Microorganisms play a crucial role in food production, health, agriculture and environmental sustainability. Yet despite the enormous diversity of microbial life on Earth, only a small fraction of microorganisms are currently used in industrial applications. As interest in probiotics, precision fermentation, agricultural biostimulants, and microbial products & solutions continues to grow, discovering novel strains is becoming increasingly important.
Identifying a promising microorganism is only the first step. To successfully bring a microbial product to market, companies need to consider functionality and performance alongside safety, regulatory requirements, and commercial feasibility from an early stage.
These themes were explored in a recent webinar co-hosted by Biosafe and Darwin Bioprospecting Excellence, where experts discussed the journey from microbial discovery to regulatory success and the decisions that can shape a strain’s commercial future long before it reaches the market.
Watch the webinar recording: From strain discovery to regulatory success: what really matters?
A vast microbial world, with much of its potential still untapped
The microbial world remains largely unexplored. Estimates suggest that Earth may host more than 10¹² microbial species, yet only a small proportion have been characterised or cultivated using conventional methods.
This presents both a scientific and commercial challenge. While the available biodiversity is vast, industries often rely on a relatively limited number of well-known microbial species and strains. That leaves considerable room for discovering organisms with new functionalities and potentially valuable applications.
To address this challenge, companies such as Darwin Bioprospecting Excellence focus on microbial bioprospecting. Over the past decade, Darwin has collected samples from more than 900 habitats worldwide, building a collection of approximately 5,000 bacterial and fungal strains originating from plants, animals, humans, soil, water and other environments.
Such collections provide access to familiar microorganisms as well as potentially novel species that may offer unique metabolic capabilities and industrial applications.
From environmental sample to functional strain
Finding a microorganism in nature is only the beginning of a much longer development journey.
The path from discovery to commercial application typically includes:
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Bioprospecting and sample collection
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Isolation and cultivation of microorganisms
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Genome sequencing and bioinformatic analysis
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Laboratory characterisation of desired properties
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Pilot-scale production
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Field trials or clinical studies
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Regulatory assessment and commercialisation
Modern genome analysis tools allow researchers to evaluate microbial potential rapidly. Functional traits such as vitamin synthesis, gut colonisation, antioxidant activity, plant growth promotion, amino acid production, and even plastic degradation can increasingly be investigated through bioinformatic analysis before extensive laboratory testing begins.
This combination of computational screening and experimental validation enables companies to focus resources on the most promising candidates.
New strains are opening new application spaces
The diversity of microorganisms translates into a wide range of potential applications.
In the health and nutrition sector, microbial strains are increasingly being selected for specific functionalities rather than general probiotic effects alone. Examples include strains capable of producing beneficial metabolites, supporting gut health, or contributing to targeted health outcomes.
One example presented during the webinar involved a GABA-producing probiotic strain used in a fermented dairy product. Gamma-aminobutyric acid (GABA) is a neurotransmitter involved in nervous system signalling, associated with relaxation and stress regulation. By combining a functional strain with a traditional fermentation strain, the developers were able to create a novel product with added value beyond basic nutrition.
Other examples included heat-resistant probiotic strains suitable for incorporation into confectionery products and probiotic strains investigated for dermatological applications.
Beyond food and health, microbial innovation is increasingly supporting sustainable agriculture and environmental solutions. Plant growth-promoting microorganisms can improve crop performance under challenging conditions such as drought, while microbial consortia are being investigated for roles in plastic degradation and other bioremediation applications.
Together, these examples show how strain discovery can unlock opportunities across a much broader range of applications than traditional fermentation processes alone.
Safety starts with knowing exactly what you have
While functionality is important, regulatory authorities require evidence that microbial products are safe for their intended use.
According to Biosafe's Managing Director Dr Pauliina Halimaa, one of the most critical foundations of microbial safety assessment is correct taxonomic identification.
Accurate species and strain identification influences almost every aspect of the subsequent evaluation process. It helps determine whether:
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The microorganism belongs to a species with Qualified Presumption of Safety (QPS) status in the European Union.
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Relevant antimicrobial resistance genes may be intrinsic to the species.
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The species is known to produce toxins or antimicrobials.
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Additional toxicological studies may be required.
Shortcuts taken during strain identification can create significant challenges later in development. For regulatory purposes, whole genome sequencing has become an essential tool for obtaining robust taxonomic information.
At this stage, precision matters. The clearer the identity and characteristics of the strain are early on, the stronger the foundation for the regulatory work that follows.
Antimicrobial resistance can shape the regulatory path
One of the most closely scrutinised aspects of microbial safety assessment is antimicrobial resistance (AMR).
Regulators require developers to investigate whether strains contain antimicrobial resistance genes and, if they do, whether these genes are considered intrinsic to the species or potentially transferable.
Whole genome sequencing plays a central role in this process. However, genomic findings alone may not always be sufficient. Additional analyses may be required to evaluate whether resistance traits could pose a risk through horizontal gene transfer.
The assessment can become particularly challenging when scientific evidence is incomplete or when the interpretation of genomic findings is uncertain. As highlighted during the webinar, regulatory authorities often apply a precautionary approach when evaluating potential safety concerns.
For product developers, this reinforces the importance of generating high-quality data early. It can help identify issues while there is still room to make informed decision about strain selection, further studies and development priorities.
Regulatory strategy begins earlier than many developers expect
A common misconception is that regulatory work starts once a promising strain has already been identified.
In practice, many of the decisions that determine regulatory success are made much earlier.
Developers should consider regulatory requirements during strain selection, characterisation, and early development phases. Factors such as strain origin, genome sequence quality, safety assessment requirements, intellectual property considerations, culture collection deposits and market-specific regulations can all influence the feasibility of commercialisation.
This makes early regulatory thinking part of a broader development strategy. Understanding potential requirements at the discovery stage can help companies prioritise the strains that offer the strongest combination of functional promise and regulatory feasibility.
Clear documentation is equally important. Even strong scientific data may be difficult for authorities to assess if study reports are incomplete, terminology is inconsistent or critical details are missing.
Successful dossiers present results in a way that helps regulators understand why the data supports product safety and addresses potential concerns.
Better decisions early can make the route to market smoother
The path from microbial discovery to market authorisation is rarely straightforward. Novel strains may offer exciting commercial opportunities, while also introducing scientific, regulatory, and technical challenges.
The key message from both Darwin Bioprospecting Excellence and Biosafe was clear: successful microbial innovation requires discovery and regulatory planning to progress hand in hand.
By combining advanced strain discovery, functional characterisation, robust safety assessment, and proactive regulatory strategy, developers can make better-informed decisions about where to invest their time and resources, and build a stronger foundation for commercialisation.
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