This was the key message from an online event hosted by Finnish regulatory and biosafety consultancy Biosafe and Spanish microbial biotech company Darwin Bioprospecting Excellence.
Pauliina Halimaa, managing director at Biosafe, and Manuel Porcar, CTO and co-founder of Darwin Bioprospecting Excellence, urged companies to integrate regulatory planning into microbial innovation from the outset.
“Discovery and regulation cannot be treated as separate processes,” Pocar said. “The regulatory pathway must be considered from the very beginning.”
According to Porcar, many companies end up using the same microbial strains largely because they are the easiest to commercialize and regulate.
“The challenge is no longer simply discovering new microorganisms,” he said. “The real challenge is identifying strains that can ultimately reach the market and deliver value in a regulated environment.”
Regulatory status has therefore become a strategic asset in microbial innovation, as strains with established Qualified Presumption of Safety (QPS) status often reach the market more quickly.
“A microorganism’s commercial value is not determined only by its biological properties,” Porcar said. “Regulatory status is often just as important.
Biodiscovery designed around Nagoya compliance
Porcar explained that companies must comply with the requirements of the Nagoya Protocol, a treaty under the Convention on Biological Diversity.
The protocol is designed to ensure that when researchers, companies or organizations use genetic resources from another country, the benefits arising from that use are shared fairly with the country and, where applicable, with the indigenous or local communities that provided the resources.
In biodiscovery, questions focus on whether the microbe is unique, produces a useful compound, and can become a drug, enzyme, or industrial product, Porcar explained. Nagoya compliance adds another question: Did you obtain this genetic resource legally and under agreed terms?
“We cannot simply travel to another country, collect samples, and commercialize them. That would be biopiracy,” Porcar explained. “Responsible innovation requires responsible access to biodiversity.”
“The key factor is often not what the strain is, but where it comes from and how access to that genetic resource was obtained.”
What does this mean for next-gen and novel strains?
Next-generation probiotics are facing a higher regulatory bar, as the industry shifts away from simply marketing products that “contain probiotics” and toward demonstrating clinically validated health outcomes, Porcar noted, adding that companies seeking to develop high-value probiotic products will need to prove efficacy through robust research.
“The next generation of probiotics will target specific outcomes such as metabolic health, women’s health, and mental wellbeing,” Porcar said. “Future probiotic development will depend increasingly on clinical validation rather than marketing claims.”
While these discoveries expand the potential for innovative microbiome-based products, regulators require additional evidence to establish their safety, including whether the organisms have a history of safe use, produce toxins, or carry antimicrobial resistance genes. Consequently, the more novel a strain is, the greater the evidence burden for commercial approval, making scientific validation an essential part of bringing next-gen probiotics to market.
“The more innovative a strain is, the more important it becomes to generate the evidence needed to support its safety and commercial use,” Porcar said.
Halimaa added that novel strains face greater regulatory scrutiny because they lack a history of safe use, requiring companies to generate extensive safety data.
This includes assessing toxigenicity, pathogenicity and antimicrobial resistance, with European Food Safety Authority (EFSA) taking a particularly precautionary approach to antimicrobial resistance and expecting robust evidence that resistance genes do not pose a safety risk.
“It is not enough to assume antimicrobials are absent,” she said. “Their absence must be demonstrated.”
Halimaa warned that mistakes made during strain selection, characterization or safety assessment can lead to significant delays and additional costs later in development.
Rather than waiting for regulators to identify gaps in an application, companies should proactively assess potential hazards and address likely regulatory concerns in their dossiers from the outset, she told the audience.
“Do not wait for EFSA’s questions,” she warned. “Anticipate where hazards and risks may be identified and address them in your dossier.”
