Richards, B. A. & Frankland, P. W. The persistence and transience of memory. Neuron 94, 1071–1084 (2017).
Zlotnik, G. & Vansintjan, A. Memory: an extended definition. Front Psychol. 10, 2523 (2019).
Kukushkin, N. V., Carney, R. E., Tabassum, T. & Carew, T. J. The massed-spaced learning effect in non-neural human cells. Nat. Commun. 15, 9635 (2024).
Witzany, G. in Memory and Learning in Plants (eds Frantisek, B. et al.) 1–16 (Springer, 2018); https://doi.org/10.1007/978-3-319-75596-0_1
De la Fuente, I. M. et al. Evidence of conditioned behavior in amoebae. Nat. Commun. 10, 3690 (2019).
Saigusa, T., Tero, A., Nakagaki, T. & Kuramoto, Y. Amoebae anticipate periodic events. Phys. Rev. Lett. 100, 018101 (2008).
Nakagaki, T., Yamada, H. & Tóth, Á Maze-solving by an amoeboid organism. Nature 407, 470–470 (2000).
Vermeersch, L. et al. Do microbes have a memory? History-dependent behavior in the adaptation to variable environments. Front. Microbiol. 13, 1004488 (2022).
Solopova, A. et al. Bet-hedging during bacterial diauxic shift. Proc. Natl Acad. Sci. USA 111, 7427–7432 (2014).
Mitchell, A. et al. Adaptive prediction of environmental changes by microorganisms. Nature 460, 220–224 (2009).
Lambert, G. et al. Correction: Memory and fitness optimization of bacteria under fluctuating environments. PLoS Genet. 10, e1004793 (2014).
Casadesús, J. & Low, D. Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. Rev. 70, 830–856 (2006).
Letourneau, J. et al. Ecological memory of prior nutrient exposure in the human gut microbiome. ISME J. 16, 2479–2490 (2022).
Globus, R. & Qimron, U. Crystal-clear memories of a bacterium. Science 357, 1096–1097 (2017).
Harvey, Z. H., Chen, Y. & Jarosz, D. F. Protein-based inheritance: epigenetics beyond the chromosome. Mol. Cell 69, 195–202 (2018).
Lambert, G. & Kussell, E. Memory and fitness optimization of bacteria under fluctuating environments. PLoS Genet. 10, e1004556 (2014).
Mitchell, A. & Pilpel, Y. A mathematical model for adaptive prediction of environmental changes by microorganisms. Proc. Natl Acad. Sci. USA 108, 7271–7276 (2011).
Veening, J.-W., Smits, W. K. & Kuipers, O. P. Bistability, epigenetics, and bet-hedging in bacteria. Annu Rev. Microbiol 62, 193–210 (2008).
Grimbergen, A. J., Siebring, J., Solopova, A. & Kuipers, O. P. Microbial bet-hedging: the power of being different. Curr. Opin. Microbiol. 25, 67–72 (2015).
Mahilkar, A., Venkataraman, P., Mall, A. & Saini, S. Experimental evolution of anticipatory regulation in Escherichia coli. Front. Microbiol. 12, 796228 (2022).
Rai, N., Kim, M. & Tagkopoulos, I. Understanding the formation and mechanism of anticipatory responses in Escherichia coli. Int. J. Mol. Sci. 23, 5985 (2022).
Tagkopoulos, I., Liu, Y.-C. & Tavazoie, S. Predictive behavior within microbial genetic networks. Science 320, 1313–1317 (2008).
Delaney, J. M. Requirement of the Escherichia coli dnaK gene for thermotolerance and protection against H2O2. J. Gen. Microbiol. 136, 2113–2118 (1990).
Badrinarayanan, A., Le, T. B. K. & Laub, M. T. Bacterial chromosome organization and segregation. Annu. Rev. Cell Dev. Biol. 31, 171–199 (2015).
Thompson, S. R., Wadhams, G. H. & Armitage, J. P. The positioning of cytoplasmic protein clusters in bacteria. Proc. Natl Acad. Sci. USA 103, 8209–8214 (2006).
Reyes-Lamothe, R. & Sherratt, D. J. The bacterial cell cycle, chromosome inheritance and cell growth. Nat. Rev. Microbiol. 17, 467–478 (2019).
Birky, W. C. & Skavaril, R. V. Random partitioning of cytoplasmic organelles at cell division: the effect of organelle and cell volume. J. Theor. Biol. 106, 441–447 (1984).
Ostovar, G. & Boedicker, J. Q. Phenotypic memory in quorum sensing. PLoS Comput. Biol. 20, e1011696 (2024).
Ishihama, A. Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks. FEMS Microbiol. Rev. 34, 628–645 (2010).
Novick, A. & Weiner, M. Enzyme induction as an all-or-none phenomenon. Proc. Natl Acad. Sci. USA 43, 553–566 (1957).
Sourjik, V. & Wingreen, N. S. Responding to chemical gradients: bacterial chemotaxis. Curr. Opin. Cell Biol. 24, 262–268 (2012).
Macnab, R. M. & Koshland, D. E. The gradient-sensing mechanism in bacterial chemotaxis. Proc. Natl Acad. Sci. USA 69, 2509–2512 (1972).
Goy, M. F., Springer, M. S. & Adler, J. Sensory transduction in Escherichia coli: role of a protein methylation reaction in sensory adaptation. Proc. Natl Acad. Sci. USA 74, 4964–4968 (1977).
Stock, J. B. & Zhang, S. The biochemistry of memory. Curr. Biol. 23, R741–R745 (2013).
Krembel, A., Colin, R. & Sourjik, V. Importance of multiple methylation sites in Escherichia coli chemotaxis. PLoS ONE 10, e0145582 (2015).
Kalinin, Y. V., Jiang, L., Tu, Y. & Wu, M. Logarithmic sensing in Escherichia coli bacterial chemotaxis. Biophys. J. 96, 2439–2448 (2009).
Gosztolai, A. & Barahona, M. Cellular memory enhances bacterial chemotactic navigation in rugged environments. Commun. Phys. 3, 47 (2020).
Govers, S. K., Mortier, J., Adam, A. & Aertsen, A. Protein aggregates encode epigenetic memory of stressful encounters in individual Escherichia coli cells. PLoS Biol. 16, e2003853 (2018).
Veening, J.-W. et al. Bet-hedging and epigenetic inheritance in bacterial cell development. Proc. Natl Acad. Sci. USA 105, 4393–4398 (2008).
Bhattacharyya, S. et al. A heritable iron memory enables decision-making in Escherichia coli. Proc. Natl Acad. Sci. USA 120, e2309082120 (2023).
Riber, L. & Hansen, L. H. Epigenetic memories: the hidden drivers of bacterial persistence? Trends Microbiol 29, 190–194 (2021).
Lim, H. N. & van Oudenaarden, A. A multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nat. Genet. 39, 269–275 (2007).
Harms, A., Maisonneuve, E. & Gerdes, K. Mechanisms of bacterial persistence during stress and antibiotic exposure. Science 354, aaf4268 (2016).
Niu, H., Gu, J. & Zhang, Y. Bacterial persisters: molecular mechanisms and therapeutic development. Signal Transduct. Target Ther. 9, 174 (2024).
Xu, Y., Liu, S., Zhang, Y. & Zhang, W. DNA adenine methylation is involved in persister formation in E. coli. Microbiol. Res. 246, 126709 (2021).
Adam, M., Murali, B., Glenn, N. O. & Potter, S. S. Epigenetic inheritance based evolution of antibiotic resistance in bacteria. BMC Evol. Biol. 8, 52 (2008).
Jõers, A. & Tenson, T. Growth resumption from stationary phase reveals memory in Escherichia coli cultures. Sci. Rep. 6, 24055 (2016).
Miyaue, S. et al. Bacterial memory of persisters: bacterial persister cells can retain their phenotype for days or weeks after withdrawal from colony–biofilm culture. Front. Microbiol. 9, 1396 (2018).
Desmond, C., Stanton, C., Fitzgerald, G. F., Collins, K. & Paul Ross, R. Environmental adaptation of probiotic lactobacilli towards improvement of performance during spray drying. Int. Dairy J. 11, 801–808 (2001).
Svenningsen, M. S., Svenningsen, S., Lo, Sørensen, M. A. & Mitarai, N. Existence of log-phase Escherichia coli persisters and lasting memory of a starvation pulse. Life Sci. Alliance 5, e202101076 (2022).
Shmidov, E. et al. Multigenerational proteolytic inactivation of restriction upon subtle genomic hypomethylation in Pseudomonas aeruginosa. Nat. Microbiol. 10, 2498–2510 (2025).
Holloway, B. W. Variations in restriction and modification of bacteriophage following increase of growth temperature of Pseudomonas aeruginosa. Virology 25, 634–642 (1965).
Ogle, K. et al. Quantifying ecological memory in plant and ecosystem processes. Ecol. Lett. 18, 221–235 (2015).
Dethlefsen, L. & Relman, D. A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl Acad. Sci. USA 108, 4554–4561 (2011).
Thaiss, C. A. et al. Persistent microbiome alterations modulate the rate of post-dieting weight regain. Nature 540, 544–551 (2016).
Palleja, A. et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat. Microbiol 3, 1255–1265 (2018).
Canarini, A. et al. Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community. Nat. Commun. 12, 5308 (2021).
Vompe, A. D. et al. Microbiome ecological memory and responses to repeated marine heatwaves clarify variation in coral bleaching and mortality. Glob. Change Biol. 30, e17088 (2024).
Smith, M. B. et al. Natural bacterial communities serve as quantitative geochemical biosensors. mBio 6, e00326–15 (2015).
Kuster, S. P. et al. Previous antibiotic exposure and antimicrobial resistance in invasive pneumococcal disease: results from prospective surveillance. Clin. Infect. Dis. 59, 944–952 (2014).
Stacy, A. et al. Infection trains the host for microbiota-enhanced resistance to pathogens. Cell 184, 615–627.e17 (2021).
Carmody, R. N. et al. Diet dominates host genotype in shaping the murine gut microbiota. Cell Host Microbe 17, 72–84 (2015).
Salonen, A. et al. Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men. ISME J. 8, 2218–2230 (2014).
Khazaei, T. et al. Metabolic multistability and hysteresis in a model aerobe–anaerobe microbiome community. Sci. Adv. 6, eaba0353 (2020).
Louca, S. & Doebeli, M. Transient dynamics of competitive exclusion in microbial communities. Environ. Microbiol. 18, 1863–1874 (2016).
Debray, R. et al. Priority effects in microbiome assembly. Nat. Rev. Microbiol. 20, 109–121 (2022).
Wallecha, A., Munster, V., Correnti, J., Chan, T. & van der Woude, M. Dam- and OxyR-dependent phase variation of agn43: essential elements and evidence for a new role of DNA methylation. J. Bacteriol. 184, 3338–3347 (2002).
Source link
