Production strains are valuable biological resources. In industrial fermentation, probiotics, food biotechnology, environmental applications or animal health, they may represent years of selection, optimisation and know-how. Sequencing these strains can provide essential information for characterisation, monitoring and decision-making.
However, production strain sequencing should not be considered only as a one-time academic exercise. It can be useful at several stages of industrial development, from strain selection to routine production monitoring.
One of the best moments to sequence a production strain is before industrial scale-up. At this stage, sequencing can help confirm strain identity, detect genomic features of interest, evaluate safety markers and establish a genomic reference for future comparisons.
This reference genome can later be used to monitor strain stability, investigate production issues or compare new isolates with the original strain.
If a production strain suddenly shows reduced performance, modified fermentation kinetics, altered metabolite production or unexpected instability, genome sequencing can help investigate whether a genomic change is involved.
Comparing the current isolate with the original reference strain may reveal SNPs, gene loss, plasmid variation, mobile element activity or structural rearrangements that could explain the change.
Microbial strains can evolve during repeated subculturing, propagation or storage. Even small genomic changes may become relevant if they affect industrial performance or reproducibility.
Sequencing after defined numbers of passages or after long-term use can help evaluate genetic drift and document whether the strain remains stable over time.
When unexpected microorganisms are detected in a production environment, genome sequencing can help determine whether they correspond to the production strain, a derivative variant, a closely related organism or an external contaminant.
Genomic comparison using ANI, SNP analysis, pangenome analysis or strain-specific markers can support traceability and help clarify the origin of microbial isolates.
Sequencing can identify strain-specific genomic markers that can later be converted into PCR or qPCR assays. This is useful when routine monitoring requires a fast and targeted detection method.
In this workflow, genomics is used for discovery and marker validation, while PCR becomes the routine tool for detection, quantification or production monitoring.
Companies often maintain several related strains or candidate isolates. Sequencing these strains can help organise a strain portfolio, identify redundancy, detect unique genomic features and prioritise candidates for future development.
This approach can support innovation strategy, intellectual property discussions, documentation and communication with partners or clients.
There is no universal frequency. The decision depends on the value of the strain, the stability of the process, the level of regulatory or quality control constraints and the risk associated with strain variation.
For high-value strains, sequencing may be useful at key milestones: before scale-up, after strain improvement, after repeated passages, when performance changes or when a new production site or process condition is introduced.
Biomanda provides bioinformatics services for microbial genomics, comparative genomics and molecular biology. Depending on the project, Biomanda can support genome assembly, genome annotation, strain comparison, SNP analysis, pangenome analysis, synteny analysis, ANI calculation, marker identification and interpretation of genomic changes.
The objective is to help companies transform production strain sequencing into practical information for stability monitoring, quality control, R&D strategy and industrial decision-making.
Production strains should be sequenced when genomic information can reduce uncertainty, support decision-making or protect the value of a microbial resource. This may occur before scale-up, during troubleshooting, after repeated passages, during contamination investigations or when developing monitoring tools.
For industrial microbiology, sequencing is not only a characterisation tool. It is a strategic approach to managing microbial strains over time.