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Villavicencio-Tejo F, Olesen MA, Navarro L, Calisto N, Iribarren C, García K, Corsini G, Quintanilla RA. Gut-Brain Axis Deregulation and Its Possible Contribution to Neurodegenerative Disorders. Neurotox Res 2023; 42:4. [PMID: 38103074 DOI: 10.1007/s12640-023-00681-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 11/10/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
The gut-brain axis is an essential communication pathway between the central nervous system (CNS) and the gastrointestinal tract. The human microbiota is composed of a diverse and abundant microbial community that compasses more than 100 trillion microorganisms that participate in relevant physiological functions such as host nutrient metabolism, structural integrity, maintenance of the gut mucosal barrier, and immunomodulation. Recent evidence in animal models has been instrumental in demonstrating the possible role of the microbiota in neurodevelopment, neuroinflammation, and behavior. Furthermore, clinical studies suggested that adverse changes in the microbiota can be considered a susceptibility factor for neurological disorders (NDs), such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). In this review, we will discuss evidence describing the role of gut microbes in health and disease as a relevant risk factor in the pathogenesis of neurodegenerative disorders, including AD, PD, HD, and ALS.
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Affiliation(s)
- Francisca Villavicencio-Tejo
- Laboratory of Neurodegenerative Diseases, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, 5to Piso, San Miguel 8910060, Santiago, Chile
| | - Margrethe A Olesen
- Laboratory of Neurodegenerative Diseases, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, 5to Piso, San Miguel 8910060, Santiago, Chile
| | - Laura Navarro
- Laboratorio de Microbiología Molecular y Compuestos Bioactivos, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Nancy Calisto
- Laboratorio de Microbiología Molecular y Compuestos Bioactivos, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Cristian Iribarren
- Laboratorio de Patógenos Gastrointestinales, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Katherine García
- Laboratorio de Patógenos Gastrointestinales, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Gino Corsini
- Laboratorio de Microbiología Molecular y Compuestos Bioactivos, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Rodrigo A Quintanilla
- Laboratory of Neurodegenerative Diseases, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, 5to Piso, San Miguel 8910060, Santiago, Chile.
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Vilca-Melendez S, Uthaug MV, Griffin JL. 1H Nuclear Magnetic Resonance: A Future Approach to the Metabolic Profiling of Psychedelics in Human Biofluids? Front Psychiatry 2021; 12:742856. [PMID: 34966300 PMCID: PMC8710695 DOI: 10.3389/fpsyt.2021.742856] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/18/2021] [Indexed: 11/25/2022] Open
Abstract
While psychedelics may have therapeutic potential for treating mental health disorders such as depression, further research is needed to better understand their biological effects and mechanisms of action when considering the development of future novel therapy approaches. Psychedelic research could potentially benefit from the integration of metabonomics by proton nuclear magnetic resonance (1H NMR) spectroscopy which is an analytical chemistry-based approach that can measure the breakdown of drugs into their metabolites and their metabolic consequences from various biofluids. We have performed a systematic review with the primary aim of exploring published literature where 1H NMR analysed psychedelic substances including psilocin, lysergic acid diethylamide (LSD), LSD derivatives, N,N-dimethyltryptamine (DMT), 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) and bufotenin. The second aim was to assess the benefits and limitations of 1H NMR spectroscopy-based metabolomics as a tool in psychedelic research and the final aim was to explore potential future directions. We found that the most current use of 1H NMR in psychedelic research has been for the structural elucidation and analytical characterisation of psychedelic molecules and that no papers used 1H NMR in the metabolic profiling of biofluids, thus exposing a current research gap and the underuse of 1H NMR. The efficacy of 1H NMR spectroscopy was also compared to mass spectrometry, where both metabonomics techniques have previously shown to be appropriate for biofluid analysis in other applications. Additionally, potential future directions for psychedelic research were identified as real-time NMR, in vivo 1H nuclear magnetic resonance spectroscopy (MRS) and 1H NMR studies of the gut microbiome. Further psychedelic studies need to be conducted that incorporate the use of 1H NMR spectroscopy in the analysis of metabolites both in the peripheral biofluids and in vivo to determine whether it will be an effective future approach for clinical and naturalistic research.
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Affiliation(s)
- Sylvana Vilca-Melendez
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Malin V. Uthaug
- The Centre for Psychedelic Research, Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of Neuropsychology and Psychopharmacology, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Julian L. Griffin
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
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Yao Q, Li H, Fan L, Zhang Y, Zhao S, Zheng N, Wang J. Dietary Regulation of the Crosstalk between Gut Microbiome and Immune Response in Inflammatory Bowel Disease. Foods 2021; 10:foods10020368. [PMID: 33567698 PMCID: PMC7915342 DOI: 10.3390/foods10020368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD), a chronic, recurring inflammatory response, is a growing global public health issue. It results from the aberrant crosstalk among environmental factors, gut microbiota, the immune system, and host genetics, with microbiota serving as the core of communication for differently-sourced signals. In the susceptible host, dysbiosis, characterized by the bloom of facultative anaerobic bacteria and the decline of community diversity and balance, can trigger an aberrant immune response that leads to reduced tolerance against commensal microbiota. In IBD, such dysbiosis has been profoundly proven in animal models, as well as clinic data analysis; however, it has not yet been conclusively ascertained whether dysbiosis actually promotes the disease or is simply a consequence of the inflammatory disorder. Better insight into the complex network of interactions between food, the intestinal microbiome, and host immune response will, therefore, contribute significantly to the diagnosis, treatment, and management of IBD. In this article, we review the ways in which the mutualistic circle of dietary nutrients, gut microbiota, and the immune system becomes anomalous during the IBD process, and discuss the roles of bacterial factors in shaping the intestinal inflammatory barrier and adjusting immune capacity.
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Affiliation(s)
- Qianqian Yao
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Y.); (H.L.); (L.F.); (Y.Z.); (S.Z.); (N.Z.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Li
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Y.); (H.L.); (L.F.); (Y.Z.); (S.Z.); (N.Z.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Linlin Fan
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Y.); (H.L.); (L.F.); (Y.Z.); (S.Z.); (N.Z.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yangdong Zhang
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Y.); (H.L.); (L.F.); (Y.Z.); (S.Z.); (N.Z.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shengguo Zhao
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Y.); (H.L.); (L.F.); (Y.Z.); (S.Z.); (N.Z.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nan Zheng
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Y.); (H.L.); (L.F.); (Y.Z.); (S.Z.); (N.Z.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiaqi Wang
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Y.); (H.L.); (L.F.); (Y.Z.); (S.Z.); (N.Z.)
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence:
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Jang YS, Nam SM, Son GE, Lee J, Park CP. Droplet‐based Continuous Flow Synthesis of Palladium Supported on Reduced Graphene Oxide. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.11966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yea Seul Jang
- Graduate School of Analytical Science and Technology (GRAST)Chungnam National University Daejeon 34134 Republic of Korea
| | - Su Min Nam
- Graduate School of Analytical Science and Technology (GRAST)Chungnam National University Daejeon 34134 Republic of Korea
| | - Go Eun Son
- Graduate School of Analytical Science and Technology (GRAST)Chungnam National University Daejeon 34134 Republic of Korea
| | - Jihoon Lee
- Department of Polymer Science and EngineeringKorea National University of Transportation Chungju 27469 Republic of Korea
| | - Chan Pil Park
- Graduate School of Analytical Science and Technology (GRAST)Chungnam National University Daejeon 34134 Republic of Korea
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Eslami-S Z, Majidzadeh-A K, Halvaei S, Babapirali F, Esmaeili R. Microbiome and Breast Cancer: New Role for an Ancient Population. Front Oncol 2020; 10:120. [PMID: 32117767 PMCID: PMC7028701 DOI: 10.3389/fonc.2020.00120] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
There are many risk factors associated with breast cancer (BC) such as the familial history of BC, using hormone replacement therapy, obesity, personal habits, and other clinical factors; however, not all BC cases are attributed to these risk factors. Recent researches show a correlation between patient microbiome and BC suggested as a new risk factor. The present review article aimed at evaluating the role of the microbiome as a risk factor in the occurrence of BC, investigating the proposed mechanisms of interaction between the microbiome and human genes involved in BC, and assessing the impact of the altered composition of breast, gut, and milk microbiome in the physiological status of normal breast as well as cancerous or non-cancerous breast lesions. The study also evaluated the growing evidence that these altered populations may hinder chemotherapeutic treatment. The role of microbiome in the development and maintenance of inflammation, estrogen metabolism, and epigenetic alterations was properly investigated. Finally, clinical and therapeutic applications of the microbiome- e.g., probiotics, microbiome genome modulation, and engineered microbiome enzymes in the management of BC were reviewed.
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Affiliation(s)
- Zahra Eslami-S
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.,Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, Montpellier, France
| | - Keivan Majidzadeh-A
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Sina Halvaei
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Fatemeh Babapirali
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.,University of Science and Culture, Basic Science and Advanced Technologies in Biology, Tehran, Iran
| | - Rezvan Esmaeili
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
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Application of 1H NMR spectroscopy to the metabolic phenotyping of rodent brain extracts: A metabonomic study of gut microbial influence on host brain metabolism. J Pharm Biomed Anal 2017; 143:141-146. [PMID: 28595107 DOI: 10.1016/j.jpba.2017.05.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 12/22/2022]
Abstract
1H NMR Spectroscopy has been applied to determine the neurochemical profiles of brain extracts from the frontal cortex and hippocampal regions of germ free and normal mice and rats. The results revealed a number of differences between germ free (GF) and conventional (CV) rats or specific pathogen-free (SPF) mice with microbiome-associated metabolic variation found to be both species- and region-dependent. In the mouse, the GF frontal cortex contained lower amounts of creatine, N-acetyl-aspartate (NAA), glycerophosphocholine and lactate, but greater amounts of choline compared to that of specific pathogen free (SPF) mice. In the hippocampus, the GF mice had greater creatine, NAA, lactate and taurine content compared to those of the SPF animals, but lower relative quantities of succinate and an unidentified lipid-related component. The GF rat frontal cortex contained higher relative quantities of lactate, creatine and NAA compared to the CV animals whilst the GF hippocampus was characterized by higher taurine and phosphocholine concentrations and lower quantities of NAA, N-acetylaspartylglutamate and choline compared to the CV animals. Of note is that, in both rat and mouse brain extracts, concentrations of hippocampal taurine were found to be greater in the absence of an established microbiome. The results provide further evidence that brain biochemistry can be influenced by gut microbial status, specifically metabolites involved in energy metabolism demonstrating biochemical dialogue between the microbiome and brain.
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Abstract
The human microbiome is a new frontier in biology and one that is helping to define what it is to be human. Recently, we have begun to understand that the "communication" between the host and its microbiome is via a metabolic superhighway. By interrogating and understanding the molecules involved we may start to know who the main players are, and how we can modulate them and the mechanisms of health and disease.
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Affiliation(s)
- Jia V Li
- Section of Biomolecular Medicine, Division of Computational & Systems Medicine, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Jonathan Swann
- Section of Biomolecular Medicine, Division of Computational & Systems Medicine, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Julian R Marchesi
- Section of Biomolecular Medicine, Division of Computational & Systems Medicine, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK; Divison of Digestive Diseases, Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, 10th Floor QEQM Building, St Mary's Hospital Campus, South Wharf Road, London W2 1NY, UK; Department of Surgery & Cancer, Centre for Digestive and Gut Health, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK; School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3XQ, UK.
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Baker L, Lanz B, Andreola F, Ampuero J, Wijeyesekera A, Holmes E, Deutz N. New technologies - new insights into the pathogenesis of hepatic encephalopathy. Metab Brain Dis 2016; 31:1259-1267. [PMID: 27696270 DOI: 10.1007/s11011-016-9906-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 09/04/2016] [Indexed: 12/16/2022]
Abstract
Hepatic encephalopathy (HE) is a neuropsychiatric syndrome which frequently accompanies acute or chronic liver disease. It is characterized by a variety of symptoms of different severity such as cognitive deficits and impaired motor functions. Currently, HE is seen as a consequence of a low grade cerebral oedema associated with the formation of cerebral oxidative stress and deranged cerebral oscillatory networks. However, the pathogenesis of HE is still incompletely understood as liver dysfunction triggers exceptionally complex metabolic derangements in the body which need to be investigated by appropriate technologies. This review summarizes technological approaches presented at the ISHEN conference 2014 in London which may help to gain new insights into the pathogenesis of HE. Dynamic in vivo 13C nuclear magnetic resonance spectroscopy was performed to analyse effects of chronic liver failure in rats on brain energy metabolism. By using a genomics approach, microRNA expression changes were identified in plasma of animals with acute liver failure which may be involved in interorgan interactions and which may serve as organ-specific biomarkers for tissue damage during acute liver failure. Genomics were also applied to analyse glutaminase gene polymorphisms in patients with liver cirrhosis indicating that haplotype-dependent glutaminase activity is an important pathogenic factor in HE. Metabonomics represents a promising approach to better understand HE, by capturing the systems level metabolic changes associated with disease in individuals, and enabling monitoring of metabolic phenotypes in real time, over a time course and in response to treatment, to better inform clinical decision making. Targeted fluxomics allow the determination of metabolic reaction rates thereby discriminating metabolite level changes in HE in terms of production, consumption and clearance.
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Affiliation(s)
- Luisa Baker
- Department of Clinical Science and Services, Royal Veterinary College, Hatfield, Hertfordshire, UK
| | - Bernard Lanz
- Laboratory for Functional and Metabolic Imaging, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Fausto Andreola
- Liver Failure Group, UCL Institute for Liver and Digestive Health, UCL Medical School, Royal Free Hospital, London, UK
| | - Javier Ampuero
- Inter-Centre Unit of Digestive Diseases, Virgen Macarena - Virgen del Rocío University Hospitals, Sevilla, Spain
- Instituto de Biomedicina de Sevilla, Sevilla, Spain
| | - Anisha Wijeyesekera
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Elaine Holmes
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Nicolaas Deutz
- Department of Health & Kinesiology, Texas A&M University, College Station, TX, USA
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Robinson O, Toledano MB, Sands C, Beckonert O, J Want E, Goldin R, Hauser ML, Fenwick A, Thursz MR, Coen M. Global metabolic changes induced by plant-derived pyrrolizidine alkaloids following a human poisoning outbreak and in a mouse model. Toxicol Res (Camb) 2016; 5:1594-1603. [PMID: 30090460 PMCID: PMC6060677 DOI: 10.1039/c6tx00221h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 08/11/2016] [Indexed: 11/26/2022] Open
Abstract
Several hundred cases of Hirmi Valley Liver Disease (HVLD), an often fatal liver injury, occurred from 2001 to 2011 in a cluster of rural villages in Tigray, Ethiopia. HVLD is principally caused by contamination of the food supply with plant derived pyrrolizidine alkaloids (PAs), with high exposure to the pesticide DDT among villagers increasing their susceptibility. In an untargeted global approach we aimed to identify metabolic changes induced by PA exposure through 1H NMR spectroscopic based metabolic profiling. We analysed spectra acquired from urine collected from HVLD cases and controls and a murine model of PA exposure and PA/DDT co-exposure, using multivariate partial least squares discriminant analysis. In the human models we identified changes in urinary concentrations of tyrosine, pyruvate, bile acids, N-acetylglycoproteins, N-methylnicotinamide and formate, hippurate, p-cresol sulphate, p-hydroxybenzoate and 3-(3-hydroxyphenyl) propionic acid. Tyrosine and p-cresol sulphate were associated with both exposure and disease. Similar changes to tyrosine, one-carbon intermediates and microbial associated metabolites were observed in the mouse model, with tyrosine correlated with the extent of liver damage. These results provide mechanistic insight and implicate the gut microflora in the human response to challenge with toxins. Pathways identified here may be useful in translational research and as "exposome" signals.
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Affiliation(s)
- Oliver Robinson
- MRC-PHE Centre for Environment and Health , School of Public Health , Imperial College London , UK
- ISGlobal , Centre for Research in Environmental Epidemiology (CREAL) , Spain
- Hospital del Mar Medical Research Institute (IMIM) , Barcelona , Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) , Spain
| | - Mireille B Toledano
- MRC-PHE Centre for Environment and Health , School of Public Health , Imperial College London , UK
| | - Caroline Sands
- Computational and Systems Medicine , Department of Surgery & Cancer , Faculty of Medicine , Imperial College London , UK .
| | - Olaf Beckonert
- Computational and Systems Medicine , Department of Surgery & Cancer , Faculty of Medicine , Imperial College London , UK .
| | - Elizabeth J Want
- Computational and Systems Medicine , Department of Surgery & Cancer , Faculty of Medicine , Imperial College London , UK .
| | - Rob Goldin
- Department of Medicine , Imperial College London , UK
| | - Michael L Hauser
- One Health Foundation , Switzerland
- Schistosomiasis Control Initiative , School of Public Health, Imperial College , London , UK
| | - Alan Fenwick
- Schistosomiasis Control Initiative , School of Public Health, Imperial College , London , UK
| | - Mark R Thursz
- Department of Medicine , Imperial College London , UK
| | - Muireann Coen
- Computational and Systems Medicine , Department of Surgery & Cancer , Faculty of Medicine , Imperial College London , UK .
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Janabi A, Biddle A, Klein D, McKeever K. Exercise training-induced changes in the gut microbiota of Standardbred racehorses. COMPARATIVE EXERCISE PHYSIOLOGY 2016. [DOI: 10.3920/cep160015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Exercise has a significant effect on different physiological systems in the body of human and animals. Only limited numbers of published studies in laboratory animals or humans have shown the effect of exercise on the gut microbiota, and no studies have shown this effect in horses. In this study, 8 horses (4 mares, 4 geldings) were exercise trained for 12 weeks, and 4 additional mares were used as a parallel seasonal control. To identify bacterial community changes over time for both groups, rectal faecal samples were collected, DNA was extracted, and the 16S rRNA gene (V3-V4) was sequenced using the Illumina Miseq platform. One-way ANOVA, Shannon diversity index, and Principal Coordinate Analysis (PCoA) were used to identify differences between and among samples. The exercise training group showed significant changes in the levels of Bacteroidetes, Proteobacteria, and Spirochaetes phyla (P<0.05), while there were no changes in the gut microbiota of the seasonal control group through the three months of the study (P>0.05). Moreover, with training two genera significantly changed in their relative abundance over time, namely Clostridium and Dysgonomonas (P<0.05). Dysgonomonas spp. was significantly changed in abundance during the exercise training period (P<0.05). Also Treponema spp. showed significant changes during the exercise training period (P<0.05). Shannon diversity index was decreased (P<0.05) in the exercise group at the beginning of the study, but then returned to pre-training levels. PCoA showed significant separation between time points of the exercise training group as far as the levels of genera and species (P<0.05) represented. Our results show that exercise training influences the gut microbiota, especially at the beginning of training.
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Affiliation(s)
- A.H.D. Janabi
- Microbial Biology Graduate Program, Rutgers-The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - A.S. Biddle
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA
| | - D. Klein
- Nutritional Sciences Graduate Program, Rutgers-The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - K.H. McKeever
- Equine Science Center, Department of Animal Science, Rutgers-The State University of New Jersey, New Brunswick, NJ 08901, USA
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11
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Cullen JM, Faiola B, Melich DH, Peterson RA, Jordan HL, Kimbrough CL, Miller RT. Acute Alpha-Naphthylisothiocyanate-induced Liver Toxicity in Germfree and Conventional Male Rats. Toxicol Pathol 2016; 44:987-97. [PMID: 27519817 DOI: 10.1177/0192623316662360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Differences in the responses of conventional and germfree male Sprague-Dawley rats to acute injury induced by alpha-naphthylisothiocyanate (ANIT), a well-characterized biliary epithelial toxicant, were evaluated. Conventional and germfree rats were dosed once orally with 50 mg/kg of ANIT or corn oil alone and serially sacrificed daily for the next 3 days. Germfree rats treated with ANIT tended to have greater increases in virtually all liver and biliary-related analytes compared with conventional rats treated with ANIT; however, significant differences were found only in a few of these analytes including increased bile acids on day 3, total bilirubin on day 4, glutamate dehydrogenase (GLDH) on day 3, and reduced paraoxonase 1 (PON1) on days 2 and 3. Histologic differences between the conventional and germfree rats were modest, but most pronounced on day 2 (24-hr post dosing). Based on subjective scoring, biliary necrosis, neutrophilic cholangitis, and portal tract edema were more severe in germfree rats at 24 hr post dosing compared with conventional rats. Biliary epithelial replication did not differ between treated groups, however. Overall, germfree rats had a modestly greater level of biliary tract injury based on subjective histologic scoring and clinical chemistry measurements following an acute exposure to the well-characterized biliary toxin, ANIT; however, the difference between the ANIT-treated germfree and conventional groups was modest and most evident only within the first day following exposure. These findings suggest that the microbiome did not significantly affect ANIT-induced acute biliary tract injury in the conditions of this study.
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Affiliation(s)
- John M Cullen
- North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Brenda Faiola
- GlaxoSmithKline, Safety Assessment, Research Triangle Park, North Carolina, USA
| | - David H Melich
- GlaxoSmithKline, Safety Assessment, Research Triangle Park, North Carolina, USA
| | - Richard A Peterson
- GlaxoSmithKline, Safety Assessment, Research Triangle Park, North Carolina, USA
| | - Holly L Jordan
- GlaxoSmithKline, Safety Assessment, Research Triangle Park, North Carolina, USA
| | - Carie L Kimbrough
- GlaxoSmithKline, Statistical Sciences, Research Triangle Park, North Carolina, USA
| | - Richard T Miller
- GlaxoSmithKline, Safety Assessment, Research Triangle Park, North Carolina, USA
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12
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Wang J, Tang L, Glenn TC, Wang JS. Aflatoxin B1 Induced Compositional Changes in Gut Microbial Communities of Male F344 Rats. Toxicol Sci 2016; 150:54-63. [PMID: 26612839 PMCID: PMC5009611 DOI: 10.1093/toxsci/kfv259] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aflatoxins are a group of potent foodborne toxicants naturally occurring in maize and groundnuts. Differential species-specific sensitivity to aflatoxins has been documented but cannot be fully explained by the differences in metabolism of these toxicants among animal species. Commensal microbial communities (microbiota) are critical to human and animal health, but few studies have assessed interactions between xenobiotic toxins and those microbiota, and its potential effects to humans and animals. Here, an exploratory dosing experiment was conducted to explore effects of Aflatoxin B1 (AFB1) on the gut microbiota in a commonly used rat model. Male F344 rats were randomly divided into groups and treated with different concentrations of AFB1. Microbial communities in fecal samples were assessed using 16S rRNA sequence analysis. We found that samples from the control group had a phylogenetically diverse community, and that increasing AFB1 doses decreased this diversity but increased evenness of community composition. In addition, the gut microbiota from different samples was clustered according to their dosing regimens. There is no community shift at the phylum level but some lactic acid bacteria were significantly depleted by AFB1. These findings suggested that AFB1 could modify the gut microbiota in a dose-dependent manner.
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Affiliation(s)
- Jincheng Wang
- *Interdisciplinary Toxicology Program and Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602 *Interdisciplinary Toxicology Program and Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602
| | - Lili Tang
- *Interdisciplinary Toxicology Program and Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602
| | - Travis C Glenn
- *Interdisciplinary Toxicology Program and Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602 *Interdisciplinary Toxicology Program and Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602
| | - Jia-Sheng Wang
- *Interdisciplinary Toxicology Program and Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602 *Interdisciplinary Toxicology Program and Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia 30602
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13
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Hou W, Zhong D, Zhang P, Li Y, Lin M, Liu G, Yao M, Liao Q, Xie Z. A strategy for the targeted metabolomics analysis of 11 gut microbiota-host co-metabolites in rat serum, urine and feces by ultra high performance liquid chromatography-tandem mass spectrometry. J Chromatogr A 2015; 1429:207-17. [PMID: 26733392 DOI: 10.1016/j.chroma.2015.12.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/27/2015] [Accepted: 12/10/2015] [Indexed: 02/06/2023]
Abstract
Microbiota-host co-metabolites are well-known to play important physiological roles, and their dysregulation has been found to be closely related to various diseases, including but not limited to inflammatory disorders. We developed herein an original and feasible method using ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The method developed enables rapid quantification of 11 key gut microbiota-host co-metabolites spanning the succinate, phenylacetylglutamine, hippurate and trimethylamine metabolic pathways within 10 min. With this method, we were able to simultaneously monitor inflammation-induced alterations of these metabolites in rat serum, urine and feces matrices. The measured levels for this panel of endogenous metabolites ranged from 0.001 to 172.8 μg m L(-1). The intra- and inter-day precision of three analytes was less than 13.1% and the accuracy was between -13.0 to 11.2% for all QC levels. The extraction recoveries in serum ranged from 85.4 to 103.2%, while the RSD was 9.0% or less for all recoveries. In addition, extraction recoveries of 11 analytes in urine and feces samples were between 85.7% and 102.0% and RSD was less than 9.5%. The method developed here has been successfully applied to the analysis of real samples from 2,4,6-trinitrobenzenesulfonic acid-induced Crohn's disease in rats. All of these results suggest that the presently developed method is sufficiently sensitive and robust to simultaneously monitor co-metabolites with diverse properties and a range of different concentrations. Therefore, this method will be expected to be useful for comprehensive studies of the pathophysiological roles and mechanisms of these key microbiota-host co-metabolites, which reflect the function of the intestine, consequently offering novel opportunities for evaluating the occurrence, development and therapeutic effects of diseases related to microbiota disturbances.
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Affiliation(s)
- Waner Hou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China; College of Chinese Traditional Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Danmin Zhong
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiting Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yemeng Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Manna Lin
- College of Chinese Traditional Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guanghui Liu
- College of Chinese Traditional Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Meicun Yao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiongfeng Liao
- College of Chinese Traditional Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Zhiyong Xie
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
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14
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Jameson E, Fu T, Brown IR, Paszkiewicz K, Purdy KJ, Frank S, Chen Y. Anaerobic choline metabolism in microcompartments promotes growth and swarming of Proteus mirabilis. Environ Microbiol 2015; 18:2886-98. [PMID: 26404097 PMCID: PMC5026066 DOI: 10.1111/1462-2920.13059] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/14/2015] [Accepted: 09/15/2015] [Indexed: 12/16/2022]
Abstract
Gammaproteobacteria are important gut microbes but only persist at low levels in the healthy gut. The ecology of Gammaproteobacteria in the gut environment is poorly understood. Here, we demonstrate that choline is an important growth substrate for representatives of Gammaproteobacteria. Using Proteus mirabilis as a model, we investigate the role of choline metabolism and demonstrate that the cutC gene, encoding a choline‐trimethylamine lyase, is essential for choline degradation to trimethylamine by targeted mutagenesis of cutC and subsequent complementation experiments. Proteus mirabilis can rapidly utilize choline to enhance growth rate and cell yield in broth culture. Importantly, choline also enhances swarming‐associated colony expansion of P. mirabilis under anaerobic conditions on a solid surface. Comparative transcriptomics demonstrated that choline not only induces choline‐trimethylamine lyase but also genes encoding shell proteins for the formation of bacterial microcompartments. Subsequent analyses by transmission electron microscopy confirmed the presence of such novel microcompartments in cells cultivated in liquid broth and hyper‐flagellated swarmer cells from solid medium. Together, our study reveals choline metabolism as an adaptation strategy for P. mirabilis and contributes to better understand the ecology of this bacterium in health and disease.
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Affiliation(s)
- Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Tiantian Fu
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Ian R Brown
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Konrad Paszkiewicz
- College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Kevin J Purdy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Stefanie Frank
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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15
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Swanson HI. Drug Metabolism by the Host and Gut Microbiota: A Partnership or Rivalry? Drug Metab Dispos 2015; 43:1499-504. [PMID: 26261284 DOI: 10.1124/dmd.115.065714] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/10/2015] [Indexed: 12/12/2022] Open
Abstract
The importance of the gut microbiome in determining not only overall health, but also in the metabolism of drugs and xenobiotics, is rapidly emerging. It is becoming increasingly clear that the gut microbiota can act in concert with the host cells to maintain intestinal homeostasis, cometabolize drugs and xenobiotics, and alter the expression levels of drug-metabolizing enzymes and transporters and the expression and activity levels of nuclear receptors. In this myriad of activities, the impact of the microbiota may be beneficial or detrimental to the host. Given that the interplay between the gut microbiota and host cells is likely subject to high interindividual variability, this work has tremendous implications for our ability to predict accurately a particular drug's pharmacokinetics and a given patient population's response to drugs. In this issue of Drug Metabolism and Disposition, a series of articles is presented that illustrate the progress and challenges that lie ahead as we unravel the intricacies associated with drug and xenobiotic metabolism by the gut microbiota. These articles highlight the underlying mechanisms that are involved and the use of in vivo and in vitro approaches that are currently available for elucidating the role of the gut microbiota in drug and xenobiotic metabolism. These articles also shed light on exciting new avenues of research that may be pursued as we consider the role of the gut microbiota as an endocrine organ, a component of the brain-gut axis, and whether the gut microbiota is an appropriate and amenable target for new drugs.
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Affiliation(s)
- Hollie I Swanson
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky
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16
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Holmes E, Wijeyesekera A, Taylor-Robinson SD, Nicholson JK. The promise of metabolic phenotyping in gastroenterology and hepatology. Nat Rev Gastroenterol Hepatol 2015. [PMID: 26194948 DOI: 10.1038/nrgastro.2015.114] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Disease risk and treatment response are determined, at the individual level, by a complex history of genetic and environmental interactions, including those with our endogenous microbiomes. Personalized health care requires a deep understanding of patient biology that can now be measured using a range of '-omics' technologies. Patient stratification involves the identification of genetic and/or phenotypic disease subclasses that require different therapeutic strategies. Stratified medicine approaches to disease diagnosis, prognosis and therapeutic response monitoring herald a new dimension in patient care. Here, we explore the potential value of metabolic profiling as applied to unmet clinical needs in gastroenterology and hepatology. We describe potential applications in a number of diseases, with emphasis on large-scale population studies as well as metabolic profiling on the individual level, using spectrometric and imaging technologies that will leverage the discovery of mechanistic information and deliver novel health care solutions to improve clinical pathway management.
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Affiliation(s)
- Elaine Holmes
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Anisha Wijeyesekera
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | | | - Jeremy K Nicholson
- MRC-NIHR National Phenome Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
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17
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Schokker D, Veninga G, Vastenhouw SA, Bossers A, de Bree FM, Kaal-Lansbergen LMTE, Rebel JMJ, Smits MA. Early life microbial colonization of the gut and intestinal development differ between genetically divergent broiler lines. BMC Genomics 2015; 16:418. [PMID: 26017153 PMCID: PMC4446945 DOI: 10.1186/s12864-015-1646-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/20/2015] [Indexed: 02/07/2023] Open
Abstract
Background Host genetic makeup plays a role in early gut microbial colonization and immune programming. Interactions between gut microbiota and host cells of the mucosal layer are of paramount importance for a proper development of host defence mechanisms. For different livestock species, it has already been shown that particular genotypes have increased susceptibilities towards disease causing pathogens. The objective of this study was to investigate the impact of genotypic variation on both early microbial colonization of the gut and functional development of intestinal tissue. From two genetically diverse chicken lines intestinal content samples were taken for microbiota analyses and intestinal tissue samples were extracted for gene expression analyses, both at three subsequent time-points (days 0, 4, and 16). Results The microbiota composition was significantly different between lines on each time point. In contrast, no significant differences were observed regarding changes in the microbiota diversity between the two lines throughout this study. We also observed trends in the microbiota data at genus level when comparing lines X and Y. We observed that approximately 2000 genes showed different temporal gene expression patterns when comparing line X to line Y. Immunological related differences seem to be only present at day 0, because at day 4 and 16 similar gene expression is observed for these two lines. However, for genes involved in cell cycle related processes the data show higher expression over the whole course of time in line Y in comparison to line X. Conclusions These data suggest the genetic background influences colonization of gut microbiota after hatch in combination with the functional development of intestinal mucosal tissue, including the programming of the immune system. The results indicate that genetically different chicken lines have different coping mechanisms in early life to cope with the outside world. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1646-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Alex Bossers
- Central Veterinary Institute, Lelystad, The Netherlands.
| | | | | | | | - Mari A Smits
- Wageningen Livestock Research, Wageningen, The Netherlands.
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18
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Jacobs J, Braun J. The Mucosal Microbiome. Mucosal Immunol 2015. [DOI: 10.1016/b978-0-12-415847-4.00005-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Jacobs JP, Braun J. Immune and genetic gardening of the intestinal microbiome. FEBS Lett 2014; 588:4102-11. [PMID: 24613921 PMCID: PMC4156569 DOI: 10.1016/j.febslet.2014.02.052] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/26/2014] [Accepted: 02/27/2014] [Indexed: 12/19/2022]
Abstract
The mucosal immune system - consisting of adaptive and innate immune cells as well as the epithelium - is profoundly influenced by its microbial environment. There is now growing evidence that the converse is also true, that the immune system shapes the composition of the intestinal microbiome. During conditions of health, this bidirectional interaction achieves a homeostasis in which inappropriate immune responses to non-pathogenic microbes are averted and immune activity suppresses blooms of potentially pathogenic microbes (pathobionts). Genetic alteration in immune/epithelial function can affect host gardening of the intestinal microbiome, contributing to the diversity of intestinal microbiota within a population and in some cases allowing for unfavorable microbial ecologies (dysbiosis) that confer disease susceptibility.
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Affiliation(s)
- Jonathan P Jacobs
- Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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20
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21
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Boelsterli UA, Lee KK. Mechanisms of isoniazid-induced idiosyncratic liver injury: emerging role of mitochondrial stress. J Gastroenterol Hepatol 2014; 29:678-87. [PMID: 24783247 DOI: 10.1111/jgh.12516] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Idiosyncratic drug-induced liver injury (DILI) is a significant adverse effect of antitubercular therapy with isoniazid (INH). Although the drug has been used for many decades, the underlying mode of action (both patient-specific and drug-specific mechanisms) leading to DILI are poorly understood. Among the patient-specific determinants of susceptibility to INH-associated DILI, the importance of HLA genetic variants has been increasingly recognized, whereas the role of polymorphisms of drug-metabolizing enzymes (NAT2 and CYP2E1) has become less important and remains controversial. However, these polymorphisms are merely correlative, and other molecular determinants of susceptibility have remained largely unknown. Regarding the drug-specific mechanisms underlying INH-induced liver injury, novel concepts have been emerging. Among these are covalent protein adduct formation via novel reactive intermediates, leading to hapten formation and a potential immune response, and interference with endogenous metabolism. Furthermore, INH and/or INH metabolites (e.g. hydrazine) can cause mitochondrial injury, which can lead to mitochondrial oxidant stress and impairment of energy homeostasis. Recent studies have revealed that underlying impairment of complex I function can trigger massive hepatocellular injury induced by otherwise nontoxic concentrations of INH superimposed on these mitochondrial deficiencies. This review discusses these emerging new paradigms of INH-induced DILI and highlights recent insights into the mechanisms, as well as points to the existing large gaps in our understanding of the pathogenesis.
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22
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Posma JM, Robinette SL, Holmes E, Nicholson JK. MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. ACTA ACUST UNITED AC 2013; 30:893-5. [PMID: 24177720 PMCID: PMC3957072 DOI: 10.1093/bioinformatics/btt612] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Summary: MetaboNetworks is a tool to create custom sub-networks in Matlab using main reaction pairs as defined by the Kyoto Encyclopaedia of Genes and Genomes and can be used to explore transgenomic interactions, for example mammalian and bacterial associations. It calculates the shortest path between a set of metabolites (e.g. biomarkers from a metabonomic study) and plots the connectivity between metabolites as links in a network graph. The resulting graph can be edited and explored interactively. Furthermore, nodes and edges in the graph are linked to the Kyoto Encyclopaedia of Genes and Genomes compound and reaction pair web pages. Availability and implementation: MetaboNetworks is available from http://www.mathworks.com/matlabcentral/fileexchange/42684. Contact:jmp111@ic.ac.uk or j.nicholson@imperial.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joram M Posma
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, UK
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23
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Zheng X, Zhao A, Xie G, Chi Y, Zhao L, Li H, Wang C, Bao Y, Jia W, Luther M, Su M, Nicholson JK, Jia W. Melamine-induced renal toxicity is mediated by the gut microbiota. Sci Transl Med 2013; 5:172ra22. [PMID: 23408055 DOI: 10.1126/scitranslmed.3005114] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Melamine poisoning has become widely publicized after a recent occurrence of renal injury in infants and children exposed to melamine-tainted milk in China. This renal damage is believed to result from kidney stones formed from melamine and uric acid or from melamine and its cocrystallizing chemical derivative, cyanuric acid. However, the composition of the stones and the mechanism by which the stones are formed in the renal tubules are unknown. We report that cyanuric acid can be produced in the gut by microbial transformation of melamine and serves as an integral component of the kidney stones responsible for melamine-induced renal toxicity in rats. Melamine-induced toxicity in rats was attenuated and melamine excretion increased after antibiotic suppression of gut microbial activity [corrected]. We further demonstrated that melamine is converted to cyanuric acid in vitro by bacteria cultured from normal rat feces; Klebsiella was subsequently identified in fecal samples by 16S ribosomal DNA sequencing. In culture, Klebsiella terrigena was shown to convert melamine to cyanuric acid directly. Rats colonized by K. terrigena showed exacerbated melamine-induced nephrotoxicity. Cyanuric acid was detected in the kidneys of rats administered melamine alone, and the concentration after Klebsiella colonization was increased. These findings suggest that the observed toxicity of melamine may be conditional on the exact composition and metabolic activities of the gut microbiota.
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Affiliation(s)
- Xiaojiao Zheng
- Center for Translational Medicine, and Shanghai Key Laboratory of Diabetes Mellitus, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
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24
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Evaluating effects of penicillin treatment on the metabolome of rats. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 932:134-43. [PMID: 23831706 DOI: 10.1016/j.jchromb.2013.05.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/28/2013] [Accepted: 05/31/2013] [Indexed: 11/20/2022]
Abstract
Penicillin (PEN) V, a well-known antibiotic widely used in the treatment of Gram-positive bacterial infections, was evaluated in this study. LC/MS- and NMR-based metabolic profiling were employed to examine the effects of PEN on the host's metabolic phenotype. Male Sprague Dawley rats were randomly divided into groups that were orally administered either 0.5% methylcellulose vehicle, 100 or 2400mg PEN/kg body weight once daily for up to 14 consecutive days. Urine, plasma and tissue were collected from groups sacrificed at 6h, 24h or 14d. The body fluids were subjected to clinical chemistry and metabolomics analysis; the tissue samples were processed for histopathology. The only notable clinical chemistry observation was that gamma glutamyltransferase (GGT) significantly decreased at 24h for both dose groups, and significantly decreased at 14d for the high-dose groups. Partial least squares discriminant analysis scores plots of the metabolomics data from urine and plasma samples showed dose- and time-dependent grouping patterns. Time- and dose-dependent decreases in urinary metabolites including indole-containing metabolites (such as 3-methyldioxyindole sulfate generated from bacterial metabolism of tryptophan), organic acids containing phenyl groups (such as hippuric acid, phenyllactic acid and 3-hydroxyanthranilic acid), and metabolites conjugated with sulfate or glucuronide (such as cresol sulfate and aminophenol sulfate) indicated that the gut microflora population was suppressed. Decreases in many host-gut microbiota urinary co-metabolites (indole- and phenyl-containing metabolites, amino acids, vitamins, nucleotides and bile acids) suggested gut microbiota play important roles in the regulation of host metabolism, including dietary nutrient absorption and reprocessing the absorbed nutrients. Decreases in urinary conjugated metabolites (sulfate, glucuronide and glycine conjugates) implied that gut microbiota might have an impact on chemical detoxification mechanisms. In all, these results clearly show that metabolic profiling is a useful tool to better understand the effects of the antibiotic penicillin has on the gut microbiota and the host.
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25
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Claus SP, Swann JR. Nutrimetabonomics:applications for nutritional sciences, with specific reference to gut microbial interactions. Annu Rev Food Sci Technol 2013; 4:381-99. [PMID: 23297777 DOI: 10.1146/annurev-food-030212-182612] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding the role of the diet in determining human health and disease is one major objective of modern nutrition. Mammalian biocomplexity necessitates the incorporation of systems biology technologies into contemporary nutritional research. Metabonomics is a powerful approach that simultaneously measures the low-molecular-weight compounds in a biological sample, enabling the metabolic status of a biological system to be characterized. Such biochemical profiles contain latent information relating to inherent parameters, such as the genotype, and environmental factors, including the diet and gut microbiota. Nutritional metabonomics, or nutrimetabonomics, is being increasingly applied to study molecular interactions between the diet and the global metabolic system. This review discusses three primary areas in which nutrimetabonomics has enjoyed successful application in nutritional research: the illumination of molecular relationships between nutrition and biochemical processes; elucidation of biomarker signatures of food components for use in dietary surveillance; and the study of complex trans-genomic interactions between the mammalian host and its resident gut microbiome. Finally, this review illustrates the potential for nutrimetabonomics in nutritional science as an indispensable tool to achieve personalized nutrition.
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Affiliation(s)
- Sandrine P Claus
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, Reading, RG6 6AP, UK
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26
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Nevedomskaya E, Pacchiarotta T, Artemov A, Meissner A, van Nieuwkoop C, van Dissel JT, Mayboroda OA, Deelder AM. (1)H NMR-based metabolic profiling of urinary tract infection: combining multiple statistical models and clinical data. Metabolomics 2012; 8:1227-1235. [PMID: 23136561 PMCID: PMC3483096 DOI: 10.1007/s11306-012-0411-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/15/2012] [Indexed: 11/29/2022]
Abstract
Urinary tract infection (UTI) encompasses a variety of clinical syndromes ranging from mild to life-threatening conditions. As such, it represents an interesting model for the development of an analytically based scoring system of disease severity and/or host response. Here we test the feasibility of this concept using (1)H NMR based metabolomics as the analytical platform. Using an exhaustively clinically characterized cohort and taking advantage of the multi-level study design, which opens possibilities for case-control and longitudinal modeling, we were able to identify molecular discriminators that characterize UTI patients. Among those discriminators a number (e.g. acetate, trimethylamine and others) showed association with the degree of bacterial contamination of urine, whereas others, such as, for instance, scyllo-inositol and para-aminohippuric acid, are more likely to be the markers of morbidity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0411-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ekaterina Nevedomskaya
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Tiziana Pacchiarotta
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Artem Artemov
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Axel Meissner
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Cees van Nieuwkoop
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
- Present Address: Department of Internal Medicine, Haga Hospital, The Hague, The Netherlands
| | - Jaap T. van Dissel
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Oleg A. Mayboroda
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - André M. Deelder
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
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27
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Date Y, Iikura T, Yamazawa A, Moriya S, Kikuchi J. Metabolic Sequences of Anaerobic Fermentation on Glucose-Based Feeding Substrates Based on Correlation Analyses of Microbial and Metabolite Profiling. J Proteome Res 2012; 11:5602-10. [DOI: 10.1021/pr3008682] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yasuhiro Date
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho,
Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
| | - Tomohiro Iikura
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
| | - Akira Yamazawa
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
- Research Planning and Management Group, Kajima Technical Research
Institute, KAJIMA Corporation, 2-19-1 Tobitakyu,
Chofu, Tokyo 182-0036, Japan
| | - Shigeharu Moriya
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
- RIKEN Advanced Science Institute, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho,
Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Bioagricultural
Sciences, Nagoya University, 1 Furo-cho,
Chikusa-ku, Nagoya, Aichi 464-0810, Japan
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Sugimoto M, Kawakami M, Robert M, Soga T, Tomita M. Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis. Curr Bioinform 2012; 7:96-108. [PMID: 22438836 PMCID: PMC3299976 DOI: 10.2174/157489312799304431] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Revised: 10/25/2011] [Accepted: 12/07/2011] [Indexed: 01/04/2023]
Abstract
Biological systems are increasingly being studied in a holistic manner, using omics approaches, to provide quantitative and qualitative descriptions of the diverse collection of cellular components. Among the omics approaches, metabolomics, which deals with the quantitative global profiling of small molecules or metabolites, is being used extensively to explore the dynamic response of living systems, such as organelles, cells, tissues, organs and whole organisms, under diverse physiological and pathological conditions. This technology is now used routinely in a number of applications, including basic and clinical research, agriculture, microbiology, food science, nutrition, pharmaceutical research, environmental science and the development of biofuels. Of the multiple analytical platforms available to perform such analyses, nuclear magnetic resonance and mass spectrometry have come to dominate, owing to the high resolution and large datasets that can be generated with these techniques. The large multidimensional datasets that result from such studies must be processed and analyzed to render this data meaningful. Thus, bioinformatics tools are essential for the efficient processing of huge datasets, the characterization of the detected signals, and to align multiple datasets and their features. This paper provides a state-of-the-art overview of the data processing tools available, and reviews a collection of recent reports on the topic. Data conversion, pre-processing, alignment, normalization and statistical analysis are introduced, with their advantages and disadvantages, and comparisons are made to guide the reader.
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Affiliation(s)
- Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
- Graduate School of Medicine and Faculty of Medicine Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masato Kawakami
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Department of Environment and Information Studies, Keio University, Fujisawa, Kanagawa 252-8520, Japan
| | - Martin Robert
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Department of Environment and Information Studies, Keio University, Fujisawa, Kanagawa 252-8520, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Department of Environment and Information Studies, Keio University, Fujisawa, Kanagawa 252-8520, Japan
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29
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McNiven EMS, German JB, Slupsky CM. Analytical metabolomics: nutritional opportunities for personalized health. J Nutr Biochem 2012; 22:995-1002. [PMID: 21999844 DOI: 10.1016/j.jnutbio.2011.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 05/31/2011] [Indexed: 02/08/2023]
Abstract
Nutrition is the cornerstone of health; survival depends on acquiring essential nutrients, and dietary components can both prevent and promote disease. Metabolomics, the study of all small molecule metabolic products in a system, has been shown to provide a detailed snapshot of the body's processes at any particular point in time, opening up the possibility of monitoring health and disease, prevention and treatment. Metabolomics has the potential to fundamentally change clinical chemistry and, by extension, the fields of nutrition, toxicology and medicine. Technological advances, combined with new knowledge of the human genome and gut microbiome, have made and will continue to make possible earlier, more accurate, less invasive diagnoses, all while enhancing our understanding of the root causes of disease and leading to a generation of dietary recommendations that enable optimal health. This article reviews the recent contributions of metabolomics to the fields of nutrition, toxicology and medicine. It is expected that these fields will eventually blend together through development of new technologies in metabolomics and genomics into a new area of clinical chemistry: personalized medicine.
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30
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Wijeyesekera A, Clarke PA, Bictash M, Brown IJ, Fidock M, Ryckmans T, Yap IKS, Chan Q, Stamler J, Elliott P, Holmes E, Nicholson JK. Quantitative UPLC-MS/MS analysis of the gut microbial co-metabolites phenylacetylglutamine, 4-cresyl sulphate and hippurate in human urine: INTERMAP Study. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2012; 4:65-72. [PMID: 23946767 PMCID: PMC3740387 DOI: 10.1039/c1ay05427a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The role of the gut microbiome in human health, and non-invasive measurement of gut dysbiosis are of increasing clinical interest. New high-throughput methods are required for the rapid measurement of gut microbial metabolites and to establish reference ranges in human populations. We used ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) -- positive and negative electrospray ionization modes, multiple reaction monitoring transitions -- to simultaneously measure three urinary metabolites (phenylacetylglutamine, 4-cresyl sulphate and hippurate) that are potential biomarkers of gut function, among multi-ethnic US men and women aged 40-59 from the INTERMAP epidemiologic study (n = 2000, two timed 24-hr urine collections/person). Metabolite concentrations were quantified via stable isotope labeled internal standards. The assay was linear in the ranges 1ng/mL (lower limit of quantification) to 1000ng/mL (phenylacetylglutamine and 4-cresyl sulfate) and 3ng/mL to 3000ng/mL (hippurate). These quantitative data provide new urinary reference ranges for population-based human samples: mean (standard deviation) 24-hr urinary excretion for phenylacetylglutamine was: 1283.0 (751.7) μmol/24-hr (men), 1145.9 (635.5) μmol/24-hr (women); for 4-cresyl sulphate, 1002.5 (737.1) μmol/24-hr (men), 1031.8 (687.9) μmol/24-hr (women); for hippurate, 6284.6 (4008.1) μmol/24-hr (men), 4793.0 (3293.3) μmol/24-hr (women). Metabolic profiling by UPLC-MS/MS in a large sample of free-living individuals has provided new data on urinary reference ranges for three urinary microbial co-metabolites, and demonstrates the applicability of this approach to epidemiological investigations.
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Affiliation(s)
- Anisha Wijeyesekera
- Section of Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, W2 1PG, UK
| | - Philip A. Clarke
- Pfizer Global Research and Development, Sandwich Laboratories, Ramsgate Road, Sandwich, Kent, CT13 9NJ, UK
| | - Magda Bictash
- Section of Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Ian J. Brown
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, W2 1PG, UK
| | - Mark Fidock
- Pfizer Global Research and Development, Sandwich Laboratories, Ramsgate Road, Sandwich, Kent, CT13 9NJ, UK
| | - Thomas Ryckmans
- Pfizer Global Research and Development, Sandwich Laboratories, Ramsgate Road, Sandwich, Kent, CT13 9NJ, UK
| | - Ivan K. S. Yap
- Section of Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, W2 1PG, UK
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, W2 1PG, UK
| | - Jeremiah Stamler
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL60611, USA
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, W2 1PG, UK
- MRC-HPA Centre for Environment and Health, Imperial College London, W2 1PG, UK
| | - Elaine Holmes
- Section of Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
- MRC-HPA Centre for Environment and Health, Imperial College London, W2 1PG, UK
| | - Jeremy K. Nicholson
- Section of Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
- MRC-HPA Centre for Environment and Health, Imperial College London, W2 1PG, UK
- Corresponding Author:
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31
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Swann JR, Tuohy KM, Lindfors P, Brown DT, Gibson GR, Wilson ID, Sidaway J, Nicholson JK, Holmes E. Variation in antibiotic-induced microbial recolonization impacts on the host metabolic phenotypes of rats. J Proteome Res 2011; 10:3590-603. [PMID: 21591676 DOI: 10.1021/pr200243t] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The interaction between the gut microbiota and their mammalian host is known to have far-reaching consequences with respect to metabolism and health. We investigated the effects of eight days of oral antibiotic exposure (penicillin and streptomycin sulfate) on gut microbial composition and host metabolic phenotype in male Han-Wistar rats (n = 6) compared to matched controls. Early recolonization was assessed in a third group exposed to antibiotics for four days followed by four days recovery (n = 6). Fluorescence in situ hybridization analysis of the intestinal contents collected at eight days showed a significant reduction in all bacterial groups measured (control, 10(10.7) cells/g feces; antibiotic-treated, 10(8.4)). Bacterial suppression reduced the excretion of mammalian-microbial urinary cometabolites including hippurate, phenylpropionic acid, phenylacetylglycine and indoxyl-sulfate whereas taurine, glycine, citrate, 2-oxoglutarate, and fumarate excretion was elevated. While total bacterial counts remained notably lower in the recolonized animals (10(9.1) cells/g faeces) compared to the controls, two cage-dependent subgroups emerged with Lactobacillus/Enterococcus probe counts dominant in one subgroup. This dichotomous profile manifested in the metabolic phenotypes with subgroup differences in tricarboxylic acid cycle metabolites and indoxyl-sulfate excretion. Fecal short chain fatty acids were diminished in all treated animals. Antibiotic treatment induced a profound effect on the microbiome structure, which was reflected in the metabotype. Moreover, the recolonization process was sensitive to the microenvironment, which may impact on understanding downstream consequences of antibiotic consumption in human populations.
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Affiliation(s)
- Jonathan R Swann
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom.
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Holmes E, Li JV, Athanasiou T, Ashrafian H, Nicholson JK. Understanding the role of gut microbiome-host metabolic signal disruption in health and disease. Trends Microbiol 2011; 19:349-59. [PMID: 21684749 DOI: 10.1016/j.tim.2011.05.006] [Citation(s) in RCA: 367] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 05/13/2011] [Indexed: 02/08/2023]
Abstract
There is growing awareness of the importance of the gut microbiome in health and disease, and recognition that the microbe to host metabolic signalling is crucial to understanding the mechanistic basis of their interaction. This opens new avenues of research for advancing knowledge on the aetiopathologic consequences of dysbiosis with potential for identifying novel microbially-related drug targets. Advances in both sequencing technologies and metabolic profiling platforms, coupled with mathematical integration approaches, herald a new era in characterizing the role of the microbiome in metabolic signalling within the host and have far reaching implications in promoting health in both the developed and developing world.
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Affiliation(s)
- Elaine Holmes
- Department of Surgery and Cancer, Imperial College London, London, UK
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Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R. Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology 2011; 140:1713-9. [PMID: 21530737 PMCID: PMC10924805 DOI: 10.1053/j.gastro.2011.02.011] [Citation(s) in RCA: 256] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 02/04/2011] [Accepted: 02/09/2011] [Indexed: 12/02/2022]
Abstract
Little was known about the development of the gastrointestinal (GI) tract microbiota, until recently, because of difficulties in obtaining sufficient sequence information from enough people or time points. Now, with decreased costs of DNA sequencing and improved bioinformatic tools, we can compare GI tract bacterial communities among individuals, of all ages from infancy to adulthood. Some key recent findings are that the initial bacterial community, even in the GI tract, depends strongly on delivery mode; that the process of early development of the microbiota is highly unstable and idiosyncratic; that the microbiota differs considerably among children from different countries; and that older adults have substantially different GI tract communities than younger adults, indicating that the GI tract microbiota can change throughout life. We relate these observations to different models of evolution including the evolution of senescence and suggest that probiotics be selected based on patient age. Studies of the microbiota in older people might tell us which probiotics could increase longevity. Drug metabolism varies among individuals with different microbial communities, so age- and region-specific clinical trials are required to ensure safety and efficacy.
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Affiliation(s)
| | - Martin J. Blaser
- Departments of Medicine and Microbiology and University Langone Medical Center, New York, NY 10016
- Veterans Affairs Medical Center, New York University Langone Medical Center, New York, NY 10016
- Department of Biology, New York University, New York, NY 10003
| | - Ruth E. Ley
- Department of Microbiology, Cornell University, Ithaca, NY 14850
| | - Rob Knight
- Howard Hughes Medical Institute, Boulder, CO 80309
- Department of Chemistry & Biochemistry, University of Colorado at Boulder, Boulder, CO 80309
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34
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Keun HC. Metabolic Profiling for Biomarker Discovery. Biomarkers 2010. [DOI: 10.1002/9780470918562.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. Proc Natl Acad Sci U S A 2010; 108 Suppl 1:4523-30. [PMID: 20837534 DOI: 10.1073/pnas.1006734107] [Citation(s) in RCA: 520] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We elucidate the detailed effects of gut microbial depletion on the bile acid sub-metabolome of multiple body compartments (liver, kidney, heart, and blood plasma) in rats. We use a targeted ultra-performance liquid chromatography with time of flight mass-spectrometry assay to characterize the differential primary and secondary bile acid profiles in each tissue and show a major increase in the proportion of taurine-conjugated bile acids in germ-free (GF) and antibiotic (streptomycin/penicillin)-treated rats. Although conjugated bile acids dominate the hepatic profile (97.0 ± 1.5%) of conventional animals, unconjugated bile acids comprise the largest proportion of the total measured bile acid profile in kidney (60.0 ± 10.4%) and heart (53.0 ± 18.5%) tissues. In contrast, in the GF animal, taurine-conjugated bile acids (especially taurocholic acid and tauro-β-muricholic acid) dominated the bile acid profiles (liver: 96.0 ± 14.5%; kidney: 96 ± 1%; heart: 93 ± 1%; plasma: 93.0 ± 2.3%), with unconjugated and glycine-conjugated species representing a small proportion of the profile. Higher free taurine levels were found in GF livers compared with the conventional liver (5.1-fold; P < 0.001). Bile acid diversity was also lower in GF and antibiotic-treated tissues compared with conventional animals. Because bile acids perform important signaling functions, it is clear that these chemical communication networks are strongly influenced by microbial activities or modulation, as evidenced by farnesoid X receptor-regulated pathway transcripts. The presence of specific microbial bile acid co-metabolite patterns in peripheral tissues (including heart and kidney) implies a broader signaling role for these compounds and emphasizes the extent of symbiotic microbial influences in mammalian homeostasis.
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36
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Abstract
Gut microbiota is an assortment of microorganisms inhabiting the length and width of the mammalian gastrointestinal tract. The composition of this microbial community is host specific, evolving throughout an individual's lifetime and susceptible to both exogenous and endogenous modifications. Recent renewed interest in the structure and function of this “organ” has illuminated its central position in health and disease. The microbiota is intimately involved in numerous aspects of normal host physiology, from nutritional status to behavior and stress response. Additionally, they can be a central or a contributing cause of many diseases, affecting both near and far organ systems. The overall balance in the composition of the gut microbial community, as well as the presence or absence of key species capable of effecting specific responses, is important in ensuring homeostasis or lack thereof at the intestinal mucosa and beyond. The mechanisms through which microbiota exerts its beneficial or detrimental influences remain largely undefined, but include elaboration of signaling molecules and recognition of bacterial epitopes by both intestinal epithelial and mucosal immune cells. The advances in modeling and analysis of gut microbiota will further our knowledge of their role in health and disease, allowing customization of existing and future therapeutic and prophylactic modalities.
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Affiliation(s)
- Inna Sekirov
- Michael Smith Laboratories, Department of Microbiology and Immunology, and Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Shannon L. Russell
- Michael Smith Laboratories, Department of Microbiology and Immunology, and Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - L. Caetano M. Antunes
- Michael Smith Laboratories, Department of Microbiology and Immunology, and Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - B. Brett Finlay
- Michael Smith Laboratories, Department of Microbiology and Immunology, and Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
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37
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Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 2010; 107:11971-5. [PMID: 20566857 DOI: 10.1073/pnas.1002601107] [Citation(s) in RCA: 2935] [Impact Index Per Article: 209.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Upon delivery, the neonate is exposed for the first time to a wide array of microbes from a variety of sources, including maternal bacteria. Although prior studies have suggested that delivery mode shapes the microbiota's establishment and, subsequently, its role in child health, most researchers have focused on specific bacterial taxa or on a single body habitat, the gut. Thus, the initiation stage of human microbiome development remains obscure. The goal of the present study was to obtain a community-wide perspective on the influence of delivery mode and body habitat on the neonate's first microbiota. We used multiplexed 16S rRNA gene pyrosequencing to characterize bacterial communities from mothers and their newborn babies, four born vaginally and six born via Cesarean section. Mothers' skin, oral mucosa, and vagina were sampled 1 h before delivery, and neonates' skin, oral mucosa, and nasopharyngeal aspirate were sampled <5 min, and meconium <24 h, after delivery. We found that in direct contrast to the highly differentiated communities of their mothers, neonates harbored bacterial communities that were undifferentiated across multiple body habitats, regardless of delivery mode. Our results also show that vaginally delivered infants acquired bacterial communities resembling their own mother's vaginal microbiota, dominated by Lactobacillus, Prevotella, or Sneathia spp., and C-section infants harbored bacterial communities similar to those found on the skin surface, dominated by Staphylococcus, Corynebacterium, and Propionibacterium spp. These findings establish an important baseline for studies tracking the human microbiome's successional development in different body habitats following different delivery modes, and their associated effects on infant health.
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38
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Han J, Antunes LCM, Finlay BB, Borchers CH. Metabolomics: towards understanding host-microbe interactions. Future Microbiol 2010; 5:153-61. [PMID: 20143941 DOI: 10.2217/fmb.09.132] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Metabolomics employs an array of analytical techniques, including high-resolution nuclear magnetic resonance spectroscopy and mass spectrometry, to simultaneously analyze hundreds to thousands of small-molecule metabolites in biological samples. In conjunction with chemoinformatics and bioinformatics tools, metabolomics enables comprehensive characterization of the metabolic phenotypes (metabotypes) of the human, and other mammalian, hosts that have co-evolved with a large number of diverse commensal microbes, especially in the intestinal tract. Correlation of the metabotypes with the microbial profiles derived from culture-independent molecular techniques is increasingly helping to decipher inherent and intimate host-microbe relationships. This integrated, systems biology approach is improving our understanding of the molecular mechanisms underlying multilevel host-microbe interactions, and promises to elucidate the etiologies of human disorders resulting from unfavorable human-microbial associations, including enteric infections.
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Affiliation(s)
- Jun Han
- University of Victoria - Genome BC Proteomics Centre, 3101-4464 Markham Street, Victoria, BC, V8Z 7X8, Canada.
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39
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Manary MJ, Heikens GT, Golden M. Kwashiorkor: more hypothesis testing is needed to understand the aetiology of oedema. Malawi Med J 2009; 21:106-7. [PMID: 20345018 PMCID: PMC3717490 DOI: 10.4314/mmj.v21i3.45630] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Mark J Manary
- Department of Pediatrics, Washington University School of Medicine, USA
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40
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The gastrointestinal microbiome: a malleable, third genome of mammals. Mamm Genome 2009; 20:395-403. [PMID: 19629594 DOI: 10.1007/s00335-009-9204-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 06/26/2009] [Indexed: 12/13/2022]
Abstract
The nonpathogenic, mutualistic bacteria of the mammalian gastrointestinal tract provide a number of benefits to the host. Recent reports have shown how the aggregate genomes of gastrointestinal bacteria provide novel benefits by functioning as the third major genome in mammals along with the nuclear and mitochondrial genomes. Consequently, efforts are underway to elucidate the complexity of the organisms comprising the unique ecosystem of the gastrointestinal tract, as well as those associated with other epidermal surfaces. The current knowledge of the gastrointestinal microbiome, its relationship to human health and disease with a particular focus on mammalian physiology, and efforts to alter its composition as a novel therapeutic approach are reviewed.
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