The gut microbiota has been proposed as an environmental factor that promotes the progression of metabolic diseases. Here, we investigated how the gut microbiota modulates the global metabolic ...differences in duodenum, jejunum, ileum, colon, liver, and two white adipose tissue depots obtained from conventionally raised (CONV‐R) and germ‐free (GF) mice using gene expression data and tissue‐specific genome‐scale metabolic models (GEMs). We created a generic mouse metabolic reaction (MMR) GEM, reconstructed 28 tissue‐specific GEMs based on proteomics data, and manually curated GEMs for small intestine, colon, liver, and adipose tissues. We used these functional models to determine the global metabolic differences between CONV‐R and GF mice. Based on gene expression data, we found that the gut microbiota affects the host amino acid (AA) metabolism, which leads to modifications in glutathione metabolism. To validate our predictions, we measured the level of AAs and N‐acetylated AAs in the hepatic portal vein of CONV‐R and GF mice. Finally, we simulated the metabolic differences between the small intestine of the CONV‐R and GF mice accounting for the content of the diet and relative gene expression differences. Our analyses revealed that the gut microbiota influences host amino acid and glutathione metabolism in mice.
Synopsis
Tissue‐specific genome‐scale metabolic models (GEMs), transcriptomic and metabolomic analyses reveal global metabolic differences between conventionally raised and germ‐free mice and show that the gut microbiota affects host amino acid and glutathione metabolism.
A generic Mouse Metabolic Reaction GEM (MMR) is created using the mouse orthologs of human genes in HMR2.
Tissue‐specific GEMs for 28 mouse tissues are reconstructed and applied for the analysis of global gene expression data.
Microbial‐induced metabolic differences in the small intestine are simulated using the relative metabolic differences (RMetD) method.
The model predictions are validated by measuring amino acid levels in the portal vein.
Tissue‐specific genome‐scale metabolic models (GEMs), transcriptomic and metabolomic analyses reveal global metabolic differences between conventionally raised and germ‐free mice and show that the gut microbiota affects host amino acid and glutathione metabolism.
Gut microbiota increases energy availability through fermentation of dietary fibers to short-chain fatty acids in conventionally raised mice. Energy deficiency in germ-free (GF) mice increases ...glucagon-like peptide-1 (GLP-1) levels, which slows intestinal transit. To further analyze the role of GLP-1-mediated signaling in this model of energy deficiency, we re-derived mice lacking GLP-1 receptor (GLP-1R KO) as GF.
GLP-1R KO mice were rederived as GF through hysterectomy and monitored for 30 weeks. Mice were subjected to rescue experiments either through feeding an energy-rich diet or colonization with a normal cecal microbiota. Histology and intestinal function were assessed at different ages. Intestinal organoids were assessed to investigate stemness.
Unexpectedly, 25% of GF GLP-1R KO mice died before 20 weeks of age, associated with enlarged ceca, increased cecal water content, increased colonic expression of apical ion transporters, reduced number of goblet cells and loss of colonic epithelial integrity. Colonocytes from GLP-1R KO mice were energy-deprived and exhibited increased ER-stress; mitochondrial fragmentation, increased oxygen levels and loss of stemness. Restoring colonic energy levels either by feeding a Western-style diet or colonization with a normal gut microbiota normalized gut phenotypes and prevented lethality.
Our findings reveal a heretofore unrecognized role for GLP-1R signaling in the maintenance of colonic physiology and survival during energy deprivation.
•Deletion of GLP-1R in germ-free mice is associated with increased lethality.•Germ-free GLP-1R KO mice have a reduced number of goblet cells in the colon.•GLP-1R signaling is essential for maintaining mitochondrial function during energy deprived states.•Absence of GLP-1R signaling in germ-free mice reduces stemness in colonic crypts.
The gut microbiota is a complex ecosystem that has coevolved with host physiology. Colonization of germ-free (GF) mice with a microbiota promotes increased vessel density in the small intestine, but ...little is known about the mechanisms involved. Tissue factor (TF) is the membrane receptor that initiates the extrinsic coagulation pathway, and it promotes developmental and tumour angiogenesis. Here we show that the gut microbiota promotes TF glycosylation associated with localization of TF on the cell surface, the activation of coagulation proteases, and phosphorylation of the TF cytoplasmic domain in the small intestine. Anti-TF treatment of colonized GF mice decreased microbiota-induced vascular remodelling and expression of the proangiogenic factor angiopoietin-1 (Ang-1) in the small intestine. Mice with a genetic deletion of the TF cytoplasmic domain or with hypomorphic TF (F3) alleles had a decreased intestinal vessel density. Coagulation proteases downstream of TF activate protease-activated receptor (PAR) signalling implicated in angiogenesis. Vessel density and phosphorylation of the cytoplasmic domain of TF were decreased in small intestine from PAR1-deficient (F2r(-/-)) but not PAR2-deficient (F2rl1(-/-)) mice, and inhibition of thrombin showed that thrombin-PAR1 signalling was upstream of TF phosphorylation. Thus, the microbiota-induced extravascular TF-PAR1 signalling loop is a novel pathway that may be modulated to influence vascular remodelling in the small intestine.
We performed integrative network analyses to identify targets that can be used for effectively treating liver diseases with minimal side effects. We first generated co‐expression networks (CNs) for ...46 human tissues and liver cancer to explore the functional relationships between genes and examined the overlap between functional and physical interactions. Since increased de novo lipogenesis is a characteristic of nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC), we investigated the liver‐specific genes co‐expressed with fatty acid synthase (FASN). CN analyses predicted that inhibition of these liver‐specific genes decreases FASN expression. Experiments in human cancer cell lines, mouse liver samples, and primary human hepatocytes validated our predictions by demonstrating functional relationships between these liver genes, and showing that their inhibition decreases cell growth and liver fat content. In conclusion, we identified liver‐specific genes linked to NAFLD pathogenesis, such as pyruvate kinase liver and red blood cell (PKLR), or to HCC pathogenesis, such as PKLR, patatin‐like phospholipase domain containing 3 (PNPLA3), and proprotein convertase subtilisin/kexin type 9 (PCSK9), all of which are potential targets for drug development.
Synopsis
Integrative network analyses identify liver‐specific drug targets that can be used to effectively treat liver diseases including nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC).
Co‐expression networks are generated for 46 human tissues and liver cancer.
Genes that are co‐expressed with fatty acid synthase (FASN) only in liver tissue are identified.
Inhibition of liver‐specific genes decreases liver fat and cell growth.
Liver‐specific genes can be targeted in order to treat NAFLD and HCC.
Integrative network analyses identify liver‐specific drug targets that can be used to effectively treat liver diseases including nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC).
ABSTRACT
Metal susceptibility assays and spot plating were used to investigate the antimicrobial activity of enantiopure Ru(phen)2dppz2+ (phen =1,10‐phenanthroline and dppz = ...dipyrido3,2‐a:2´,3´‐cphenazine) and μ‐bidppz(phen)4Ru24+ (bidppz =11,11´‐bis(dipyrido3,2‐a:2´,3´‐cphenazinyl)), on Gram‐negative Escherichia coli and Gram‐positive Bacillus subtilis as bacterial models. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) were determined for both complexes: while μ‐bidppz(phen)4Ru24+ only showed a bactericidal effect at the highest concentrations tested, the antimicrobial activity of Ru(phen)2dppz2+ against B. subtilis was comparable to that of tetracyline. In addition, the Δ‐enantiomer of Ru(phen)2dppz2+ showed a 2‐fold higher bacteriostatic and bactericidal effect compared to the Λ‐enantiomer. This was in accordance with the enantiomers relative binding affinity for DNA, thus strongly indicating DNA binding as the mode of action.
Metal susceptibility assays and spot plating were used to investigate the antimicrobial activity of enantiopure Ru(phen)(2)dppz(2+) (phen =1,10-phenanthroline and dppz = dipyrido3,2-a:2 ',3 ...'-cphenazine) and -bidppz(phen)(4)Ru-2(4+) (bidppz =11,11 '-bis(dipyrido3,2-a:2 ',3 '-cphenazinyl)), on Gram-negative Escherichia coli and Gram-positive Bacillus subtilis as bacterial models. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) were determined for both complexes: while -bidppz(phen)(4)Ru-2(4+) only showed a bactericidal effect at the highest concentrations tested, the antimicrobial activity of Ru(phen)(2)dppz(2+) against B. subtilis was comparable to that of tetracyline. In addition, the -enantiomer of Ru(phen)(2)dppz(2+) showed a 2-fold higher bacteriostatic and bactericidal effect compared to the -enantiomer. This was in accordance with the enantiomers relative binding affinity for DNA, thus strongly indicating DNA binding as the mode of action.
Metal susceptibility assays and spot plating were used to investigate the antimicrobial activity of enantiopure Ru(phen)
dppz
(phen =1,10-phenanthroline and dppz = dipyrido3,2-a:2´,3´-cphenazine) and ...μ-bidppz(phen)
Ru
(bidppz =11,11´-bis(dipyrido3,2-a:2´,3´-cphenazinyl)), on Gram-negative Escherichia coli and Gram-positive Bacillus subtilis as bacterial models. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) were determined for both complexes: while μ-bidppz(phen)
Ru
only showed a bactericidal effect at the highest concentrations tested, the antimicrobial activity of Ru(phen)
dppz
against B. subtilis was comparable to that of tetracyline. In addition, the Δ-enantiomer of Ru(phen)
dppz
showed a 2-fold higher bacteriostatic and bactericidal effect compared to the Λ-enantiomer. This was in accordance with the enantiomers relative binding affinity for DNA, thus strongly indicating DNA binding as the mode of action.
Metal susceptibility assays and spot plating were used to investigate the antimicrobial activity of enantiopure Ru(phen) sub(2)dppz super(2+) (phen =1,10-phenanthroline and dppz = ...dipyrido3,2-a:2,3-cphenazine) and mu -bidppz(phen) sub(4)Ru sub(2) super(4) super(+) (bidppz =11,11-bis(dipyrido3,2-a:2,3-cphenazinyl)), on Gram-negative Escherichia coli and Gram-positive Bacillus subtilis as bacterial models. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) were determined for both complexes: while mu -bidppz(phen) sub(4)Ru sub(2) super(4) super(+) only showed a bactericidal effect at the highest concentrations tested, the antimicrobial activity of Ru(phen) sub(2)dppz super(2+) against B. subtilis was comparable to that of tetracyline. In addition, the Delta -enantiomer of Ru(phen) sub(2)dppz super(2+) showed a 2-fold higher bacteriostatic and bactericidal effect compared to the Lambda -enantiomer. This was in accordance with the enantiomers relative binding affinity for DNA, thus strongly indicating DNA binding as the mode of action.
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