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Microbial Genomics logo Microbial Genomics

Volume 11, Issue 5

Assessing the safety of microbiome perturbations Open Access

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, 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 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 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): artificial intelligence (AI)/ML , clinical studies , gut , in vitro models , microbiome , oral , safety assessment and skin
Funding
This study was supported by the:
  • Wellcome Trust (Award 220876/Z/20/Z)
    • Principal Award Recipient: J HallLindsay
  • Biotechnology and Biological Sciences Research Council (Award BB/X011054/1)
    • Principal Award Recipient: J HallLindsay
  • H2020 European Research Council (Award 101115994)
    • Principal Award Recipient: BrowneHilary
  • Strategic Research Council (Award 330887)
    • Principal Award Recipient: LahtiLeo
  • EIT Health (Award 952914)
    • Principal Award Recipient: LahtiLeo
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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Assessing the safety of microbiome perturbations
M Gen 11, 001405 (2025); https://doi.org/10.1099/mgen.0.001405
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