXL is used in microbiome research here.

Picking production strains

To produce good probiotics, microorganisms must pass safety testing and strict acceptance criteria. Strains identified as production strains must be non-pathogenic, have a stable viability and have the ability to be produced at a large scale [9].

PIXL can identify and pick colonies based on phenotype, with a colony-picking tip that can scrape, mix and scratch to select even the most tenacious strains. Perfect for identification and picking of production strains, with a pinning transfer efficiency of 99.78%. Providing consistency in picking that you wouldn’t get from doing it by hand. 

“We are screening for strains that could be useful either as production strains or as probiotics. The PIXL, we have so far used to spot our strains on 96 well agar plates for assaying.”

~ Sandra Kittelmann at Wilmar International.

Explore how PIXL can accelerate your screening workflows

Colony pick with the standard PIXL set up


Is for users looking to automate manual colony picking with an intuitive and user-friendly robot.

PIXL in Anerobic Chamber with automated setup

PIXL with Anaerobic Chamber

A customised anaerobic chamber designed for PIXL with user experience in mind, making integration seamless.