How to Automate the Microbiology Lab - A rapidmicrobiology Special Focus

In this rapidmicrobiology special focus, we showcase solutions to automate and improve workflows in the routine microbiology laboratory. Labs can now ditch repetitive tasks, which can instead be performed by robots that never get tired or make mistakes, generating data that flows seamlessly between instruments and freeing technicians to focus on analyses that do need the human touch rather than manual chores.

Whether you’re looking to boost throughput, cut down on human error, or simply reclaim your sanity from endless sample prep, automating your lab could be the game-changer you’re looking for. In this guide, we’ll explore some options for automating a microbiology testing lab - from choosing the right technology to workflow redesign to building a culture that embraces change. 

Starting at the beginning with media preparation, still a process that takes up a lot of time and space, our expert insights interview with INTEGRA’s Product Manager Gerald Posch explains how, from Petri dishes to microplates via bottles and tubes, there is a media prep and fill solution to meet most applications.

The ready-to-rehydrate Easy Plate system from Kikkoman Biochemifa automates colony counting and analysis in food microbiology, eliminating the variability and inefficiencies associated with manual counting.

Discover how Bio-Rad's integrated EZ-Check workflow is helping laboratories to test and release food samples faster without compromising reliability.

If you are building a business case for the automation of microbial quality control (QC) in your pharmaceutical manufacturing facility, be sure to read the interview with Dr Frederic Berkermann, Commercial Project Lead EMEA for Merck’s automation and robotics solutions, on the financial and strategic considerations.

Streamlining bioproduction quality control with automated workflows, BioMérieux’s portfolio includes options for environmental monitoring, endotoxin and mycoplasma testing.

Deciding to adopt automation can be scary, Lonza takes the pressure off with their ‘Partner in Change’ toolkit, take advantage of their experience in implementing their modular automated endotoxin testing incrementally – one step at a time.

In partnerships with leading engineering and pharmaceutical companies, Merck has developed an award-winning solution that fully automates the repetitive routine tasks in bioburden testing, delivering reliable results with full traceability.

Remove an entire category of risk from cleanroom environmental monitoring by using remote robotic monitoring instead of personnel. MicronView's EMC robot line offers modules for non-viable particle counting, particle counting and viable air sampling, real-time bioaerosol monitoring, and automated decontamination, with the latter coming in late 2026.

No one can cover automation without mentioning AI; Clever Culture has issued a whitepaper on how to pivot to an AI-based culture plate reading system. Covering the full lifecycle from selection and qualification to ongoing monitoring and change management, this paper provides clear guidance on meeting regulatory requirements whilst unlocking the efficiency and consistency benefits of automation in pharmaceutical manufacturing.

Discover how automation with ScanStation can transform your laboratory and optimize your productivity. Compliant with 21 CFR Part 11 and GMP Annex 11 standards, the system ensures complete traceability thanks to account management, electronic signatures and audit trails.

Don Whitley partners with Copan on their WASPLab® system, which provides a practical, evidence-based solution to address the challenges faced by high-throughput labs. Rather than targeting a single step, it integrates the entire diagnostic pathway, from sample reception, inoculation and streaking through to incubation, imaging, and digital interpretation.

Don’t miss out on some insightful webinars on automation. Symcel will be presenting on Symcel’s biocalorimetry technology, which detects metabolic heat with extreme sensitivity, enabling rapid and reliable growth-based microbial testing with results in hours. Automated continuous detection and clear positive/negative results at very low detection limits across complex food, beverage, consumer goods, ingredients, and industrial matrices with results in hours. Plus, we feature webinars from Merck and Clever Culture Systems.

Discover how the integrated EZ-Check workflow, helps laboratories to test and release food samples faster without compromising reliability. Join this practical webinar to see how automation streamlines sample preparation and PCR workflows for efficient, scalable pathogen testing.
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In this interview, INTEGRA’s Product Manager Gerald Posch explains how automation is helping microbiology labs streamline media preparation and dispensing, leading to more efficient laboratory workflows.
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In this interview with Dr Frederic Berkermann, Commercial Project Lead EMEA for Merck’s automation and robotics solutions, we discuss the financial and strategic considerations of automating microbial quality control (QC) in pharmaceutical manufacturing.
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Automation is revolutionizing microbiology labs by enhancing workflows from sampling to data management. bioMérieux's solutions, like 3P® ENTERPRISE and BIOFIRE® SPOTFIRE®, provide reliable results, help reduce errors, and support faster decision-making.
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Making the transition to automated endotoxin testing starts with a strong case for change. Learn how Lonza partners with QC leaders to identify risks, build justification, and prepare with the Partner in Change toolkit.
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Don’t be left behind, Bioburden Automation is on its way! Merck is pioneering this revolution in microbial QC. Discover how robotics, automation, and digitalization boost efficiency, compliance, and reliability in pharmaceutical manufacturing.
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MicronView's EMC robot line brings scalable automation to cleanroom environmental monitoring. Built on a shared platform with interchangeable modules, each robot targets a specific monitoring need, from particle counting to real-time bioaerosol detection.
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Automate colony counting with Kikkoman’s Easy Plate. Improve accuracy, eliminate operator variability, and accelerate microbiology workflows with batch scanning and intelligent analysis.
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Despite advances in clinical diagnostics, culture interpretation still relies heavily on skilled scientists to review plates, interpret growth, and make judgement calls built on experience. Full laboratory automation with the Copan WASPLab® provides a practical, evidence-based solution to these challenges.
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Discover how the calScreener® and new caloTrace® biocalorimetry systems enable rapid, reliable and automated growth-based microbial testing across complex food, beverage, consumer goods, ingredients, and industrial matrices with results in hours.
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In this whitepaper, get a clear framework to assess AI systems beyond “black box” concerns to equip your team with a clear approach to successfully adopt AI-enabled automated culture plate reading and reporting technology using a practical, risk-based validation approach.  
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ScanStation supports rapid microbiology workflows by combining controlled incubation with continuous, automated imaging, enabling earlier detection of microbial growth compared with traditional end-point incubation methods.  
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From Hands-On to High-Tech: A Practical Roadmap for Implementing AI in Pharma QC
Taking place on 27th May, this webinar will guide you through a roadmap for implementing AI-enabled automation into the microbiology workflow. From initial planning to commercial use, the session lays the foundation for adopters to maximize value while maintaining compliance and control during the implementation process. Register now to join the live webinar or view the recording.
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From Manual to Automated QC: Key Considerations, Challenges and Solutions 
Pharma QC faces pressure for faster, reliable results and turns to automation. This webinar covers evaluating and implementing automated rapid technologies, staffing/volume case studies, selecting the right solution and partner, and why now is the time to invest. 
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New Rapid Microbial Testing System with Results in Hours
Discover how the calScreener® and new caloTrace® biocalorimetry systems enable rapid, reliable and automated microbial testing across complex food, beverage, consumer goods, ingredients, and industrial matrices with results in hours.
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