The Microbiome and Butyrate Regulate Energy Metabolism and Autophagy in the Mammalian Colon

“INTRODUCTION Diverse microbial communities reside at various sites within the human body (Camp et al., 2009; Eckburg et al., 2005; Savage, 1977).”

“These microbiota and their genomes, referred to collectively as the microbiome, are being characterized by metagenomic sequencing as part of the Human Microbiome Project (Gill et al., 2006; Hildebrandt et al., 2009; Kurokawa et al., 2007; Qin et al.; Turnbaugh et al., 2009; Turnbaugh et al., 2007).”

“These studies support the idea that microbes increase host metabolic efficiency (Backhed et al., 2004; Turnbaugh et al., 2008; Turnbaugh and Gordon, 2009; Turnbaugh et al., 2009; Turnbaugh et al., 2006).”

“These microbiota and their genomes, referred to collectively as the microbiome, are being characterized by metagenomic sequencing as part of the Human Microbiome Project (Gill et al., 2006; Hildebrandt et al., 2009; Kurokawa et al., 2007; Qin et al.; Turnbaugh et al., 2009; Turnbaugh et al., 2007).”

“These microbiota and their genomes, referred to collectively as the microbiome, are being characterized by metagenomic sequencing as part of the Human Microbiome Project (Gill et al., 2006; Hildebrandt et al., 2009; Kurokawa et al., 2007; Qin et al.; Turnbaugh et al., 2009; Turnbaugh et al., 2007).”

“In response to nutrient deprivation, AMPK activation induces autophagy, which is a catabolic process where the cell degrades its own cellular components in an attempt to maintain energy homeostasis (He and Klionsky, 2009; Yang and Klionsky, 2009).”

“These studies support the idea that microbes increase host metabolic efficiency (Backhed et al., 2004; Turnbaugh et al., 2008; Turnbaugh and Gordon, 2009; Turnbaugh et al., 2009; Turnbaugh et al., 2006).”

“In fact, butyrate enema therapy has been shown to ameliorate the inflammation associated with colitis in mouse models and in human clinical trials (Hamer et al., 2008).”

“These results are consistent with previous studies from liver and heart of nonfasted GF and CONV-R mice (Bäckhed et al., 2007; Crawford et al., 2009).”

“The vast majority of microbes are bacteria that reside in the gut and are estimated to number 100 trillion, which is 10-fold greater than all of somatic and germ cells in the human body (Savage, 1977; Turnbaugh and Gordon, 2009).”

“To investigate the effect of the microbiome in host metabolism, germfree (GF) animals lacking microbiota have been studied (Gordon and Pesti, 1971; Hooper and Gordon, 2001; Wostmann, 1981).”

“NMR Metabolomics Colonocytes were processed with the methanolchloroform-water method (Beckonert et al., 2007), and the polar phase was lyophilized, stored at 80 C, thawed and suspended in 550 ml of a 1.”

“These microbiota and their genomes, referred to collectively as the microbiome, are being characterized by metagenomic sequencing as part of the Human Microbiome Project (Gill et al., 2006; Hildebrandt et al., 2009; Kurokawa et al., 2007; Qin et al.; Turnbaugh et al., 2009; Turnbaugh et al., 2007).”

“The lumen of the colon has the highest density of microbes in the body, and specific bacteria belonging to genera such as Clostridium, Eubacterium, and Butyrivibrio ferment dietary fiber into butyrate at very high (mM) concentrations (Barcenilla et al., 2000; Pryde et al., 2002).”

“Butyrate is noteworthy because it is a histone deacetylase (HDAC) inhibitor that regulates gene expression and also serves as the primary energy source for the colonic epithelium (Boffa et al., 1978; Candido et al., 1978; Dashwood et al., 2006; Garcea and Alberts, 1980; Roediger, 1980, 1982).”

“Butyrate is noteworthy because it is a histone deacetylase (HDAC) inhibitor that regulates gene expression and also serves as the primary energy source for the colonic epithelium (Boffa et al., 1978; Candido et al., 1978; Dashwood et al., 2006; Garcea and Alberts, 1980; Roediger, 1980, 1982).”

“The lumen of the colon has the highest density of microbes in the body, and specific bacteria belonging to genera such as Clostridium, Eubacterium, and Butyrivibrio ferment dietary fiber into butyrate at very high (mM) concentrations (Barcenilla et al., 2000; Pryde et al., 2002).”

“The vast majority of microbes are bacteria that reside in the gut and are estimated to number 100 trillion, which is 10-fold greater than all of somatic and germ cells in the human body (Savage, 1977; Turnbaugh and Gordon, 2009).”

“For example, Angpt14/Fiaf is upregulated in GF compared to CONVwhileGpx2, ApoB, Aqp4, and Pla2g4c are downregulated (Bäckhed et al., 2004; Chowdhury et al., 2007; Cresci et al., 2010; Esworthy et al., 2003; Rawls et al., 2004).”

“AMPK can induce autophagy by phosphorylating (Thr198) and stabilizing the cyclin-dependent kinase inhibitor 1B (p27) (Liang et al., 2007).”

“In response to nutrient deprivation, AMPK activation induces autophagy, which is a catabolic process where the cell degrades its own cellular components in an attempt to maintain energy homeostasis (He and Klionsky, 2009; Yang and Klionsky, 2009).”

“These microbiota and their genomes, referred to collectively as the microbiome, are being characterized by metagenomic sequencing as part of the Human Microbiome Project (Gill et al., 2006; Hildebrandt et al., 2009; Kurokawa et al., 2007; Qin et al.; Turnbaugh et al., 2009; Turnbaugh et al., 2007).”

“Propionate is a SCFA that enters the TCA through succinyl-CoA functions as an energy source and an HDAC inhibitor (Hinnebusch et al., 2002; Waldecker et al., 2008).”

“Propionate is a SCFA that enters the TCA cycle through succinyl-CoA to function as an energy source and an HDAC inhibitor (Hinnebusch et al., 2002; Waldecker et al., 2008).”

“Quantificationwasperformedwith redundant spectral counting where spectral counts (SCs) for an individual protein are normalized to the overall spectra collected in each fraction for the individual and then by total spectral counts for all proteins (Carvalho et al., 2008a, 2008b; Kislinger et al., 2006).”

“For example, GF mice must consume 10–30% more food to maintain the same body weight as CONV-R controls (Backhed et al., 2004; Gordon and Pesti, 1971).”

“These results are consistent with previous studies from liver and heart of non-fasted GF and CONV-R mice (Backhed et al., 2007; Crawford et al., 2009).”

“3 M urea lysis buffer (Reyes et al., 1997) with NaF and Na orthovanadate and incubated on wet ice for 30 min.”

“To investigate the effect of the microbiome in host metabolism, germfree (GF) animals lacking microbiota have been studied (Gordon and Pesti, 1971; Hooper and Gordon, 2001; Wostmann, 1981).”

“Butyrate is noteworthy because it is a histone deacetylase (HDAC) inhibitor that regulates gene expression and also serves as the primary energy source for the colonic epithelium (Boffa et al., 1978; Candido et al., 1978; Dashwood et al., 2006; Garcea and Alberts, 1980; Roediger, 1980, 1982).”

“For example, Angpt14/Fiaf is upregulated in GF compared to CONVwhileGpx2, ApoB, Aqp4, and Pla2g4c are downregulated (Bäckhed et al., 2004; Chowdhury et al., 2007; Cresci et al., 2010; Esworthy et al., 2003; Rawls et al., 2004).”

“…using redundant spectral counting where spectral counts (SC) for an individual protein are normalized to the overall spectra collected in each fraction for the individual and then by total spectral counts for all proteins(Carvalho et al., 2008a; Carvalho et al., 2008b; Kislinger et al., 2006).”

“Isolation of Colonocytes Colonic epithelial cells were isolated as previously described (Roediger and Truelove, 1979) in order to exclude cell types other than colonocytes such as immune cells, smooth muscle, and enteric neurons.”

“For example, Angpt14/Fiaf is upregulated in GF compared to CONVwhileGpx2, ApoB, Aqp4, and Pla2g4c are downregulated (Bäckhed et al., 2004; Chowdhury et al., 2007; Cresci et al., 2010; Esworthy et al., 2003; Rawls et al., 2004).”

“In addition to colonizing GF mice with a complete microbiota, we also colonized GF mice with a butyrate-producing bacterial strain called Butyrivibrio fibrisolvens (Diez-Gonzalez et al., 1999; Rumney et al., 1995).”

“…using redundant spectral counting where spectral counts (SC) for an individual protein are normalized to the overall spectra collected in each fraction for the individual and then by total spectral counts for all proteins(Carvalho et al., 2008a; Carvalho et al., 2008b; Kislinger et al., 2006).”

“To demonstrate that microbiota directly affect metabolism, individual tissues from GF and CONV-R mice must be assessed for differences in key metabolic parameters (Camp et al., 2009).”

“Butyrate is noteworthy because it is a histone deacetylase (HDAC) inhibitor that regulates gene expression and also serves as the primary energy source for the colonic epithelium (Boffa et al., 1978; Candido et al., 1978; Dashwood et al., 2006; Garcea and Alberts, 1980; Roediger, 1980, 1982).”

“For example, Angpt14/Fiaf is upregulated in GF compared to CONVwhileGpx2, ApoB, Aqp4, and Pla2g4c are downregulated (Bäckhed et al., 2004; Chowdhury et al., 2007; Cresci et al., 2010; Esworthy et al., 2003; Rawls et al., 2004).”

“In addition to colonizing GF mice with a complete microbiota, we also colonized GF mice with a butyrate-producing bacterial strain called Butyrivibrio fibrisolvens (Diez-Gonzalez et al., 1999; Rumney et al., 1995).”

“…from fiber and other complex carbohydrates toward processed, simple carbohydrates, the incidence of colorectal cancer (CRC) and inflammatory bowel diseases (IBD) such as ulcerative colitis and Crohn’s Disease have increased (Garcea and Alberts, 1980; Hamer et al., 2008; Latella and Caprilli, 1991).”

“Donohoe et al. ( 18 ) showed that colonocytes of germ-free mice exhibit a defi cit in mitochondrial respiration and undergo autophagy.”

“Recolonization of GF mice with butyrate-producing bacteria and butyrate treatment of GF colonocytes ex-vivo, increases oxidative phosphorylation and suppresses autophagy to normal levels (17), implying the importance of host-microbe interaction in energy metabolism of colonic epithelium.”