Fig. 2

Potential applications of bacterial epigenetics in microbiome engineering. A Mimicking host DNA methylation patterns and recoding DNA sequences with synonymous nucleotide modifications or single-nucleotide polymorphisms (SNPs) have facilitated the evasion of R-M barrier in bacteria. B DNA MTases can serve as reporter systems for monitoring protein expression levels, achieved by their integration with methylation-sensitive restriction enzyme digestion and subsequent high-throughput sequencing. C Epigenetic regulatory systems utilizing DNA methyltransferases have been devised to sense targeted signals and maintain an epigenetic memory of cellular states. D Natural bacterial DNA methylation and methylation-sensitive Type II REases have been harnessed to selectively enrich genomes of specific bacterial subgroups within microbiomes. E Type IV secretion systems (T4SS), combined with DNA methylation patterns, could offer precision in gene transmission to specific microbes. The use of DNA methylation patterns ensures that gene delivery is confined to targeted microbial clusters, thereby enhancing target specificity. F A fusion protein of DCM (DNA cytosine methyltransferase) and the RNA polymerase subunit b, along with methylated DNA sequencing, has been employed to trace genome-wide gene transcription over time