Beyond the agar plate – the next generation microbiological analysis
22 April 2026 | Suzanne Jordan, Section Lead Molecular Microbiology and Methods
Some microbiological investigations call for next generation analysis to reach the answers that you need.
Microbiologists have many analytical techniques at their fingertips for rapid pathogen detection and troubleshooting safety and contamination issues. Traditional culture-based microbiology methods provide a good understanding of most challenges typically encountered in industry, but molecular technologies have enhanced capabilities for deeper dive investigations and more complex problems.
This blog explores one of the DNA sequence-based approaches, microbial population profiling, and how it can assist the food and drink industry in troubleshooting quality and safety questions.
What is DNA sequencing?
Over recent decades, technologies have evolved to analyse the blueprint of life, deoxyribonucleic acid (DNA), which is present in all living organisms. DNA sequencing is the process of determining the nucleic acid sequence of the DNA being analysed. When applied to microbiology, it enables us to read the total genetic code of microorganisms and offers the opportunity of analysing samples without the need for culturing.
There are several potential applications of DNA sequencing in food microbiology, ranging from the analysis of single isolates during epidemiological investigations to the study of the whole microflora in food and environmental samples (which is known as metagenomics or population profiling).
What is microbial population profiling?
Population profiling provides information on the relative abundance of microorganisms present in the sample, i.e. which microbial genera or species are present, and the proportion of each one in the total population (microbiome). The analysis can either be targeted to specific types of organisms, i.e. bacteria or yeasts and moulds, or left open to cover all microorganisms.
DNA sequence-based analysis offers two key benefits over traditional microbial techniques:
- Culture independent analysis that eliminates bias introduced from the selection of conditions used for microbial growth, and;
- The capability to provide a comprehensive picture of the microflora present in a sample (as well as the diversity of genera or species a sample contains).
How can population profiling help the food industry?
Microbial population profiling can be carried out on a diverse selection of samples, including food and beverage products, their process intermediates, as well as environmental swabs and process wash water.
Due to the flexibility of the approach, the technique can be applied to various situations occurring in industry.
Example applications include:
- Identification of potential causes of product spoilage: By comparing the microbial population profiles generated from control and spoilt samples, the possible causes of product spoilage can be highlighted even if the organism responsible does not grow on microbiological media.
- Investigating population changes over product shelf-life or during fermentation processes: Analysis of samples taken over time can determine how the microflora changes during fermentation of products such as sourdough, or how organisms vary over product shelf-life (which could be used to compare data between products packed under different environments).
- Assessing batch-to-batch variability in new or novel ingredients: A batch-to-batch comparison of the microflora of ingredients such as plant proteins (to understand microbial variability that could impact the growth of pathogens and spoilage organisms) could assist in the assessment of possible risks during new product development.
- Trending factory environment ecology over time or investigating biofilms: By analysing samples taken from different locations in the production environment, at varying time points, it is possible to identify potential trends in contamination. It also allows comparison of pre- and post-clean to evaluate cleaning efficacy.
Using microbial population profiling for these applications eliminates biases introduced by culturing, and benefits from a comprehensive picture of the microbial populations present in the samples.
Get next generation microbiology support
To get you the microbiology answers that you need, we offer bacterial population profiling and fungal population profiling for food, alcoholic and alcohol-free beverages, food packaging and environmental samples.
Our microbial population profiling analysis packages can be tailored to the solutions you need, and are not limited to the applications listed above. If you have alternative sample types, or a situation where understanding the microbial population present could assist in your investigations or product development, please get in touch.
Microbiology: Protect your business and your customers
Protect your customers and your brand from risk with Campden BRI’s unique wrap around testing and advisory microbiology solutions.
This is just part of how we can support the food safety assurance of your end-to-end supply chain. Our wraparound support includes consultancy (microbiology and hygiene) and product testing, as well as help with process control, decontamination methods, food safety and quality management systems, incident management, root cause analysis and more.
For existing products, product development and exploring new ingredient / product categories and manufacturing processes, we can help with optimal risk reduction strategies.
We can advise on your testing and methodology requirements for your specific situation and product, and can conduct microbiological testing, either for routine analysis, or in response to an issue.
When it comes to hygiene and preventing contamination from the food processing / production environment, we can support with hygienic design, cleaning and environmental monitoring plans (EMP).
For pathogens of concern, we develop, validate and help implement effective decontamination methods into client facilities. We also support clients with process control design, implementation and validation – from a microbiological / decontamination perspective and more broadly.
About Suzanne Jordan
Suzanne has worked here at Campden BRI since 2005, following nine years of PhD and postdoctoral research experience in food microbiology and molecular biology of food microorganisms.
Suzanne is the lead for third party microbiological method validation studies for AOAC, MicroVal and NordVal, is a Retailer-approved Method Review Co-ordinator, and is involved in several research and contract projects for developing and evaluating new methodology. Alongside this, she is an industrial PhD supervisor for a project on the of fine-tuning dietary fibre to target gut microbiota accessibility.
During her career to date she has participated in multidisciplinary research projects involving European partners, developed expertise in a range of molecular techniques, and presented her research at an international level and in peer-reviewed journals.
How can we help?
If you’d like to find out more about microbial population profiling, get in touch to discuss your needs.
Food microbiology
Protect your customers and your brand from risk with our unique wrap around testing and advisory microbiology solutions
