Insights from a Strain Engineer: Perspectives from a Strain Engineer and Bioinformatician

Lexin Ann Morales     

Lexin recently spoke to Deeksha Shetty, a Strain Engineer and Bioinformatician at Genecis Bioindustries Inc. Her role evolves in bioinformatics, fermentation, and targeted genetic modification. When not in the lab, Deeksha enjoys playing chess, painting, and sketching.

Deeksha emphasized the importance of understanding the bigger goal of the company or to see how a specific strain can help align with company goals.

Bioinformatics plays a pivotal role in the field of strain engineering, serving as a powerful companion in the quest to design and optimize microbial strains for various applications. This interdisciplinary science leverages computational tools and biological insights to analyze, interpret, and manage complex biological data. In the context of strain engineering, bioinformaticians utilize their expertise to decipher genomic information, identify key genes, and predict metabolic pathways. This knowledge guides scientists in tailoring microbial strains for specific purposes, such as the production of biofuels, pharmaceuticals, or sustainable food sources. By integrating bioinformatics with strain engineering, researchers can harness the full potential of genetic and metabolic manipulation to create innovative and sustainable solutions for a wide range of industries.

What is the experience of working as a Strain Engineer and Bioinformatician like?

My daily responsibilities are diverse, combining genetic engineering, genomic data analysis, and bioprocess optimization.

I do strain modification using cutting-edge CRISPR-Cas9 technology. Additionally, whenever required  I use computational tools to perform genomic analysis like 16S analysis, WGS, or RNA Seq which help me understand the precise genetic modifications achieved through strain modification techniques but also provide valuable insights into the broader implications of gene deletions or insertions. The other aspect of the role is to ensure that engineered strains perform consistently and at scale which helped me to get a deeper understanding of both the microorganisms being engineered and the bioprocess itself.  This way, I can get a complete picture of how it might impact our process. ”

The combination of bioinformatics and strain engineering: The best things about this role

Through my academic and industrial experiences, I have thoroughly enjoyed the skills I have acquired. The combination of bioinformatics and strain engineering allows me to understand what's happening within the genome. My passion lies in using computational tools to gain meaningful insights, and I'm able to do just that through these techniques. Applying these multidisciplinary skills to solve problems is what I find enjoyable.

Genetic complexity: A continuous challenge

In strain engineering, genetic complexity is a challenge. Despite advanced tools like CRISPR-Cas9, off-target effects are possible and can disrupt cellular metabolic processes. While technology helps minimize this, genetic complexity remains a challenge. It is imperative that our engineered strains align with company goals and market demands. The optimization of growth conditions, including nutrient availability, temperature, and pH for high yields and cost efficiency, is time-consuming. Scaling up strains can be challenging, considering factors like bioreactor types, resistance to shear stress, contamination management, and adapting to evolving  raw materials. Data analysis is vital due to the growing data volume, requiring advanced computational and statistical skills for meaningful data analysis. Interdisciplinary collaboration and effective communication are essential. Furthermore, the strategic utilisation of computational tools offers promise in navigating these challenges and enhancing our strain engineering capabilities. Regulatory and ethical concerns regarding genetically modified organisms must also be addressed.

Key learnings to prepare for challenges? Preparation and prioritization

To address these challenges, it's important to act now rather than waiting--we make sure we're already well-prepared to tackle these challenges. For example, I encountered a situation in Asia where the price of a diabetic drug was significantly reduced. In such instances, strain engineers can play a pivotal role in cost cutting strategies that maintain the business’s seamless operations smoothly. This way, we become more impactful in improving clinical trials, reducing material expenses and optimising resource utilization. Embracing adaptability and agility is key to navigating the ever-evolving landscape of biotechnology challenges.

In strain engineering, effective communication and collaboration is foundational

As a strain engineer, my priority is aligning a specific strain's capabilities with the company's broader objectives. To achieve this, I emphasize clear communication, ensuring that even individuals without a scientific background can understand the information. I avoid complex scientific jargon and instead use plain language and analogies to convey technical findings. The key is demonstrating how the strain's characteristics can impact the company's overarching goals--this approach helps me effectively communicate with stakeholders.

"Sometimes, we can get so immersed in our work that we lose sight of the bigger picture. Collaborating with these teams helps us tailor our strains to meet the company's requirements and market demands."

As a Strain Engineer, I believe in collaborating not only with the strain engineering team but also closely with the fermentation, downstream processing, materials, and marketing team. Effective collaboration helps to address challenges that may arise, like ensuring that downstream processes can effectively purify our products.. By communicating well, it allows us to understand each other's challenges and find innovative solutions together.

Explore, network, and patience: Key skills for success

My advice for success? Explore and start networking early. When I was a graduate student, I didn't have a clear idea of the opportunities outside my field, and I was unfamiliar with certain areas like fermentation. However, networking and learning from professionals in various fields opened up new perspectives for me. I realized the importance of fermentation and gained insights into the significance of statistical knowledge and computational tools for data analysis. Patience and resilience are crucial when conducting experiments and dealing with data. It's easy to get absorbed in details, so focusing on the bigger picture is essential. Stay updated with developments in your area through literature reviews. Networking can also lead to unconventional problem-solving approaches. Seeking out mentors as part of your networking efforts can provide invaluable guidance and support, helping you navigate your academic and professional journey more effectively. So, my top suggestion for graduate students is to actively network and explore diverse opportunities.

Anything that you are looking forward to in the future of strain engineering?

I'm genuinely excited about leveraging my computational skills and exploring the potential of machine learning and AI in enhancing my strain engineering techniques. Additionally, I am also interested in applying machine learning to analyze fermentation data, going beyond traditional experimentation. This avenue opens the possibility of predictive modelling for outcomes,  a direction I'm keen to explore and upskill myself in.

I've been actively researching and studying within this domain, and have also participated in a data science boot camp and relevant courses. These experiences have provided me with a strong foundation in SQL, Python, machine learning and big data technologies like AWS, poised to revolutionize our approach to strain engineering and data interpretation.

Furthermore, I hold a deep interest in utilizing bioinformatics, AI, and machine learning in drug discovery and microbial evolution studies. My goal is to seamlessly integrate my wet lab knowledge with my proficiency in the dry lab, thereby blending practical experimentation with computational methodologies to drive innovation in research. I am looking forward to the future of strain engineering with these exciting possibilities.

Deeksha Shetty is a Strain Engineer and Bioinformaticcian based in Toronto. This article is based on the series: Insights from a Strain Engineer by Gravel. Subscribe via our LinkedIn newsletter and email newsletter for the latest updates weekly.