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Diet-microbiome interactions and the regulation of the epigenome
CHAPTER
Diet-microbiome interactions and the regulation of the epigenome
24
Iara Cassandra V. Ibay1, Elesa Poteres1, Allison Isabelli1, Kristina Martinez-Guryn Midwestern University, Downers Grove, IL, USA
1. Introduction The gut microbiota has been implicated in the development of several life-altering diseases such as obesity, diabetes, inflammatory bowel disease, and cardiovascular diseases. However, the mechanisms that link gut microbiota composition and function to disease outcome are only beginning to be discovered. One such mechanism that may drive disease development in response to altered gut microbiota is epigenetic modification. The interaction between gut microbiota and epigenetics is further influenced by dietary-induced shifts in the gut microbiota. Collectively, these factors drive epigenetic programs that influence the development of disease. The goal of this chapter is to describe (1) the general characteristics of the gut microbiota, (2) the dietary impact on the gut microbiota, (3) the microbial impact on epigenetics, and (4) mechanisms underlying diet-microbe interactions on the host epigenome and consequences for host health.
2. Characteristics of the gut microbiota While microbes are present on virtually every part of the body, the gastrointestinal tract (GI) houses approximately 70% of our total microbial population [1]. The gastrointestinal tract is rich in nutrients and non-digestible food components making it an ideal site for bacterial colonization. It has been reported that the gut microbiota is comprised of over 35,000 bacterial species belonging to prominent phyla including: Firmicutes, Bacteroidetes, Actinobacteria, Verrucomicriobia, and Proteobacteria [2,3]. Location of phyla within the GI tract is variable as certain factors such as chemical composition and nutrient gradients help govern the location of certain bacteria [4,5]. The acidic environment, bile acid and oxygen levels, and antimicrobials present in the small intestine contribute to its lack of overall microbiota diversity. Therefore, facultative anaerobes that can withstand these conditions dominate this region of the gut [4,5], and although fewer in number, may elicit significant changes in host physiology. Abundant phyla of the small intestine include Firmicutes and Proteobacteria [5,6]. The large intestine houses most microbes found in the body due to its large surface area and more conducive conditions for bacterial growth. While Firmicutes and Bacteroidetes dominate, the large 1
These authors contributed equally.
Nutritional Epigenomics. https://doi.org/10.1016/B978-0-12-816843-1.00024-2 Copyright © 2019 Elsevier Inc. All rights reserved.
401
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Chapter 24 Diet-microbiome interactions and epigenome regulation
intestine consists of an array of anaerobes that utilize undigested carbohydrates and resources for continual colonization [3,4]. The gut microbiome also exhibits vast differences in mucosal and luminal bacterial populations. An abundance of Bacteroidetes, Bifidobacterium, Streptococcus and many other microbes populate luminal areas, while mucosal-associated locations are sparser housing a limited amount of species such as Clostridium, Lactobacillus, Enterococcus, and Akkermansia [3]. A high level of inter-individual variability exists in gut microbiota composition and can influence the level of microbial metabolites that are generated given the presence of particular substrates [7]. While each individual’s microbiome is vastly unique, some researchers believe that all humans possess a core set of bacteria [5]. This conservation of bacteria suggests that bacteria perform necessary functional processes critical for host survival. These include protection against pathogens, bile acid deconjugation, short chain fatty acid (SCFA) production via metabolism of indigestible carbohydrates, nutrient digestion and absorption, promotion of epithelial integrity and immune function. However, gut dysbiosis, or the deleterious shift in community composition or presence of harmful pathogens, can disrupt normal physiology processes leading to disease. Gaining a greater understanding of these unique biomes and their functions within the host will provide greater opportunities for personalized medicine in the future.
3. Impact of gut microbes on epigenetics It is becoming more appreciated that the gut microbiome can influence epigenetic modifications in the host or that the host epigenome can influence gut microbiota composition [8]. Epigenetics involves alterations in gene expression that are not due to direct changes in the DNA sequence. Instead, modifications to gene expression occur through (1) post-translational modifications on amino acids on histone proteins, (2) methylation of DNA, (3) altered expression of enzymes that regulate methylation [i.e., DNA methyltransferase (DNMT) or ten-elven translocation (TET)] and acetylation [(i.e., HDACs and histone acetyltransferases (HATs)], or (4) by microRNA activity at the post-transcriptional level. Post-translational modifications (PTMs) of histones, such as methylation, acetylation, ubiquitination, phosphorylation and SUMOylation, among others contribute to the activation and repression of genes. Acetylation of histone tails typically opens up chromatin and allows for gene transcription, whereas deacetylation mediated by HDACs strengthens the association of DNA with histones and prevents gene transcription [9]. The classically studied diet-microbe-host epigenetic interaction is that of microbe-derived butyrate and inhibition of HDAC activity [10,11]. Other interactions involve microbe-mediated DNA methylation, HDAC deacetylation and methylation, as well as the influence of host epigenetics on microbial colonization [8,9,12]. It was demonstrated by Alenghat et al. [12] that deficiency in HDAC3 in intestinal epithelial cells (IECs) resulted in altered gene expression, histone acetylation, and decreased intestinal barrier function. These HDAC3-IEC deficient mice (HDAC3DIEC) were re-derived germ free and were consequently protected from dysfunction of the intestinal barrier, directly implying a microbial role in this process [12]. HDAC3DIEC mice also displayed significant alterations in gut microbiota composition in this study, suggesting that an altered host epigenome elicits pressures on microbial ecology of the gut [12].
4. Dietary impact on the gut microbiota
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This phenomenon was also revealed in a study by Cortese et al. investigating both the impact of gut microbes on epigenetic modification in intestinal epithelial cells but also the impact of epigenetics on microbial colonization in a model of neonatal necrotizing enterocolitis (NEC). NEC is an inflammatory bowel disease that affects premature infants. In this study, IECs were treated with probiotic and pathogenic bacteria, which elicited DNA modifications in over 200 regions. In addition, prenatal exposure to the glucocorticoid dexamethasone triggered the altered epigenome of the host and dictated the colonization of microbiota including a slight increase in Firmicutes and slight decrease in Bacteroidetes as well as changes at lower taxonomic levels [8]. These studies highlight the cross-talk between the gut microbiota and the host epigenome [8,12].
4. Dietary impact on the gut microbiota Interactions between diet and gut microbiota have been well-established. Diet can dramatically alter gut microbial composition and function and have the potential to elicit changes in microbial phyla in as little as 24e48 h [13]. For instance, humans fed a diet rich in animal-based foods and low in fiber displayed a shift in beta diversity in fecal microbiota after only 2 days and also displayed reduced SCFA levels [14]. Similar rapid changes in the gut microbiota due to high fat diets have been reported in mice [15,16]. Another study in mice demonstrated that a diet deficient in microbe-accessible carbohydrates led to the generational loss of bacterial species. This model was proposed to represent how microbial communities may shift in human populations over time with the prolonged consumption of western-style diets low in dietary fiber [17]. Whether or not the loss of bacterial species over generations was influenced by epigenetic changes in the host has yet to be investigated in this model. It was also recently reported in our own work that HF diets can dramatically influence the gut microbiota along the length of the intestine such as increasing the abundance of Clostridiaceae, particularly in the jejunum and ileum, which influenced the level of lipid absorption in conventionalized animals [6]. This work underscores the importance of considering the site at which microbial communities are assessed in relation to the host response. Taken together, dramatic shifts in dietary intake can profoundly and rapidly impact the gut microbiota composition and function and may have long-term and functional consequences for the host. Dietary fiber, including insoluble and soluble fiber, is an essential component of a healthy diet having a number of health benefits including decreasing plasma lipid levels, providing satiety, and promoting gut regularity. Soluble fiber undergoes fermentation by gut bacteria to synthesize SCFAs including butyrate, acetate, and propionate which are important players in maintaining homeostasis within the host [18]. Although acetate and propionate have important roles for the host, benefits of butyrate are many including increased integrity of the gut epithelium, brain health, regulation of circadian rhythm, and metabolism [18]. Mechanisms include activation of g-protein coupled receptors (GPCRs), acting as an energy source for gut epithelial cells, and inhibition of HDAC activity. The latter has been associated with prevention of colon cancer [19] and Western diet-induced obesity [20]. Butyrate represents a well-studied link between gut microbiota and epigenetic regulation and will be discussed in greater detail in the next section. Other dietary components that have been found to elicit changes in the gut microbiota and host epigenetics include glucosinolates from cruciferous vegetables as well as dietary fat; these will be further discussed in the following section.
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Chapter 24 Diet-microbiome interactions and epigenome regulation
5. Diet-microbe interactions that regulate the epigenome 5.1 Short chain fatty acids Metabolism of dietary fiber leads to the production of SCFAs that have been widely shown to influence host physiology. Butyrate reaches mM concentrations in the intestinal lumen and has a wide variety of effects on host systems. A well-defined mechanism of action of butyrate is HDAC inhibition which influences the progression of colon cancer and inflammatory bowel disease (IBD). Butyrate-mediated inhibition of HDAC activity decreases epithelial cell proliferation and induces of apoptosis [10,11,21]. Intriguingly, butyrate does not inhibit cell growth of normal colonic cells. Donohoe et al. [10] proposed that this is because butyrate is metabolized though beta oxidation in normal cells whereas cancer cells primarily undergo aerobic glycolysis. This allows for a build-up of intracellular butyrate particularly in the nucleus where it inhibits HDAC activity. Donohoe et al. [10] also found that butyrate had additional roles in epigenetic regulation by increasing histone acetylation through being metabolized into acetyl CoA and stimulating HAT activity, and thus epigenetically regulates the expression of target genes. They later showed that supplementing mice with B. fibrisolvens while being fed a high fiber diet (rich in inulin) protected them from AOM/DSS-induced tumor growth compared to control groups (Donohoe et al. 2014), presumably through increased SCFA production. Butyrate-mediated HDAC inhibition is a classic and well-known diet-microbe interaction that influences host epigenetics.
5.2 Isothiocyanates Bacteria with thioglucosidase activity metabolize glucosinolates into ITCs which have been shown to have anti-cancer effects through epigenetic modifications [21]. Foods rich in glucosinolates include cruciferous vegetables such as broccoli. It was recently demonstrated that consumption of 200 g of cooked broccoli (w2 cups) for 18 days significantly altered microbiota composition, characterized by a 9% decrease in Firmicutes and a 10% increase in Bacteroidetes, in human subjects [22]. Notably, interindividual variability in gut microbiota composition determines the level of ITC produced as demonstrated by Li et al. [7]. Here, human participants were fed a standardized meal containing 200 g cooked broccoli and stool samples were collected from those with the highest and lowest ITC excretion levels. These samples were incubated with glucoraphanin, a major glucosinolate from broccoli, in an ex vivo experiment and it was found that high-ITC excreted stool metabolized more glucoraphanin than low-ITC excreted stool. This is an important consideration, as ITCs have been shown to reduce tumor growth via altering DNA methylation and histone acetylation [21]. One particular ITC, sulforaphane, has been shown to have chemoprotective effects in colon, breast, and prostate cancer models [23e26]. For instance, sulforaphane prevents carcinogenesis in rodent models by inhibiting HDAC activity and increasing acetylation of histones in the colon [23]. Taken together, ITCs represent an important diet-microbe interaction that have direct effects on the epigenome.
5.3 Dietary fat As previously discussed, extensive research has demonstrated that diets high in fat and even the fatty acid composition of the diet can alter the composition and function of the gut microbiota. Recent work by Whitt et al. [27] showed that HDAC3 in intestinal epithelial cells may promote the development of
References
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obesity, as IEC-specific disruption of HDAC3 protected against obesity, glucose intolerance, and elevated plasma lipids in a murine diet-induced obesity (DIO) model [27]. Administration of butyrate led to significant weight loss in control mice but not HDAC3DIEC mice, suggesting that intact HDAC3 is necessary for the weight loss-promoting effects of butyrate. In addition, HDAC3 levels from intestinal biopsy samples correlated with patient weight. Altogether this study presents compelling evidence for diet-microbe interactions that suggest consuming a high fat diet that decreases butyrate levels may lead to increased HDAC3 activity in IECs, thereby promoting an obese phenotype [27]. Krautkramer et al. [20] showed that conventionally-raised or germ free (GF) mice conventionalized with conventionally-raised (ConvR) microbiota have significantly greater histone acetylation and methylation compared to GF animals, suggesting a direct role of microbes in regulating histone modification. A diet-microbe-host interaction was also demonstrated in this study, whereby a Western Diet high in fat and sugar decreased SCFA levels as well as decreased histone acetylation in the colon, liver, and white adipose tissue (WAT). Delivery of SCFAs to GF mice restored histone acetylation and methylation. Interestingly, RNA seq analysis revealed that the hepatic gene profile was similarly altered with SCFA supplementation in GF mice as compared to those ConvR or ConvD. This study demonstrated a direct association between host diet, microbiota-derived SCFA, and host epigenetic function [20]. Taken together, these recent reports suggest an important interaction between dietary consumption, gut microbiota, and host epigenetic programming.
6. Conclusion A wealth of literature exists demonstrating the dramatic impact of diet on gut microbiota and emerging studies have provided evidence for diet-microbe interactions that impact epigenetic modifications that ultimately have important implications for host health and disease development. Another key consideration for applying this information to personalized healthcare is that one’s microbiota dictates the types and levels of microbial byproducts generated, given a particular diet (e.g., high fiber vs. high fat), that may confer physiological benefits. This speaks to the importance of a personalized approach to healthcare that may involve the assessment of the gut microbiota to determine treatment plans or dietary recommendations for inclusion of particular foods or the use of a combination of probiotics and prebiotics until better options become available. However, this is an early field of investigation and further studies are needed to characterize diet-microbe-host interactions that could have important implications for various immune, cancer, and metabolic-related diseases through epigenetic modifications.
References [1] Sekirov I, Russell SL, Antunes CMFB. Gut microbiota in health and disease. Physiol Rev 2010;90:859e904. [2] Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci Unit States Am 2007;104(34):13780e5. [3] Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Reddy DN. Role of the normal gut microbiota. World J Gastroenterol 2015;21(29):8836e47.
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[4] Thursby E, Juge N. Introduction to the human gut microbiota [Internet] Biochem J 2017;474(11):1823e36. Available from: http://biochemj.org/lookup/doi/10.1042/BCJ20160510. [5] Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol 2015;14(1):20e32. [6] Martinez-Guryn K, Hubert N, Frazier K, Urlass S, Musch MW, Ojeda P, et al. Small intestine microbiota regulate host digestive and absorptive adaptive responses to dietary lipids. Cell Host Microbe 2018;23(4): 458e469.e5. [7] Li F, Hullar MAJ, Beresford SAA, Lampe JW. Variation of glucoraphanin metabolism in vivo and ex vivo by human gut bacteria. Br J Nutr 2011;106(3):408e16. [8] Cortese R, Lu L, Yu Y, Ruden D, Claud EC. Epigenome-Microbiome crosstalk: a potential new paradigm influencing neonatal susceptibility to disease. Epigenetics 2016;11(3):205e15. [9] Alenghat T. NIH public access. Toxicol Pathol 2015;43(1):101e6. [10] Donohoe DR, Garge N, Zhang X, Sun W, O’Connell TM, Bunger MK, et al. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab [Internet] 2011;13(5): 517e26. Available from: https://doi.org/10.1016/j.cmet.2011.02.018. [11] Donohoe DR, Holley D, Collins LB, Montgomery SA, Whitmore AC, Hillhouse A, et al. A gnotobiotic mouse model demonstrates that dietary fiber protects against colorectal tumorigenesis in a microbiota- and butyrate-dependent manner. Cancer Discov 2014;4(12):1387e97. [12] Alenghat T, Osborne LC, Saenz SA, Kobuley D, Ziegler CGK, Mullican SE, et al. Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis [Internet] Nature 2013;504(7478): 153e7. Available from: https://doi.org/10.1038/nature12687. [13] Ojeda P, Bobe A, Dolan K, Leone V, Martinez K. Nutritional modulation of gut microbiota - the impact on metabolic disease pathophysiology [Internet] J Nutr Biochem 2016;28:191e200. Available from: https://doi. org/10.1016/j.jnutbio.2015.08.013. [14] David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome [Internet] Nature 2014;505(7484):559e63. Available from: https://doi.org/10.1038/nature12820. [15] Carmody RN, Gerber GK, Luevano JM, Gatti DM, Somes L, Svenson KL, et al. Diet dominates host genotype in shaping the murine gut microbiota [Internet] Cell Host Microbe 2015;17(1):72e84. Available from: https://doi.org/10.1016/j.chom.2014.11.010. [16] Howe A, Ringus DL, Williams RJ, Choo ZN, Greenwald SM, Owens SM, et al. Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice [Internet] ISME J 2016; 10(5):1217e27. Available from: https://doi.org/10.1038/ismej.2015.183. [17] Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL. Diet-induced extinctions in the gut microbiota compound over generations [Internet] Nature 2016;529(7585):212e5. Available from: https://doi.org/10.1038/nature16504. [18] Bourassa MW, Alim I, Bultman SJ, Ratan RR. Butyrate, neuroepigenetics and the gut microbiome: can a high fiber diet improve brain health? [Internet] Neurosci Lett 2016;625:56e63. Available from: https://doi. org/10.1016/j.neulet.2016.02.009. [19] Davie JR. Nutritional proteomics in cancer prevention. Nutr Proteomics Cancer Prev 2003;133(7 Suppl. l): 2485e93. [20] Krautkramer KA, Kreznar JH, Romano KA, Vivas EI, Barrett-Wilt GA, Rabaglia ME, et al. Diet-microbiota interactions mediate global epigenetic programming in multiple host tissues [Internet] Mol Cell 2016;64(5): 982e92. Available from: https://doi.org/10.1016/j.molcel.2016.10.025. [21] Hullar MAJ, Fu BC. Diet, the {gut} {microbiome}, and {epigenetics} [Internet] Cancer J 2014;20(3):170e5. Available from: http://content.wkhealth.com/linkback/openurl?sid¼WKPTLP:landingpage&an¼00130404201405000-00002.
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[22] Kaczmarek JL, Liu X, Charron CS, Novotny JA, Jeffery EH, Seifried HE, et al. Broccoli consumption affects the human gastrointestinal microbiota [Internet] J Nutr Biochem 2019;63:27e34. Available from: http:// www.ncbi.nlm.nih.gov/pubmed/30317146%0Ahttps://linkinghub.elsevier.com/retrieve/pii/S095528631830 3000. [23] Myzak MC. Sulforaphane inhibits histone deacetylase in vivo and suppresses tumorigenesis in Apcmin mice [Internet] FASEB J 2006;19(10):1e19. Available from: https://doi.org/10.1096/fj.05-4785fje. [24] Myzak MC, Karplus PA, Chung F, Dashwood RH. A novel mechanism of chemoprotection by sulforaphane. Cancer Res 2004;(541):5767e74. [25] Myzak MC, Hardin K, Wang R, Dashwood RH, Ho E. Sulforaphane inhibits histone deacetylase activity in BPH-1, LnCaP and PC-3 prostate epithelial cells. Carcinogenesis 2006;27(4):811e9. [26] Meeran SM, Patel SN, Tollefsbol TO. Sulforaphane causes epigenetic repression of hTERT expression in human breast cancer cell lines. PLoS One 2010;5(7). [27] Whitt J, Woo V, Lee P, Moncivaiz J, Haberman Y, Denson L, et al. Disruption of epithelial HDAC3 in intestine prevents diet-induced obesity in mice. Gastroenterology 2018;155(2):501e13.
Diet-microbiome interactions and the regulation of the epigenome
24
Iara Cassandra V. Ibay1, Elesa Poteres1, Allison Isabelli1, Kristina Martinez-Guryn Midwestern University, Downers Grove, IL, USA
1. Introduction The gut microbiota has been implicated in the development of several life-altering diseases such as obesity, diabetes, inflammatory bowel disease, and cardiovascular diseases. However, the mechanisms that link gut microbiota composition and function to disease outcome are only beginning to be discovered. One such mechanism that may drive disease development in response to altered gut microbiota is epigenetic modification. The interaction between gut microbiota and epigenetics is further influenced by dietary-induced shifts in the gut microbiota. Collectively, these factors drive epigenetic programs that influence the development of disease. The goal of this chapter is to describe (1) the general characteristics of the gut microbiota, (2) the dietary impact on the gut microbiota, (3) the microbial impact on epigenetics, and (4) mechanisms underlying diet-microbe interactions on the host epigenome and consequences for host health.
2. Characteristics of the gut microbiota While microbes are present on virtually every part of the body, the gastrointestinal tract (GI) houses approximately 70% of our total microbial population [1]. The gastrointestinal tract is rich in nutrients and non-digestible food components making it an ideal site for bacterial colonization. It has been reported that the gut microbiota is comprised of over 35,000 bacterial species belonging to prominent phyla including: Firmicutes, Bacteroidetes, Actinobacteria, Verrucomicriobia, and Proteobacteria [2,3]. Location of phyla within the GI tract is variable as certain factors such as chemical composition and nutrient gradients help govern the location of certain bacteria [4,5]. The acidic environment, bile acid and oxygen levels, and antimicrobials present in the small intestine contribute to its lack of overall microbiota diversity. Therefore, facultative anaerobes that can withstand these conditions dominate this region of the gut [4,5], and although fewer in number, may elicit significant changes in host physiology. Abundant phyla of the small intestine include Firmicutes and Proteobacteria [5,6]. The large intestine houses most microbes found in the body due to its large surface area and more conducive conditions for bacterial growth. While Firmicutes and Bacteroidetes dominate, the large 1
These authors contributed equally.
Nutritional Epigenomics. https://doi.org/10.1016/B978-0-12-816843-1.00024-2 Copyright © 2019 Elsevier Inc. All rights reserved.
401
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Chapter 24 Diet-microbiome interactions and epigenome regulation
intestine consists of an array of anaerobes that utilize undigested carbohydrates and resources for continual colonization [3,4]. The gut microbiome also exhibits vast differences in mucosal and luminal bacterial populations. An abundance of Bacteroidetes, Bifidobacterium, Streptococcus and many other microbes populate luminal areas, while mucosal-associated locations are sparser housing a limited amount of species such as Clostridium, Lactobacillus, Enterococcus, and Akkermansia [3]. A high level of inter-individual variability exists in gut microbiota composition and can influence the level of microbial metabolites that are generated given the presence of particular substrates [7]. While each individual’s microbiome is vastly unique, some researchers believe that all humans possess a core set of bacteria [5]. This conservation of bacteria suggests that bacteria perform necessary functional processes critical for host survival. These include protection against pathogens, bile acid deconjugation, short chain fatty acid (SCFA) production via metabolism of indigestible carbohydrates, nutrient digestion and absorption, promotion of epithelial integrity and immune function. However, gut dysbiosis, or the deleterious shift in community composition or presence of harmful pathogens, can disrupt normal physiology processes leading to disease. Gaining a greater understanding of these unique biomes and their functions within the host will provide greater opportunities for personalized medicine in the future.
3. Impact of gut microbes on epigenetics It is becoming more appreciated that the gut microbiome can influence epigenetic modifications in the host or that the host epigenome can influence gut microbiota composition [8]. Epigenetics involves alterations in gene expression that are not due to direct changes in the DNA sequence. Instead, modifications to gene expression occur through (1) post-translational modifications on amino acids on histone proteins, (2) methylation of DNA, (3) altered expression of enzymes that regulate methylation [i.e., DNA methyltransferase (DNMT) or ten-elven translocation (TET)] and acetylation [(i.e., HDACs and histone acetyltransferases (HATs)], or (4) by microRNA activity at the post-transcriptional level. Post-translational modifications (PTMs) of histones, such as methylation, acetylation, ubiquitination, phosphorylation and SUMOylation, among others contribute to the activation and repression of genes. Acetylation of histone tails typically opens up chromatin and allows for gene transcription, whereas deacetylation mediated by HDACs strengthens the association of DNA with histones and prevents gene transcription [9]. The classically studied diet-microbe-host epigenetic interaction is that of microbe-derived butyrate and inhibition of HDAC activity [10,11]. Other interactions involve microbe-mediated DNA methylation, HDAC deacetylation and methylation, as well as the influence of host epigenetics on microbial colonization [8,9,12]. It was demonstrated by Alenghat et al. [12] that deficiency in HDAC3 in intestinal epithelial cells (IECs) resulted in altered gene expression, histone acetylation, and decreased intestinal barrier function. These HDAC3-IEC deficient mice (HDAC3DIEC) were re-derived germ free and were consequently protected from dysfunction of the intestinal barrier, directly implying a microbial role in this process [12]. HDAC3DIEC mice also displayed significant alterations in gut microbiota composition in this study, suggesting that an altered host epigenome elicits pressures on microbial ecology of the gut [12].
4. Dietary impact on the gut microbiota
403
This phenomenon was also revealed in a study by Cortese et al. investigating both the impact of gut microbes on epigenetic modification in intestinal epithelial cells but also the impact of epigenetics on microbial colonization in a model of neonatal necrotizing enterocolitis (NEC). NEC is an inflammatory bowel disease that affects premature infants. In this study, IECs were treated with probiotic and pathogenic bacteria, which elicited DNA modifications in over 200 regions. In addition, prenatal exposure to the glucocorticoid dexamethasone triggered the altered epigenome of the host and dictated the colonization of microbiota including a slight increase in Firmicutes and slight decrease in Bacteroidetes as well as changes at lower taxonomic levels [8]. These studies highlight the cross-talk between the gut microbiota and the host epigenome [8,12].
4. Dietary impact on the gut microbiota Interactions between diet and gut microbiota have been well-established. Diet can dramatically alter gut microbial composition and function and have the potential to elicit changes in microbial phyla in as little as 24e48 h [13]. For instance, humans fed a diet rich in animal-based foods and low in fiber displayed a shift in beta diversity in fecal microbiota after only 2 days and also displayed reduced SCFA levels [14]. Similar rapid changes in the gut microbiota due to high fat diets have been reported in mice [15,16]. Another study in mice demonstrated that a diet deficient in microbe-accessible carbohydrates led to the generational loss of bacterial species. This model was proposed to represent how microbial communities may shift in human populations over time with the prolonged consumption of western-style diets low in dietary fiber [17]. Whether or not the loss of bacterial species over generations was influenced by epigenetic changes in the host has yet to be investigated in this model. It was also recently reported in our own work that HF diets can dramatically influence the gut microbiota along the length of the intestine such as increasing the abundance of Clostridiaceae, particularly in the jejunum and ileum, which influenced the level of lipid absorption in conventionalized animals [6]. This work underscores the importance of considering the site at which microbial communities are assessed in relation to the host response. Taken together, dramatic shifts in dietary intake can profoundly and rapidly impact the gut microbiota composition and function and may have long-term and functional consequences for the host. Dietary fiber, including insoluble and soluble fiber, is an essential component of a healthy diet having a number of health benefits including decreasing plasma lipid levels, providing satiety, and promoting gut regularity. Soluble fiber undergoes fermentation by gut bacteria to synthesize SCFAs including butyrate, acetate, and propionate which are important players in maintaining homeostasis within the host [18]. Although acetate and propionate have important roles for the host, benefits of butyrate are many including increased integrity of the gut epithelium, brain health, regulation of circadian rhythm, and metabolism [18]. Mechanisms include activation of g-protein coupled receptors (GPCRs), acting as an energy source for gut epithelial cells, and inhibition of HDAC activity. The latter has been associated with prevention of colon cancer [19] and Western diet-induced obesity [20]. Butyrate represents a well-studied link between gut microbiota and epigenetic regulation and will be discussed in greater detail in the next section. Other dietary components that have been found to elicit changes in the gut microbiota and host epigenetics include glucosinolates from cruciferous vegetables as well as dietary fat; these will be further discussed in the following section.
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Chapter 24 Diet-microbiome interactions and epigenome regulation
5. Diet-microbe interactions that regulate the epigenome 5.1 Short chain fatty acids Metabolism of dietary fiber leads to the production of SCFAs that have been widely shown to influence host physiology. Butyrate reaches mM concentrations in the intestinal lumen and has a wide variety of effects on host systems. A well-defined mechanism of action of butyrate is HDAC inhibition which influences the progression of colon cancer and inflammatory bowel disease (IBD). Butyrate-mediated inhibition of HDAC activity decreases epithelial cell proliferation and induces of apoptosis [10,11,21]. Intriguingly, butyrate does not inhibit cell growth of normal colonic cells. Donohoe et al. [10] proposed that this is because butyrate is metabolized though beta oxidation in normal cells whereas cancer cells primarily undergo aerobic glycolysis. This allows for a build-up of intracellular butyrate particularly in the nucleus where it inhibits HDAC activity. Donohoe et al. [10] also found that butyrate had additional roles in epigenetic regulation by increasing histone acetylation through being metabolized into acetyl CoA and stimulating HAT activity, and thus epigenetically regulates the expression of target genes. They later showed that supplementing mice with B. fibrisolvens while being fed a high fiber diet (rich in inulin) protected them from AOM/DSS-induced tumor growth compared to control groups (Donohoe et al. 2014), presumably through increased SCFA production. Butyrate-mediated HDAC inhibition is a classic and well-known diet-microbe interaction that influences host epigenetics.
5.2 Isothiocyanates Bacteria with thioglucosidase activity metabolize glucosinolates into ITCs which have been shown to have anti-cancer effects through epigenetic modifications [21]. Foods rich in glucosinolates include cruciferous vegetables such as broccoli. It was recently demonstrated that consumption of 200 g of cooked broccoli (w2 cups) for 18 days significantly altered microbiota composition, characterized by a 9% decrease in Firmicutes and a 10% increase in Bacteroidetes, in human subjects [22]. Notably, interindividual variability in gut microbiota composition determines the level of ITC produced as demonstrated by Li et al. [7]. Here, human participants were fed a standardized meal containing 200 g cooked broccoli and stool samples were collected from those with the highest and lowest ITC excretion levels. These samples were incubated with glucoraphanin, a major glucosinolate from broccoli, in an ex vivo experiment and it was found that high-ITC excreted stool metabolized more glucoraphanin than low-ITC excreted stool. This is an important consideration, as ITCs have been shown to reduce tumor growth via altering DNA methylation and histone acetylation [21]. One particular ITC, sulforaphane, has been shown to have chemoprotective effects in colon, breast, and prostate cancer models [23e26]. For instance, sulforaphane prevents carcinogenesis in rodent models by inhibiting HDAC activity and increasing acetylation of histones in the colon [23]. Taken together, ITCs represent an important diet-microbe interaction that have direct effects on the epigenome.
5.3 Dietary fat As previously discussed, extensive research has demonstrated that diets high in fat and even the fatty acid composition of the diet can alter the composition and function of the gut microbiota. Recent work by Whitt et al. [27] showed that HDAC3 in intestinal epithelial cells may promote the development of
References
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obesity, as IEC-specific disruption of HDAC3 protected against obesity, glucose intolerance, and elevated plasma lipids in a murine diet-induced obesity (DIO) model [27]. Administration of butyrate led to significant weight loss in control mice but not HDAC3DIEC mice, suggesting that intact HDAC3 is necessary for the weight loss-promoting effects of butyrate. In addition, HDAC3 levels from intestinal biopsy samples correlated with patient weight. Altogether this study presents compelling evidence for diet-microbe interactions that suggest consuming a high fat diet that decreases butyrate levels may lead to increased HDAC3 activity in IECs, thereby promoting an obese phenotype [27]. Krautkramer et al. [20] showed that conventionally-raised or germ free (GF) mice conventionalized with conventionally-raised (ConvR) microbiota have significantly greater histone acetylation and methylation compared to GF animals, suggesting a direct role of microbes in regulating histone modification. A diet-microbe-host interaction was also demonstrated in this study, whereby a Western Diet high in fat and sugar decreased SCFA levels as well as decreased histone acetylation in the colon, liver, and white adipose tissue (WAT). Delivery of SCFAs to GF mice restored histone acetylation and methylation. Interestingly, RNA seq analysis revealed that the hepatic gene profile was similarly altered with SCFA supplementation in GF mice as compared to those ConvR or ConvD. This study demonstrated a direct association between host diet, microbiota-derived SCFA, and host epigenetic function [20]. Taken together, these recent reports suggest an important interaction between dietary consumption, gut microbiota, and host epigenetic programming.
6. Conclusion A wealth of literature exists demonstrating the dramatic impact of diet on gut microbiota and emerging studies have provided evidence for diet-microbe interactions that impact epigenetic modifications that ultimately have important implications for host health and disease development. Another key consideration for applying this information to personalized healthcare is that one’s microbiota dictates the types and levels of microbial byproducts generated, given a particular diet (e.g., high fiber vs. high fat), that may confer physiological benefits. This speaks to the importance of a personalized approach to healthcare that may involve the assessment of the gut microbiota to determine treatment plans or dietary recommendations for inclusion of particular foods or the use of a combination of probiotics and prebiotics until better options become available. However, this is an early field of investigation and further studies are needed to characterize diet-microbe-host interactions that could have important implications for various immune, cancer, and metabolic-related diseases through epigenetic modifications.
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