Table 3.

Gut Microbiota Involved with Epigenetic Alterations in CRC

Epigenetic modification	Microbiota studied	Model	Key findings	REFs
Methylation	Murine gut microbiota	GF mice	The methylation of WIF1, PENK, and NPY were associated with CRC dysbiosis.	[94]
	Murine gut microbiota	Lgr5-EGFP-CreER mice	Gene methylation was increased by microbiota transplantation.	[148]
	L. acidophilus, B. infantis, and Klebsiella species	Human intestinal epithelial cells (IECs)	Microbiota treatment resulted in differential methylation changes in 200 regions of DNA.	[149]
	Murine gut microbiota	GF mice	The number of changes in the methylation status of genes increased with age of GF mice.	[150]
	ETBF	MinApcΔ716+/− mice	ETBF-induced tumors contained methylated tumor suppressor genes.	[151]
Histone modifications	Murine gut microbiota	wild-type mice	Histone marks H3K4me1 and H3K27ac were enriched at poised or active enhancers.	[152]
	Antibiotic-treated murine microbiota	GF mice	De novo generation of oscillating histone marks and rhythmically expressed genes.	[153]
	Murine gut microbiota	wild-type mice	Bacterial presence resulted in numerous changes in histone acetylation in the proximal colon tissue.	[154]
	Murine gut microbiota	GF mice	The location of H3K4 methylation marks was modified when gut microbes colonized.	[155]
	Antibiotic-treated murine microbiota	GF mice	Derived SCFAs promoted H3K18 crotonylation by inhibiting HDACs.	[156]
Non-coding RNAs	E. coli strains or fecal-derived murine microbiota	GF mice	Distinct changes in lncRNA signatures occurred after GF mice were reconstituted with normal mouse microbiota or with E. coli alone.	[105]
	F. nucleatum	CRC xenograft model	F. nucleatum caused resistance to oxaliplatin and 5-FU via downregulation of miR-4802 and miR-18a.	[108]
	Murine gut microbiota	GF mice	A total of 19 miRNAs in IESCs significantly differed in expression depending on microbial status.	[157]
	Murine gut microbiota	GF mice	Microbiota-dependent miR-21–5p expression in IECs regulated intestinal epithelial permeability via ARF4.	[107]
	Antibiotic-treated murine microbiota	GF mice	miRNAs let-7b, miR-141, and miR-200a expression were significantly reduced in GF mice.	[106]
	Murine gut microbiota	IEC-miRNA-deficient mice	The presence of gut microbes was associated with decreased production of miRNAs.	[158]