51
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From Association to Causality: the Role of the Gut Microbiota and Its Functional Products on Host Metabolism. Mol Cell 2020; 78:584-596. [PMID: 32234490 DOI: 10.1016/j.molcel.2020.03.005] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/30/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022]
Abstract
Many genomic studies have revealed associations between the gut microbiota composition and host metabolism. These observations led to the idea that a causal relationship could exist between the microbiota and metabolic diseases, a concept supported by studies showing compositional changes in the microbial community in metabolic diseases and transmissibility of host phenotype via microbiota transfer. Accumulating data suggest that the microbiota may affect host metabolic phenotypes through the production of metabolites. These bioactive microbial metabolites, sensitive fingerprints of microbial function, can act as inter-kingdom signaling messengers via penetration into host blood circulation and tissues. These fingerprints may be used for diagnostic purposes, and increased understanding of strain specificity in producing microbial metabolites can identify bacterial strains or specific metabolites that can be used for therapeutic purposes. Here, we will review data supporting the causal role of the gut microbiota in metabolism and discuss mechanisms and potential clinical implications.
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52
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Yin X, Gibbons H, Rundle M, Frost G, McNulty BA, Nugent AP, Walton J, Flynn A, Brennan L. The Relationship between Fish Intake and Urinary Trimethylamine-N-Oxide. Mol Nutr Food Res 2020; 64:e1900799. [PMID: 31863680 DOI: 10.1002/mnfr.201900799] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/05/2019] [Indexed: 12/14/2022]
Abstract
SCOPE Fish intake is reported to be associated with certain health benefits; however, accurate assessment of fish intake is still problematic. The objective of this study is to identify fish intake biomarkers and examine relationships with health parameters in a free-living population. METHODS AND RESULTS In the NutriTech study, ten participants randomized into the fish group consume increasing quantities of fish for 3 days per week for 3 weeks. Urine is analyzed by NMR spectroscopy. Trimethylamine-N-oxide (TMAO), dimethylamine, and dimethyl sulfone are identified and display significant dose-response with intake (p < 0.05). Fish consumption yields a greater increase in urinary TMAO compared to red meat. Biomarker-derived fish intake is calculated in the National Adult Nutrition Survey cross-sectional study. However, the correlation between fish intake and TMAO (r = 0.148, p < 0.01) and that between fish intake and calculated fish intake (r = 0.142, p < 0.01) are poor. In addition, TMAO shows significantly positive correlation with serum insulin and insulin resistance in males and the relationship is more pronounced for males with high dietary fat intake. CONCLUSION Urinary TMAO displays a strong dose-response relationship with fish intake; however, use of TMAO alone is insufficient to determine fish intake in a free-living population.
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Affiliation(s)
- Xiaofei Yin
- UCD School of Agriculture and Food Science, Institute of Food and Health, University College Dublin, Dublin, Ireland
| | - Helena Gibbons
- UCD School of Agriculture and Food Science, Institute of Food and Health, University College Dublin, Dublin, Ireland
| | - Milena Rundle
- Faculty of Medicine, Department of Medicine, Imperial College London, London, UK
| | - Gary Frost
- Faculty of Medicine, Department of Medicine, Imperial College London, London, UK
| | - Breige A McNulty
- UCD School of Agriculture and Food Science, Institute of Food and Health, University College Dublin, Dublin, Ireland
| | - Anne P Nugent
- UCD School of Agriculture and Food Science, Institute of Food and Health, University College Dublin, Dublin, Ireland.,Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Northern Ireland
| | - Janette Walton
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland.,Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - Albert Flynn
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Lorraine Brennan
- UCD School of Agriculture and Food Science, Institute of Food and Health, University College Dublin, Dublin, Ireland
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Trimethylamine N-Oxide Binds and Activates PERK to Promote Metabolic Dysfunction. Cell Metab 2019; 30:1141-1151.e5. [PMID: 31543404 DOI: 10.1016/j.cmet.2019.08.021] [Citation(s) in RCA: 252] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/02/2019] [Accepted: 08/26/2019] [Indexed: 12/20/2022]
Abstract
The gut-microbe-derived metabolite trimethylamine N-oxide (TMAO) is increased by insulin resistance and associated with several sequelae of metabolic syndrome in humans, including cardiovascular, renal, and neurodegenerative disease. The mechanism by which TMAO promotes disease is unclear. We now reveal the endoplasmic reticulum stress kinase PERK (EIF2AK3) as a receptor for TMAO: TMAO binds to PERK at physiologically relevant concentrations; selectively activates the PERK branch of the unfolded protein response; and induces the transcription factor FoxO1, a key driver of metabolic disease, in a PERK-dependent manner. Furthermore, interventions to reduce TMAO, either by manipulation of the gut microbiota or by inhibition of the TMAO synthesizing enzyme, flavin-containing monooxygenase 3, can reduce PERK activation and FoxO1 levels in the liver. Taken together, these data suggest TMAO and PERK may be central to the pathogenesis of the metabolic syndrome.
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54
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Chen R, Wang J, Zhan R, Zhang L, Wang X. Fecal metabonomics combined with 16S rRNA gene sequencing to analyze the changes of gut microbiota in rats with kidney-yang deficiency syndrome and the intervention effect of You-gui pill. JOURNAL OF ETHNOPHARMACOLOGY 2019; 244:112139. [PMID: 31401318 DOI: 10.1016/j.jep.2019.112139] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/20/2019] [Accepted: 08/04/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE A myriad of evidence have shown that kidney-yang deficiency syndrome (KYDS) is associated with metabolic disorders of the intestinal microbiota, while TCMs can treat KYDS by regulating gut microbiota metabolism. However, the specific interplay between KYDS and intestinal microbiota, and the intrinsic regulation mechanism of You-gui pill (YGP) on KYDS' gut microbiota remains largely unknown so far. MATERIALS AND METHODS In the present study, fecal metabonomics combined with 16S rRNA gene sequencing analysis were used to explore the mutual effect between KYDS and intestinal flora, and the intrinsic regulation mechanism of YGP on KYDS's gut microbiota. Rats' feces from control (CON) group, KYDS group and YGP group were collected, and metabolomic analysis was performed using 1H NMR technique combined with multivariate statistical analysis to obtain differential metabolites. Simultaneously, 16S rRNA gene sequencing analysis based on the Illumina HiSeq sequencing platform and ANOVA analysis were used to analyze the composition of the intestinal microbiota in the stool samples and to screen for the significant altered microbiota at the genus level. After that, MetaboAnalyst database and PICRUSt software were apply to conduct metabolic pathway analysis and functional prediction analysis of the screened differential metabolites and intestinal microbiota, respectively. What's more, Pearson correlation analysis was performed on these differential metabolites and gut microbiota. RESULTS Using fecal metabonomics, KYDS was found to be associated with 21 differential metabolites and seven potential metabolic pathways. These metabolites and metabolic pathways were mainly involved in amino acid metabolism, energy metabolism, methylamine metabolism, bile acid metabolism and urea cycle, and short-chain fatty acid metabolism. Through 16S rRNA gene sequencing analysis, we found that KYDS was related to eleven different intestinal microbiotas. These gut microbiota were mostly involved in amino acid metabolism, energy metabolism, nervous, endocrine, immune and digestive system, lipid metabolism, and carbohydrate metabolism. Combined fecal metabonomics and 16S rRNA gene sequencing analysis, we further discovered that KYDS was primarily linked to three gut microbiotas (i.e. Bacteroides, Desulfovibrio and [Eubacterium]_coprostanoligenes_group) and eleven related metabolites (i.e. deoxycholate, n-butyrate, valine, isoleucine, acetate, taurine, glycine, α-gluconse, β-glucose, glycerol and tryptophan) mediated various metabolic disorders (amino acid metabolism, energy metabolism, especially methylamine metabolism, bile acid metabolism and urea cycle, short-chain fatty acid metabolism. nervous, endocrine, immune and digestive system, lipid metabolism, and carbohydrate metabolism). YGP, however, had the ability to mediate four kinds of microbes (i.e. Ruminiclostridium_9, Ruminococcaceae_UCG-007, Ruminococcaceae_UCG-010, and uncultured_bacterium_f_Bacteroidales_S24-7_group) and ten related metabolites (i.e. deoxycholate, valine, isoleucine, alanine, citrulline, acetate, DMA, TMA, phenylalanine and tryptophan) mediated amino acid metabolism, especially methylamine metabolism, bile acid metabolism and urea cycle, short-chain fatty acid metabolism, endocrine, immune and digestive system, and lipid metabolism, thereby exerting a therapeutic effect on KYDS rats. CONCLUSION Overall, our findings have preliminary confirmed that KYDS is closely related to metabolic and microbial dysbiosis, whereas YGP can improve the metabolic disorder of KYDS by acting on intestinal microbiota. Meanwhile, this will lay the foundation for the further KYDS's metagenomic research and the use of intestinal microbiotas as drug targets to treat KYDS.
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Affiliation(s)
- Ruiqun Chen
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Jia Wang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Runhua Zhan
- Shool of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Lei Zhang
- College of Medical Information Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
| | - Xiufeng Wang
- College of Medical Information Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, PR China.
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Adolph TE, Mayr L, Grabherr F, Schwärzler J, Tilg H. Pancreas–Microbiota Cross Talk in Health and Disease. Annu Rev Nutr 2019; 39:249-266. [DOI: 10.1146/annurev-nutr-082018-124306] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The pancreas controls metabolism through endocrine and exocrine functions. Pancreatic diseases comprise a spectrum of mild to life-threatening conditions, including acute and chronic pancreatitis, diabetes, and pancreatic cancer, which affect endocrine and exocrine pancreatic function and impose a substantial disease burden on individuals. Increasing experimental evidence demonstrates that the intestinal microbiota has an important impact on pancreatic function and diseases. This influence may be conferred by bacterial metabolites, such as short-chain fatty acids, or the modulation of immune responses. In turn, pancreatic factors, such as the excretion of antimicrobials, might have a substantial impact on the composition and functional properties of the gut microbiota. Here, we summarize experimental and clinical approaches used to untie the intricate pancreas–microbiota cross talk. Future advances will allow clinicians to manipulate the intestinal microbiota and guide patient management in pancreatic diseases.
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Affiliation(s)
- Timon E. Adolph
- Department of Internal Medicine I (Gastroenterology, Hepatology, Endocrinology and Metabolism), Medical University Innsbruck, Innsbruck 6020, Austria
| | - Lisa Mayr
- Department of Internal Medicine I (Gastroenterology, Hepatology, Endocrinology and Metabolism), Medical University Innsbruck, Innsbruck 6020, Austria
| | - Felix Grabherr
- Department of Internal Medicine I (Gastroenterology, Hepatology, Endocrinology and Metabolism), Medical University Innsbruck, Innsbruck 6020, Austria
| | - Julian Schwärzler
- Department of Internal Medicine I (Gastroenterology, Hepatology, Endocrinology and Metabolism), Medical University Innsbruck, Innsbruck 6020, Austria
| | - Herbert Tilg
- Department of Internal Medicine I (Gastroenterology, Hepatology, Endocrinology and Metabolism), Medical University Innsbruck, Innsbruck 6020, Austria
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Parker A, Fonseca S, Carding SR. Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health. Gut Microbes 2019; 11:135-157. [PMID: 31368397 PMCID: PMC7053956 DOI: 10.1080/19490976.2019.1638722] [Citation(s) in RCA: 401] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/22/2019] [Accepted: 06/26/2019] [Indexed: 02/03/2023] Open
Abstract
The human gastrointestinal (gut) microbiota comprises diverse and dynamic populations of bacteria, archaea, viruses, fungi, and protozoa, coexisting in a mutualistic relationship with the host. When intestinal homeostasis is perturbed, the function of the gastrointestinal tract and other organ systems, including the brain, can be compromised. The gut microbiota is proposed to contribute to blood-brain barrier disruption and the pathogenesis of neurodegenerative diseases. While progress is being made, a better understanding of interactions between gut microbes and host cells, and the impact these have on signaling from gut to brain is now required. In this review, we summarise current evidence of the impact gut microbes and their metabolites have on blood-brain barrier integrity and brain function, and the communication networks between the gastrointestinal tract and brain, which they may modulate. We also discuss the potential of microbiota modulation strategies as therapeutic tools for promoting and restoring brain health.
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Affiliation(s)
- Aimée Parker
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - Sonia Fonseca
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
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Zhao ZH, Xin FZ, Zhou D, Xue YQ, Liu XL, Yang RX, Pan Q, Fan JG. Trimethylamine N-oxide attenuates high-fat high-cholesterol diet-induced steatohepatitis by reducing hepatic cholesterol overload in rats. World J Gastroenterol 2019; 25:2450-2462. [PMID: 31171889 PMCID: PMC6543245 DOI: 10.3748/wjg.v25.i20.2450] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Trimethylamine N-oxide (TMAO) has been shown to be involved in cardiovascular disease (CVD). However, its role in nonalcoholic steatohepatitis (NASH) is unknown. AIM To determine the effect of TMAO on the progression of NASH. METHODS A rat model was induced by 16-wk high-fat high-cholesterol (HFHC) diet feeding and TMAO was administrated by daily oral gavage for 8 wk. RESULTS Oral TMAO intervention attenuated HFHC diet-induced steatohepatitis in rats. Histological evaluation showed that TMAO treatment significantly alleviated lobular inflammation and hepatocyte ballooning in the livers of rats fed a HFHC diet. Serum levels of alanine aminotransferase and aspartate aminotransferase were also decreased by TMAO treatment. Moreover, hepatic endoplasmic reticulum (ER) stress and cell death were mitigated in HFHC diet-fed TMAO-treated rats. Hepatic and serum levels of cholesterol were both decreased by TMAO treatment in rats fed a HFHC diet. Furthermore, the expression levels of intestinal cholesterol transporters were detected. Interestingly, cholesterol influx-related Niemann-Pick C1-like 1 was downregulated and cholesterol efflux-related ABCG5/8 were upregulated by TMAO treatment in the small intestine. Gut microbiota analysis showed that TMAO could alter the gut microbial profile and restore the diversity of gut flora. CONCLUSION These data suggest that TMAO may modulate the gut microbiota, inhibit intestinal cholesterol absorption, and ameliorate hepatic ER stress and cell death under cholesterol overload, thereby attenuating HFHC diet-induced steatohepatitis in rats. Further studies are needed to evaluate the influence on CVD and define the safe does of TMAO treatment.
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Affiliation(s)
- Ze-Hua Zhao
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Feng-Zhi Xin
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Da Zhou
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Ya-Qian Xue
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao-Lin Liu
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Rui-Xu Yang
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Qin Pan
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Jian-Gao Fan
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
- Shanghai Key Lab of Pediatric Gastroenterology and Nutrition, Shanghai 200092, China
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Zhou D, Fan JG. Microbial metabolites in non-alcoholic fatty liver disease. World J Gastroenterol 2019; 25:2019-2028. [PMID: 31114130 PMCID: PMC6506577 DOI: 10.3748/wjg.v25.i17.2019] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 02/06/2023] Open
Abstract
The prevalence of non-alcoholic fatty liver disease (NAFLD) is rising exponentially worldwide. The spectrum of NAFLD includes non-alcoholic fatty liver, non-alcoholic steatohepatitis, liver cirrhosis, and even hepatocellular carcinoma. Evidence shows that microbial metabolites play pivotal roles in the onset and progression of NAFLD. In this review, we discuss how microbe-derived metabolites, such as short-chain fatty acids, endogenous ethanol, bile acids and so forth, contribute to the pathogenesis of NAFLD.
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Affiliation(s)
- Da Zhou
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai Institute of Liver Disease, Shanghai 200032, China
| | - Jian-Gao Fan
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Key Lab of Pediatric Gastroenterology and Nutrition, Shanghai 200092, China
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Abdul Rahim MBH, Chilloux J, Martinez-Gili L, Neves AL, Myridakis A, Gooderham N, Dumas ME. Diet-induced metabolic changes of the human gut microbiome: importance of short-chain fatty acids, methylamines and indoles. Acta Diabetol 2019; 56:493-500. [PMID: 30903435 PMCID: PMC6451719 DOI: 10.1007/s00592-019-01312-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/21/2019] [Indexed: 02/07/2023]
Abstract
The human gut is a home for more than 100 trillion bacteria, far more than all other microbial populations resident on the body's surface. The human gut microbiome is considered as a microbial organ symbiotically operating within the host. It is a collection of different cell lineages that are capable of communicating with each other and the host and has an ability to undergo self-replication for its repair and maintenance. As the gut microbiota is involved in many host processes including growth and development, an imbalance in its ecological composition may lead to disease and dysfunction in the human. Gut microbial degradation of nutrients produces bioactive metabolites that bind target receptors, activating signalling cascades, and modulating host metabolism. This review covers current findings on the nutritional and pharmacological roles of selective gut microbial metabolites, short-chain fatty acids, methylamines and indoles, as well as discussing nutritional interventions to modulate the microbiome.
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Affiliation(s)
- Mohd Badrin Hanizam Abdul Rahim
- Division of Systems and Digestive Medicine, Department of Surgery and Cancer, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Julien Chilloux
- Division of Systems and Digestive Medicine, Department of Surgery and Cancer, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Laura Martinez-Gili
- Division of Systems and Digestive Medicine, Department of Surgery and Cancer, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Ana L Neves
- Division of Systems and Digestive Medicine, Department of Surgery and Cancer, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Antonis Myridakis
- Division of Systems and Digestive Medicine, Department of Surgery and Cancer, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Nigel Gooderham
- Division of Systems and Digestive Medicine, Department of Surgery and Cancer, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Marc-Emmanuel Dumas
- Division of Systems and Digestive Medicine, Department of Surgery and Cancer, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
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Lees HJ, Swann JR, Poucher S, Holmes E, Wilson ID, Nicholson JK. Obesity and Cage Environment Modulate Metabolism in the Zucker Rat: A Multiple Biological Matrix Approach to Characterizing Metabolic Phenomena. J Proteome Res 2019; 18:2160-2174. [PMID: 30939873 DOI: 10.1021/acs.jproteome.9b00040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Obesity and its comorbidities are increasing worldwide imposing a heavy socioeconomic burden. The effects of obesity on the metabolic profiles of tissues (liver, kidney, pancreas), urine, and the systemic circulation were investigated in the Zucker rat model using 1H NMR spectroscopy coupled to multivariate statistical analysis. The metabolic profiles of the obese ( fa/ fa) animals were clearly differentiated from the two phenotypically lean phenotypes, ((+/+) and ( fa/+)) within each biological compartment studied, and across all matrices combined. No significant differences were observed between the metabolic profiles of the genotypically distinct lean strains. Obese Zucker rats were characterized by higher relative concentrations of blood lipid species, cross-compartmental amino acids (particularly BCAAs), urinary and liver metabolites relating to the TCA cycle and glucose metabolism; and lower amounts of urinary gut microbial-host cometabolites, and intermatrix metabolites associated with creatine metabolism. Further to this, the obese Zucker rat metabotype was defined by significant metabolic alterations relating to disruptions in the metabolism of choline across all compartments analyzed. The cage environment was found to have a significant effect on urinary metabolites related to gut-microbial metabolism, with additional cage-microenvironment trends also observed in liver, kidney, and pancreas. This study emphasizes the value in metabotyping multiple biological matrices simultaneously to gain a better understanding of systemic perturbations in metabolism, and also underscores the need for control or evaluation of cage environment when designing and interpreting data from metabonomic studies in animal models.
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Affiliation(s)
- Hannah J Lees
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Jonathan R Swann
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Simon Poucher
- AstraZeneca Pharmaceuticals , Mereside , Alderley Park , Macclesfield , SK10 4TG , United Kingdom
| | - Elaine Holmes
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Ian D Wilson
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College London , London , SW7 2AZ , United Kingdom
| | - Jeremy K Nicholson
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College London , London , SW7 2AZ , United Kingdom
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Clarke G, Sandhu KV, Griffin BT, Dinan TG, Cryan JF, Hyland NP. Gut Reactions: Breaking Down Xenobiotic-Microbiome Interactions. Pharmacol Rev 2019; 71:198-224. [PMID: 30890566 DOI: 10.1124/pr.118.015768] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2025] Open
Abstract
The microbiome plays a key role in health and disease, and there has been considerable interest in therapeutic targeting of the microbiome as well as mining this rich resource in drug discovery efforts. However, a growing body of evidence suggests that the gut microbiota can itself influence the actions of a range of xenobiotics, in both beneficial and potentially harmful ways. Traditionally, clinical studies evaluating the pharmacokinetics of new drugs have mostly ignored the important direct and indirect effects of the gut microbiome on drug metabolism and efficacy. Despite some important observations from xenobiotic metabolism in general, there is only an incomplete understanding of the scope of influence of the microbiome specifically on drug metabolism and absorption, and how this might influence systemic concentrations of parent compounds and toxic metabolites. The significance of both microbial metabolism of xenobiotics and the impact of the gut microbiome on host hepatic enzyme systems is nonetheless gaining traction and presents a further challenge in drug discovery efforts, with implications for improving treatment outcomes or counteracting adverse drug reactions. Microbial factors must now be considered when determining drug pharmacokinetics and the impact that an evolving and dynamic microbiome could have in this regard. In this review, we aim to integrate the contribution of the gut microbiome in health and disease to xenobiotic metabolism focusing on therapeutic interventions, pharmacological drug action, and chemical biotransformations that collectively will have implications for the future practice of precision medicine.
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Affiliation(s)
- Gerard Clarke
- APC Microbiome Ireland (G.C., K.V.S., B.T.G., T.G.D., J.F.C., N.P.H.), INFANT Research Centre (G.C.), Department of Psychiatry and Neurobehavioural Science (G.C., T.G.D.), School of Pharmacy (B.T.G.), and Departments of Anatomy and Neuroscience (J.F.C.), Pharmacology and Therapeutics (N.P.H.), and Physiology (N.P.H.), University College Cork, Cork, Ireland
| | - Kiran V Sandhu
- APC Microbiome Ireland (G.C., K.V.S., B.T.G., T.G.D., J.F.C., N.P.H.), INFANT Research Centre (G.C.), Department of Psychiatry and Neurobehavioural Science (G.C., T.G.D.), School of Pharmacy (B.T.G.), and Departments of Anatomy and Neuroscience (J.F.C.), Pharmacology and Therapeutics (N.P.H.), and Physiology (N.P.H.), University College Cork, Cork, Ireland
| | - Brendan T Griffin
- APC Microbiome Ireland (G.C., K.V.S., B.T.G., T.G.D., J.F.C., N.P.H.), INFANT Research Centre (G.C.), Department of Psychiatry and Neurobehavioural Science (G.C., T.G.D.), School of Pharmacy (B.T.G.), and Departments of Anatomy and Neuroscience (J.F.C.), Pharmacology and Therapeutics (N.P.H.), and Physiology (N.P.H.), University College Cork, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland (G.C., K.V.S., B.T.G., T.G.D., J.F.C., N.P.H.), INFANT Research Centre (G.C.), Department of Psychiatry and Neurobehavioural Science (G.C., T.G.D.), School of Pharmacy (B.T.G.), and Departments of Anatomy and Neuroscience (J.F.C.), Pharmacology and Therapeutics (N.P.H.), and Physiology (N.P.H.), University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland (G.C., K.V.S., B.T.G., T.G.D., J.F.C., N.P.H.), INFANT Research Centre (G.C.), Department of Psychiatry and Neurobehavioural Science (G.C., T.G.D.), School of Pharmacy (B.T.G.), and Departments of Anatomy and Neuroscience (J.F.C.), Pharmacology and Therapeutics (N.P.H.), and Physiology (N.P.H.), University College Cork, Cork, Ireland
| | - Niall P Hyland
- APC Microbiome Ireland (G.C., K.V.S., B.T.G., T.G.D., J.F.C., N.P.H.), INFANT Research Centre (G.C.), Department of Psychiatry and Neurobehavioural Science (G.C., T.G.D.), School of Pharmacy (B.T.G.), and Departments of Anatomy and Neuroscience (J.F.C.), Pharmacology and Therapeutics (N.P.H.), and Physiology (N.P.H.), University College Cork, Cork, Ireland
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Zhao ZH, Lai JKL, Qiao L, Fan JG. Role of gut microbial metabolites in nonalcoholic fatty liver disease. J Dig Dis 2019; 20:181-188. [PMID: 30706694 DOI: 10.1111/1751-2980.12709] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/08/2019] [Accepted: 01/30/2019] [Indexed: 12/11/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common, multifactorial liver disease that has emerged as a global challenge due to its increasing prevalence and lack of sustainable treatment options. Gut microbiota possess vital functions in fermenting dietary nutrients and synthesizing bioactive molecules. This function is of great importance in maintaining health because these microbial metabolites are essential in regulating energy metabolism, immune response, and other vital physiological processes. Altered gut flora can result in a change in gut microbial metabolites, affecting the onset and progression of multiple diseases. In this review we summarize the metabolites that may have beneficial or harmful effects on the development and progression of NAFLD. This will help us better understand the possible mechanisms underlying the pathogenesis of NAFLD and facilitate the identification of potential therapeutic approaches for NAFLD.
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Affiliation(s)
- Ze Hua Zhao
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jonathan King-Lam Lai
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
| | - Liang Qiao
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
| | - Jian Gao Fan
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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63
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Brial F, Le Lay A, Hedjazi L, Tsang T, Fearnside JF, Otto GW, Alzaid F, Wilder SP, Venteclef N, Cazier JB, Nicholson JK, Day C, Burt AD, Gut IG, Lathrop M, Dumas ME, Gauguier D. Systems Genetics of Hepatic Metabolome Reveals Octopamine as a Target for Non-Alcoholic Fatty Liver Disease Treatment. Sci Rep 2019; 9:3656. [PMID: 30842494 PMCID: PMC6403227 DOI: 10.1038/s41598-019-40153-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/17/2019] [Indexed: 12/14/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is often associated with obesity and type 2 diabetes. To disentangle etiological relationships between these conditions and identify genetically-determined metabolites involved in NAFLD processes, we mapped 1H nuclear magnetic resonance (NMR) metabolomic and disease-related phenotypes in a mouse F2 cross derived from strains showing resistance (BALB/c) and increased susceptibility (129S6) to these diseases. Quantitative trait locus (QTL) analysis based on single nucleotide polymorphism (SNP) genotypes identified diet responsive QTLs in F2 mice fed control or high fat diet (HFD). In HFD fed F2 mice we mapped on chromosome 18 a QTL regulating liver micro- and macrovesicular steatosis and inflammation, independently from glucose intolerance and adiposity, which was linked to chromosome 4. Linkage analysis of liver metabolomic profiling data identified a QTL for octopamine, which co-localised with the QTL for liver histopathology in the cross. Functional relationship between these two QTLs was validated in vivo in mice chronically treated with octopamine, which exhibited reduction in liver histopathology and metabolic benefits, underlining its role as a mechanistic biomarker of fatty liver with potential therapeutic applications.
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Affiliation(s)
- Francois Brial
- Sorbonne University, University Paris Descartes, University Paris Diderot, INSERM UMR_S 1138, Cordeliers Research Centre, 75006, Paris, France
| | - Aurélie Le Lay
- Sorbonne University, University Paris Descartes, University Paris Diderot, INSERM UMR_S 1138, Cordeliers Research Centre, 75006, Paris, France
| | - Lyamine Hedjazi
- Sorbonne University, University Paris Descartes, University Paris Diderot, INSERM UMR_S 1138, Cordeliers Research Centre, 75006, Paris, France
| | - Tsz Tsang
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jane F Fearnside
- School of Health and Related Research, The University of Sheffield, 30 Regent Court, Sheffield, S10 2TA, United Kingdom
| | - Georg W Otto
- Genetics and Genomic Medicine, University College London Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, United Kingdom
| | - Fawaz Alzaid
- Sorbonne University, University Paris Descartes, University Paris Diderot, INSERM UMR_S 1138, Cordeliers Research Centre, 75006, Paris, France
| | - Steven P Wilder
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, United Kingdom
- Genomics Plc, King Charles House, Oxford, Park End Street, OX1 1JD, United Kingdom
| | - Nicolas Venteclef
- Sorbonne University, University Paris Descartes, University Paris Diderot, INSERM UMR_S 1138, Cordeliers Research Centre, 75006, Paris, France
| | - Jean-Baptiste Cazier
- Centre for Computational Biology, Medical School, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Jeremy K Nicholson
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, United Kingdom
- The Australian National Phenome Centre, Murdoch University, Perth, WA6150, Australia
| | - Chris Day
- Faculty of Medical Sciences, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Alastair D Burt
- Faculty of Medical Sciences, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ivo G Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, 08028, Barcelona, Spain
| | - Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Marc-Emmanuel Dumas
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, United Kingdom
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Dominique Gauguier
- Sorbonne University, University Paris Descartes, University Paris Diderot, INSERM UMR_S 1138, Cordeliers Research Centre, 75006, Paris, France.
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, United Kingdom.
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, United Kingdom.
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada.
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64
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Heianza Y, Sun D, Li X, DiDonato JA, Bray GA, Sacks FM, Qi L. Gut microbiota metabolites, amino acid metabolites and improvements in insulin sensitivity and glucose metabolism: the POUNDS Lost trial. Gut 2019; 68:263-270. [PMID: 29860242 PMCID: PMC6275143 DOI: 10.1136/gutjnl-2018-316155] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Alterations in gut microbiota have been linked to host insulin resistance, diabetes and impaired amino acid metabolism. We investigated whether changes in gut microbiota-dependent metabolite of trimethylamine N-oxide (TMAO) and its nutrient precursors (choline and L-carnitine) were associated with improvements in glucose metabolism and diabetes-related amino acids in a weight-loss diet intervention. DESIGN We included 504 overweight and obese adults who were randomly assigned to one of four energy-reduced diets varying in macronutrient intake. The 6-month changes (Δ) in TMAO, choline and L-carnitine levels after the intervention were calculated. RESULTS Greater decreases in choline and L-carnitine were significantly (p<0.05) associated with greater improvements in fasting insulin concentrations and homeostasis model assessment of insulin resistance (HOMA-IR) at 6 months. The reduction of choline was significantly related to 2-year improvements in glucose and insulin resistance. We found significant linkages between dietary fat intake and ΔTMAO for changes in fasting glucose, insulin and HOMA-IR (pinteraction <0.05); a greater increase in TMAO was related to lesser improvements in the outcomes among participants who consumed a high-fat diet. In addition, ΔL-carnitine and Δcholine were significantly related to changes in amino acids (including branched-chain and aromatic amino acids). Interestingly, the associations of ΔTMAO, Δcholine and ΔL-carnitine with diabetes-related traits were independent of the changes in amino acids. CONCLUSION Our findings underscore the importance of changes in TMAO, choline and L-carnitine in improving insulin sensitivity during a weight-loss intervention for obese patients. Dietary fat intake may modify the associations of TMAO with insulin sensitivity and glucose metabolism. TRIAL REGISTRATION NUMBER NCT00072995.
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Affiliation(s)
- Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Dianjianyi Sun
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Joseph A. DiDonato
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH
| | - George A Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA
| | - Frank M Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
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65
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Danneskiold-Samsøe NB, Dias de Freitas Queiroz Barros H, Santos R, Bicas JL, Cazarin CBB, Madsen L, Kristiansen K, Pastore GM, Brix S, Maróstica Júnior MR. Interplay between food and gut microbiota in health and disease. Food Res Int 2019; 115:23-31. [DOI: 10.1016/j.foodres.2018.07.043] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 07/01/2018] [Accepted: 07/28/2018] [Indexed: 12/14/2022]
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66
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Yue SJ, Liu J, Wang AT, Meng XT, Yang ZR, Peng C, Guan HS, Wang CY, Yan D. Berberine alleviates insulin resistance by reducing peripheral branched-chain amino acids. Am J Physiol Endocrinol Metab 2019; 316:E73-E85. [PMID: 30422704 DOI: 10.1152/ajpendo.00256.2018] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Increased circulating branched-chain amino acids (BCAAs) have been involved in the pathogenesis of obesity and insulin resistance (IR). However, evidence relating berberine (BBR), gut microbiota, BCAAs, and IR is limited. Here, we showed that BBR could effectively rectify steatohepatitis and glucose intolerance in high-fat diet (HFD)-fed mice. BBR reorganized gut microbiota populations under both the normal chow diet (NCD) and HFD. Particularly, BBR noticeably decreased the relative abundance of BCAA-producing bacteria, including order Clostridiales; families Streptococcaceae, Clostridiaceae, and Prevotellaceae; and genera Streptococcus and Prevotella. Compared with the HFD group, predictive metagenomics indicated a reduction in the proportion of gut microbiota genes involved in BCAA biosynthesis but the enrichment genes for BCAA degradation and transport by BBR treatment. Accordingly, the elevated serum BCAAs of HFD group were significantly decreased by BBR. Furthermore, the Western blotting results implied that BBR could promote the BCAA catabolism in the liver and epididymal white adipose tissues of HFD-fed mice by activation of the multienzyme branched-chain α-ketoacid dehydrogenase complex (BCKDC), whereas by inhibition of the phosphorylation state of BCKDHA (E1α subunit) and branched-chain α-ketoacid dehydrogenase kinase (BCKDK). The ex vivo assay further confirmed that BBR could increase BCAA catabolism in both AML12 hepatocytes and 3T3-L1 adipocytes. Finally, data from healthy subjects and diabetics confirmed that BBR could improve glycemic control and modulate circulating BCAAs. Together, our findings clarified BBR improving IR associated not only with gut microbiota alteration in BCAA biosynthesis but also with BCAA catabolism in liver and adipose tissues.
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Affiliation(s)
- Shi-Jun Yue
- Beijing Key Laboratory of Bio-Characteristic Profiling for Evaluation of Rational Drug Use, Beijing Shijitan Hospital, Capital Medical University , Beijing , China
- Key Laboratory of Marine Drugs (Ministry of Education of China), School of Medicine and Pharmacy, Ocean University of China , Qingdao , China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao , China
| | - Juan Liu
- Beijing Key Laboratory of Bio-Characteristic Profiling for Evaluation of Rational Drug Use, Beijing Shijitan Hospital, Capital Medical University , Beijing , China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine , Chengdu , China
| | - Ai-Ting Wang
- Beijing Key Laboratory of Bio-Characteristic Profiling for Evaluation of Rational Drug Use, Beijing Shijitan Hospital, Capital Medical University , Beijing , China
| | - Xin-Tong Meng
- Beijing Key Laboratory of Bio-Characteristic Profiling for Evaluation of Rational Drug Use, Beijing Shijitan Hospital, Capital Medical University , Beijing , China
| | - Zhi-Rui Yang
- Beijing Key Laboratory of Bio-Characteristic Profiling for Evaluation of Rational Drug Use, Beijing Shijitan Hospital, Capital Medical University , Beijing , China
| | - Cheng Peng
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine , Chengdu , China
| | - Hua-Shi Guan
- Key Laboratory of Marine Drugs (Ministry of Education of China), School of Medicine and Pharmacy, Ocean University of China , Qingdao , China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao , China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs (Ministry of Education of China), School of Medicine and Pharmacy, Ocean University of China , Qingdao , China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao , China
| | - Dan Yan
- Beijing Key Laboratory of Bio-Characteristic Profiling for Evaluation of Rational Drug Use, Beijing Shijitan Hospital, Capital Medical University , Beijing , China
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Brial F, Le Lay A, Dumas ME, Gauguier D. Implication of gut microbiota metabolites in cardiovascular and metabolic diseases. Cell Mol Life Sci 2018; 75:3977-3990. [PMID: 30101405 PMCID: PMC6182343 DOI: 10.1007/s00018-018-2901-1] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 12/18/2022]
Abstract
Evidence from the literature keeps highlighting the impact of mutualistic bacterial communities of the gut microbiota on human health. The gut microbita is a complex ecosystem of symbiotic bacteria which contributes to mammalian host biology by processing, otherwise, indigestible nutrients, supplying essential metabolites, and contributing to modulate its immune system. Advances in sequencing technologies have enabled structural analysis of the human gut microbiota and allowed detection of changes in gut bacterial composition in several common diseases, including cardiometabolic disorders. Biological signals sent by the gut microbiota to the host, including microbial metabolites and pro-inflammatory molecules, mediate microbiome-host genome cross-talk. This rapidly expanding line of research can identify disease-causing and disease-predictive microbial metabolite biomarkers, which can be translated into novel biodiagnostic tests, dietary supplements, and nutritional interventions for personalized therapeutic developments in common diseases. Here, we review results from the most significant studies dealing with the association of products from the gut microbial metabolism with cardiometabolic disorders. We underline the importance of these postbiotic biomarkers in the diagnosis and treatment of human disorders.
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Affiliation(s)
- Francois Brial
- Sorbonne University, University Paris Descartes, INSERM UMR_S1138, Cordeliers Research Centre, 15 rue de l'Ecole de Médecine, 75006, Paris, France
| | - Aurélie Le Lay
- Sorbonne University, University Paris Descartes, INSERM UMR_S1138, Cordeliers Research Centre, 15 rue de l'Ecole de Médecine, 75006, Paris, France
| | - Marc-Emmanuel Dumas
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, UK
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Dominique Gauguier
- Sorbonne University, University Paris Descartes, INSERM UMR_S1138, Cordeliers Research Centre, 15 rue de l'Ecole de Médecine, 75006, Paris, France.
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, UK.
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada.
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68
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Integration of the human exposome with the human genome to advance medicine. Biochimie 2018; 152:155-158. [DOI: 10.1016/j.biochi.2018.06.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 06/26/2018] [Indexed: 11/19/2022]
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69
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Glucose and Fat Tolerance Tests Induce Differential Responses in Plasma Choline Metabolites in Healthy Subjects. Nutrients 2018; 10:nu10091209. [PMID: 30200465 PMCID: PMC6165136 DOI: 10.3390/nu10091209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/24/2018] [Accepted: 08/26/2018] [Indexed: 12/12/2022] Open
Abstract
Plasma choline shows associations with plasma glucose and lipids. We studied changes of choline metabolites after oral glucose tolerance test (OGTT) and fat tolerance test (OFTT). Eighteen healthy subjects (mean age 54.3 years; BMI 26.8 kg/m2) underwent 2 tests. First, OFTT (80 g fat) was applied and blood was collected at baseline and 4 h after OFTT. Seven days later, 75 g glucose was applied and blood was collected at baseline and 2 h after OGTT. Plasma concentrations of choline, betaine, trimethylamine N-oxide (TMAO), dimethylglycine, S-adenosylmethionine (SAM), lipids and glucose were measured. After OFTT, plasma choline declined (10.6 to 9.2 µmol/L; p = 0.004), betaine declined (33.4 to 31.7 µmol/L; p = 0.003), TMAO slightly increased (4.1 to 5.6 µmol/L; p = 0.105), glucose declined (5.39 to 4.98 mmol/L; p < 0.001), and triglycerides increased (1.27 to 2.53 mmol/L; p < 0.001). After OGTT, plasma choline increased (10.1 to 11.1 µmol/L; p < 0.001), TMAO declined (4.0 to 3.5 µmol/L; p = 0.029), dimethylglycine declined (2.0 to 1.7 µmol/L; p = 0.005), SAM declined (103 to 96 nmol/L; p = 0.041), but betaine, glucose, and SAM were unchanged. In conclusion, OFTT lowered plasma betaine and choline and caused heterogeneous changes in plasma TMAO. OGTT reduced the flow of methyl groups and plasma TMAO.
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70
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Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women. Nat Med 2018; 24:1070-1080. [PMID: 29942096 PMCID: PMC6140997 DOI: 10.1038/s41591-018-0061-3] [Citation(s) in RCA: 484] [Impact Index Per Article: 69.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2018] [Indexed: 02/07/2023]
Abstract
Hepatic steatosis is a multifactorial condition that is often observed in obese patients and is a prelude to non-alcoholic fatty liver disease. Here, we combine shotgun sequencing of fecal metagenomes with molecular phenomics (hepatic transcriptome and plasma and urine metabolomes) in two well-characterized cohorts of morbidly obese women recruited to the FLORINASH study. We reveal molecular networks linking the gut microbiome and the host phenome to hepatic steatosis. Patients with steatosis have low microbial gene richness and increased genetic potential for the processing of dietary lipids and endotoxin biosynthesis (notably from Proteobacteria), hepatic inflammation and dysregulation of aromatic and branched-chain amino acid metabolism. We demonstrated that fecal microbiota transplants and chronic treatment with phenylacetic acid, a microbial product of aromatic amino acid metabolism, successfully trigger steatosis and branched-chain amino acid metabolism. Molecular phenomic signatures were predictive (area under the curve = 87%) and consistent with the gut microbiome having an effect on the steatosis phenome (>75% shared variation) and, therefore, actionable via microbiome-based therapies.
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71
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Hoyles L, Jiménez-Pranteda ML, Chilloux J, Brial F, Myridakis A, Aranias T, Magnan C, Gibson GR, Sanderson JD, Nicholson JK, Gauguier D, McCartney AL, Dumas ME. Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota. MICROBIOME 2018; 6:73. [PMID: 29678198 PMCID: PMC5909246 DOI: 10.1186/s40168-018-0461-0] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/13/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND The dietary methylamines choline, carnitine, and phosphatidylcholine are used by the gut microbiota to produce a range of metabolites, including trimethylamine (TMA). However, little is known about the use of trimethylamine N-oxide (TMAO) by this consortium of microbes. RESULTS A feeding study using deuterated TMAO in C57BL6/J mice demonstrated microbial conversion of TMAO to TMA, with uptake of TMA into the bloodstream and its conversion to TMAO. Microbial activity necessary to convert TMAO to TMA was suppressed in antibiotic-treated mice, with deuterated TMAO being taken up directly into the bloodstream. In batch-culture fermentation systems inoculated with human faeces, growth of Enterobacteriaceae was stimulated in the presence of TMAO. Human-derived faecal and caecal bacteria (n = 66 isolates) were screened on solid and liquid media for their ability to use TMAO, with metabolites in spent media analysed by 1H-NMR. As with the in vitro fermentation experiments, TMAO stimulated the growth of Enterobacteriaceae; these bacteria produced most TMA from TMAO. Caecal/small intestinal isolates of Escherichia coli produced more TMA from TMAO than their faecal counterparts. Lactic acid bacteria produced increased amounts of lactate when grown in the presence of TMAO but did not produce large amounts of TMA. Clostridia (sensu stricto), bifidobacteria, and coriobacteria were significantly correlated with TMA production in the mixed fermentation system but did not produce notable quantities of TMA from TMAO in pure culture. CONCLUSIONS Reduction of TMAO by the gut microbiota (predominantly Enterobacteriaceae) to TMA followed by host uptake of TMA into the bloodstream from the intestine and its conversion back to TMAO by host hepatic enzymes is an example of metabolic retroconversion. TMAO influences microbial metabolism depending on isolation source and taxon of gut bacterium. Correlation of metabolomic and abundance data from mixed microbiota fermentation systems did not give a true picture of which members of the gut microbiota were responsible for converting TMAO to TMA; only by supplementing the study with pure culture work and additional metabolomics was it possible to increase our understanding of TMAO bioconversions by the human gut microbiota.
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Affiliation(s)
- Lesley Hoyles
- Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, London, SW7 2AZ UK
| | - Maria L. Jiménez-Pranteda
- Food Microbial Sciences Unit, Department of Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, Faculty of Life Sciences, The University of Reading, Whiteknights Campus, Reading, RG6 6UR UK
| | - Julien Chilloux
- Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, London, SW7 2AZ UK
| | - Francois Brial
- Sorbonne Universities, University Pierre & Marie Curie, University Paris Descartes, Sorbonne Paris Cité, INSERM UMR_S 1138, Cordeliers Research Centre, Paris, France
| | - Antonis Myridakis
- Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, London, SW7 2AZ UK
| | - Thomas Aranias
- Sorbonne Universities, University Pierre & Marie Curie, University Paris Descartes, Sorbonne Paris Cité, INSERM UMR_S 1138, Cordeliers Research Centre, Paris, France
| | - Christophe Magnan
- Sorbonne Paris Cité, Université Denis Diderot, Unité de Biologie Fonctionnelle et Adaptative, CNRS UMR 8251, 75205 Paris, France
| | - Glenn R. Gibson
- Food Microbial Sciences Unit, Department of Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, Faculty of Life Sciences, The University of Reading, Whiteknights Campus, Reading, RG6 6UR UK
| | - Jeremy D. Sanderson
- Department of Gastroenterology, Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
| | - Jeremy K. Nicholson
- Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, London, SW7 2AZ UK
| | - Dominique Gauguier
- Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, London, SW7 2AZ UK
- Sorbonne Universities, University Pierre & Marie Curie, University Paris Descartes, Sorbonne Paris Cité, INSERM UMR_S 1138, Cordeliers Research Centre, Paris, France
| | - Anne L. McCartney
- Food Microbial Sciences Unit, Department of Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, Faculty of Life Sciences, The University of Reading, Whiteknights Campus, Reading, RG6 6UR UK
| | - Marc-Emmanuel Dumas
- Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, London, SW7 2AZ UK
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72
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Ciciliot S, Albiero M, Campanaro S, Poncina N, Tedesco S, Scattolini V, Dalla Costa F, Cignarella A, Vettore M, Di Gangi IM, Bogialli S, Avogaro A, Fadini GP. Interplay between gut microbiota and p66Shc affects obesity-associated insulin resistance. FASEB J 2018; 32:4004-4015. [PMID: 29466053 DOI: 10.1096/fj.201701409r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 66 kDa isoform of the mammalian Shc gene promotes adipogenesis, and p66Shc-/- mice accumulate less body weight than wild-type (WT) mice. As the metabolic consequences of the leaner phenotype of p66Shc-/- mice is debated, we hypothesized that gut microbiota may be involved. We confirmed that p66Shc-/- mice gained less weight than WT mice when on a high-fat diet (HFD), but they were not protected from insulin resistance and glucose intolerance. p66Shc deletion significantly modified the composition of gut microbiota and their modification after an HFD. This was associated with changes in gene expression of Il-1b and regenerating islet-derived protein 3 γ ( Reg3g) in the gut and in systemic trimethylamine N-oxide and branched chain amino acid levels, despite there being no difference in intestinal structure and permeability. Depleting gut microbiota at the end of HFD rendered both strains more glucose tolerant but improved insulin sensitivity only in p66Shc-/- mice. Microbiota-depleted WT mice cohoused with microbiota-competent p66Shc-/- mice became significantly more insulin resistant than WT mice cohoused with WT mice, despite no difference in weight gain. These findings reconcile previous inconsistent observations on the metabolic phenotype of p66Shc-/- mice and illustrate the complex microbiome-host-genotype interplay under metabolic stress.-Ciciliot, S., Albiero, M., Campanaro, S., Poncina, N., Tedesco, S., Scattolini, V., Dalla Costa, F., Cignarella, A., Vettore, M., Di Gangi, I. M., Bogialli, S., Avogaro, A., Fadini, G. P. Interplay between gut microbiota and p66Shc affects obesity-associated insulin resistance.
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Affiliation(s)
| | | | | | - Nicol Poncina
- Venetian Institute of Molecular Medicine, Padua, Italy
| | | | - Valentina Scattolini
- Venetian Institute of Molecular Medicine, Padua, Italy.,Department of Medicine, University of Padova, Padua, Italy; and
| | | | | | - Monica Vettore
- Department of Medicine, University of Padova, Padua, Italy; and
| | | | - Sara Bogialli
- Department of Chemistry, University of Padova, Padua, Italy
| | - Angelo Avogaro
- Department of Medicine, University of Padova, Padua, Italy; and
| | - Gian Paolo Fadini
- Venetian Institute of Molecular Medicine, Padua, Italy.,Department of Medicine, University of Padova, Padua, Italy; and
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Gu Q, Veselkov K. Bi-clustering of metabolic data using matrix factorization tools. Methods 2018; 151:12-20. [PMID: 29438828 PMCID: PMC6297113 DOI: 10.1016/j.ymeth.2018.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/04/2018] [Accepted: 02/06/2018] [Indexed: 01/08/2023] Open
Abstract
We propose a positive matrix factorization bi-clustering strategy for metabolic data. The approach automatically determines the number and composition of bi-clusters. We demonstrate its superior performance compared to other techniques.
Metabolic phenotyping technologies based on Nuclear Magnetic Spectroscopy (NMR) and Mass Spectrometry (MS) generate vast amounts of unrefined data from biological samples. Clustering strategies are frequently employed to provide insight into patterns of relationships between samples and metabolites. Here, we propose the use of a non-negative matrix factorization driven bi-clustering strategy for metabolic phenotyping data in order to discover subsets of interrelated metabolites that exhibit similar behaviour across subsets of samples. The proposed strategy incorporates bi-cross validation and statistical segmentation techniques to automatically determine the number and structure of bi-clusters. This alternative approach is in contrast to the widely used conventional clustering approaches that incorporate all molecular peaks for clustering in metabolic studies and require a priori specification of the number of clusters. We perform the comparative analysis of the proposed strategy with other bi-clustering approaches, which were developed in the context of genomics and transcriptomics research. We demonstrate the superior performance of the proposed bi-clustering strategy on both simulated (NMR) and real (MS) bacterial metabolic data.
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Affiliation(s)
- Quan Gu
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK
| | - Kirill Veselkov
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK.
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74
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Madsen L, Myrmel LS, Fjære E, Liaset B, Kristiansen K. Links between Dietary Protein Sources, the Gut Microbiota, and Obesity. Front Physiol 2017; 8:1047. [PMID: 29311977 PMCID: PMC5742165 DOI: 10.3389/fphys.2017.01047] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/30/2017] [Indexed: 12/22/2022] Open
Abstract
The association between the gut microbiota and obesity is well documented in both humans and in animal models. It is also demonstrated that dietary factors can change the gut microbiota composition and obesity development. However, knowledge of how diet, metabolism and gut microbiota mutually interact and modulate energy metabolism and obesity development is still limited. Epidemiological studies indicate an association between intake of certain dietary protein sources and obesity. Animal studies confirm that different protein sources vary in their ability to either prevent or induce obesity. Different sources of protein such as beans, vegetables, dairy, seafood, and meat differ in amino acid composition. Further, the type and level of other factors, such as fatty acids and persistent organic pollutants (POPs) vary between dietary protein sources. All these factors can modulate the composition of the gut microbiota and may thereby influence their obesogenic properties. This review summarizes evidence of how different protein sources affect energy efficiency, obesity development, and the gut microbiota, linking protein-dependent changes in the gut microbiota with obesity.
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Affiliation(s)
- Lise Madsen
- National Institute of Nutrition and Seafood Research, Bergen, Norway.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,BGI-Shenzhen, Shenzhen, China
| | - Lene S Myrmel
- National Institute of Nutrition and Seafood Research, Bergen, Norway
| | - Even Fjære
- National Institute of Nutrition and Seafood Research, Bergen, Norway
| | - Bjørn Liaset
- National Institute of Nutrition and Seafood Research, Bergen, Norway
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,BGI-Shenzhen, Shenzhen, China
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Fabbiano S, Suárez-Zamorano N, Trajkovski M. Host-Microbiota Mutualism in Metabolic Diseases. Front Endocrinol (Lausanne) 2017; 8:267. [PMID: 29056925 PMCID: PMC5635267 DOI: 10.3389/fendo.2017.00267] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/21/2017] [Indexed: 12/23/2022] Open
Abstract
The intestinal microbiota is a plastic ecosystem that is shaped by environmental and genetic factors, interacting with virtually all tissues of the host. Many signals result from the interplay between the microbiota with its mammalian symbiont that can lead to altered metabolism. Disruptions in the microbial composition are associated with a number of comorbidities linked to the metabolic syndrome. Promoting the niche expansion of beneficial bacteria through diet and supplements can improve metabolic disorders. Reintroducing bacteria through probiotic treatment or fecal transplant is a strategy under active investigation for multiple pathological conditions. Here, we review the recent knowledge of microbiota's contribution to host pathology, the modulation of the microbiota by dietary habits, and the potential therapeutic benefits of reshaping the gut bacterial landscape in context of metabolic disorders such as obesity.
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Affiliation(s)
- Salvatore Fabbiano
- Faculty of Medicine, Department of Cell Physiology and Metabolism, University of Geneva, Centre Médical Universitaire (CMU), Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Diabetes Center, Geneva, Switzerland
| | - Nicolas Suárez-Zamorano
- Faculty of Medicine, Department of Cell Physiology and Metabolism, University of Geneva, Centre Médical Universitaire (CMU), Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Diabetes Center, Geneva, Switzerland
| | - Mirko Trajkovski
- Faculty of Medicine, Department of Cell Physiology and Metabolism, University of Geneva, Centre Médical Universitaire (CMU), Geneva, Switzerland
- Faculty of Medicine, University of Geneva, Diabetes Center, Geneva, Switzerland
- Institute for Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
- *Correspondence: Mirko Trajkovski,
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