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Muhlebach MS, Sha W, MacIntosh B, Kelley TJ, Muenzer J. Metabonomics reveals altered metabolites related to inflammation and energy utilization at recovery of cystic fibrosis lung exacerbation. Metabol Open 2019; 3:100010. [PMID: 32812947 PMCID: PMC7424819 DOI: 10.1016/j.metop.2019.100010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/31/2019] [Accepted: 06/01/2019] [Indexed: 02/07/2023] Open
Abstract
Background Cystic fibrosis lung disease is characterized by chronic bacterial infections in the setting of mucus abnormalities. Patients experience periodic exacerbations that manifest with increased respiratory symptoms that require intensification of therapy with enhanced airway clearance and intravenous (IV) antibiotics. Objectives In an observational study we tested if the profile of metabolites in serum distinguished the pre-from post-exacerbation state and which systemically measurable pathways were affected during the process to recovery. Methods Serum collected within 48 h of start and completion, respectively of IV antibiotics was collected from people with CF ages 6–30 years. Three day food records were collected prior to each sample. To reduce variation between subjects only subjects who had pancreatic insufficiency, had similar CF mutations, and did not have CF liver disease or diabetes were included. Metabolomic profiling was conducted by Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy with metabolites being identified based on retention time/index, mass to charge ratio and comparison to known compounds. Biostatistical analyses used paired t-test with correction for multiple comparisons and orthogonal partial least square discriminant analysis. Results Thirty subjects (20 male) with a mean ± SEM age of 15.3 ± 1.2 years participated, 17 of whom had matched food-records. Lung function was significantly improved post-therapy compared to pre-therapy, (mean ± SEM) 75 ± 4% vs. 68 ± 4% predicted (n = 26). Serum metabonomics showed distinction of the pre-vs. post-therapy groups with 123 compounds contributing to the differentiation pre-versus post-antibiotics by multiple biostatistical analyses. Compounds and pathways affected included bile acids and microbial derived amino acid metabolites, increases in lipid classes of the glycerophospholipid, glycerolipids, cholesterol, phopsholipids, and most pronounced, the class of sphingolipids. Changes in n6/n3 fatty acids, decreased polyamines but increased metabolites in the nitric oxide pathway, and changes in the tryptophan-kynurenine pathway indicated decreased inflammation at resolution of exacerbation. Conclusions Changes in serum metabolites that distinguished CF pulmonary exacerbation vs. resolution of symptoms showed evidence of decreased inflammation and improvement from a catabolic state. Serum metabonomics distinguishes cystic fibrosis exacerbation to resolution state. Distinguishing pathways indicate alterations in (gut) microbiome and bile acids. Serum metabolites at resolution show decreased inflammation and oxidative stress. Lipid markers indicate improvement from a catabolic state at exacerbation.
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Key Words
- AA, arachidonate
- ARG, arginase
- BA, bile acids
- BHBA, 3-hydroxybutyrate
- CF, cystic fibrosis
- CFTR, Cystic Fibrosis Transmembrane Regulator
- CRP, C-reactive protein
- DHA, docosahexaenoate
- ESI, electrospray ionization
- FDR, false discovery rate
- FEV1, forced expiratory volume in 1st second
- IDO, indoleamine-2-3-dioxygenase
- IV, intravenous
- NOS, nitric oxide synthase
- ODC, ornithine decarboxylase
- OPLS-DA, orthogonal partial least square discriminant analysis
- QC, quality control
- RI, retention time/index
- UNC, University of North Carolina at Chapel Hill
- UPLC, ultrahigh performance liquid chromatography-tandem mass spectroscopy
- VIP, variable influence on projection score
- n3-DPA, docosapentaenoate
- q, significance at a 5% FDR cut-off
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Affiliation(s)
- Marianne S Muhlebach
- Dept. Pediatrics, Division Pulmonary Medicine, University of North Carolina at Chapel Hill, 450 MacNider, 330 S. Columbia Road, Chapel Hill, NC, 27599-7217, USA.,Marsico Lung Institute, Chapel Hill, NC, USA
| | - Wei Sha
- Bioinformatics Services Division, Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 150 Research Campus Dr, Kannapolis, NC 28081, NC, USA
| | - Beth MacIntosh
- Metabolic and Nutrition Research Core, UNC Healthcare, Nutrition and Food Services Department, 102 Mason Farm Rd, CB#7777, Chapel Hill, NC, USA
| | - Thomas J Kelley
- Departments of Pediatrics/Pharmacology, Case Western Reserve University, 833 BRB, 10900, Euclid Ave, Cleveland, OH, USA
| | - Joseph Muenzer
- Dept. Pediatrics, Division Metabolism and Genetics, University of North Carolina at Chapel Hill, USA
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Menni C, Hernandez MM, Vital M, Mohney RP, Spector TD, Valdes AM. Circulating levels of the anti-oxidant indoleproprionic acid are associated with higher gut microbiome diversity. Gut Microbes 2019; 10:688-695. [PMID: 31030641 PMCID: PMC6866703 DOI: 10.1080/19490976.2019.1586038] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The gut microbiome has recently emerged as an important regulator of insulin resistance and abdominal obesity. The tryptophan metabolite generated by the gut microbiome, indoleproprionic acid (IPA) has been shown to predict the onset of type 2 diabetes. IPA is a metabolite produced by gut microbes from dietary tryptophan that exhibits a high degree of inter-individual variation. The microbiome composition parameters that are associated with circulating levels of this potent anti-oxidant have however not been investigated to date in human populations. In 1018 middle-aged women from the TwinsUK cohort, we assessed the relationship between serum IPA levels and gut microbiome composition targeting the 16S rRNA gene. Microbiome alpha-diversity was positively correlated with serum indoleproprionic acid levels (Shannon Diversity: Beta[95%CI] = 0.19[0.13;0.25], P = 6.41 × 10-10) after adjustment for covariates. Sixteen taxa and 12 operational taxonomic units (OTUs) associated with IPA serum levels. Among these are positive correlations with the butyrate-producing Faecalibacterium prausnitzii, the class Mollicutes and the order RF39 of the Tenericutes, and Coprococcus Negative correlations instead were observed with Eubacterium dolichum previously shown to correlate with visceral fat mass and several genera in the Lachnospiraceae family such as Blautia and Ruminococcus previously shown to correlate with obesity. Microbiome composition parameters explained ~20% of the variation in circulating levels of IPA, whereas nutritional and host genetic parameters explained only ~4%. Our data confirm an association between IPA circulating levels and metabolic syndrome parameters and indicate that gut microbiome composition influences IPA levels.
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Affiliation(s)
- Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK,CONTACT Ana M Valdes School of Medicine, University of Nottingham, Clinical Sciences Bldg, City Hospital, Hucknall Rd, Nottingham NG5 1PB, UK
| | | | - Marius Vital
- Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Robert P. Mohney
- Discovery and Translational Sciences, Metabolon Inc, Raleigh-Durham, NC, USA
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Ana M. Valdes
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK,MSK Theme, NIHR Nottingham Biomedical Research Centre, Nottingham, UK,School of Medicine, Nottingham City Hospital, Nottingham, UK
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53
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Tam V, Turcotte M, Meyre D. Established and emerging strategies to crack the genetic code of obesity. Obes Rev 2019; 20:212-240. [PMID: 30353704 DOI: 10.1111/obr.12770] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 12/11/2022]
Abstract
Tremendous progress has been made in the genetic elucidation of obesity over the past two decades, driven largely by technological, methodological and organizational innovations. Current strategies for identifying obesity-predisposing loci/genes, including cytogenetics, linkage analysis, homozygosity mapping, admixture mapping, candidate gene studies, genome-wide association studies, custom genotyping arrays, whole-exome sequencing and targeted exome sequencing, have achieved differing levels of success, and the identified loci in aggregate explain only a modest fraction of the estimated heritability of obesity. This review outlines the successes and limitations of these approaches and proposes novel strategies, including the use of exceptionally large sample sizes, the study of diverse ethnic groups and deep phenotypes and the application of innovative methods and study designs, to identify the remaining obesity-predisposing genes. The use of both established and emerging strategies has the potential to crack the genetic code of obesity in the not-too-distant future. The resulting knowledge is likely to yield improvements in obesity prediction, prevention and care.
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Affiliation(s)
- V Tam
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - M Turcotte
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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54
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Bowyer RCE, Jackson MA, Le Roy CI, Ni Lochlainn M, Spector TD, Dowd JB, Steves CJ. Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study. Microorganisms 2019; 7:E17. [PMID: 30641975 PMCID: PMC6351927 DOI: 10.3390/microorganisms7010017] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 12/12/2022] Open
Abstract
Socioeconomic inequalities in health and mortality are well established, but the biological mechanisms underlying these associations are less understood. In parallel, the gut microbiome is emerging as a potentially important determinant of human health, but little is known about its broader environmental and social determinants. We test the association between gut microbiota composition and individual- and area-level socioeconomic factors in a well-characterized twin cohort. In this study, 1672 healthy volunteers from twin registry TwinsUK had data available for at least one socioeconomic measure, existing fecal 16S rRNA microbiota data, and all considered co-variables. Associations with socioeconomic status (SES) were robust to adjustment for known health correlates of the microbiome; conversely, these health-microbiome associations partially attenuated with adjustment for SES. Twins discordant for IMD (Index of Multiple Deprivation) were shown to significantly differ by measures of compositional dissimilarity, with suggestion the greater the difference in twin pair IMD, the greater the dissimilarity of their microbiota. Future research should explore how SES might influence the composition of the gut microbiota and its potential role as a mediator of differences associated with SES.
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Affiliation(s)
- Ruth C E Bowyer
- The Department of Twin Research, Kings College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
| | - Matthew A Jackson
- The Department of Twin Research, Kings College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX1 3QR, UK.
| | - Caroline I Le Roy
- The Department of Twin Research, Kings College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
| | - Mary Ni Lochlainn
- The Department of Twin Research, Kings College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
- Clinical Age Research Unit, Kings College Hospital Foundation Trust, London SE5 9RS, UK.
| | - Tim D Spector
- The Department of Twin Research, Kings College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
| | - Jennifer B Dowd
- Department of Global Health & Social Medicine, King's Building, King's College London, Strand, London WC2R 2LS, UK.
- CUNY Graduate School of Public Health and Health Policy, 55 W 125th Street, New York, NY 10027, USA.
| | - Claire J Steves
- The Department of Twin Research, Kings College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
- Department of Ageing and Health, St Thomas' Hospital, 9th floor, North Wing, Westminster Bridge Road, London SE1 7EH, UK.
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55
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Forster GM, Stockman J, Noyes N, Heuberger AL, Broeckling CD, Bantle CM, Ryan EP. A Comparative Study of Serum Biochemistry, Metabolome and Microbiome Parameters of Clinically Healthy, Normal Weight, Overweight, and Obese Companion Dogs. Top Companion Anim Med 2018; 33:126-135. [PMID: 30502863 DOI: 10.1053/j.tcam.2018.08.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/30/2018] [Accepted: 08/11/2018] [Indexed: 12/20/2022]
Abstract
The aim of this study was to compare fecal microbiome, plasma, fecal and urine metabolomes, and serum biochemistry of adult companion dogs according to body condition scores. Blood, serum/plasma, urine, and fecal samples were collected from 66 clinically healthy, adult companion dogs of either normal weight (NW), overweight (OW), or obese dogs (OB). analyses included fecal microbiome analyses via 16S ribosomal RNA gene amplicon; sequencing, nontargeted plasma, fecal, and urine metabolomics using liquid chromatography/gas chromatography-mass; spectrometry, and serum biochemistry for each dog. Few significant differences in serum biochemistry and fecal microbiome Operational Taxonomic Unit (OTU) were found between weight groups and there was high OTU variation between individual dogs. NW dogs had higher relative abundance of the genus Eubacterium (log-fold change 4.3, adjusted P value = .003) and lower relative abundance of the family Bifidobacteriaceae (log-fold change -3.6, adjusted P value = .02) compared to OB dogs. The microbiome of NW dogs had higher OTU richness compared with OB dogs. Metabolome analysis showed 185 plasma, 37 fecal, and 45 urine metabolites that significantly differed between NW and OW or OB dogs. There were notable significant differences in relative abundance of several plasma phospholipid moieties and fecal volatile fatty acids between weight phenotypes. The combinations of host and gut microbiota and metabolic shifts suggest a pattern that could help detection of early metabolic changes in overweight dogs before the development of obesity related disease. The results of this study support the need for continued investigation into sensitive measures of metabolic aberrancies in overweight dogs.
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Affiliation(s)
- Genevieve M Forster
- College of Veterinary Medicine and Biomedical Sciences, Departments of Clinical Sciences, Colorado State University, Fort Collins, CO, USA; College of Veterinary Medicine and Biomedical Sciences, Environmental and Radiological Health Sciences Colorado State University, Fort Collins, CO, USA
| | - Jonathan Stockman
- College of Veterinary Medicine and Biomedical Sciences, Departments of Clinical Sciences, Colorado State University, Fort Collins, CO, USA; College of Veterinary Medicine and Biomedical Sciences, Environmental and Radiological Health Sciences Colorado State University, Fort Collins, CO, USA
| | - Noelle Noyes
- College of Veterinary Medicine and Biomedical Sciences, Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Adam L Heuberger
- College of Agricultural Sciences, Departments of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Corey D Broeckling
- College of Agricultural Sciences, Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, USA
| | - Collin M Bantle
- College of Veterinary Medicine and Biomedical Sciences, Environmental and Radiological Health Sciences Colorado State University, Fort Collins, CO, USA
| | - Elizabeth P Ryan
- College of Veterinary Medicine and Biomedical Sciences, Environmental and Radiological Health Sciences Colorado State University, Fort Collins, CO, USA.
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56
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Menni C, Lin C, Cecelja M, Mangino M, Matey-Hernandez ML, Keehn L, Mohney RP, Steves CJ, Spector TD, Kuo CF, Chowienczyk P, Valdes AM. Gut microbial diversity is associated with lower arterial stiffness in women. Eur Heart J 2018; 39:2390-2397. [PMID: 29750272 PMCID: PMC6030944 DOI: 10.1093/eurheartj/ehy226] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/06/2017] [Accepted: 04/06/2018] [Indexed: 12/11/2022] Open
Abstract
Aims The gut microbiome influences metabolic syndrome (MetS) and inflammation and is therapeutically modifiable. Arterial stiffness is poorly correlated with most traditional risk factors. Our aim was to examine whether gut microbial composition is associated with arterial stiffness. Methods and results We assessed the correlation between carotid-femoral pulse wave velocity (PWV), a measure of arterial stiffness, and gut microbiome composition in 617 middle-aged women from the TwinsUK cohort with concurrent serum metabolomics data. Pulse wave velocity was negatively correlated with gut microbiome alpha diversity (Shannon index, Beta(SE)= -0.25(0.07), P = 1 × 10-4) after adjustment for covariates. We identified seven operational taxonomic units associated with PWV after adjusting for covariates and multiple testing-two belonging to the Ruminococcaceae family. Associations between microbe abundances, microbe diversity, and PWV remained significant after adjustment for levels of gut-derived metabolites (indolepropionate, trimethylamine oxide, and phenylacetylglutamine). We linearly combined the PWV-associated gut microbiome-derived variables and found that microbiome factors explained 8.3% (95% confidence interval 4.3-12.4%) of the variance in PWV. A formal mediation analysis revealed that only a small proportion (5.51%) of the total effect of the gut microbiome on PWV was mediated by insulin resistance and visceral fat, c-reactive protein, and cardiovascular risk factors after adjusting for age, body mass index, and mean arterial pressure. Conclusions Gut microbiome diversity is inversely associated with arterial stiffness in women. The effect of gut microbiome composition on PWV is only minimally mediated by MetS. This first human observation linking the gut microbiome to arterial stiffness suggests that targeting the microbiome may be a way to treat arterial ageing.
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Affiliation(s)
- Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas' Hospital, London, UK
| | - Chihung Lin
- Division of Rheumatology, Allergy and Immunology, Chang Gung Memorial Hospital, Fuxing Street, Guishan Dist., Taoyuan City, Taiwan
| | - Marina Cecelja
- Department of Clinical Pharmacology, British Heart Foundation Centre, King’s College London, St Thomas' Hospital, London, UK
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas' Hospital, London, UK
- NIHR Biomedical Research Centre at Guy’s and St Thomas’ Foundation Trust, St Thomas’ Hospital, London, UK
| | - Maria Luisa Matey-Hernandez
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas' Hospital, London, UK
| | - Louise Keehn
- Department of Clinical Pharmacology, British Heart Foundation Centre, King’s College London, St Thomas' Hospital, London, UK
| | | | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas' Hospital, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas' Hospital, London, UK
| | - Chang-Fu Kuo
- Division of Rheumatology, Allergy and Immunology, Chang Gung Memorial Hospital, Fuxing Street, Guishan Dist., Taoyuan City, Taiwan
- School of Medicine, Nottingham City Hospital, Hucknall Road, Nottingham, UK
| | - Phil Chowienczyk
- Department of Clinical Pharmacology, British Heart Foundation Centre, King’s College London, St Thomas' Hospital, London, UK
| | - Ana M Valdes
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas' Hospital, London, UK
- School of Medicine, Nottingham City Hospital, Hucknall Road, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, Derby Rd, Nottingham, UK
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57
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Zierer J, Jackson MA, Kastenmüller G, Mangino M, Long T, Telenti A, Mohney RP, Small KS, Bell JT, Steves CJ, Valdes AM, Spector TD, Menni C. The fecal metabolome as a functional readout of the gut microbiome. Nat Genet 2018; 50:790-795. [PMID: 29808030 PMCID: PMC6104805 DOI: 10.1038/s41588-018-0135-7] [Citation(s) in RCA: 407] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/05/2018] [Indexed: 01/07/2023]
Abstract
The human gut microbiome plays a key role in human health 1 , but 16S characterization lacks quantitative functional annotation 2 . The fecal metabolome provides a functional readout of microbial activity and can be used as an intermediate phenotype mediating host-microbiome interactions 3 . In this comprehensive description of the fecal metabolome, examining 1,116 metabolites from 786 individuals from a population-based twin study (TwinsUK), the fecal metabolome was found to be only modestly influenced by host genetics (heritability (H2) = 17.9%). One replicated locus at the NAT2 gene was associated with fecal metabolic traits. The fecal metabolome largely reflects gut microbial composition, explaining on average 67.7% (±18.8%) of its variance. It is strongly associated with visceral-fat mass, thereby illustrating potential mechanisms underlying the well-established microbial influence on abdominal obesity. Fecal metabolic profiling thus is a novel tool to explore links among microbiome composition, host phenotypes, and heritable complex traits.
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Affiliation(s)
- Jonas Zierer
- Department for Twin Research & Genetic Epidemiology, King's College London, London, UK
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA
| | - Matthew A Jackson
- Department for Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Massimo Mangino
- Department for Twin Research & Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Tao Long
- Human Longevity, Inc, San Diego, CA, USA
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | | | - Kerrin S Small
- Department for Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department for Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department for Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Ana M Valdes
- Department for Twin Research & Genetic Epidemiology, King's College London, London, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham, UK
- School of Medicine, University of Nottingham, Nottingham, UK
| | - Tim D Spector
- Department for Twin Research & Genetic Epidemiology, King's College London, London, UK.
| | - Cristina Menni
- Department for Twin Research & Genetic Epidemiology, King's College London, London, UK.
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58
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Chen EB, Cason C, Gilbert JA, Ho KJ. Current State of Knowledge on Implications of Gut Microbiome for Surgical Conditions. J Gastrointest Surg 2018; 22:1112-1123. [PMID: 29623674 PMCID: PMC5966332 DOI: 10.1007/s11605-018-3755-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023]
Abstract
The role of the microbiome in human health has become a central tenant of current medical research, infiltrating a diverse disciplinary base whereby microbiology, computer science, ecology, gastroenterology, immunology, neurophysiology and psychology, metabolism, and cardiovascular medicine all intersect. Traditionally, commensal gut microbiota have been assumed to play a significant role only in the metabolic processing of dietary nutrients and host metabolites, the fortification of gut epithelial barrier function, and the development of mucosal immunity. However, over the last 20 years, new technologies and renewed interest have uncovered a considerably broader influence of the microbiota on health maintenance and disease development, many of which are of particular relevance for surgeons. This article provides a broad overview of the current state of knowledge and a review of the technology that helped in their formation.
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Affiliation(s)
- Edmund B Chen
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cori Cason
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jack A Gilbert
- Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Karen J Ho
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Division of Vascular Surgery, Feinberg School of Medicine, Northwestern University, 676 North St. Clair Street, Suite 650, Chicago, IL, 60611, USA.
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59
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Bowyer RCE, Jackson MA, Pallister T, Skinner J, Spector TD, Welch AA, Steves CJ. Use of dietary indices to control for diet in human gut microbiota studies. MICROBIOME 2018; 6:77. [PMID: 29695307 PMCID: PMC5918560 DOI: 10.1186/s40168-018-0455-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 03/28/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Environmental factors have a large influence on the composition of the human gut microbiota. One of the most influential and well-studied is host diet. To assess and interpret the impact of non-dietary factors on the gut microbiota, we endeavoured to determine the most appropriate method to summarise community variation attributable to dietary effects. Dietary habits are multidimensional with internal correlations. This complexity can be simplified by using dietary indices that quantify dietary variance in a single measure and offer a means of controlling for diet in microbiota studies. However, to date, the applicability of different dietary indices to gut microbiota studies has not been assessed. Here, we use food frequency questionnaire (FFQ) data from members of the TwinsUK cohort to create three different dietary measures applicable in western-diet populations: The Healthy Eating Index (HEI), the Mediterranean Diet Score (MDS) and the Healthy Food Diversity index (HFD-Index). We validate and compare these three indices to determine which best summarises dietary influences on gut microbiota composition. RESULTS All three indices were independently validated using established measures of health, and all were significantly associated with microbiota measures; the HEI had the highest t values in models of alpha diversity measures, and had the highest number of associations with microbial taxa. Beta diversity analyses showed the HEI explained the greatest variance of microbiota composition. In paired tests between twins discordant for dietary index score, the HEI was associated with the greatest variation of taxa and twin dissimilarity. CONCLUSIONS We find that the HEI explains the most variance in, and has the strongest association with, gut microbiota composition in a western (UK) population, suggesting that it may be the best summary measure to capture gut microbiota variance attributable to habitual diet in comparable populations.
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Affiliation(s)
- Ruth C. E. Bowyer
- The Department of Twin Research, Kings College London, 3-4th Floor South Wing Block D, St Thomas’ Hospital, Westminster Bridge Road, London, SE1 7EH UK
| | - Matthew A. Jackson
- The Department of Twin Research, Kings College London, 3-4th Floor South Wing Block D, St Thomas’ Hospital, Westminster Bridge Road, London, SE1 7EH UK
| | - Tess Pallister
- The Department of Twin Research, Kings College London, 3-4th Floor South Wing Block D, St Thomas’ Hospital, Westminster Bridge Road, London, SE1 7EH UK
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC-WHO), 150 Cours Albert Thomas, 69008 Lyon, France
| | - Jane Skinner
- Norwich Medical School 2.02, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | - Tim D. Spector
- The Department of Twin Research, Kings College London, 3-4th Floor South Wing Block D, St Thomas’ Hospital, Westminster Bridge Road, London, SE1 7EH UK
| | - Ailsa A. Welch
- Norwich Medical School 2.02, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | - Claire J. Steves
- The Department of Twin Research, Kings College London, 3-4th Floor South Wing Block D, St Thomas’ Hospital, Westminster Bridge Road, London, SE1 7EH UK
- Clinical Age Research Unit, Kings College Hospital Foundation Trust, London, UK
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60
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Moran-Ramos S, López-Contreras BE, Canizales-Quinteros S. Gut Microbiota in Obesity and Metabolic Abnormalities: A Matter of Composition or Functionality? Arch Med Res 2017; 48:735-753. [PMID: 29292011 DOI: 10.1016/j.arcmed.2017.11.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/15/2017] [Indexed: 12/18/2022]
Abstract
The obesity pandemic and the metabolic complications derived from it represent a major public health challenge worldwide. Although obesity is a multifactorial disease, research from the past decade suggests that the gut microbiota interacts with host genetics and diet, as well as with other environmental factors, and thus contributes to the development of obesity and related complications. Despite abundant research on animal models, substantial evidence from humans has only started to accumulate over the past few years. Thus, the aim of the present review is to discuss structural and functional characteristics of the gut microbiome in human obesity, challenges associated with multi-omic technologies, and advances in identifying microbial metabolites with a direct link to obesity and metabolic complications. To date, studies suggests that obesity is related to low microbial diversity and taxon depletion sometimes resulting from an interaction with host dietary habits and genotype. These findings support the idea that the depletion or absence of certain taxa leaves an empty niche, likely leading to compromised functionality and thus promoting dysbiosis. Although the role of altered gut microbiota as cause or consequence of obesity remains controversial, research on microbial genomes and metabolites points towards an increased extraction of energy from the diet in obesity and suggests that metabolites, such as trimethylamine-N-oxide or branched-chain amino acids, participate in metabolic complications. Future research should be focused on structural and functional levels to unravel the mechanism linking gut microbiota and obesity.
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Affiliation(s)
- Sofia Moran-Ramos
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Ciudad de México, México; Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica, Ciudad de México, México.
| | - Blanca E López-Contreras
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/Instituto Nacional de Medicina Genómica, Ciudad de México, México.
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Pallister T, Jackson MA, Martin TC, Zierer J, Jennings A, Mohney RP, MacGregor A, Steves CJ, Cassidy A, Spector TD, Menni C. Hippurate as a metabolomic marker of gut microbiome diversity: Modulation by diet and relationship to metabolic syndrome. Sci Rep 2017; 7:13670. [PMID: 29057986 PMCID: PMC5651863 DOI: 10.1038/s41598-017-13722-4] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/25/2017] [Indexed: 01/07/2023] Open
Abstract
Reduced gut microbiome diversity is associated with multiple disorders including metabolic syndrome (MetS) features, though metabolomic markers have not been investigated. Our objective was to identify blood metabolite markers of gut microbiome diversity, and explore their relationship with dietary intake and MetS. We examined associations between Shannon diversity and 292 metabolites profiled by the untargeted metabolomics provider Metabolon Inc. in 1529 females from TwinsUK using linear regressions adjusting for confounders and multiple testing (Bonferroni: P < 1.71 × 10-4). We replicated the top results in an independent sample of 420 individuals as well as discordant identical twin pairs and explored associations with self-reported intakes of 20 food groups. Longitudinal changes in circulating levels of the top metabolite, were examined for their association with food intake at baseline and with MetS at endpoint. Five metabolites were associated with microbiome diversity and replicated in the independent sample. Higher intakes of fruit and whole grains were associated with higher levels of hippurate cross-sectionally and longitudinally. An increasing hippurate trend was associated with reduced odds of having MetS (OR: 0.795[0.082]; P = 0.026). These data add further weight to the key role of the microbiome as a potential mediator of the impact of dietary intake on metabolic status and health.
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Affiliation(s)
- Tess Pallister
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Matthew A Jackson
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Tiphaine C Martin
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jonas Zierer
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.,Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Amy Jennings
- Department of Nutrition & Preventive Medicine, Norwich Medical School, University of East Anglia, Norwich, UK
| | | | - Alexander MacGregor
- Department of Nutrition & Preventive Medicine, Norwich Medical School, University of East Anglia, Norwich, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Aedin Cassidy
- Department of Nutrition & Preventive Medicine, Norwich Medical School, University of East Anglia, Norwich, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, SE1 7EH, UK.
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