Microbiomes must sit at the heart of EU rules for modified microbes, scientists tell Brussels

Members of Applied Microbiology International have urged the European Commission to place microbial communities at the centre of environmental risk assessments for genetically modified microorganisms, in the society’s response to the consultation on the forthcoming EU Biotech Act. The submission, drawing on contributions from several of the society’s members, addresses proposed amendments to the EU Directive governing the deliberate release of genetically modified microorganisms into the environment. While it represents a diverse range of views, the response generally highlights opportunities to streamline regulation while insisting on robust scientific safeguards to protect environmental and public health.

The central message is that microorganisms should not be considered in isolation. Regulatory assessments, the members argue, must account for the interactions of any released organism with the wider microbiomes in which it will exist, from soil and aquatic ecosystems to the human gut. Microbial communities underpin essential global processes, including nutrient cycling, ecosystem resilience and climate regulation, and the society contends that these functions, together with the potential effects of modified organisms on them, must be explicitly reflected in the regulatory framework rather than treated as an afterthought.

To that end, the members recommend updating environmental risk assessment requirements to reflect advances in environmental microbiology and microbial ecology. Assessments should consider how a modified microorganism could affect the composition and function of existing microbial communities, the ecosystem services those communities deliver and long-term ecological resilience. The submission also calls for greater attention to the persistence and spread of modified microorganisms, their potential to establish themselves in new environments, and the possibility of horizontal gene transfer, a concern that becomes particularly acute where transferred genetic material could contribute to the spread of antimicrobial resistance.

Monitoring is another focal point. Some members highlight the need for approaches suited to microbial applications: alongside conventional microbiological methods, technologies such as metagenomics, metatranscriptomics and environmental DNA analysis could help researchers detect changes in microbial diversity, gene transfer and ecosystem processes following an environmental release. These tools read the genetic and transcriptional signatures of entire communities, offering a way to observe whether a released strain has altered the structure or function of a resident microbiome in ways that targeted, event-specific tests would miss.

The response also recognises the potential benefits of a proportionate, risk-based approach to biotechnology regulation. Several members broadly support introducing a simplified authorisation pathway for low-risk modified microorganisms, provided that appropriate safeguards are in place, although the submission records differing and much more cautious views as well. Where a simplified pathway is used, the members suggest safeguards should include evidence of genetic stability, consideration of potential harm, and assessment of an organism’s environmental behaviour and its interactions with native microbiomes. The submission further stresses that Qualified Presumption of Safety status, which draws on established knowledge of particular microbial groups, should not be treated as sufficient evidence of environmental safety on its own.

Authorisation duration drew pointed concern. Members raised objections to proposals for unlimited-duration authorisations, particularly if these were combined with exemptions from post-market environmental monitoring. The response recommends retaining proportionate mechanisms for periodic review, or introducing clear triggers for reassessment when new scientific evidence emerges, so that long-term environmental risks and emerging findings can be addressed after an organism has already been released rather than only before.

Detection and traceability present a further technical challenge. Where genetic modifications cannot be detected using conventional event-specific methods, some members support considering alternative approaches, but only under clear, harmonised criteria across EU Member States. Flexibility in detection, the submission argues, must not undermine traceability, monitoring or risk management, since the ability to identify and track a released organism underpins both regulatory oversight and any response to unexpected effects in the field.

The submission also calls for future technical requirements to be developed with input from across the microbiological sciences, including microbial ecology, molecular microbiology, virology, mycology, antimicrobial resistance and public health. Expertise in synthetic biology, environmental monitoring and analytical chemistry will also be important as biotechnology advances. Members further highlight the potential of artificial intelligence and digital environmental surveillance to support predictive ecological modelling, analyse complex datasets and improve the early detection of unexpected environmental effects, alongside a regulatory framework that supports responsible innovation while remaining responsive to scientific advances and environmental risks.

The society’s key recommendations cover eight areas. The Directive should use clear, scientifically robust and future-proof definitions of microorganisms that reflect modern microbial classification, emerging synthetic biology technologies and complex organisms such as symbiotic partnerships. Environmental risk assessments should consider effects on existing microbiomes, ecosystem functions and resilience, with requirements reflecting the diverse applications of microbial biotechnology, including bioremediation and wastewater treatment, rather than focusing primarily on plant-based scenarios. On authorisation duration, the members recommend proportionate periodic reviews or clearly defined review triggers to address emerging scientific evidence and long-term environmental risks.

The remaining recommendations address detection, low-risk pathways, monitoring, expertise and artificial intelligence. Where identifying a specific genetic modification is technically impossible, alternative detection approaches should be permitted under clear, harmonised EU-wide criteria without undermining traceability, monitoring or risk management. Members broadly support simplified authorisation for low-risk organisms but recommend additional safeguards covering genetic stability, non-pathogenicity, potential horizontal gene transfer, environmental persistence and interactions with native microbiomes. Monitoring waivers should be exceptional, evidence-based and decided case by case, with Qualified Presumption of Safety status alone deemed insufficient to establish environmental safety and monitoring kept proportionate to risk, particularly for organisms released into the environment. Future technical requirements should draw on multidisciplinary expertise with independent scientific oversight and periodic review, and AI-assisted surveillance, predictive ecological modelling and machine learning could strengthen environmental monitoring and help identify unexpected ecological effects. Applied Microbiology International, the oldest microbiology society in the UK with more than half of its membership outside the country, describes itself as serving microbiologists in universities, private industry and research institutes worldwide, and says it amplifies the collective influence of applied microbiologists to inform international, evidence-based decision making.

Subject of Research: Microbiome-focused environmental risk assessment for genetically modified microorganisms under proposed EU biotechnology regulation

Article Title: ​Applied Microbiology International members call for microbiome-focused approach to EU biotechnology regulation

Article References: ​Applied Microbiology International members call for microbiome-focused approach to EU biotechnology regulation. Original publication (Bibliographic details unavailable.)

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Keywords: genetically modified microorganisms, microbiome, EU Biotech Act, environmental risk assessment, horizontal gene transfer, antimicrobial resistance, metagenomics, post-market environmental monitoring, Qualified Presumption of Safety, synthetic biology, artificial intelligence, biotechnology regulation