Insider Insights with Dr. Sushmita Sudarshan

With a PhD in microbiology and years at the lab bench, Sushmita Sudarshan knows better than most what it means to spend hours pipetting plates and picking colonies by hand. Today, as a scientist working on automation solutions like the QPix® FLEX™ Microbial Colony Picking System, she’s helping transform those painstaking manual workflows into streamlined, sterile, and reproducible processes.

In this post from our Insider Insights series—where experts share both their quick reactions and deep reflections on what it’ll take to prepare scientists for what’s next—Sushmita reflects on what automation means not just for labs and data, but for the people behind the science; freeing researchers to spend less time on routine tasks and more time exploring complex biological questions that could change the world.

https://vids.moleculardevices.com/watch/yM5gwYWF2c4LBRaxe4K7jT

Inquiring minds want to know:

How have you seen the development of automation in microbial research impact or improve the everyday lives of our customers?

Quick reaction: Automation is like giving researchers a reliable lab partner who never forgets a step, keeps everything sterile, and ensures experiments stay on track.

Deep reflection: Microbial research underpins everything from antibiotic discovery and microbiome profiling to synthetic biology and sustainable manufacturing. Each of these fields involves intricate, repetitive workflows that have to stay sterile and precise, because you’re often working with bacteria, viruses, phages, and other microbes where contamination risk is huge. These fields rely on workflows that are not only repetitive and time-sensitive but are also highly prone to human error. Whether you're working with anaerobes, filamentous strains, or spore-formers, even a single lapse in sterility or traceability can derail an entire experiment.

Automation steps in to handle these critical but manual parts of the process: pipetting, colony picking, plating—all within a controlled chamber that reduces contamination, keeps traceable records, and ensures reproducibility. What excites me most is that innovations like the QPix FLEX system make this level of precision accessible to labs of all sizes—whether you’re a small lab or a global company tackling big questions.

The QPix FLEX Microbial Colony Picking System offers end-to-end automation inside and outside hypoxic chambers.

For our customers, this means higher throughput, faster data generation, fewer failed experiments, and more time spent on discovery rather than troubleshooting. Whether you're running library screens or optimizing a single strain, the QPix FLEX system helps labs of all sizes scale their impact without scaling complexity.

Why do you find this exciting?

Quick reaction: This is exciting because I’ve lived the manual side of this work and I know firsthand how that grind can drain your energy and leave less space to think creatively, collaborate, or chase the questions that really light you up. The QPix FLEX system doesn’t just automate—it empowers. By streamlining colony picking, streaking, and imaging, it frees researchers from the grind of manual workflows and gives them back the time and clarity to focus on what really matters: designing smarter experiments, running more sophisticated assays, and pushing the boundaries of microbial innovation.

Deep reflection: During my PhD, I spent countless hours doing things like pipetting media into 96-well plates and manually plating and picking colonies. These tasks are essential to the integrity and success of microbial workflows, demanding precision, consistency, and care. But they’re also time-intensive and often repetitive, which means they can pull scientists away from the work that drives progress: designing experiments, interpreting data, and driving innovation. By automating these steps, we free up researchers to focus on what they do best: asking bold questions, solving complex problems, and advancing science.

When scientists have tools that automate routine tasks, it frees them to focus on the creative and strategic work that drives breakthroughs. A few of my favorite examples illustrate this beautifully. One is the microbial production of insulin. Once extracted from animal pancreases, it is now synthesized by engineered E.coli—a leap made possible by recombinant DNA technology and the time researchers had to innovate. Another is the development of biodegradable plastics from Pseudomonas strains, offering a sustainable alternative to petrochemical polymers.

These weren’t just technical wins. They were paradigm shifts born from curiosity, creativity, and the time to explore. That, to me, is the true power of automation. It buys back time for scientists to imagine, innovate, and discover what’s next.

By automating colony picking, streaking for single colonies, and liquid handling, the QPix FLEX workcell streamlines workflows that are foundational to assays in synthetic biology, microbiome research, protein engineering, and food safety. Its high-resolution color imaging system enables precise classification of colonies based on morphology and RGB color intensity, which is especially valuable for phenotype-based selection and microbial diversity screening. The ability to detect colonies as small as 0.2 mm and group them by visual characteristics allows researchers to perform more refined assays, such as screening for pigment production, enzyme activity, or antibiotic resistance.

In synthetic biology, for example, QPix FLEX supports high-throughput screening of genetically engineered strains, enabling rapid identification of successful constructs. In microbiome culturomics, its anaerobic compatibility allows researchers to isolate and characterize fastidious organisms that thrive in low-oxygen environments. And for protein expression assays, the system can automate hit picking and media dispensing, accelerating the identification of high-yield clones. This isn’t just a tool—it’s a platform for scientific acceleration.

Grouping of blue E.coli and pink Klebsiella aerogenes colonies plated on 4 region OmniTrays. Image source: Application note describing how the QPix FLEX Microbial Colony Picker ensures efficient Color-Based Colony Grouping for Microbial Research and Screening.

Automation gives scientists the freedom to reimagine what’s possible and that’s how breakthroughs happen. So yes, this excites me deeply, because when scientists are freed from the grind of repetitive tasks, they’re empowered to imagine, innovate, and discover what’s next. And that, to me, is the true power of automation.

What trends or customer feedback have driven innovation in this area?

Quick reaction: Scientists told us what really slows them down: sterility issues, stubborn contaminants, instruments that aren’t compatible with or need babysitting in hypoxic chambers, and tools that don’t fit into existing workflows—and we listened.

Deep reflection: Sterility in microbial workflows isn’t just a best practice. It’s a survival strategy, especially when working with spore-formers like Clostridium or Bacillus, or aerosol-prone organisms that can linger in the air and cross-contaminate plates. Traditional metal picking pins, while reusable, require rigorous cleaning between runs and, on some occasions, even that is not enough. To address this, the QPix FLEX system introduced sterile disposable picking pins, which eliminate the need for pin sterilization and reduce the risk of carryover contamination. Combined with UV decontamination—which cycles between runs to reduce surface bioburden—it minimizes contamination risk with minimal manual intervention.

Pre-pick (A) and post-pick (B) images of the source plate for picking process. Picked colonies counted with ImageJ software (C). Image source: Application note describing how the QPix FLEX Microbial Colony Picker ensures colony picking accuracy and efficiency in a contamination-free environment, preventing microbial cross-transfer.

For example, in microbiome culturomics, where researchers isolate hundreds of colonies from stool or soil samples, even a single contaminant can skew downstream sequencing. Disposable pins allow for single-use sterility, preserving sample integrity without compromising throughput.

Flexibility was another recurring theme. Scientists didn’t want to overhaul their protocols to accommodate rigid instrument specs. The QPix FLEX system responded with adaptive software that supports user-defined plate maps and colony morphology parameters—like edge sharpness, circularity, and color contrast—so researchers can fine-tune selection criteria for engineered and rare or slow-growing colonies.

Barcode tracking was added to prevent mislabeling during runs. For example, a lab screening engineered E.col i variants can use barcode-linked metadata to trace colony origin, growth conditions, and/or plasmid constructs—ensuring full traceability from plate to freezer stock.

These upgrades weren’t theoretical. They came from direct customer feedback. And the QPix FLEX system isn’t just a colony picker. It’s a response to the nuanced, real-world challenges scientists face every day.

What common research challenges do customers face now, and how can automation in microbial research open new opportunities?

Quick reaction: Manual work introduces errors and inconsistency. One small mistake upstream can cost months of downstream effort.

Deep reflection: Let’s be honest. Manual work in the lab isn’t just tedious—it’s risky. If you’ve ever pipetted liquid media or culture samples into dozens of plates, you know the moment I’m talking about. By plate 30, your hand’s cramping, your focus is slipping, and suddenly you’re not sure if sample A went into well B or C. That tiny lapse? It can derail weeks of work. Sequencing prep, MALDI-TOF analysis, protein engineering—all of it compromised by one upstream error. I’ve been there. It’s frustrating, costly, and completely avoidable.

That’s why automation is about more than speed. It enables scientific resilience. When every colony is picked with accuracy, liquids are handled with precision, every plate barcode is tracked, and every step is logged, you’re not just working faster—you’re building a workflow that’s traceable, reproducible, and scalable.

https://vids.moleculardevices.com/watch/xdUPbCQux2FvdZcL7g5916

This matters more than ever. Microbial research is pushing boundaries in strain engineering, antibiotic discovery, and probiotic development. These aren’t projects where “close enough” is good enough. Reproducibility is a requirement—for regulatory approval, for scientific credibility, and for your own peace of mind. Automation transforms the lab from a place of potential error into a platform for confident innovation, and it ensures that when breakthroughs happen, they’re built on a foundation of rigor and reliability.

In a world where automation in microbial research reaches its full potential, what do you envision happens next?

Quick reaction: I see every lab—big or small—able to contribute to breakthroughs because they all have access to flexible, reliable automation.

Deep reflection: True potential builds more complex systems while also democratizing access. Today, some of the best ideas come from small academic labs. But without automation, they’re limited in how far they can take those ideas. Imagine if every lab had tools to run high-quality, reproducible experiments, without needing massive funding.

What I envision is a shift from automation as a luxury, to automation as infrastructure. When microbial research labs—regardless of size—gain access to flexible, modular systems, we start seeing real parity in experimental capability, from small academic labs to big pharma and biotech companies. With integrated automation—like colony picking with hit-selection, metadata traceability, and sterile sample prep—researchers can execute high-fidelity screens, validate hits faster, and scale protocols without compromising reproducibility.

While increasing capacity, we also want to enable consistent, traceable workflows that support complex biological questions. Whether the goal is antibiotic discovery, synthetic pathway optimization, or strain characterization, automation needs to adapt to the lab’s priorities—be it throughput, sterility, or platform integration. That’s how we unlock broader participation in translational science and accelerate the development of solutions to urgent microbial challenges, such as faster discovery of new antibiotics at a time when resistance is rising, or quicker development of bio-manufactured products that benefit everyone. If tools can adapt to different needs, we’ll see more diverse, creative research, and more solutions to complex biological problems.

Inspired by what you’ve read? Learn more about automation in microbial research here.

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