Assessing the safety of microbiome perturbations

Metris, Aline, Walker, Alan, Showering, Alicia, Doolan, Andrea, McBain, Andrew, Ampatzoglou, Antonis, Murphy, Barry, O'Neill, Catherine, Shortt, Colette, Darby, Elizabeth, Aldis, Gary, Hillebrand, Greg, Brown, Helen, Browne, Hilary, Tiesman, Jay, Leng, Joy, Lahti, Leo, Jakubovics, Nicholas, Hasselwander, Oliver, Finn, Robery, Klamert, Silvia, Korcsmaros, Tamas and Hall, Lindsay 2025. Assessing the safety of microbiome perturbations. Microbial Genomics 11 (5) , 001405. 10.1099/mgen.0.001405

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Abstract

Everyday actions such as eating, tooth brushing, or applying cosmetics inherently modulate our microbiome. Advances in sequencing technologies now facilitate detailed microbial profiling, driving intentional microbiome-targeted product development. Inspired by an academic-industry workshop held in January 2024, this review explores the oral, skin, and gut microbiomes, focusing on the potential long-term implications of perturbations. Key challenges in microbiome safety assessment include confounding factors (ecological variability, host influences, and external conditions like geography and diet) and biases from experimental measurements and bioinformatics analyses. The taxonomic composition of the microbiome has been associated with both health and disease, and perturbations like regular disruption of the dental biofilm are essential for preventing caries and inflammatory gum disease. However, further research is required to understand the potential long-term impacts of microbiome disturbances, particularly in vulnerable populations including infants. We propose that emerging technologies, such as omics technologies to characterize microbiome functions rather than taxa, leveraging artificial intelligence to interpret clinical study data, and in vitro models to characterize and measure host–microbiome interaction endpoints, could all enhance the risk assessments. The workshop emphasized the importance of detailed documentation, transparency, and openness in computational models to reduce uncertainties. Harmonization of methods could help bridge regulatory gaps and streamline safety assessments but should remain flexible enough to allow innovation and technological advancements. Continued scientific collaboration and public engagement are critical for long-term microbiome monitoring, which is essential to advancing safety assessments of microbiome perturbations.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Schools > Biosciences
Publisher:	Microbiology Society
ISSN:	2057-5858
Date of First Compliant Deposit:	23 May 2025
Date of Acceptance:	27 March 2025
Last Modified:	23 May 2025 15:00
URI:	https://orca.cardiff.ac.uk/id/eprint/178437

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