A2 Refereed review article in a scientific journal
Assessing the safety of microbiome perturbations
Authors: Metris, Aline; Walker, Alan W.; Showering, Alicia; Doolan, Andrea; McBain, Andrew J.; Ampatzoglou, Antonis; Murphy, Barry; O'Neill, Catherine; Shortt, Colette; Darby, Elizabeth M.; Aldis, Gary; Hillebrand, Greg G.; Brown, Helen L.; Browne, Hilary P.; Tiesman, Jay P.; Leng, Joy; Lahti, Leo; Jakubovics, Nicholas S.; Hasselwander, Oliver; Finn, Robert D.; Klamert, Silvia; Korcsmaros, Tamas; Hall, Lindsay J.
Publisher: Microbiology Society
Publication year: 2025
Journal: Microbial genomics
Journal name in source: Microbial Genomics
Article number: 001405
Volume: 11
Issue: 5
eISSN: 2057-5858
DOI: https://doi.org/10.1099/mgen.0.001405
Web address : https://doi.org/10.1099/mgen.0.001405
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/498432675
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, focussing 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 micro-biome 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. Harmonisation 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.
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Funding information in the publication:
A.W.W. and the Rowett Institute receive core funding from the Scottish Government’s Rural and Environment Science and Analytical Services Division (RESAS). L.J.H. is supported by a Wellcome Trust Investigator Award 220876/Z/20/Z and together with T.K. a Biotechnology and Biological Sciences Research Council (BBSRC) Institute Strategic Programme Food, Microbiome and Health BB/X011054/1 and its constituent project BBS/E/F/000PR13631. H.P.B. is funded by European Research Council Starter Grant: SYNergize 101115994. L.L. is supported by the Research Council of Finland (decision 330887) and the European Union’s Horizon 2020 research and innovation programme (grant 952914). T.K. is supported by the NIHR Imperial Biomedical Research Centre (BRC) and its Organoid Facility. The views expressed are those of the authors and not necessarily those of the NIHR or the UK Department of Health and Social Care. The workshop was organized and funded by the Microbiology Society and Unilever PLC.
