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Exploring the concept of bacterial memory

Nature Microbiology volume 10, pages 3049–3058 (2025)Cite this article

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Abstract

Bacteria have multiple mechanisms through which they sense changes in their environment and respond appropriately. In some instances, bacteria appear to retain an imprint of past events that can influence future behaviour, resembling a form of memory. This Perspective explores this concept of bacterial memory at the genetic, epigenetic, biochemical and ecological levels. We discuss how memory can prime bacteria to respond appropriately to recurring stimuli, providing fitness benefits in fluctuating environments. At the cellular level, there is evidence for memory storage mechanisms involving mutations, DNA methylation, or the inheritance of metabolites or proteins that provide a means of accessing past experiences. Complex bacterial communities can exhibit ecological memories of past environments, stored as microbiota population changes that persist or lag after acute environmental change. We review the emerging evidence supporting these concepts of microbial memory, outline some of the key molecular mechanisms, and identify research gaps and potential future applications.

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Fig. 1: Mechanisms of bacterial memory and ecological memory.
Fig. 2: Anticipatory regulation strategies.
Fig. 3: Protein-based inheritance confers phenotypic memory.
Fig. 4: Response memory of the lactose operon.
Fig. 5: DNA methylation-dependent gene regulation.
Fig. 6: Ecological memory in response to diet switching.

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Acknowledgements

This research was conducted with the financial support of Research Ireland under grant no. SFI/12/RC/2273_P2 and the Weston Family Foundation.

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Authors and Affiliations

  1. APC Microbiome Ireland, Biosciences Institute, University College, Cork, Ireland

    Killian Scanlon, Fergus Shanahan, R. Paul Ross & Colin Hill

  2. School of Microbiology, University Cork College, Cork, Ireland

    Killian Scanlon, R. Paul Ross & Colin Hill

  3. Department of Medicine, University College Cork, Cork, Ireland

    Fergus Shanahan

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  1. Killian Scanlon
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  2. Fergus Shanahan
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  4. Colin Hill
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All authors conceptualized the content of the paper. K.S wrote the draft paper. F.S., R.P.R. and C.H. reviewed and edited the paper.

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Correspondence to Colin Hill.

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Nature Microbiology thanks Yitzhak Pilpel, Tanel Tenson and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Scanlon, K., Shanahan, F., Ross, R.P. et al. Exploring the concept of bacterial memory. Nat Microbiol 10, 3049–3058 (2025). https://doi.org/10.1038/s41564-025-02185-3

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