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Shi Z, Yang X, Shi X, Zhang D, Zhao D, Hao Y, Yang J, Bie X, Yan W, Chen G, Chen L, Liu X, Zheng H, Zhang K. Identification and verification of the role of key metabolites and metabolic pathways on ASFV replication. iScience 2024; 27:109345. [PMID: 38500823 PMCID: PMC10946325 DOI: 10.1016/j.isci.2024.109345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/06/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
African swine fever virus (ASFV) infection usually causes viremia within a few days. However, the metabolic changes in pig serum after ASFV infection remain unclear. In this study, serum samples collected from ASFV-infected pigs at different times were analyzed using pseudotargeted metabolomics method. Metabolomic analysis revealed the dopaminergic synapse pathway has the highest rich factor in both ASFV5 and ASFV10 groups. By disrupting the dopamine synaptic pathway, dopamine receptor antagonists inhibited ASFV replication and L-dopa promoted ASFV replication. In addition, guanosine, one of the top20 changed metabolites in both ASFV5 and ASFV10 groups suppressed the replication of ASFV. Taken together, this study revealed the changed serum metabolite profiles of ASFV-infected pigs at various times after infection and verified the effect of the changed metabolites and metabolic pathways on ASFV replication. These findings may contribute to understanding the pathogenic mechanisms of ASFV and the development of target drugs to control ASF.
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Affiliation(s)
- Zunji Shi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Xing Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Xijuan Shi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Dajun Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Dengshuai Zhao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Yu Hao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Jinke Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Xintian Bie
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Wenqian Yan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Guohui Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Lingling Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Xiangtao Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
| | - Keshan Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
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2
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Mattos-Graner RO, Klein MI, Alves LA. The complement system as a key modulator of the oral microbiome in health and disease. Crit Rev Microbiol 2024; 50:138-167. [PMID: 36622855 DOI: 10.1080/1040841x.2022.2163614] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/10/2023]
Abstract
In this review, we address the interplay between the complement system and host microbiomes in health and disease, focussing on oral bacteria known to contribute to homeostasis or to promote dysbiosis associated with dental caries and periodontal diseases. Host proteins modulating complement activities in the oral environment and expression profiles of complement proteins in oral tissues were described. In addition, we highlight a sub-set of bacterial proteins involved in complement evasion and/or dysregulation previously characterized in pathogenic species (or strains), but further conserved among prototypical commensal species of the oral microbiome. Potential roles of these proteins in host-microbiome homeostasis and in the emergence of commensal strain lineages with increased virulence were also addressed. Finally, we provide examples of how commensal bacteria might exploit the complement system in competitive or cooperative interactions within the complex microbial communities of oral biofilms. These issues highlight the need for studies investigating the effects of the complement system on bacterial behaviour and competitiveness during their complex interactions within oral and extra-oral host sites.
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Affiliation(s)
- Renata O Mattos-Graner
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Sao Paulo, Brazil
| | - Marlise I Klein
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Sao Paulo, Brazil
| | - Lívia Araújo Alves
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP), Sao Paulo, Brazil
- School of Dentistry, Cruzeiro do Sul University (UNICSUL), Sao Paulo, Brazil
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3
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Yan H, Xu G, Bei L, Jiang S, Zhang R. Duck hepatitis A virus type 1 infection induces hepatic metabolite and gut microbiota changes in ducklings. Poult Sci 2024; 103:103265. [PMID: 38042039 PMCID: PMC10711513 DOI: 10.1016/j.psj.2023.103265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/24/2023] [Accepted: 11/02/2023] [Indexed: 12/04/2023] Open
Abstract
Duck hepatitis A virus type 1 (DHAV-1) can cause severe liver damage in infected ducklings and is a fatal and contagious pathogen that endangers the Chinese duck industry. The objective of this study was to explore the correlation mechanism of liver metabolism-gut microbiota in DHAV-1 infection. Briefly, liquid chromatography-mass spectrometry and 16S rDNA sequencing combined with multivariate statistical analysis were used to evaluate the effects of DHAV-1 infection on liver metabolism, gut microbiota regulation, and other potential mechanisms in ducklings. In DHAV-1-infected ducklings at 72 h postinfection, changes were found in metabolites associated with key metabolic pathways such as lipid metabolism, sugar metabolism, and nucleotide metabolism, which participated in signaling networks and ultimately affecting the function of the liver. The abundance and composition of gut microbiota were also changed, and gut microbiota is significantly involved in lipid metabolism in the liver. The evident correlation between gut microbiota and liver metabolites indicates that DHAV-host gut microbiome interactions play important roles in the development of duck viral hepatitis (DVH).
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Affiliation(s)
- Hui Yan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Guige Xu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Lei Bei
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Shijin Jiang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Ruihua Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China.
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4
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Zhao N, Zhao M, Jin H. Microplastic-induced gut microbiota and serum metabolic disruption in Sprague-Dawley rats. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 320:121071. [PMID: 36646405 DOI: 10.1016/j.envpol.2023.121071] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/13/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Toxic effects of exposure to microplastics (MPs) on living organisms and humans have attracted global concern. However, most previous studies exposed animals to only one type of MP (mainly polystyrene) to assess the health risk of MPs for animals. Therefore, we conducted a laboratory gavage experiment on rats based on the types and concentration of MPs to which humans are exposed in their daily life. The purpose of this study is to use Sprague-Dawley (SD) rat models to assess the potential health risks in mammals from co-exposure to various MPs. In the present study, SD rats were exposed to 12 mg/kg bw/day mixed-MPs (containing 10 types of MPs) for 42 days, and then examined the alteration of gut microbes and serum metabolites. The results showed that 6 gut microbes at the family level (f_Muribaculaceae, f_Oscillospiraceae, f_Bacteroidaceae, f_Neisseriaceae, f_Prevotellaceae, and f_Veillonellaceae) were significantly perturbed (t-test, p < 0.05) in rats after MP exposure. After MP intervention, 47 metabolites significantly regulated in SD rat serum, mainly including lipids and lipid-like molecules (e.g., fatty acids), organic acids and derivatives (e.g., phosphoric acids), and isoflavonoids (e.g., daidzein). These findings contribute to assessing the health risks of various MP co-exposure in mammals in the actual environment and provide a novel insight into the toxicity mechanism of MPs.
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Affiliation(s)
- Nan Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Meirong Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Hangbiao Jin
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, PR China.
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Dooling SW, Sgritta M, Wang IC, Duque ALRF, Costa-Mattioli M. The Effect of Limosilactobacillus reuteri on Social Behavior Is Independent of the Adaptive Immune System. mSystems 2022; 7:e0035822. [PMID: 36286493 PMCID: PMC9765170 DOI: 10.1128/msystems.00358-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/22/2022] [Indexed: 12/25/2022] Open
Abstract
Gut microbes can modulate almost all aspects of host physiology throughout life. As a result, specific microbial interventions are attracting considerable attention as potential therapeutic strategies for treating a variety of conditions. Nonetheless, little is known about the mechanisms through which many of these microbes work. Recently, we and others have found that the commensal bacterium Limosilactobacillus reuteri (formerly Lactobacillus reuteri) reverses social deficits in several mouse models (genetic, environmental, and idiopathic) for neurodevelopmental disorders in a vagus nerve-, oxytocin-, and biopterin-dependent manner. Given that gut microbes can signal to the brain through the immune system and L. reuteri promotes wound healing via the adaptive immune response, we sought to determine whether the prosocial effect mediated by L. reuteri also depends on adaptive immunity. Here, we found that the effects of L. reuteri on social behavior and related changes in synaptic function are independent of the mature adaptive immune system. Interestingly, these findings indicate that the same microbe (L. reuteri) can affect different host phenotypes through distinct mechanisms. IMPORTANCE Because preclinical animal studies support the idea that gut microbes could represent novel therapeutics for brain disorders, it is essential to fully understand the mechanisms by which gut microbes affect their host's physiology. Previously, we discovered that treatment with Limosilactobacillus reuteri selectively improves social behavior in different mouse models for autism spectrum disorder through the vagus nerve, oxytocin reward signaling in the brain, and biopterin metabolites (BH4) in the gut. However, given that (i) the immune system remains a key pathway for host-microbe interactions and that (ii) L. reuteri has been shown to facilitate wound healing through the adaptive immune system, we examined here whether the prosocial effects of L. reuteri require immune signaling. Unexpectedly, we found that the mature adaptive immune system (i.e., conventional B and T cells) is not required for L. reuteri to reverse social deficits and related changes in synaptic function. Overall, these findings add new insight into the mechanism through which L. reuteri modulates brain function and behavior. More importantly, they highlight that a given bacterial species can modulate different phenotypes (e.g., wound healing versus social behavior) through separate mechanisms.
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Affiliation(s)
- Sean W. Dooling
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Martina Sgritta
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, Texas, USA
| | - I-Ching Wang
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ana Luiza Rocha Faria Duque
- Department of Food and Nutrition, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Mauro Costa-Mattioli
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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6
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Bai J, Xiong T, Wang X, Cheng Y, Luo R, Yang X, Fu C. Potential mechanisms of Lian-Zhi-Fan solution for TNBS-induced ulcerative colitis in rats via a metabolomics approach. Front Pharmacol 2022; 13:1014117. [DOI: 10.3389/fphar.2022.1014117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Lian-Zhi-Fan (LZF) decoction is a hospital-prescribed traditional Chinese medicine botanical drug prepared by the fermentation of decocted Coptidis Rhizome (Huanglian), Gardeniae Fructus (Zhizi), and alum (Baifan). It has been used clinically in China for the treatment of anal fistula, perianal abscess, ulcerative colitis (UC), and other anorectal diseases for hundreds of years. However, due to the complexity of traditional Chinese medicine, the potential mechanisms of LZF in the treatment of UC have remained unknown. This study primarily investigated the remarkable pharmacological effects of LZF on TNBS-induced UC rats. To explore the complex targets and regulatory mechanisms of metabolic networks under LZF intervention, a metabolomics approach mediated by HPLC/Q-TOF-MS analysis was used to screen the different metabolites and their metabolic pathways in the serum in order to characterize the possible anti-UC mechanisms of LZF. After rectal administration of LZF for seven consecutive days, significant amelioration effects on body weight loss, DAI score, and colon inflammation were found in UC rats. Based on this, further metabolomics identified 14 potential biomarkers in the treatment of UC with LZF, of which five possessed diagnostic significance: L-alanine, taurocholic acid, niacinamide, cholic acid, and L-valine. These metabolites are mainly involved in 12 metabolic pathways, including nicotate and nicotinamide metabolism, glycospholipid metabolism, arginine and proline metabolism, primary bile acid biosynthesis, and pantothenate and CoA biosynthesis. These metabolic pathways suggest that LZF ameliorates UC by regulating amino acid metabolism, fat metabolism, and energy production. This study provides a useful approach for exploring the potential mechanisms of herbal prescription in UC treatment mediated by metabolomics.
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7
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Tu P, Chi L, Bian X, Gao B, Ru H, Lu K. A Black Raspberry-Rich Diet Protects From Dextran Sulfate Sodium-Induced Intestinal Inflammation and Host Metabolic Perturbation in Association With Increased Aryl Hydrocarbon Receptor Ligands in the Gut Microbiota of Mice. Front Nutr 2022; 9:842298. [PMID: 35734371 PMCID: PMC9208328 DOI: 10.3389/fnut.2022.842298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Dietary modulation of the gut microbiota recently received considerable attention, and ligand activation of aryl hydrocarbon receptor (AHR) plays a pivotal role in intestinal immunity. Importantly, black raspberry (BRB, Rubus occidentalis) is associated with a variety of beneficial health effects. We aim to investigate effects of a BRB-rich diet on dextran sulfate sodium (DSS)-induced intestinal inflammation and to determine whether its consequent anti-inflammatory effects are relevant to modulation of the gut microbiota, especially its production of AHR ligands. A mouse model of DSS-induced intestinal inflammation was used in the present study. C57BL/6J mice were fed either AIN-76A or BRB diet. Composition and functions of the gut microbiota were assessed by 16S rRNA sequencing and comparative metagenome analysis. Metabolic profiles of host and the gut microbiome were assessed by serum and fecal metabolomic profiling and identification. BRB diet was found to ameliorate DSS-induced intestinal inflammation and host metabolic perturbation. BRB diet also protected from DSS-induced perturbation in diversity and composition in the gut microbiota. BRB diet promoted AHR ligand production by the gut microbiota, as revealed by increased levels of fecal AHR activity in addition to increased levels of two known AHR ligands, hemin and biliverdin. Accordingly, enrichment of bacterial genes and pathways responsible for production of hemin and biliverdin were found, specific gut bacteria that are highly correlated with abundances of hemin and biliverdin were also identified. BRB dietary intervention ameliorated intestinal inflammation in mice in association with promotion of AHR ligand production by the gut microbiota.
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Affiliation(s)
- Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Xiaoming Bian
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, United States
| | - Bei Gao
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, United States
| | - Hongyu Ru
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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8
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Ma H, Niu Y. Metabolomic Profiling Reveals New Insight of Fowl Adenovirus Serotype 4 Infection. Front Microbiol 2022; 12:784745. [PMID: 35111140 PMCID: PMC8801735 DOI: 10.3389/fmicb.2021.784745] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022] Open
Abstract
Highly pathogenic fowl adenovirus serotype 4 (FAdV-4) is the causative agent of hydropericardium syndrome (HPS), which is characterized by pericardial effusion and hepatitis, and is one of the foremost causes of economic losses to the poultry industry over the last 30 years. However, the metabolic changes in cells in response to FAdV-4 infection remain unclear. In order to understand the metabolic interactions between the host cell and virus, we utilized ultra-high-performance liquid chromatography/quadrupole time-of-flight tandem mass spectrometry to analyze the metabolic profiles with hepatocellular carcinoma cell line (LMH) infected with FAdV-4. The results showed that FAdV-4 could restore metabolic networks in LMH cells and tricarboxylic acid cycle, glycolysis, and metabolism of purines, pyrimidines, alanine, aspartate, glutamate, and amino sugar and nucleotide sugar moieties. Moreover, FAdV-4 production was significantly reduced in LMH cells cultured in glucose or glutamine-deficient medium. These observations highlighted the importance of host cell metabolism in virus replication. Therefore, similarities and disparities in FAdV-4-regulation of the metabolism of host cells could help improve targeted drug and reduce infection.
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González-Loyola A, Bovay E, Kim J, Lozano TW, Sabine A, Renevey F, Arroz-Madeira S, Rapin A, Wypych TP, Rota G, Durot S, Velin D, Marsland B, Guarda G, Delorenzi M, Zamboni N, Luther SA, Petrova TV. FOXC2 controls adult lymphatic endothelial specialization, function, and gut lymphatic barrier preventing multiorgan failure. SCIENCE ADVANCES 2021; 7:7/29/eabf4335. [PMID: 34272244 PMCID: PMC8284898 DOI: 10.1126/sciadv.abf4335] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 06/01/2021] [Indexed: 05/02/2023]
Abstract
The mechanisms maintaining adult lymphatic vascular specialization throughout life and their role in coordinating inter-organ communication to sustain homeostasis remain elusive. We report that inactivation of the mechanosensitive transcription factor Foxc2 in adult lymphatic endothelium leads to a stepwise intestine-to-lung systemic failure. Foxc2 loss compromised the gut epithelial barrier, promoted dysbiosis and bacterial translocation to peripheral lymph nodes, and increased circulating levels of purine metabolites and angiopoietin-2. Commensal microbiota depletion dampened systemic pro-inflammatory cytokine levels, corrected intestinal lymphatic dysfunction, and improved survival. Foxc2 loss skewed the specialization of lymphatic endothelial subsets, leading to populations with mixed, pro-fibrotic identities and to emergence of lymph node-like endothelial cells. Our study uncovers a cross-talk between lymphatic vascular function and commensal microbiota, provides single-cell atlas of lymphatic endothelial subtypes, and reveals organ-specific and systemic effects of dysfunctional lymphatics. These effects potentially contribute to the pathogenesis of diseases, such as inflammatory bowel disease, cancer, or lymphedema.
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Affiliation(s)
- Alejandra González-Loyola
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Epalinges 1066, Switzerland
| | - Esther Bovay
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Epalinges 1066, Switzerland
| | - Jaeryung Kim
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Epalinges 1066, Switzerland
| | - Tania Wyss Lozano
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Epalinges 1066, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Amélie Sabine
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Epalinges 1066, Switzerland
| | - Francois Renevey
- Department of Biochemistry, University of Lausanne, Epalinges 1066, Switzerland
| | - Silvia Arroz-Madeira
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Epalinges 1066, Switzerland
| | - Alexis Rapin
- École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Tomasz P Wypych
- Department of Immunology and Pathology, Monash University, Melbourne 3800, Australia
| | - Giorgia Rota
- Department of Biochemistry, University of Lausanne, Epalinges 1066, Switzerland
| | - Stephan Durot
- Institute of Molecular Systems Biology ETH, Zurich 8093, Switzerland
| | - Dominique Velin
- Service of Gastroenterology and Hepatology, Department of Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne 1011, Switzerland
| | - Benjamin Marsland
- Department of Immunology and Pathology, Monash University, Melbourne 3800, Australia
| | - Greta Guarda
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Mauro Delorenzi
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Epalinges 1066, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology ETH, Zurich 8093, Switzerland
| | - Sanjiv A Luther
- Department of Biochemistry, University of Lausanne, Epalinges 1066, Switzerland
| | - Tatiana V Petrova
- Department of Oncology, University of Lausanne and Ludwig Institute for Cancer Research Lausanne, Epalinges 1066, Switzerland.
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10
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Mao L, Fang S, Zhao M, Liu W, Jin H. Effects of Bisphenol A and Bisphenol S Exposure at Low Doses on the Metabolome of Adolescent Male Sprague-Dawley Rats. Chem Res Toxicol 2021; 34:1578-1587. [PMID: 34019419 DOI: 10.1021/acs.chemrestox.1c00018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Toxic effects induced upon exposure to low-dose bisphenol A (BPA) or bisphenol S (BPS) remains controversial. In this study, metabolomics was used to examine the metabolomic perturbation arising from 28 days of exposure to BPA or BPS at 50 μg/kg bw/day in Sprague-Dawley (SD) rats. Endogenous metabolite profiling revealed a clear discrimination of metabolome in the rat plasma among BPA-treatment, BPS-treatment, and control groups. BPA exposure induced the up-regulation of 19 metabolites and down-regulation of 32 metabolites in plasma of SD rats, compared with the control. BPS exposure induced the up-regulation of 15 metabolites and the down-regulation of 33 metabolites in the plasma of SD rats, compared with the control. Joint pathway analysis suggested marked perturbations in the citrate cycle, butanoate metabolism, and alanine, aspartate, and glutamate metabolism for BPA-exposed rats as well as glycerophospholipid metabolism for BPS-exposed rats. These findings provide novel insights into associations between the metabolomic perturbation and phenotypic changes arising from BPA and BPS exposure.
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Affiliation(s)
- Lingling Mao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Shuhong Fang
- College of Resources and Environment, Chengdu University of Information Technology, Chengdu 610225, P. R. China
| | - Meirong Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Weiping Liu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, Institution of Environmental Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Hangbiao Jin
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
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Ma Y, Zhang Y, Xiang J, Xiang S, Zhao Y, Xiao M, Du F, Ji H, Kaboli PJ, Wu X, Li M, Wen Q, Shen J, Yang Z, Li J, Xiao Z. Metagenome Analysis of Intestinal Bacteria in Healthy People, Patients With Inflammatory Bowel Disease and Colorectal Cancer. Front Cell Infect Microbiol 2021; 11:599734. [PMID: 33738265 PMCID: PMC7962608 DOI: 10.3389/fcimb.2021.599734] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/15/2021] [Indexed: 12/24/2022] Open
Abstract
Objectives Several reports suggesting that the intestinal microbiome plays a key role in the development of inflammatory bowel disease (IBD) or colorectal cancer (CRC), but the changes of intestinal bacteria in healthy people, patients with IBD and CRC are not fully explained. The study aimed to investigate changes of intestinal bacteria in healthy subjects, patients with IBD, and patients with CRC. Materials We collected data from the European Nucleotide Archive on healthy people and patients with colorectal cancer with the study accession number PRJEB6070, PRJEB7774, PRJEB27928, PRJEB12449, and PRJEB10878, collected IBD patient data from the Integrated Human Microbiome Project from the Human Microbiome Project Data Portal. We performed metagenome-wide association studies on the fecal samples from 290 healthy subjects, 512 IBD patients, and 285 CRC patients. We used the metagenomics dataset to study bacterial community structure, relative abundance, functional prediction, differentially abundant bacteria, and co-occurrence networks. Results The bacterial community structure in both IBD and CRC was significantly different from healthy subjects. Our results showed that IBD patients had low intestinal bacterial diversity and CRC patients had high intestinal bacterial diversity compared to healthy subjects. At the phylum level, the relative abundance of Firmicutes in IBD decreased significantly, while the relative abundance of Bacteroidetes increased significantly. At the genus level, the relative abundance of Bacteroides in IBD was higher than in healthy people and CRC. Compared with healthy people and CRC, the main difference of intestinal bacteria in IBD patients was Bacteroidetes, and compared with healthy people and IBD, the main difference of intestinal bacteria in CRC patients was in Fusobacteria, Verrucomicrobia, and Proteobacteria. The main differences in the functional composition of intestinal bacteria in healthy people, IBD and CRC patients were L-homoserine and L-methionine biosynthesis, 5-aminoimidazole ribonucleotide biosynthesis II, L-methionine biosynthesis I, and superpathway of L-lysine, L-threonine, and L-methionine biosynthesis I. The results of stratified showed that the abundance of Firmicutes, Bacteroidetes, and Actinobacteria involved in metabolic pathways has significantly changed. Besides, the association network of intestinal bacteria in healthy people, IBD, and CRC patients has also changed. Conclusions In conclusion, compared with healthy people, the taxonomic and functional composition of intestinal bacteria in IBD and CRC patients was significantly changed.
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Affiliation(s)
- Yongshun Ma
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yao Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Jianghou Xiang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| | - Shixin Xiang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Mintao Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Huijiao Ji
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Parham Jabbarzadeh Kaboli
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Qinglian Wen
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Zhongmin Yang
- Department of Oncology and Hematology, Hospital (T.C.M) Affiliated to Southwest Medical University, Luzhou, China
| | - Jing Li
- Department of Oncology and Hematology, Hospital (T.C.M) Affiliated to Southwest Medical University, Luzhou, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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12
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Bauset C, Gisbert-Ferrándiz L, Cosín-Roger J. Metabolomics as a Promising Resource Identifying Potential Biomarkers for Inflammatory Bowel Disease. J Clin Med 2021; 10:jcm10040622. [PMID: 33562024 PMCID: PMC7915257 DOI: 10.3390/jcm10040622] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a relapsing chronic disorder of the gastrointestinal tract characterized by disruption of epithelial barrier function and excessive immune response to gut microbiota. The lack of biomarkers providing early diagnosis or defining the status of the pathology difficulties an accurate assessment of the disease. Given the different metabolomic profiles observed in IBD patients, metabolomics may reveal prime candidates to be studied, which may help in understanding the pathology and identifying novel therapeutic targets. In this review, we summarize the most current advances describing the promising metabolites such as lipids or amino acids found through untargeted metabolomics from serum, faecal, urine and biopsy samples.
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Affiliation(s)
- Cristina Bauset
- Department of Pharmacology and CIBER, Faculty of Medicine, University of Valencia, 46010 Valencia, Spain; (C.B.); (L.G.-F.)
| | - Laura Gisbert-Ferrándiz
- Department of Pharmacology and CIBER, Faculty of Medicine, University of Valencia, 46010 Valencia, Spain; (C.B.); (L.G.-F.)
| | - Jesús Cosín-Roger
- Hospital Dr. Peset, Fundación para la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, FISABIO, 46017 Valencia, Spain
- Correspondence: ; Tel.: +34-963851234
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13
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Li Y, Yin W, Zhan Y, Jia Y, Cui D, Zhang W, Chang Y. Comparative metabolome analysis provides new insights into increased larval mortality under seawater acidification in the sea urchin Strongylocentrotus intermedius. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141206. [PMID: 32777501 DOI: 10.1016/j.scitotenv.2020.141206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
Mortality and metabolic responses of four-armed larvae of Strongylocentrotus intermedius under CO2-induced seawater acidification were investigated. Gametes of S. intermedius were fertilized and developed to the four-armed larval stage in either current natural seawater pH levels (as Control; pH = 7.99 ± 0.01) or laboratory-controlled acidified conditions (OA1: ΔpH = -0.3 units; OA2: ΔpH = -0.4 units; OA3: ΔpH = -0.5 units) according to the predictions of the Intergovernmental Panel on Climate Change (IPCC). The degrees of spicule exposure and asymmetry and mortality of four-armed larvae of S. intermedius were observed; each had a significant linearly increasing trend as the seawater pH level decreased. Comparative metabolome analysis identified a total of 87 significantly differentially expressed metabolites (SDMs, UP: 57, DOWN: 30) in OA-treated groups compared with the control group. Twenty-three SDMs, including carnitine, lysophosphatidylcholine (LPC) 18:3, lysophosphatidyl ethanolamine (LPE) 16:1, glutathione (GSH) and L-ascorbate, exhibited a linear increasing trend with decreasing seawater pH. Nine SDMs exhibited a linear decreasing trend as the seawater pH declined, including hypoxanthine, guanine and thymidine. Among all SDMs, we further mined 48 potential metabolite biomarkers responding to seawater acidification in four-armed larvae of S. intermedius. These potential metabolite biomarkers were mainly enriched in five pathways: glycerophospholipid metabolism, glutathione metabolism, purine metabolism, pyrimidine metabolism and the tricarboxylic acid cycle (TCA cycle). Our results will enrich our knowledge of the molecular mechanisms employed by sea urchins in response to CO2-induced seawater acidification.
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Affiliation(s)
- Yingying Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Wenlu Yin
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yaoyao Zhan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China.
| | - Yujie Jia
- College of Basic Medical Science, Dalian Medical University, Dalian, Liaoning 116044, PR China
| | - Dongyao Cui
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China.
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14
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Duan H, Yu L, Tian F, Zhai Q, Fan L, Chen W. Gut microbiota: A target for heavy metal toxicity and a probiotic protective strategy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140429. [PMID: 32629250 DOI: 10.1016/j.scitotenv.2020.140429] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/02/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
There is growing epidemiological evidence that heavy metals (HMs) may contribute to the progression of various metabolic diseases and that the etiology and progression of these diseases is partly due to HM-induced perturbations of the gut microbiota. Importantly, the gut microbiota are the first line of defense against the toxic effects of HMs, and there is a bidirectional relationship between the two. Thus, HM exposure alters the composition and metabolic profile of the gut microbiota at the functional level, and in turn, the gut microbiota alter the uptake and metabolism of HMs by acting as a physical barrier to HM absorption and by altering the pH, oxidative balance, and concentrations of detoxification enzymes or proteins involved in HM metabolism. Moreover, the gut microbiota can affect the integrity of the intestinal barrier, which may also in turn affect the absorption of HMs. Specifically, probiotic have been shown to reduce the absorption of HMs in the intestinal tract via the enhancement of intestinal HM sequestration, detoxification of HMs in the gut, changing the expression of metal transporter proteins, and maintaining the gut barrier function. This review is a summary of the bidirectional relationship between HMs and gut microbiota and of the probiotic-based protective strategies against HM-induced gut dysbiosis, with reference to strategies used in the food industry or for medically alleviating HM toxicity.
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Affiliation(s)
- Hui Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Liuping Fan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, China
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15
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Garand M, Kumar M, Huang SSY, Al Khodor S. A literature-based approach for curating gene signatures in multifaceted diseases. J Transl Med 2020; 18:279. [PMID: 32650786 PMCID: PMC7350750 DOI: 10.1186/s12967-020-02408-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/05/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND AND AIMS The task of identifying a representative and yet manageable target gene list for assessing the pathogenesis of complicated and multifaceted diseases is challenging. Using Inflammatory Bowel Disease (IBD) as an example, we conceived a bioinformatic approach to identify novel genes associated with the various disease subtypes, in combination with known clinical control genes. METHODS From the available literature, we used Acumenta Literature LabTM (LitLab), network analyses, and LitLab Gene Retriever to assemble a gene pool that has a high likelihood of representing immunity-related subtype-specific signatures of IBD. RESULTS We generated six relevant gene lists and 21 intersections that contain genes with unique literature associations to Crohn's Disease (n = 60), Ulcerative Colitis (n = 17), and unclassified (n = 45) subtypes of IBD. From this gene pool, we then filtered and constructed, using network analysis, a final list of 142 genes that are the most representative of the disease and its subtypes. CONCLUSIONS In this paper, we present the bioinformatic construction of a gene panel that putatively contains subtype signatures of IBD, a multifactorial disease. These gene signatures will be tested as biomarkers to classify patients with IBD, which has been a clinically challenging task. Such approach to diagnose and monitor complicated disease pathogenesis is a stepping-stone towards personalized care.
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Affiliation(s)
| | - Manoj Kumar
- Research Department, Sidra Medicine, Doha, Qatar
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16
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Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome. Proc Natl Acad Sci U S A 2020; 117:13839-13845. [PMID: 32471946 PMCID: PMC7306764 DOI: 10.1073/pnas.1922498117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Deep molecular phenotyping of individuals provides the opportunity for biological insight into host physiology. As the human microbiome is increasingly being recognized as an important determinant of host health, understanding the host–microbiome relationship in a multiomics context may pave the way forward for targeted interventions. In this study, we analyze gut microbial composition of 101 individuals over the course of a year, alongside clinical markers and serum metabolomics. We establish association between specific gut compositional states and host health biomarkers (e.g., of inflammation). Finally, we provide evidence for an apparent transition barrier between these compositional states. A deeper understanding of microbiome dynamics and the associated variation in host phenotypes furthers our ability to engineer effective interventions that optimize wellness. The Pioneer 100 Wellness Project involved quantitatively profiling 108 participants’ molecular physiology over time, including genomes, gut microbiomes, blood metabolomes, blood proteomes, clinical chemistries, and data from wearable devices. Here, we present a longitudinal analysis focused specifically around the Pioneer 100 gut microbiomes. We distinguished a subpopulation of individuals with reduced gut diversity, elevated relative abundance of the genus Prevotella, and reduced levels of the genus Bacteroides. We found that the relative abundances of Bacteroides and Prevotella were significantly correlated with certain serum metabolites, including omega-6 fatty acids. Primary dimensions in distance-based redundancy analysis of clinical chemistries explained 18.5% of the variance in bacterial community composition, and revealed a Bacteroides/Prevotella dichotomy aligned with inflammation and dietary markers. Finally, longitudinal analysis of gut microbiome dynamics within individuals showed that direct transitions between Bacteroides-dominated and Prevotella-dominated communities were rare, suggesting the presence of a barrier between these states. One implication is that interventions seeking to transition between Bacteroides- and Prevotella-dominated communities will need to identify permissible paths through ecological state-space that circumvent this apparent barrier.
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Translational Potential of Metabolomics on Animal Models of Inflammatory Bowel Disease-A Systematic Critical Review. Int J Mol Sci 2020; 21:ijms21113856. [PMID: 32485793 PMCID: PMC7312423 DOI: 10.3390/ijms21113856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 12/16/2022] Open
Abstract
In the development of inflammatory bowel disease (IBD), the gut microbiota has been established as a key factor. Recently, metabolomics has become important for understanding the functional relevance of gut microbial changes in disease. Animal models for IBD enable the study of factors involved in disease development. However, results from animal studies may not represent the human situation. The aim of this study was to investigate whether results from metabolomics studies on animal models for IBD were similar to those from studies on IBD patients. Medline and Embase were searched for relevant studies up to May 2017. The Covidence systematic review software was used for study screening, and quality assessment was conducted for all included studies. Data showed a convergence of ~17% for metabolites differentiated between IBD and controls in human and animal studies with amino acids being the most differentiated metabolite subclass. The acute dextran sodium sulfate model appeared as a good model for analysis of systemic metabolites in IBD, but analytical platform, age, and biological sample type did not show clear correlations with any significant metabolites. In conclusion, this systematic review highlights the variation in metabolomics results, and emphasizes the importance of expanding the applied detection methods to ensure greater coverage and convergence between the various different patient phenotypes and animal models of inflammatory bowel disease.
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18
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Tikka C, Manthari RK, Ommati MM, Niu R, Sun Z, Zhang J, Wang J. Immune disruption occurs through altered gut microbiome and NOD2 in arsenic induced mice: Correlation with colon cancer markers. CHEMOSPHERE 2020; 246:125791. [PMID: 31927375 DOI: 10.1016/j.chemosphere.2019.125791] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/27/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
The gut microbial compositions are easily affected by the environmental chemicals like arsenic (As) leading to dysbiosis. The dysbiosis of gut microbiome has associated with numerous diseases; among which cancer is one of the major diseases. The meticulous mechanism underlying As- altered gut microbiome, Nucleotide domine containing protein 2 (NOD2) and how altered gut microbiome disturbs the intestinal homeostasis to regulate colon cancer markers remains unclear. For this, one hundred twenty 8-week old age male mice were divided into two exposure periods (3 and 6 months), and each exposure group animals were further divided into four groups as control (received only distilled H2O), low (0.15 mg As2O3/L), medium (1.5 mg As2O3/L) and high (15 mg As2O3/L) dose (each group containing 15 mice) administrated for 3 and 6 months. The results showed that As exposure highly altered gut microbiome with a significant depletion in NOD2 in contrast to control groups. Moreover, the dendritic cells (CD11a, CD103, CX3CR1) and macrophages (F4/80) were significantly increased by As exposure. Interestingly, increased trend of inflammatory cytokines (TNF-α, IFN-γ, IL-17) and depleted anti-inflammatory cytokines (IL-10) was observed in As exposed mice. Furthermore, the colon cancer markers β-catenin has increased while APC was arrested by As both in 3 and 6 months treated animals. Many studies reported that As altered gut microbial compositions, in this study, our results suggested that altered gut microbiome indirectly regulates colon cancer marker through immune system destruction mediated by inflammatory cytokines.
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Affiliation(s)
- Chiranjeevi Tikka
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Ram Kumar Manthari
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Mohammad Mehdi Ommati
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China; Department of Life Science, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Ruiyan Niu
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Zilong Sun
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Jianhai Zhang
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China
| | - Jundong Wang
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
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Mazumdar C, Driggers EM, Turka LA. The Untapped Opportunity and Challenge of Immunometabolism: A New Paradigm for Drug Discovery. Cell Metab 2020; 31:26-34. [PMID: 31839485 DOI: 10.1016/j.cmet.2019.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 10/24/2019] [Accepted: 11/14/2019] [Indexed: 12/14/2022]
Abstract
Here, we explore the manipulation of immune cell metabolism as a strategy in target discovery and drug development for immune-mediated diseases. Comparing exploitation of metabolic pathways to kill tumor cells for cancer treatment with the reprogramming of immune cells to treat autoimmune diseases highlights differences that confer several advantages to the latter (including a more favorable therapeutic index and greater target stability). We discuss technological capabilities and gaps, including the challenge of relating in vitro observations to in vivo biology. Finally, we conclude by identifying future opportunities that will move the field forward and accelerate drug discovery.
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Integrating omics for a better understanding of Inflammatory Bowel Disease: a step towards personalized medicine. J Transl Med 2019; 17:419. [PMID: 31836022 PMCID: PMC6909475 DOI: 10.1186/s12967-019-02174-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/08/2019] [Indexed: 02/06/2023] Open
Abstract
Background Inflammatory Bowel Disease (IBD) is a multifactorial chronic disease. Understanding only one aspect of IBD pathogenesis does not reflect the complex nature of IBD nor will it improve its clinical management. Therefore, it is vital to dissect the interactions between the different players in IBD pathogenesis in order to understand the biology of the disease and enhance its clinical outcomes. Aims To provide an overview of the available omics data used to assess the potential mechanisms through which various players are contributing to IBD pathogenesis and propose a precision medicine model to fill the current knowledge gap in IBD. Results Several studies have reported microbial dysbiosis, immune and metabolic dysregulation in IBD patients, however, this data is not sufficient to create signatures that can differentiate between the disease subtypes or between disease relapse and remission. Conclusions We summarized the current knowledge in the application of omics in IBD patients, and we showed that the current knowledge gap in IBD hinders the improvements of clinical decision for treatment as well as the prediction of disease relapse. We propose one way to fill this gap by implementing integrative analysis of various omics datasets generated from one patient at a single time point.
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Lai Y, Xue J, Liu CW, Gao B, Chi L, Tu P, Lu K, Ru H. Serum Metabolomics Identifies Altered Bioenergetics, Signaling Cascades in Parallel with Exposome Markers in Crohn's Disease. Molecules 2019; 24:E449. [PMID: 30691236 PMCID: PMC6385106 DOI: 10.3390/molecules24030449] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/15/2019] [Accepted: 01/22/2019] [Indexed: 02/08/2023] Open
Abstract
: Inflammatory bowel disease (IBD) has stimulated much interest due to its surging incidences and health impacts in the U.S. and worldwide. However, the exact cause of IBD remains incompletely understood, and biomarker is lacking towards early diagnostics and effective therapy assessment. To tackle these, the emerging high-resolution mass spectrometry (HRMS)-based metabolomics shows promise. Here, we conducted a pilot untargeted LC/MS metabolomic profiling in Crohn's disease, for which serum samples of both active and inactive cases were collected, extracted, and profiled by a state-of-the-art compound identification workflow. Results show a distinct metabolic profile of Crohn's from control, with most metabolites downregulated. The identified compounds are structurally diverse, pointing to important pathway perturbations ranging from energy metabolism (e.g., β-oxidation of fatty acids) to signaling cascades of lipids (e.g., DHA) and amino acid (e.g., L-tryptophan). Importantly, an integral role of gut microbiota in the pathogenesis of Crohn's disease is highlighted. Xenobiotics and their biotransformants were widely detected, calling for massive exposomic profiling for future cohort studies as such. This study endorses the analytical capacity of untargeted metabolomics for biomarker development, cohort stratification, and mechanistic interpretation; the findings might be valuable for advancing biomarker research and etiologic inquiry in IBD.
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Affiliation(s)
- Yunjia Lai
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Jingchuan Xue
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Bei Gao
- NIH West Coast Metabolomics Center, University of California at Davis, Davis, CA 95616, USA.
| | - Liang Chi
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Kun Lu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, CB #7431, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Hongyu Ru
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27695, USA.
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Murgia A, Hinz C, Liggi S, Denes J, Hall Z, West J, Santoru ML, Piras C, Manis C, Usai P, Atzori L, Griffin JL, Caboni P. Italian cohort of patients affected by inflammatory bowel disease is characterised by variation in glycerophospholipid, free fatty acids and amino acid levels. Metabolomics 2018; 14:140. [PMID: 30830399 DOI: 10.1007/s11306-018-1439-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/05/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND Inflammatory bowel disease is a group of pathologies characterised by chronic inflammation of the intestine and an unclear aetiology. Its main manifestations are Crohn's disease and ulcerative colitis. Currently, biopsies are the most used diagnostic tests for these diseases and metabolomics could represent a less invasive approach to identify biomarkers of disease presence and progression. OBJECTIVES The lipid and the polar metabolite profile of plasma samples of patients affected by inflammatory bowel disease have been compared with healthy individuals with the aim to find their metabolomic differences. Also, a selected sub-set of samples was analysed following solid phase extraction to further characterise differences between pathological samples. METHODS A total of 200 plasma samples were analysed using drift tube ion mobility coupled with time of flight mass spectrometry and liquid chromatography for the lipid metabolite profile analysis, while liquid chromatography coupled with triple quadrupole mass spectrometry was used for the polar metabolite profile analysis. RESULTS Variations in the lipid profile between inflammatory bowel disease and healthy individuals were highlighted. Phosphatidylcholines, lyso-phosphatidylcholines and fatty acids were significantly changed among pathological samples suggesting changes in phospholipase A2 and arachidonic acid metabolic pathways. Variations in the levels of cholesteryl esters and glycerophospholipids were also found. Furthermore, a decrease in amino acids levels suggests mucosal damage in inflammatory bowel disease. CONCLUSIONS Given good statistical results and predictive power of the model produced in our study, metabolomics can be considered as a valid tool to investigate inflammatory bowel disease.
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Affiliation(s)
- Antonio Murgia
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Christine Hinz
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Sonia Liggi
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Jùlìa Denes
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Zoe Hall
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - James West
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | | | - Cristina Piras
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Cristina Manis
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Paolo Usai
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Luigi Atzori
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Pierluigi Caboni
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
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Zhou J, Tang L, Shen CL, Wang JS. Green tea polyphenols modify gut-microbiota dependent metabolisms of energy, bile constituents and micronutrients in female Sprague-Dawley rats. J Nutr Biochem 2018; 61:68-81. [PMID: 30189365 DOI: 10.1016/j.jnutbio.2018.07.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/09/2018] [Accepted: 07/25/2018] [Indexed: 12/26/2022]
Abstract
Our recent metagenomics analysis has uncovered remarkable modifying effects of green tea polyphenols (GTP) on gut-microbiota community structure and energy conversion related gene orthologs in rats. How these genomic changes could further influence host health is still unclear. In this work, the alterations of gut-microbiota dependent metabolites were studied in the GTP-treated rats. Six groups of female SD rats (n=12/group) were administered drinking water containing 0%, 0.5%, and 1.5% GTP (wt/vol). Their gut contents were collected at 3 and 6 months and were analyzed via high performance liquid chromatography (HPLC) and gas chromatography (GC)-mass spectrometry (MS). GC-MS based metabolomics analysis captured 2668 feature, and 57 metabolites were imputatively from top 200 differential features identified via NIST fragmentation database. A group of key metabolites were quantitated using standard calibration methods. Compared with control, the elevated components in the GTP-treated groups include niacin (8.61-fold), 3-phenyllactic acid (2.20-fold), galactose (3.13-fold), mannose (2.05-fold), pentadecanoic acid (2.15-fold), lactic acid (2.70-fold), and proline (2.15-fold); the reduced components include cholesterol (0.29-fold), cholic acid (0.62-fold), deoxycholic acid (0.41-fold), trehalose (0.14-fold), glucose (0.46-fold), fructose (0.12-fold), and alanine (0.61-fold). These results were in line with the genomic alterations of gut-microbiome previously discovered by metagenomics analysis. The alterations of these metabolites suggested the reduction of calorific carbohydrates, elevation of vitamin production, decreases of bile constituents, and modified metabolic pattern of amino acids in the GTP-treated animals. Changes in gut-microbiota associated metabolism may be a major contributor to the anti-obesity function of GTP.
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Affiliation(s)
- Jun Zhou
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia; Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602.
| | - Lili Tang
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia; Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602.
| | - Chwan-Li Shen
- Department of Pathology, Texas Technology University Health Sciences Center, Lubbock, TX 79430.
| | - Jia-Sheng Wang
- Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia; Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602.
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24
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Lyons J, Brubaker DK, Ghazi PC, Baldwin KR, Edwards A, Boukhali M, Strasser SD, Suarez-Lopez L, Lin YJ, Yajnik V, Kissil JL, Haas W, Lauffenburger DA, Haigis KM. Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis. Sci Signal 2018; 11:eaan3580. [PMID: 29487189 PMCID: PMC6719711 DOI: 10.1126/scisignal.aan3580] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic disorder of the gastrointestinal tract that has limited treatment options. To gain insight into the pathogenesis of chronic colonic inflammation (colitis), we performed a multiomics analysis that integrated RNA microarray, total protein mass spectrometry (MS), and phosphoprotein MS measurements from a mouse model of the disease. Because we collected all three types of data from individual samples, we tracked information flow from RNA to protein to phosphoprotein and identified signaling molecules that were coordinately or discordantly regulated and pathways that had complex regulation in vivo. For example, the genes encoding acute-phase proteins were expressed in the liver, but the proteins were detected by MS in the colon during inflammation. We also ascertained the types of data that best described particular facets of chronic inflammation. Using gene set enrichment analysis and trans-omics coexpression network analysis, we found that each data set provided a distinct viewpoint on the molecular pathogenesis of colitis. Combining human transcriptomic data with the mouse multiomics data implicated increased p21-activated kinase (Pak) signaling as a driver of colitis. Chemical inhibition of Pak1 and Pak2 with FRAX597 suppressed active colitis in mice. These studies provide translational insights into the mechanisms contributing to colitis and identify Pak as a potential therapeutic target in IBD.
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Affiliation(s)
- Jesse Lyons
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas K Brubaker
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phaedra C Ghazi
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Katherine R Baldwin
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Pediatric Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Amanda Edwards
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Myriam Boukhali
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha Dale Strasser
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lucia Suarez-Lopez
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yi-Jang Lin
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Vijay Yajnik
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Joseph L Kissil
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Wilhelm Haas
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin M Haigis
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA.
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Harvard Digestive Disease Center, Harvard Medical School, Boston, MA 02115, USA
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25
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Bian X, Chi L, Gao B, Tu P, Ru H, Lu K. Gut Microbiome Response to Sucralose and Its Potential Role in Inducing Liver Inflammation in Mice. Front Physiol 2017; 8:487. [PMID: 28790923 PMCID: PMC5522834 DOI: 10.3389/fphys.2017.00487] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/26/2017] [Indexed: 12/20/2022] Open
Abstract
Sucralose is the most widely used artificial sweetener, and its health effects have been highly debated over the years. In particular, previous studies have shown that sucralose consumption can alter the gut microbiota. The gut microbiome plays a key role in processes related to host health, such as food digestion and fermentation, immune cell development, and enteric nervous system regulation. Inflammation is one of the most common effects associated with gut microbiome dysbiosis, which has been linked to a series of human diseases, such as diabetes and obesity. The aim of this study was to investigate the structural and functional effects of sucralose on the gut microbiota and associated inflammation in the host. In this study, C57BL/6 male mice received sucralose in their drinking water for 6 months. The difference in gut microbiota composition and metabolites between control and sucralose-treated mice was determined using 16S rRNA gene sequencing, functional gene enrichment analysis and metabolomics. Inflammatory gene expression in tissues was analyzed by RT-PCR. Alterations in bacterial genera showed that sucralose affects the gut microbiota and its developmental dynamics. Enrichment of bacterial pro-inflammatory genes and disruption in fecal metabolites suggest that 6-month sucralose consumption at the human acceptable daily intake (ADI) may increase the risk of developing tissue inflammation by disrupting the gut microbiota, which is supported by elevated pro-inflammatory gene expression in the liver of sucralose-treated mice. Our results highlight the role of sucralose-gut microbiome interaction in regulating host health-related processes, particularly chronic inflammation.
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Affiliation(s)
- Xiaoming Bian
- Department of Environmental Health Science, University of GeorgiaAthens, GA, United States
| | - Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel HillChapel Hill, NC, United States
| | - Bei Gao
- Department of Environmental Health Science, University of GeorgiaAthens, GA, United States
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel HillChapel Hill, NC, United States
| | - Hongyu Ru
- Department of Population Health and Pathobiology, North Carolina State UniversityRaleigh, NC, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel HillChapel Hill, NC, United States
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26
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Bian X, Tu P, Chi L, Gao B, Ru H, Lu K. Saccharin induced liver inflammation in mice by altering the gut microbiota and its metabolic functions. Food Chem Toxicol 2017; 107:530-539. [PMID: 28472674 DOI: 10.1016/j.fct.2017.04.045] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 12/17/2022]
Abstract
Maintaining the balance of the gut microbiota and its metabolic functions is vital for human health, however, this balance can be disrupted by various external factors including food additives. A range of food and beverages are sweetened by saccharin, which is generally considered to be safe despite controversial debates. However, recent studies indicated that saccharin perturbed the gut microbiota. Inflammation is frequently associated with disruptions of the gut microbiota. The aim of this study is to investigate the relationship between host inflammation and perturbed gut microbiome by saccharin. C57BL/6J male mice were treated with saccharin in drinking water for six months. Q-PCR was used to detect inflammatory markers in mouse liver, while 16S rRNA gene sequencing and metabolomics were used to reveal changes of the gut microbiota and its metabolomic profiles. Elevated expression of pro-inflammatory iNOS and TNF-α in liver indicated that saccharin induced inflammation in mice. The altered gut bacterial genera, enriched orthologs of pathogen-associated molecular patterns, such as LPS and bacterial toxins, in concert with increased pro-inflammatory metabolites suggested that the saccharin-induced liver inflammation could be associated with the perturbation of the gut microbiota and its metabolic functions.
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Affiliation(s)
- Xiaoming Bian
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, United States
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, 27599, United States
| | - Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, 27599, United States
| | - Bei Gao
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, United States
| | - Hongyu Ru
- Department of Population Health and Pathobiology, North Carolina State Univeristy, Raleigh 27506, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, 27599, United States.
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27
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Gong W, Jia J, Zhang B, Mi S, Zhang L, Xie X, Guo H, Shi J, Tu C. Serum Metabolomic Profiling of Piglets Infected with Virulent Classical Swine Fever Virus. Front Microbiol 2017; 8:731. [PMID: 28496435 PMCID: PMC5406397 DOI: 10.3389/fmicb.2017.00731] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/07/2017] [Indexed: 12/14/2022] Open
Abstract
Classical swine fever (CSF) is a highly contagious swine infectious disease and causes significant economic losses for the pig industry worldwide. The objective of this study was to determine whether small molecule metabolites contribute to the pathogenesis of CSF. Birefly, serum metabolomics of CSFV Shimen strain-infected piglets were analyzed by ultraperformance liquid chromatography/electrospray ionization time-of-flight mass spectrometry (UPLC/ESI-Q-TOF/MS) in combination with multivariate statistical analysis. In CSFV-infected piglets at days 3 and 7 post-infection changes were found in metabolites associated with several key metabolic pathways, including tryptophan catabolism and the kynurenine pathway, phenylalanine metabolism, fatty acid and lipid metabolism, the tricarboxylic acid and urea cycles, branched-chain amino acid metabolism, and nucleotide metabolism. Several pathways involved in energy metabolism including fatty acid biosynthesis and β-oxidation, branched-chain amino acid metabolism, and the tricarboxylic acid cycle were significantly inhibited. Changes were also observed in several metabolites exclusively associated with gut microbiota. The metabolomic profiles indicate that CSFV-host gut microbiome interactions play a role in the development of CSF.
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Affiliation(s)
- Wenjie Gong
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China.,Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State UniversityManhattan, KS, USA
| | - Junjie Jia
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Bikai Zhang
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Shijiang Mi
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Li Zhang
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Xiaoming Xie
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Huancheng Guo
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China
| | - Jishu Shi
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State UniversityManhattan, KS, USA
| | - Changchun Tu
- Department of Virology, Institute of Military Veterinary, Academy of Military Medical SciencesChangchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou, China
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28
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Gao B, Bian X, Mahbub R, Lu K. Sex-Specific Effects of Organophosphate Diazinon on the Gut Microbiome and Its Metabolic Functions. ENVIRONMENTAL HEALTH PERSPECTIVES 2017; 125:198-206. [PMID: 27203275 PMCID: PMC5289904 DOI: 10.1289/ehp202] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/27/2015] [Accepted: 04/18/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND There is growing recognition of the significance of the gut microbiome to human health, and the association between a perturbed gut microbiome with human diseases has been established. Previous studies also show the role of environmental toxicants in perturbing the gut microbiome and its metabolic functions. The wide agricultural use of diazinon, an organophosphate insecticide, has raised serious environmental health concerns since it is a potent neurotoxicant. With studies demonstrating the presence of a microbiome-gut-brain axis, it is possible that gut microbiome perturbation may also contribute to diazinon toxicity. OBJECTIVES We investigated the impact of diazinon exposure on the gut microbiome composition and its metabolic functions in C57BL/6 mice. METHODS We used a combination of 16S rRNA gene sequencing, metagenomics sequencing, and mass spectrometry-based metabolomics profiling in a mouse model to examine the functional impact of diazinon on the gut microbiome. RESULTS 16S rRNA gene sequencing revealed that diazinon exposure significantly perturbed the gut microbiome, and metagenomic sequencing found that diazinon exposure altered the functional metagenome. Moreover, metabolomics profiling revealed an altered metabolic profile arising from exposure. Of particular significance, these changes were more pronounced for male mice than for female mice. CONCLUSIONS Diazinon exposure perturbed the gut microbiome community structure, functional metagenome, and associated metabolic profiles in a sex-specific manner. These findings may provide novel insights regarding perturbations of the gut microbiome and its functions as a potential new mechanism contributing to diazinon neurotoxicity and, in particular, its sex-selective effects. Citation: Gao B, Bian X, Mahbub R, Lu K. 2017. Sex-specific effects of organophosphate diazinon on the gut microbiome and its metabolic functions. Environ Health Perspect 125:198-206; http://dx.doi.org/10.1289/EHP202.
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Affiliation(s)
| | | | | | - Kun Lu
- Address correspondence to K. Lu, 140 Environmental Health Science Building, University of Georgia, Athens, GA 30602 USA. Telephone: (706) 542-1001. E-mail:
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Dunn AB, Dunlop AL, Hogue CJ, Miller A, Corwin EJ. The Microbiome and Complement Activation: A Mechanistic Model for Preterm Birth. Biol Res Nurs 2017; 19:295-307. [PMID: 28073296 DOI: 10.1177/1099800416687648] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Preterm birth (PTB, <37 completed weeks' gestation) is one of the leading obstetrical problems in the United States, affecting approximately one of every nine births. Even more concerning are the persistent racial disparities in PTB, with particularly high rates among African Americans. There are several recognized pathophysiologic pathways to PTB, including infection and/or exaggerated systemic or local inflammation. Intrauterine infection is a causal factor linked to PTB thought to result most commonly from inflammatory processes triggered by microbial invasion of bacteria ascending from the vaginal microbiome. Trials to treat various infections have shown limited efficacy in reducing PTB risk, suggesting that other complex mechanisms, including those associated with inflammation, may be involved in the relationship between microbes, infection, and PTB. The complement system, a key mediator of the inflammatory response, is an innate defense mechanism involved in both normal physiologic processes that occur during pregnancy implantation and processes that promote the elimination of pathogenic microbes. Recent research has demonstrated an association between this system and PTB. The purpose of this article is to present a mechanistic model of inflammation-associated PTB, which hypothesizes a relationship between the microbiome and dysregulation of the complement system. Exploring the relationships between the microbial environment and complement biomarkers may elucidate a potentially modifiable biological pathway to PTB.
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Affiliation(s)
- Alexis B Dunn
- 1 Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA
| | - Anne L Dunlop
- 1 Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA
| | - Carol J Hogue
- 2 Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Andrew Miller
- 3 School of Medicine, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Elizabeth J Corwin
- 1 Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA
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30
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Zhang F, Xu C, Ning L, Hu F, Shan G, Chen H, Yang M, Chen W, Yu J, Xu G. Exploration of Serum Proteomic Profiling and Diagnostic Model That Differentiate Crohn's Disease and Intestinal Tuberculosis. PLoS One 2016; 11:e0167109. [PMID: 27997555 PMCID: PMC5173341 DOI: 10.1371/journal.pone.0167109] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/07/2016] [Indexed: 01/30/2023] Open
Abstract
AIM To explore the diagnostic models of Crohn's disease (CD), Intestinal tuberculosis (ITB) and the differential diagnostic model between CD and ITB by analyzing serum proteome profiles. METHODS Serum proteome profiles from 30 CD patients, 21 ITB patients and 30 healthy controls (HCs) were analyzed by using weak cationic magnetic beads combined with MALDI-TOF-MS technique to detect the differentially expressed proteins of serum samples. Three groups were made and compared accordingly: group of CD patients and HCs, group of ITB patients and HCs, group of CD patients and ITB patients. Wilcoxon rank sum test was used to screen the ten most differentiated protein peaks (P < 0.05). Genetic algorithm combining with support vector machine (SVM) was utilized to establish the optimal diagnostic models for CD, ITB and the optimal differential diagnostic model between CD and ITB. The predictive effects of these models were evaluated by Leave one out (LOO) cross validation method. RESULTS There were 236 protein peaks differently expressed between group of CD patients and HCs, 305 protein peaks differently expressed between group of ITB patients and HCs, 332 protein peaks differently expressed between group of CD patients and ITB patients. Ten most differentially expressed peaks were screened out between three groups respectively (P < 0.05) to establish diagnostic models and differential diagnostic model. A diagnostic model comprising of four protein peaks (M/Z 4964, 3029, 2833, 2900) can well distinguish CD patients and HCs, with a specificity and sensitivity of 96.7% and 96.7% respectively. A diagnostic model comprising four protein peaks (M/Z 3030, 2105, 2545, 4210) can well distinguish ITB patients and HCs, with a specificity and sensitivity of 93.3% and 95.2% respectively. A differential diagnostic model comprising three potential biomarkers protein peaks (M/Z 4267, 4223, 1541) can well distinguish CD patients and ITB patients, with a specificity and sensitivity of 76.2% and 80.0% respectively. Among the eleven protein peaks from the diagnostic models and differential diagnostic model, two have been successfully purified and identified, Those two peaks were M/Z 2900 from the diagnostic model between CD and HCs and M/Z 1541 from the differential diagnostic model between CD and ITB. M/Z 2900 was identified as appetite peptide, M/Z 1541 was identified as Lysyl oxidase-like 2 (LOXL-2). CONCLUSION The differently expressed protein peaks analyzed by serum proteome with weak cationic magnetic beads combined MALDI-TOF-MS technique can effectively distinguish CD patients and HCs, ITB patients and HCs, CD patients and ITB patients. The diagnostic model between CD patients and HCs consisting of four protein peaks (M/Z 4964, 3029, 2833, 2900), the diagnostic model between ITB patients and HCs comprising four protein peaks (M/Z 3030, 2105, 2545, 4210) and the differential diagnostic model between CD patients and ITB patients comprising three protein peaks (M/Z 4267, 4223, 1541) had high specificity and sensitivity and can contribute to diagnoses of CD, ITB and the differential diagnosis between CD and ITB. Two proteins from the diagnostic model of CD and the differential diagnostic model between CD and ITB were identified. Further experiments are required using a larger cohort of samples.
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Affiliation(s)
- Fenming Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Chengfu Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Longgui Ning
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Fengling Hu
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Guodong Shan
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Hongtan Chen
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Ming Yang
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Wenguo Chen
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jiekai Yu
- Department of Tumor Research Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Guoqiang Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- * E-mail:
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Chi ZC. Helicobacter hepaticus and bowel disease progression. Shijie Huaren Xiaohua Zazhi 2016; 24:3018-3025. [DOI: 10.11569/wcjd.v24.i19.3018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
There are six main kinds of Helicobacter (H.) associated with human infection, namely, H. pylori, H. bizzozeronii, H. cinaedi, H. canis, H. canadensis, and H. feils. In recent years, there have been a number of research and clinical reports of H. hepaticus and H. Bilis. In this paper, we review the bacteriology of Helicobacter hepaticus and its association with the pathogenesis of enteropathy.
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Yin L, Yu KS, Lu K, Yu X. Benzyl butyl phthalate promotes adipogenesis in 3T3-L1 preadipocytes: A High Content Cellomics and metabolomic analysis. Toxicol In Vitro 2016; 32:297-309. [PMID: 26820058 DOI: 10.1016/j.tiv.2016.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/12/2016] [Accepted: 01/20/2016] [Indexed: 01/15/2023]
Abstract
Benzyl butyl phthalate (BBP) has been known to induce developmental and reproductive toxicity. However, its association with dysregulation of adipogenesis has been poorly investigated. The present study aimed to examine the effect of BBP on the adipogenesis, and to elucidate the underlying mechanisms using the 3T3-L1 cells. The capacity of BBP to promote adipogenesis was evaluated by multiple staining approaches combined with a High Content Cellomics analysis. The dynamic changes of adipogenic regulatory genes and proteins were examined, and the metabolite profile was identified using GC/MC based metabolomic analysis. The High Content analysis showed BBP in contrast with Bisphenol A (BPA), a known environmental obesogen, increased lipid droplet accumulation in a similar dose-dependent manner. However, the size of the lipid droplets in BBP-treated cells was significantly larger than those in cells treated with BPA. BBP significantly induced mRNA expression of transcriptional factors C/EBPα and PPARγ, their downstream genes, and numerous adipogenic proteins in a dose and time-dependent manner. Furthermore, GC/MC metabolomic analysis revealed that BBP exposure perturbed the metabolic profiles that are associated with glyceroneogenesis and fatty acid synthesis. Altogether, our current study clearly demonstrates that BBP promoted the differentiation of 3T3-L1 through the activation of the adipogenic pathway and metabolic disturbance.
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Affiliation(s)
- Lei Yin
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Kevin Shengyang Yu
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Kun Lu
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Xiaozhong Yu
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States.
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Li R, Li F, Feng Q, Liu Z, Jie Z, Wen B, Xu X, Zhong S, Li G, He K. An LC-MS based untargeted metabolomics study identified novel biomarkers for coronary heart disease. MOLECULAR BIOSYSTEMS 2016; 12:3425-3434. [PMID: 27713999 DOI: 10.1039/c6mb00339g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This work leads to candidate diagnosis biomarker discovery in coronary heart disease which can be developed as a non-invasive and feasible method for CHD diagnosis.
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Affiliation(s)
- Ruijun Li
- Department of Cardiology
- Chinese PLA General Hospital
- Beijing
- China
| | - Fengyu Li
- BGI Education Center
- University of Chinese Academy of Sciences
- Shenzhen
- China
- BGI-Shenzhen
| | - Qiang Feng
- BGI-Shenzhen
- Shenzhen
- China
- Department of Biology
- University of Copenhagen
| | | | | | - Bo Wen
- BGI-Shenzhen
- Shenzhen
- China
| | - Xun Xu
- BGI-Shenzhen
- Shenzhen
- China
| | - Shilong Zhong
- Medical Research Center of Guangdong General Hospital
- Guangzhou
- China
- Guangdong Cardiovascular Institute
- Guangdong Academy of Medical Sciences
| | | | - Kunlun He
- Department of Cardiology
- Chinese PLA General Hospital
- Beijing
- China
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Zhu WN, Long HY. Application of metabonomics in research of inflammatory bowel disease. Shijie Huaren Xiaohua Zazhi 2015; 23:2084-2090. [DOI: 10.11569/wcjd.v23.i13.2084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is a chronic non-specific inflammatory disorder of the gastrointestinal tract. The etiology and pathogenesis of IBD are still not entirely understood today and are thought to be caused by the interaction of multiple factors, including environmental, genetic, infectious and immune factors. The lack of typical clinical features also leads to a difficult diagnosis of IBD. In recent years, metabonomics is becoming a very important way to find biomarkers and investigate disease mechanisms. In this paper we review the main technologies of metabonomics and their present application in IBD.
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Afrin LB, Khoruts A. Mast Cell Activation Disease and Microbiotic Interactions. Clin Ther 2015; 37:941-53. [PMID: 25773459 DOI: 10.1016/j.clinthera.2015.02.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/03/2015] [Accepted: 02/03/2015] [Indexed: 02/07/2023]
Abstract
PURPOSE This article reviews the diagnostically challenging presentation of mast cell activation disease (MCAD) and current thoughts regarding interactions between microbiota and MCs. METHODS A search for all studies on interactions between mast cells, mast cell activation disease, and microbiota published on pubmed.gov and scholar.google.com between 1960 and 2015 was conducted using the search terms mast cell, mastocyte, mastocytosis, mast cell activation, mast cell activation disease, mast cell activation syndrome, microbiome, microbiota. A manual review of the references from identified studies was also conducted. Studies were excluded if they were not accessible electronically or by interlibrary loan. FINDINGS Research increasingly is revealing essential involvement of MCs in normal human biology and in human disease. Via many methods, normal MCs-present sparsely in every tissue-sense their environment and reactively exert influences that, directly and indirectly, locally and remotely, improve health. The dysfunctional MCs of the "iceberg" of MCAD, on the other hand, sense abnormally, react abnormally, activate constitutively, and sometimes (in mastocytosis, the "tip" of the MCAD iceberg) even proliferate neoplastically. MCAD causes chronic multisystem illness generally, but not necessarily, of an inflammatory ± allergic theme and with great variability in behavior among patients and within any patient over time. Furthermore, the range of signals to which MCs respond and react include signals from the body's microbiota, and regardless of whether an MCAD patient has clonal mastocytosis or the bulk of the iceberg now known as MC activation syndrome (also suspected to be clonal but without significant MC proliferation), dysfunctional MCs interact as dysfunctionally with those microbiota as they interact with other human tissues, potentially leading to many adverse consequences. IMPLICATIONS Interactions between microbiota and MCs are complex at baseline. The potential for both pathology and benefit may be amplified when compositionally variant microbiota interact with aberrant MCs in various types of MCAD. More research is needed to better understand and leverage these interactions.
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Affiliation(s)
- Lawrence B Afrin
- Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, Minnesota.
| | - Alexander Khoruts
- Division of Gastroenterology and Center for Immunology, BioTechnology Institute, University of Minnesota, Minneapolis, Minnesota
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Application of metabolomics in autoimmune diseases: Insight into biomarkers and pathology. J Neuroimmunol 2015; 279:25-32. [DOI: 10.1016/j.jneuroim.2015.01.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/09/2014] [Accepted: 01/05/2015] [Indexed: 12/31/2022]
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Gautam A, D’Arpa P, Donohue DE, Muhie S, Chakraborty N, Luke BT, Grapov D, Carroll EE, Meyerhoff JL, Hammamieh R, Jett M. Acute and chronic plasma metabolomic and liver transcriptomic stress effects in a mouse model with features of post-traumatic stress disorder. PLoS One 2015; 10:e0117092. [PMID: 25629821 PMCID: PMC4309402 DOI: 10.1371/journal.pone.0117092] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/18/2014] [Indexed: 12/18/2022] Open
Abstract
Acute responses to intense stressors can give rise to post-traumatic stress disorder (PTSD). PTSD diagnostic criteria include trauma exposure history and self-reported symptoms. Individuals who meet PTSD diagnostic criteria often meet criteria for additional psychiatric diagnoses. Biomarkers promise to contribute to reliable phenotypes of PTSD and comorbidities by linking biological system alterations to behavioral symptoms. Here we have analyzed unbiased plasma metabolomics and other stress effects in a mouse model with behavioral features of PTSD. In this model, C57BL/6 mice are repeatedly exposed to a trained aggressor mouse (albino SJL) using a modified, resident-intruder, social defeat paradigm. Our recent studies using this model found that aggressor-exposed mice exhibited acute stress effects including changed behaviors, body weight gain, increased body temperature, as well as inflammatory and fibrotic histopathologies and transcriptomic changes of heart tissue. Some of these acute stress effects persisted, reminiscent of PTSD. Here we report elevated proteins in plasma that function in inflammation and responses to oxidative stress and damaged tissue at 24 hrs post-stressor. Additionally at this acute time point, transcriptomic analysis indicated liver inflammation. The unbiased metabolomics analysis showed altered metabolites in plasma at 24 hrs that only partially normalized toward control levels after stress-withdrawal for 1.5 or 4 wks. In particular, gut-derived metabolites were altered at 24 hrs post-stressor and remained altered up to 4 wks after stress-withdrawal. Also at the 4 wk time point, hyperlipidemia and suppressed metabolites of amino acids and carbohydrates in plasma coincided with transcriptomic indicators of altered liver metabolism (activated xenobiotic and lipid metabolism). Collectively, these system-wide sequelae to repeated intense stress suggest that the simultaneous perturbed functioning of multiple organ systems (e.g., brain, heart, intestine and liver) can interact to produce injuries that lead to chronic metabolic changes and disorders that have been associated with PTSD.
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Affiliation(s)
- Aarti Gautam
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, Tacoma, WA 98402, United States of America
| | - Peter D’Arpa
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, Tacoma, WA 98402, United States of America
| | - Duncan E. Donohue
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, Tacoma, WA 98402, United States of America
| | - Seid Muhie
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Nabarun Chakraborty
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, Tacoma, WA 98402, United States of America
| | - Brian T. Luke
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Dmitry Grapov
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA, United States of America
| | - Erica E. Carroll
- Army Institute for Public Health, Aberdeen Proving Ground, Aberdeen, MD 21010–5403, United States of America
| | - James L. Meyerhoff
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, Tacoma, WA 98402, United States of America
| | - Rasha Hammamieh
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Marti Jett
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
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Abstract
: The human intestinal microbiome plays a critical role in human health and disease, including the pathogenesis of inflammatory bowel disease (IBD). Numerous studies have identified altered bacterial diversity and abundance at varying taxonomic levels through biopsies and fecal samples of patients with IBD and diseased model animals. However, inconsistent observations regarding the microbial compositions of such patients have hindered the efforts in assessing the etiological role of specific bacterial species in the pathophysiology of IBD. These observations highlight the importance of minimizing the confounding factors associated with IBD and the need for a standardized methodology to analyze well-defined microbial sampling sources in early IBD diagnosis. Furthermore, establishing the linkage between microbiota compositions with their function within the host system can provide new insights on the pathogenesis of IBD. Such research has been greatly facilitated by technological advances that include functional metagenomics coupled with proteomic and metabolomic profiling. This review provides updates on the composition of the microbiome in IBD and emphasizes microbiota dysbiosis-involved mechanisms. We highlight functional roles of specific bacterial groups in the development and management of IBD. Functional analyses of the microbiome may be the key to understanding the role of microbiota in the development and chronicity of IBD and reveal new strategies for therapeutic intervention.
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Huttenhower C, Kostic AD, Xavier RJ. Inflammatory bowel disease as a model for translating the microbiome. Immunity 2014; 40:843-54. [PMID: 24950204 DOI: 10.1016/j.immuni.2014.05.013] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Indexed: 02/06/2023]
Abstract
The inflammatory bowel diseases (IBDs) are among the most closely studied chronic inflammatory disorders that involve environmental, host genetic, and commensal microbial factors. This combination of features has made IBD both an appropriate and a high-priority platform for translatable research in host-microbiome interactions. Decades of epidemiology have identified environmental risk factors, although most mechanisms of action remain unexplained. The genetic architecture of IBD has been carefully dissected in multiple large populations, identifying several responsible host epithelial and immune pathways but without yet a complete systems-level explanation. Most recently, the commensal gut microbiota have been found to be both ecologically and functionally perturbed during the disease, but with as-yet-unexplained heterogeneity among IBD subtypes and individual patients. IBD thus represents perhaps the most comprehensive current model for understanding the human microbiome's role in complex inflammatory disease. Here, we review the influences of the microbiota on IBD and its potential for translational medicine.
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Affiliation(s)
- Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Aleksandar D Kostic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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40
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Venkatesh M, Mukherjee S, Wang H, Li H, Sun K, Benechet AP, Qiu Z, Maher L, Redinbo MR, Phillips RS, Fleet JC, Kortagere S, Mukherjee P, Fasano A, Le Ven J, Nicholson JK, Dumas ME, Khanna KM, Mani S. Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and Toll-like receptor 4. Immunity 2014; 41:296-310. [PMID: 25065623 DOI: 10.1016/j.immuni.2014.06.014] [Citation(s) in RCA: 638] [Impact Index Per Article: 63.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 05/30/2014] [Indexed: 02/07/2023]
Abstract
Intestinal microbial metabolites are conjectured to affect mucosal integrity through an incompletely characterized mechanism. Here we showed that microbial-specific indoles regulated intestinal barrier function through the xenobiotic sensor, pregnane X receptor (PXR). Indole 3-propionic acid (IPA), in the context of indole, is a ligand for PXR in vivo, and IPA downregulated enterocyte TNF-α while it upregulated junctional protein-coding mRNAs. PXR-deficient (Nr1i2(-/-)) mice showed a distinctly "leaky" gut physiology coupled with upregulation of the Toll-like receptor (TLR) signaling pathway. These defects in the epithelial barrier were corrected in Nr1i2(-/-)Tlr4(-/-) mice. Our results demonstrate that a direct chemical communication between the intestinal symbionts and PXR regulates mucosal integrity through a pathway that involves luminal sensing and signaling by TLR4.
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Affiliation(s)
- Madhukumar Venkatesh
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Subhajit Mukherjee
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hongwei Wang
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hao Li
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Katherine Sun
- Department of Pathology, Montefiore Medical Center, Bronx, NY 10467, USA
| | - Alexandre P Benechet
- Department of Immunology, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Zhijuan Qiu
- Department of Immunology, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Leigh Maher
- Department of Immunology, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert S Phillips
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - James C Fleet
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
| | - Sandhya Kortagere
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Paromita Mukherjee
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Alessio Fasano
- Department of Pediatrics, MassGeneral Hospital for Children, Harvard Medical School, Boston, MA 02114, USA
| | - Jessica Le Ven
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Jeremy K Nicholson
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Marc E Dumas
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Kamal M Khanna
- Department of Immunology, University of Connecticut Health Center, Farmington, CT 06030, USA.
| | - Sridhar Mani
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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Smith MI, Turpin W, Tyler AD, Silverberg MS, Croitoru K. Microbiome analysis - from technical advances to biological relevance. F1000PRIME REPORTS 2014; 6:51. [PMID: 25184041 PMCID: PMC4108955 DOI: 10.12703/p6-51] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The development of culture-independent techniques and next-generation sequencing has led to a staggering rise in the number of microbiome studies over the last decade. Although it remains important to identify the taxa of microbes present in a variety of environmental samples, including the gut microbiomes of healthy and diseased individuals, the next stage of microbiome research will need to focus on uncovering the role of the microbiome rather than its mere composition. Here, we introduce techniques that go beyond identifying the taxa present within a sample and examine the biological function of the microbiome or the host-microbiome interaction.
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Affiliation(s)
- Michelle I Smith
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5
| | - Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5 ; Institute of Medical Science, Department of Medicine University of Toronto, Toronto, ON Canada, M5S 1A8
| | - Andrea D Tyler
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5 ; Institute of Medical Science, Department of Medicine University of Toronto, Toronto, ON Canada, M5S 1A8
| | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue, Room 437, Toronto, ON Canada, M5G 1X5 ; Institute of Medical Science, Department of Medicine University of Toronto, Toronto, ON Canada, M5S 1A8
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Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. ENVIRONMENTAL HEALTH PERSPECTIVES 2014; 122:284-91. [PMID: 24413286 PMCID: PMC3948040 DOI: 10.1289/ehp.1307429] [Citation(s) in RCA: 377] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 01/09/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND The human intestine is host to an enormously complex, diverse, and vast microbial community-the gut microbiota. The gut microbiome plays a profound role in metabolic processing, energy production, immune and cognitive development, epithelial homeostasis, and so forth. However, the composition and diversity of the gut microbiome can be readily affected by external factors, which raises the possibility that exposure to toxic environmental chemicals leads to gut microbiome alteration, or dysbiosis. Arsenic exposure affects large human populations worldwide and has been linked to a number of diseases, including cancer, diabetes, and cardiovascular disorders. OBJECTIVES We investigated the impact of arsenic exposure on the gut microbiome composition and its metabolic profiles. METHODS We used an integrated approach combining 16S rRNA gene sequencing and mass spectrometry-based metabolomics profiling to examine the functional impact of arsenic exposure on the gut microbiome. RESULTS 16S rRNA gene sequencing revealed that arsenic significantly perturbed the gut microbiome composition in C57BL/6 mice after exposure to 10 ppm arsenic for 4 weeks in drinking water. Moreover, metabolomics profiling revealed a concurrent effect, with a number of gut microflora-related metabolites being perturbed in multiple biological matrices. CONCLUSIONS Arsenic exposure not only alters the gut microbiome community at the abundance level but also substantially disturbs its metabolic profiles at the function level. These findings may provide novel insights regarding perturbations of the gut microbiome and its functions as a potential new mechanism by which arsenic exposure leads to or exacerbates human diseases. CITATION Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG. 2014. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ Health Perspect 122:284-291; http://dx.doi.org/10.1289/ehp.1307429.
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Affiliation(s)
- Kun Lu
- Department of Biological Engineering
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Dawiskiba T, Deja S, Mulak A, Ząbek A, Jawień E, Pawełka D, Banasik M, Mastalerz-Migas A, Balcerzak W, Kaliszewski K, Skóra J, Barć P, Korta K, Pormańczuk K, Szyber P, Litarski A, Młynarz P. Serum and urine metabolomic fingerprinting in diagnostics of inflammatory bowel diseases. World J Gastroenterol 2014; 20:163-174. [PMID: 24415869 PMCID: PMC3886005 DOI: 10.3748/wjg.v20.i1.163] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/21/2013] [Accepted: 12/06/2013] [Indexed: 02/06/2023] Open
Abstract
AIM: To evaluate the utility of serum and urine metabolomic analysis in diagnosing and monitoring of inflammatory bowel diseases (IBD).
METHODS: Serum and urine samples were collected from 24 patients with ulcerative colitis (UC), 19 patients with the Crohn’s disease (CD) and 17 healthy controls. The activity of UC was assessed with the Simple Clinical Colitis Activity Index, while the activity of CD was determined using the Harvey-Bradshaw Index. The analysis of serum and urine samples was performed using proton nuclear magnetic resonance (NMR) spectroscopy. All spectra were exported to Matlab for preprocessing which resulted in two data matrixes for serum and urine. Prior to the chemometric analysis, both data sets were unit variance scaled. The differences in metabolite fingerprints were assessed using partial least-squares-discriminant analysis (PLS-DA). Receiver operating characteristic curves and area under curves were used to evaluate the quality and prediction performance of the obtained PLS-DA models. Metabolites responsible for separation in models were tested using STATISTICA 10 with the Mann-Whitney-Wilcoxon test and the Student’s t test (α = 0.05).
RESULTS: The comparison between the group of patients with active IBD and the group with IBD in remission provided good PLS-DA models (P value 0.002 for serum and 0.003 for urine). The metabolites that allowed to distinguish these groups were: N-acetylated compounds and phenylalanine (up-regulated in serum), low-density lipoproteins and very low-density lipoproteins (decreased in serum) as well as glycine (increased in urine) and acetoacetate (decreased in urine). The significant differences in metabolomic profiles were also found between the group of patients with active IBD and healthy control subjects providing the PLS-DA models with a very good separation (P value < 0.001 for serum and 0.003 for urine). The metabolites that were found to be the strongest biomarkers included in this case: leucine, isoleucine, 3-hydroxybutyric acid, N-acetylated compounds, acetoacetate, glycine, phenylalanine and lactate (increased in serum), creatine, dimethyl sulfone, histidine, choline and its derivatives (decreased in serum), as well as citrate, hippurate, trigonelline, taurine, succinate and 2-hydroxyisobutyrate (decreased in urine). No clear separation in PLS-DA models was found between CD and UC patients based on the analysis of serum and urine samples, although one metabolite (formate) in univariate statistical analysis was significantly lower in serum of patients with active CD, and two metabolites (alanine and N-acetylated compounds) were significantly higher in serum of patients with CD when comparing jointly patients in the remission and active phase of the diseases. Contrary to the results obtained from the serum samples, the analysis of urine samples allowed to distinguish patients with IBD in remission from healthy control subjects. The metabolites of importance included in this case up-regulated acetoacetate and down-regulated citrate, hippurate, taurine, succinate, glycine, alanine and formate.
CONCLUSION: NMR-based metabolomic fingerprinting of serum and urine has the potential to be a useful tool in distinguishing patients with active IBD from those in remission.
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Mangerich A, Dedon PC, Fox JG, Tannenbaum SR, Wogan GN. Chemistry meets biology in colitis-associated carcinogenesis. Free Radic Res 2013; 47:958-86. [PMID: 23926919 PMCID: PMC4316682 DOI: 10.3109/10715762.2013.832239] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The intestine comprises an exceptional venue for a dynamic and complex interplay of numerous chemical and biological processes. Here, multiple chemical and biological systems, including the intestinal tissue itself, its associated immune system, the gut microbiota, xenobiotics, and metabolites meet and interact to form a sophisticated and tightly regulated state of tissue homoeostasis. Disturbance of this homeostasis can cause inflammatory bowel disease (IBD)-a chronic disease of multifactorial etiology that is strongly associated with increased risk for cancer development. This review addresses recent developments in research into chemical and biological mechanisms underlying the etiology of inflammation-induced colon cancer. Beginning with a general overview of reactive chemical species generated during colonic inflammation, the mechanistic interplay between chemical and biological mediators of inflammation, the role of genetic toxicology, and microbial pathogenesis in disease development are discussed. When possible, we systematically compare evidence from studies utilizing human IBD patients with experimental investigations in mice. The comparison reveals that many strong pathological and mechanistic correlates exist between mouse models of colitis-associated cancer, and the clinically relevant situation in humans. We also summarize several emerging issues in the field, such as the carcinogenic potential of novel inflammation-related DNA adducts and genotoxic microbial factors, the systemic dimension of inflammation-induced genotoxicity, and the complex role of genome maintenance mechanisms during these processes. Taken together, current evidence points to the induction of genetic and epigenetic alterations by chemical and biological inflammatory stimuli ultimately leading to cancer formation.
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Affiliation(s)
- Aswin Mangerich
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Department of Biology, Molecular Toxicology Group, University of Konstanz, D-78457 Konstanz, Germany
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Center for Environmental Health Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - James G. Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Division of Comparative Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Center for Environmental Health Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Steven R. Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Center for Environmental Health Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Gerald N. Wogan
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
- Center for Environmental Health Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
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Abstract
PURPOSE OF REVIEW The assessment of metabolite profiles in biofluids has become a powerful method for the detection of biomarker molecules and disease mechanisms. This review outlines the recent advances in the use of metabolomic techniques to study inflammatory bowel diseases (IBDs). RECENT FINDINGS The last few years have seen an increase in the studies of experimental and human IBD focusing on the search for small metabolites, such as amino acids, bases, and tricarboxylic acid cycle intermediates. Experimental methods for the screening of metabolites in serum, urine, fecal extracts, and colon tissue include H NMR spectroscopy, gas chromatography-mass spectrometry, and liquid chromatography methods. Several studies demonstrate that IBD patients and healthy individuals, as well as the IBD subtypes, can be distinguished using metabolic profiling. Metabolomic data of fecal extracts and urine have revealed disruptions in bacterial populations, findings that are indicative of a possible involvement of the microbiome in the development of IBDs. SUMMARY Metabolites from biofluids can be detected in IBDs by different experimental methods that allow successful separation of IBD subtypes from healthy cohorts. Knowledge of a unique metabolomic fingerprint in IBDs could be useful for diagnosis, treatment, and detection of disease mechanisms.
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Chemical and cytokine features of innate immunity characterize serum and tissue profiles in inflammatory bowel disease. Proc Natl Acad Sci U S A 2013; 110:E2332-41. [PMID: 23754421 DOI: 10.1073/pnas.1222669110] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel disease (IBD) arises from inappropriate activation of the mucosal immune system resulting in a state of chronic inflammation with causal links to colon cancer. Helicobacter hepaticus-infected Rag2(-/-) mice emulate many aspects of human IBD, and our recent work using this experimental model highlights the importance of neutrophils in the pathology of colitis. To define molecular mechanisms linking colitis to the identity of disease biomarkers, we performed a translational comparison of protein expression and protein damage products in tissues of mice and human IBD patients. Analysis in inflamed mouse colons identified the neutrophil- and macrophage-derived damage products 3-chlorotyrosine (Cl-Tyr) and 3-nitrotyrosine, both of which increased with disease duration. Analysis also revealed higher Cl-Tyr levels in colon relative to serum in patients with ulcerative colitis and Crohn disease. The DNA chlorination damage product, 5-chloro-2'-deoxycytidine, was quantified in diseased human colon samples and found to be present at levels similar to those in inflamed mouse colons. Multivariate analysis of these markers, together with serum proteins and cytokines, revealed a general signature of activated innate immunity in human IBD. Signatures in ulcerative colitis sera were strongly suggestive of neutrophil activity, and those in Crohn disease and mouse sera were suggestive of both macrophage and neutrophil activity. These data point to innate immunity as a major determinant of serum and tissue profiles and provide insight into IBD disease processes.
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Yu SL, An YJ, Yang HJ, Kang MS, Kim HY, Wen H, Jin X, Kwon HN, Min KJ, Lee SK, Park S. Alanine-Metabolizing Enzyme Alt1 Is Critical in Determining Yeast Life Span, As Revealed by Combined Metabolomic and Genetic Studies. J Proteome Res 2013; 12:1619-27. [DOI: 10.1021/pr300979r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Sung-Lim Yu
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Yong Jin An
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Hey-ji Yang
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Mi-Sun Kang
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Ho-Yeol Kim
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - He Wen
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Xing Jin
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Hyuk Nam Kwon
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Kyung-Jin Min
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Sung-Keun Lee
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
| | - Sunghyouk Park
- Inha
Research Institute for Medical Sciences, ‡Department of Biochemistry, and §Department of
Pharmacology, Center for Advanced Medical Education by
BK21 project, College of Medicine and ∥Department of Biological Sciences, Inha University, Incheon, Korea, 400-712
- College
of Pharmacy and #Natural Product Research Institute, Seoul National University, San 56-1 Sillim-dong, Gwanak-gu,
Seoul, Korea, 151-742
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