Table 2 Summary of recent papers (2015–present) addressing the impact of gut microbes on the colon epithelial cell genome or epigenome
Key findings | Bacteria studied | Model system | Relevant CRC genes or pathways identified | Technique used to examine genome or epigenome |
|---|---|---|---|---|
DNA damage | ||||
 Colibactin-induced intrastrand DNA crosslinking upon exposure to cells [57] | pks + E. coli | HeLa cells | None highlighted | Cross-linking assay in cells, acellular DNA-cross-linking assay |
 pks + E. coli worked synergistically with ETBF to cause increased DNA damage and increased tumor formation in a mouse model of CRC [59] | pks + E. coli and ETBF | Mice | None highlighted | Immunohistochemistry |
 When inoculated with ETBF, Apcmin/+/Msh2−/− mice produced more tumors than Apcmin/+ mice. The increase in tumor burden was not seen in the absence of ETBF inoculation, suggesting that MMR proteins are important in preventing tumorigenesis after ETBF infection [61] | ETBF | Mice | None highlighted | Transgenic mouse model |
 CECs exposed to macrophages that were previously exposed to E. faecalis showed an increased rate of mutagenesis and an increased rate of aneuploidy and chromosomal translocation, indicative of CIN [63] | E. faecalis | Young adult mouse colonic (YAMC) ECs | Several cancer driver genes, including Arid1b, Cdkn2a, Daxx, Gata3, Map3k1, Notch1, Pten, Smad2 and others | Mutant fraction assay, FACS |
Methylation | ||||
 In a porcine model, in which premature infant pigs were given antibiotics immediately after birth, 80 DMRs were identified and were associated with genes involved in phagocytosis, the innate immune response, and other pathways [73] | Antibiotic-treated porcine gut microbiome | Premature infant pigs | Pathways related to innate immune response and phagocytosis | RRBS, BSP |
 Treatment of human intestinal ECs with Lactobacillus acidophilus, Bifidobacterium infantis, and Klebsiella species resulted in methylation changes in several hundred genes of interest [74] | L. acidophilus, B. infantis and Klebsiella species | Human intestinal EC lines (H4 and NCM460) | Pathways related to nucleotide binding (immature ECs) and chromatin organization (mature ECs) | Infinium Human Methylation 450 BeadChip |
 Fecal microbial transplant to reintroduce microbes into GF mice resulted in increased gene methylation [75] | Murine gut microbiome | Mice | None highlighted | Bisulfite pyrosequencing |
 The gene methylation status of GF mice differed from that of conventional mice. The number of genes with changes in both gene expression and methylation status increased as mice aged [76] | Murine gut microbiome | Mice | Pathways related to cellular proliferation or regeneration (Pik3cd, Rb1, Grb10, Plagl1, Nfix, Tab3) and immune response (Atp7a, Atf4, Bcl3) | RRBS |
 ETBF-induced tumors contained more hypermethylated DMRs and fewer hypomethylated DMRs than spontaneous tumors [61] | ETBF | Mice | Hoxa5, Polg, Runx1, Runx3, CD37, Stx11, Tceb2, Lgr6, Cdx1, and Fut4 genes | MBD-seq, pyrosequencing, qMSP |
Chromatin structure | ||||
 Investigators found no differential DNase hypersensitivity sites in the jejunum of GF mice. They did, however, find changes in the histone marks H3K4me1 and H3K27ac, which are generally enriched at poised or active enhancers, respectively [87] | Murine gut microbiome | Mice | Transcription factors belonging to the IRF family, STAT family, and ETS family | DNase-seq, ChIP-seq |
 Several hundred promoters and enhancers lost rhythmicity after antibiotic treatment, and a near equal number gained de novo rhythmic behavior [92] | Antibiotic-treated murine gut microbiome | Mice | None highlighted | ChIP-seq |
 Bacterial presence resulted in numerous changes in histone acetylation and methylation in the proximal colon tissue of GF mice. SCFAs produced by gut microbes might have mediated this effect [93] | Murine gut microbiome | Mice | None highlighted | Electrospray ionization tandem mass spectrometry |
 The location of H3K4 methylation marks was modified when gut microbes colonized GF mice [94] | Murine gut microbiome | Mice | Genes involved in maintaining the innate mucosal barrier, ROS generation, ephrin signaling, and others | ChIP-seq |
 In mice treated with antibiotics for 3 days, H3K18 crotonylation in the colon was decreased. This was associated with a concomitant decrease in HDAC2 protein expression, which was mediated by the SCFAs butyrate and crotonate. These SCFAs promote H3K18 crotonylation by inhibiting HDACs [96] | Antibiotic-treated murine gut microbiome | Mice, mouse small intestinal enteroids, human CRC cell lines (HCT116) | Pathways related to endometrial cancer, prostate cancer, pancreatic cancer, CRC, TGF-β signaling and stem cell pluripotency | ChIP-seq |
Non-coding RNAs | ||||
 Using GF mice, the presence of gut microbes was associated with decreased production of miRNAs, which were shown to be produced by intestinal ECs, goblet cells and Paneth cells [107] | Murine gut microbiome | Mice | None highlighted | NanoString nCounter |
 Absence (GF mice) of the gut microbiota resulted in lower levels of expression of the miRNAs let-7b, miR-141, and miR-200a. Depletion (antibiotic-treated rats) of gut microbiota resulted in lower levels of miRNAs let-7b, miR-141, miR-200a, and miR-1224 after 6 weeks of treatment [108] | Murine gut microbiome, antibiotic-treated murine gut microbiome | Mice, rats | let-7b, miR-141, miR-200a, and miR-1224 | qRT-PCR |
 miR-21-5p was expressed at higher levels in the small and large intestine of conventional mice than in GF mice. Exposing HT-29 and SW480 cells (two CRC cell lines) to Bacteroides acidifaciens type A43 and Lactobacillus johnsonii 129 resulted in an upregulation of miR-21-5p [112] | Murine gut microbiome, B. acidifaciens type A43 and L. johnsonii 129 | Mice, human CRC cell lines (HT-29, SW480) | miR-21-5p | Microarray |
 19 miRNAs were differentially expressed in IESCs of GF mice when compared to conventionalized mice. miR-375-3p was downregulated in conventionalized mice [115] | Murine gut microbiome | Mice, mouse small intestinal enteroids | miR-375-3p | RNA-seq |
 Several miRNAs were downregulated in Fusobacterium nucleatum-rich tumor samples from patients with recurrent CRC. A CRC xenograft model was used to show that F. nucleatum causes resistance to oxaliplatin and 5-FU via downregulation of miR-4802 and miR-18a* [117] | F. nucleatum | Mice, CRC cell lines (HCT116 and HT29) | miR-4802 (newly associated with CRC) and miR-18a* (belongs to the miR-17-92 cluster) | RNA-seq |
 lncRNAs in the mouse duodenum, jejunum, ileum, and colon were altered in GF mice when compared to conventional mice [118] | Murine gut microbiome | Mice | Pathways related to GPCR signaling and TGF signaling | RNA-seq |
 When GF mice were reconstituted with normal mouse microbiota or with E. coli alone, fairly distinct changes in lncRNA signatures occurred, with only 8% of the differentially expressed lncRNAs overlapping [119] | Murine gut microbiome, E. coli | Mice | None highlighted | Affymetrix mouse exon microarray |