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Probiotic lactobacilli mediated changes in global epigenetic signatures of human intestinal epithelial cells during Escherichia coli challenge

Abstract

Host genome environment association is critical for proper development and functioning of an individual. Microbiota and probiotics within the cellular vicinity may serve such critical stimuli that can bring out different epigenetic mediated host responses. The aim of present study was to explore the changes in epigenetic signatures of Caco-2 cells by probiotic strains (Lactobacillus rhamnosus MTCC 5897: LR, Lactobacillus fermentum MTCC 5898: LF and their mixture: RF), respectively, or during challenge with Escherichia coli (ATCC 14948) using exclusion, competition and displacement assays. Adenocarcinoma intestinal epithelial Caco-2 cells were treated with LR, LF, RF and E. coli for 6 h, respectively. Caco-2 cells were also challenged with E. coli and probiotic lactobacilli during exclusion, competition and displacement assays. Finally, global epigenetic modifications by acetylation of H4 and H3 histone proteins and DNA methylation patterns were determined. Probiotic-treated Caco-2 cells displayed significant (p < 0.01) reduction in percent global H4 and H3 acetylation, respectively, in contrast to their elevated (p < 0.05) levels after E. coli infection. On the other hand, a remarkable (p < 0.01) decrease in percent H4 and H3 acetylation were observed when E. coli were excluded, competed or displaced by lactobacilli strains. No changes in the global DNA methylation patterns were observed in Caco-2 cells after exposure to probiotic strains or E. coli, respectively, but surprisingly, their levels increased significantly (p < 0.05) when lactobacilli-treated cells were challenged with E. coli during exclusion or competition than displacement assays. Probiotic L. rhamnosus and L. fermentum modulated the host epigenetic signatures via global histone acetylation individually or during E. coli challenge by exclusion, competition and displacement assays. Whilst on the other hand changes in global DNA methylation patterns were obtained significantly during probiotic treatment with E. coli in exclusion and competition protocols.

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Funding

We are grateful to Department of BioTechnology, Ministry of Science and Technology, New Delhi, for providing the necessary funds (BT/PR15109/PFN/20/1174/2015).

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Correspondence to Rajeev Kapila.

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Bhat, M.I., Kumari, A., Kapila, S. et al. Probiotic lactobacilli mediated changes in global epigenetic signatures of human intestinal epithelial cells during Escherichia coli challenge. Ann Microbiol 69, 603–612 (2019). https://doi.org/10.1007/s13213-019-01451-0

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Keywords

  • DNA methylation
  • Epigenome
  • Histone acetylation
  • Lactobacilli
  • Caco-2