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Chienwichai P, Tipthara P, Tarning J, Limpanont Y, Chusongsang P, Chusongsang Y, Kiangkoo N, Adisakwattana P, Reamtong O. Identification of trans-genus biomarkers for early diagnosis of intestinal schistosomiasis and progression of gut pathology in a mouse model using metabolomics. PLoS Negl Trop Dis 2024; 18:e0011966. [PMID: 38381759 PMCID: PMC10880994 DOI: 10.1371/journal.pntd.0011966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Schistosomiasis is one of the most devastating human diseases worldwide. The disease is caused by six species of Schistosoma blood fluke; five of which cause intestinal granulomatous inflammation and bleeding. The current diagnostic method is inaccurate and delayed, hence, biomarker identification using metabolomics has been applied. However, previous studies only investigated infection caused by one Schistosoma spp., leaving a gap in the use of biomarkers for other species. No study focused on understanding the progression of intestinal disease. Therefore, we aimed to identify early gut biomarkers of infection with three Schistosoma spp. and progression of intestinal pathology. We infected 3 groups of mice, 3 mice each, with Schistosoma mansoni, Schistosoma japonicum or Schistosoma mekongi and collected their feces before and 1, 2, 4 and 8 weeks after infection. Metabolites in feces were extracted and identified using mass spectrometer-based metabolomics. Metabolites were annotated and analyzed with XCMS bioinformatics tool and Metaboanalyst platform. From >36,000 features in all conditions, multivariate analysis found a distinct pattern at each time point for all species. Pathway analysis reported alteration of several lipid metabolism pathways as infection progressed. Disturbance of the glycosaminoglycan degradation pathway was found with the presence of parasite eggs, indicating involvement of this pathway in disease progression. Biomarkers were discovered using a combination of variable importance for projection score cut-off and receiver operating characteristic curve analysis. Five molecules met our criteria and were present in all three species: 25-hydroxyvitamin D2, 1α-hydroxy-2β-(3-hydroxypropoxy) vitamin D3, Ganoderic acid Md, unidentified feature with m/z 455.3483, and unidentified feature with m/z 456.3516. These molecules were proposed as trans-genus biomarkers of early schistosomiasis. Our findings provide evidence for disease progression in intestinal schistosomiasis and potential biomarkers, which could be beneficial for early detection of this disease.
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Affiliation(s)
- Peerut Chienwichai
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Phornpimon Tipthara
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Joel Tarning
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Yanin Limpanont
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Phiraphol Chusongsang
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yupa Chusongsang
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nuttapohn Kiangkoo
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Shayya NW, Bandick R, Busmann LV, Mousavi S, Bereswill S, Heimesaat MM. Metabolomic signatures of intestinal colonization resistance against Campylobacter jejuni in mice. Front Microbiol 2023; 14:1331114. [PMID: 38164399 PMCID: PMC10757985 DOI: 10.3389/fmicb.2023.1331114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Campylobacter jejuni stands out as one of the leading causes of bacterial enteritis. In contrast to humans, specific pathogen-free (SPF) laboratory mice display strict intestinal colonization resistance (CR) against C. jejuni, orchestrated by the specific murine intestinal microbiota, as shown by fecal microbiota transplantation (FMT) earlier. Methods Murine infection models, comprising SPF, SAB, hma, and mma mice were employed. FMT and microbiota depletion were confirmed by culture and culture-independent analyses. Targeted metabolome analyses of fecal samples provided insights into the associated metabolomic signatures. Results In comparison to hma mice, the murine intestinal microbiota of mma and SPF mice (with CR against C. jejuni) contained significantly elevated numbers of lactobacilli, and Mouse Intestinal Bacteroides, whereas numbers of enterobacteria, enterococci, and Clostridium coccoides group were reduced. Targeted metabolome analysis revealed that fecal samples from mice with CR contained increased levels of secondary bile acids and fatty acids with known antimicrobial activities, but reduced concentrations of amino acids essential for C. jejuni growth as compared to control animals without CR. Discussion The findings highlight the role of microbiota-mediated nutrient competition and antibacterial activities of intestinal metabolites in driving murine CR against C. jejuni. The study underscores the complex dynamics of host-microbiota-pathogen interactions and sets the stage for further investigations into the mechanisms driving CR against enteric infections.
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Huang D, Yang Y, Song W, Jiang C, Zhang Y, Zhang A, Lin Z, Ke X. Untargeted metabonomic analysis of a cerebral stroke model in rats: a study based on UPLC-MS/MS. Front Neurosci 2023; 17:1084813. [PMID: 37614341 PMCID: PMC10442664 DOI: 10.3389/fnins.2023.1084813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/18/2023] [Indexed: 08/25/2023] Open
Abstract
Introduction Brain tissue damage caused by ischemic stroke can trigger changes in the body's metabolic response, and understanding the changes in the metabolic response of the gut after stroke can contribute to research on poststroke brain function recovery. Despite the increase in international research on poststroke metabolic mechanisms and the availability of powerful research tools in recent years, there is still an urgent need for poststroke metabolic studies. Metabolomic examination of feces from a cerebral ischemia-reperfusion rat model can provide new insights into poststroke metabolism and identify key metabolic pathways, which will help reveal diagnostic and therapeutic targets as well as inspire pathophysiological studies after stroke. Methods We randomly divided 16 healthy adult pathogen-free male Sprague-Dawley (SD) rats into the normal group and the study group, which received middle cerebral artery occlusion/reperfusion (MCAO/R). Ultra-performance liquid chromatography-tandem mass spectrometry (UPLCMS/MS) was used to determine the identities and concentrations of metabolites across all groups, and filtered high-quality data were analyzed for differential screening and differential metabolite functional analysis. Results After 1 and 14 days of modeling, compared to the normal group, rats in the study group showed significant neurological deficits (p < 0.001) and significantly increased infarct volume (day 1: p < 0.001; day 14: p = 0.001). Mass spectra identified 1,044 and 635 differential metabolites in rat feces in positive and negative ion modes, respectively, which differed significantly between the normal and study groups. The metabolites with increased levels identified in the study group were involved in tryptophan metabolism (p = 0.036678, p < 0.05), arachidonic acid metabolism (p = 0.15695), cysteine and methionine metabolism (p = 0.24705), and pyrimidine metabolism (p = 0.3413), whereas the metabolites with decreased levels were involved in arginine and proline metabolism (p = 0.15695) and starch and sucrose metabolism (p = 0.52256). Discussion We determined that UPLC-MS/MS could be employed for untargeted metabolomics research. Moreover, tryptophan metabolic pathways may have been disordered in the study group. Alterations in the tryptophan metabolome may provide additional theoretical and data support for elucidating stroke pathogenesis and selecting pathways for intervention.
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Affiliation(s)
- Dunbing Huang
- Department of Rehabilitation Medicine, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yihan Yang
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Wei Song
- Department of Rehabilitation Medicine, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Cai Jiang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
- Second Rehabilitation Department, Fujian Provincial Hospital, Fuzhou, China
- Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, China
- Fujian Key Laboratory of Geriatrics Diseases, Fujian Provincial Hospital, Fuzhou, China
- Department of Complementary Medicine, University of Johannesburg, Johannesburg, South Africa
| | - Yuhao Zhang
- Department of Rehabilitation Medicine, Nanjing Lishui District Hospital of Traditional Chinese medicine, Nanjing, China
| | - Anren Zhang
- Department of Rehabilitation Medicine, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhonghua Lin
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
- Second Rehabilitation Department, Fujian Provincial Hospital, Fuzhou, China
- Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, China
- Fujian Key Laboratory of Geriatrics Diseases, Fujian Provincial Hospital, Fuzhou, China
- Department of Complementary Medicine, University of Johannesburg, Johannesburg, South Africa
| | - Xiaohua Ke
- Department of Rehabilitation Medicine, Shanghai Fourth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
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Kelly PE, Ng HJ, Farrell G, McKirdy S, Russell RK, Hansen R, Rattray Z, Gerasimidis K, Rattray NJW. An Optimised Monophasic Faecal Extraction Method for LC-MS Analysis and Its Application in Gastrointestinal Disease. Metabolites 2022; 12:1110. [PMID: 36422250 PMCID: PMC9698041 DOI: 10.3390/metabo12111110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 12/28/2023] Open
Abstract
Liquid chromatography coupled with mass spectrometry (LC-MS) metabolomic approaches are widely used to investigate underlying pathogenesis of gastrointestinal disease and mechanism of action of treatments. However, there is an unmet requirement to assess faecal metabolite extraction methods for large-scale metabolomics studies. Current methods often rely on biphasic extractions using harmful halogenated solvents, making automation and large-scale studies challenging. The present study reports an optimised monophasic faecal extraction protocol that is suitable for untargeted and targeted LC-MS analyses. The impact of several experimental parameters, including sample weight, extraction solvent, cellular disruption method, and sample-to-solvent ratio, were investigated. It is suggested that a 50 mg freeze-dried faecal sample should be used in a methanol extraction (1:20) using bead beating as the means of cell disruption. This is revealed by a significant increase in number of metabolites detected, improved signal intensity, and wide metabolic coverage given by each of the above extraction parameters. Finally, we addressed the applicability of the method on faecal samples from patients with Crohn's disease (CD) and coeliac disease (CoD), two distinct chronic gastrointestinal diseases involving metabolic perturbations. Untargeted and targeted metabolomic analysis demonstrated the ability of the developed method to detect and stratify metabolites extracted from patient groups and healthy controls (HC), highlighting characteristic changes in the faecal metabolome according to disease. The method developed is, therefore, suitable for the analysis of patients with gastrointestinal disease and can be used to detect and distinguish differences in the metabolomes of CD, CoD, and HC.
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Affiliation(s)
- Patricia E. Kelly
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow G4 0RE, UK
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
| | - H Jene Ng
- School of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow Royal Infirmary, Glasgow G12 8QQ, UK
| | - Gillian Farrell
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow G4 0RE, UK
| | - Shona McKirdy
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
- School of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow Royal Infirmary, Glasgow G12 8QQ, UK
| | - Richard K. Russell
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
- Royal Hospital for Children and Young People, 50 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Richard Hansen
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
- Royal Hospital for Children, 1345 Govan Road, Glasgow G52 4TF, UK
| | - Zahra Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow G4 0RE, UK
| | - Konstantinos Gerasimidis
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
- School of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow Royal Infirmary, Glasgow G12 8QQ, UK
| | - Nicholas J. W. Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow G4 0RE, UK
- Bacteria, Immunology, Nutrition, Gastroenterology and Omics (BINGO) Group, University of Glasgow, Glasgow G12 8QQ, UK
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Moschino L, Verlato G, Duci M, Cavicchiolo ME, Guiducci S, Stocchero M, Giordano G, Fascetti Leon F, Baraldi E. The Metabolome and the Gut Microbiota for the Prediction of Necrotizing Enterocolitis and Spontaneous Intestinal Perforation: A Systematic Review. Nutrients 2022; 14:nu14183859. [PMID: 36145235 PMCID: PMC9506026 DOI: 10.3390/nu14183859] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/26/2022] Open
Abstract
Necrotizing enterocolitis (NEC) is the most devastating gastrointestinal emergency in preterm neonates. Research on early predictive biomarkers is fundamental. This is a systematic review of studies applying untargeted metabolomics and gut microbiota analysis to evaluate the differences between neonates affected by NEC (Bell’s stage II or III), and/or by spontaneous intestinal perforation (SIP) versus healthy controls. Five studies applying metabolomics (43 cases, 95 preterm controls) and 20 applying gut microbiota analysis (254 cases, 651 preterm controls, 22 term controls) were selected. Metabolomic studies utilized NMR spectroscopy or mass spectrometry. An early urinary alanine/histidine ratio >4 showed good sensitivity and predictive value for NEC in one study. Samples collected in proximity to NEC diagnosis demonstrated variable pathways potentially related to NEC. In studies applying untargeted gut microbiota analysis, the sequencing of the V3−V4 or V3 to V5 regions of the 16S rRNA was the most used technique. At phylum level, NEC specimens were characterized by increased relative abundance of Proteobacteria compared to controls. At genus level, pre-NEC samples were characterized by a lack or decreased abundance of Bifidobacterium. Finally, at the species level Bacteroides dorei, Clostridium perfringens and perfringens-like strains dominated early NEC specimens, whereas Clostridium butyricum, neonatale and Propionibacterium acnei those at disease diagnosis. Six studies found a lower Shannon diversity index in cases than controls. A clear separation of cases from controls emerged based on UniFrac metrics in five out of seven studies. Importantly, no studies compared NEC versus SIP. Untargeted metabolomics and gut microbiota analysis are interrelated strategies to investigate NEC pathophysiology and identify potential biomarkers. Expression of quantitative measurements, data sharing via biorepositories and validation studies are fundamental to guarantee consistent comparison of results.
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Affiliation(s)
- Laura Moschino
- Neonatal Intensive Care Unit, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
- Institute of Paediatric Research, Città della Speranza, Laboratory of Mass Spectrometry and Metabolomics, 35127 Padova, Italy
- Correspondence: ; Tel.: +39-049-821-3548
| | - Giovanna Verlato
- Neonatal Intensive Care Unit, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Miriam Duci
- Paediatric Surgery, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Maria Elena Cavicchiolo
- Neonatal Intensive Care Unit, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Silvia Guiducci
- Neonatal Intensive Care Unit, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Matteo Stocchero
- Institute of Paediatric Research, Città della Speranza, Laboratory of Mass Spectrometry and Metabolomics, 35127 Padova, Italy
- Laboratory of Mass Spectrometry and Metabolomics, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Giuseppe Giordano
- Institute of Paediatric Research, Città della Speranza, Laboratory of Mass Spectrometry and Metabolomics, 35127 Padova, Italy
- Laboratory of Mass Spectrometry and Metabolomics, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Francesco Fascetti Leon
- Paediatric Surgery, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
| | - Eugenio Baraldi
- Neonatal Intensive Care Unit, Department of Women’s and Children’s Health, Padova University Hospital, 35128 Padova, Italy
- Institute of Paediatric Research, Città della Speranza, Laboratory of Mass Spectrometry and Metabolomics, 35127 Padova, Italy
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Fecal amine metabolite analysis before onset of severe necrotizing enterocolitis in preterm infants: a prospective case-control study. Sci Rep 2022; 12:12310. [PMID: 35853977 PMCID: PMC9296556 DOI: 10.1038/s41598-022-16351-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 07/08/2022] [Indexed: 11/08/2022] Open
Abstract
Infants developing necrotizing enterocolitis (NEC) have a different metabolomic profile compared to controls. The potential of specific metabolomics, i.e. amino acids and amino alcohols (AAA), as early diagnostic biomarkers for NEC is largely unexplored. In this multicenter prospective case-control study, longitudinally collected fecal samples from preterm infants (born <30 weeks of gestation) from 1-3 days before diagnosis of severe NEC (Bell's stage IIIA/IIIB), were analyzed by targeted high-performance liquid chromatography (HPLC). Control samples were collected from gestational and postnatal age-matched infants. Thirty-one NEC cases (15 NEC IIIA;16 NEC IIIB) with 1:1 matched controls were included. Preclinical samples of infants with NEC were characterized by five increased essential amino acids-isoleucine, leucine, methionine, phenylalanine and valine. Lysine and ethanolamine ratios were lower prior to NEC, compared to control samples. A multivariate model was rendered based on isoleucine, lysine, ethanolamine, tryptophan and ornithine, modestly discriminating cases from controls (AUC 0.67; p < 0.001). Targeted HPLC pointed to several specific AAA alterations in samples collected 1-3 days before NEC onset, compared to controls. Whether this reflects metabolic alterations and has a role in early biomarker development for NEC, has yet to be elucidated.
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Garzarelli V, Ferrara F, Primiceri E, Chiriacò MS. Biofluids manipulation methods for liquid biopsy in minimally-invasive assays. MethodsX 2022; 9:101759. [PMID: 35774416 PMCID: PMC9237943 DOI: 10.1016/j.mex.2022.101759] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/10/2022] [Indexed: 12/05/2022] Open
Abstract
The Liquid Biopsy (LB) is an opportunity for non-invasive diagnosis and prognosis of various diseases. To date, it isn't possible to consider that tissue biopsy can represent a pathology entirety. Then, body fluids are rich in a large number and variety of biomarkers and they can provide information about several diseases.Recently, other biological fluids, easy to be collected are rising for their significant content of biomarkers and for the possibility to collect and manipulate them without the intervention of medical staff. The management of biological fluids requires suitable storage methods. Temperature, storage time and physical stresses due to sample handling can lead to chemical and physical changes that may induce sample degradation and incorrect analysis. The reliability of a diagnostic or screening test depends on its sensitivity and specificity. As the liquid biopsy is a 'snapshot' of a pathophysiological condition, it is crucial that its components do not degrade due to the improper handling of the body fluid. In this review, some handling methods of Saliva, Urine, Stool, Seminal Fluid, Tears and Sweat samples will be described, as well as protocols to facilitate the analysis of metabolites, nucleic acids, proteins and Extracellular Vesicles (EVs) from those unusual body fluids.
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Affiliation(s)
- Valeria Garzarelli
- University of Salento, Dept. of Mathematics & Physics E. de Giorgi, Via Arnesano, 73100, Lecce, Italy.,CNR NANOTEC - Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy
| | - Francesco Ferrara
- CNR NANOTEC - Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy.,STMicroelectronics s.r.l., via per Monteroni, 73100, Lecce, Italy
| | - Elisabetta Primiceri
- CNR NANOTEC - Institute of Nanotechnology, via per Monteroni, 73100, Lecce, Italy
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Gegner HM, Mechtel N, Heidenreich E, Wirth A, Cortizo FG, Bennewitz K, Fleming T, Andresen C, Freichel M, Teleman AA, Kroll J, Hell R, Poschet G. Deep Metabolic Profiling Assessment of Tissue Extraction Protocols for Three Model Organisms. Front Chem 2022; 10:869732. [PMID: 35548679 PMCID: PMC9083328 DOI: 10.3389/fchem.2022.869732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022] Open
Abstract
Metabolic profiling harbors the potential to better understand various disease entities such as cancer, diabetes, Alzheimer’s, Parkinson’s disease or COVID-19. To better understand such diseases and their intricate metabolic pathways in human studies, model animals are regularly used. There, standardized rearing conditions and uniform sampling strategies are prerequisites towards a successful metabolomic study that can be achieved through model organisms. Although metabolomic approaches have been employed on model organisms before, no systematic assessment of different conditions to optimize metabolite extraction across several organisms and sample types has been conducted. We address this issue using a highly standardized metabolic profiling assay analyzing 630 metabolites across three commonly used model organisms (Drosophila, mouse, and zebrafish) to find an optimal extraction protocol for various matrices. Focusing on parameters such as metabolite coverage, concentration and variance between replicates we compared seven extraction protocols. We found that the application of a combination of 75% ethanol and methyl tertiary-butyl ether (MTBE), while not producing the broadest coverage and highest concentrations, was the most reproducible extraction protocol. We were able to determine up to 530 metabolites in mouse kidney samples, 509 in mouse liver, 422 in zebrafish and 388 in Drosophila and discovered a core overlap of 261 metabolites in these four matrices. To enable other scientists to search for the most suitable extraction protocol in their experimental context and interact with this comprehensive data, we have integrated our data set in the open-source shiny app “MetaboExtract”. Hereby, scientists can search for metabolites or compound classes of interest, compare them across the different tested extraction protocols and sample types as well as find reference concentration values.
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Affiliation(s)
- Hagen M. Gegner
- Metabolomics Core Technology Platform, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Nils Mechtel
- Metabolomics Core Technology Platform, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Elena Heidenreich
- Metabolomics Core Technology Platform, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Angela Wirth
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Fabiola Garcia Cortizo
- Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katrin Bennewitz
- European Center for Angioscience (ECAS), Department of Vascular Biology and Tumor Angiogenesis, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Fleming
- Department of Internal Medicine I and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany
| | - Carolin Andresen
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM GGmbH), Heidelberg, Germany
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Aurelio A. Teleman
- Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jens Kroll
- European Center for Angioscience (ECAS), Department of Vascular Biology and Tumor Angiogenesis, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Rüdiger Hell
- Metabolomics Core Technology Platform, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Gernot Poschet
- Metabolomics Core Technology Platform, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
- *Correspondence: Gernot Poschet,
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Fornasaro S, Esposito A, Florian F, Pallavicini A, De Leo L, Not T, Lagatolla C, Mezzarobba M, Di Silvestre A, Sergo V, Bonifacio A. Spectroscopic investigation of faeces with surface-enhanced Raman scattering: a case study with coeliac patients on gluten-free diet. Anal Bioanal Chem 2022; 414:3517-3527. [PMID: 35258650 PMCID: PMC9018641 DOI: 10.1007/s00216-022-03975-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 11/06/2022]
Abstract
Surface-enhanced Raman scattering (SERS) spectra of faecal samples can be obtained by adding AuNP to their methanol extracts according to the reported protocol, and display bands that are due to bilirubin-like species but also to xanthine and hypoxanthine, two metabolic products secreted by gut bacteria. A total of 27 faecal samples from three different groups, i.e. coeliac patients (n = 9), coeliac patients on gluten-free diet (n = 10) and a control group (n = 8), were characterized with both SERS spectroscopy and 16S rRNA sequencing analysis. Significant differences are present between SERS spectra of coeliac patients and those on gluten-free diet, with a marked increase in the relative intensity of both xanthine and hypoxanthine for the latter. Interestingly, these differences do not correlate with bacterial composition as derived from 16S rRNA sequencing.
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Affiliation(s)
- Stefano Fornasaro
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Alessandro Esposito
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Fiorella Florian
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Luigina De Leo
- Institute for Maternal Child Health-IRCCS "Burlo Garofolo" Trieste, via dell'Istria 65/1, 34100, Trieste, Italy
| | - Tarcisio Not
- Institute for Maternal Child Health-IRCCS "Burlo Garofolo" Trieste, via dell'Istria 65/1, 34100, Trieste, Italy
| | - Cristina Lagatolla
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Marica Mezzarobba
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Alessia Di Silvestre
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Valter Sergo
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Alois Bonifacio
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy.
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Coto L, Sousa C, Cebolla A. Individual variability in patterns and dynamics of fecal gluten immunogenic peptides excretion after low gluten intake. Eur J Nutr 2022; 61:2033-2049. [PMID: 34993643 PMCID: PMC8739026 DOI: 10.1007/s00394-021-02765-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022]
Abstract
Purpose Determination of Gluten Immunogenic Peptides (GIP) in feces is a direct tool for gluten exposure detection. The sensitivity of GIP detection methods for cases of unintentional low gluten intakes is unknown. We studied the interindividual variability in the kinetic of excretion under homogeneously controlled dietary conditions, and the sensitivity of fecal GIP tests after low amounts of punctual gluten ingestions. Methods Participants (n = 20) followed the same gluten-free menu for 12 days in which two separated doses of gluten (50 mg and 2 g) were ingested and all the depositions were collected. GIP from stool samples were analyzed by ELISA and lateral flow immunoassay (LFIA) tests. Results Most participants had detectable GIP after 50 mg and 2 g gluten ingestions using ELISA test (72.2% and 95%, respectively), whereas the LFIA test showed less sensitivity (22.2% and 80%, respectively). GIP were detected at higher either frequency or concentration in the range of 12–36 h after 50 mg intake, and 12–84 h after 2 g consumption. Considering this period, diagnostic sensitivity of GIP detection after a single 50 mg ingestion may be significatively increased analyzing three stool samples per individual. High variability among participants was found in the time and amount of GIP excretion; however, some individuals showed common patterns for both gluten intakes. Conclusion Sporadic gluten exposure detection may require several fecal samples to achieve level of sensitivity above 90%. Interindividual variability in the dynamic of GIP excretion may suggest patterns of gluten metabolism.
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Affiliation(s)
- Laura Coto
- Biomedal S.L., Polígono Industrial Parque Plata, Calle Calzada Romana, 40, 41900, Camas, Sevilla, Spain
- Human Nutrition and Food Science Doctoral Program, University of Granada, 18011, Granada, Spain
| | - Carolina Sousa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012, Seville, Spain
| | - Angel Cebolla
- Biomedal S.L., Polígono Industrial Parque Plata, Calle Calzada Romana, 40, 41900, Camas, Sevilla, Spain.
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Ivanova L, Rangel-Huerta OD, Tartor H, Gjessing MC, Dahle MK, Uhlig S. Fish Skin and Gill Mucus: A Source of Metabolites for Non-Invasive Health Monitoring and Research. Metabolites 2021; 12:28. [PMID: 35050150 PMCID: PMC8781917 DOI: 10.3390/metabo12010028] [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: 11/24/2021] [Revised: 12/16/2021] [Accepted: 12/25/2021] [Indexed: 11/28/2022] Open
Abstract
Mucous membranes such as the gill and skin mucosa in fish protect them against a multitude of environmental factors. At the same time, changes in the molecular composition of mucus may provide valuable information about the interaction of the fish with their environment, as well as their health and welfare. In this study, the metabolite profiles of the plasma, skin and gill mucus of freshwater Atlantic salmon (Salmo salar) were compared using liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). Several normalization procedures aimed to reduce unwanted variation in the untargeted data were tested. In addition, the basal metabolism of skin and gills, and the impact of the anesthetic benzocaine for euthanisation were studied. For targeted metabolomics, the commercial AbsoluteIDQ p400 HR kit was used to evaluate the potential differences in metabolic composition in epidermal mucus as compared to the plasma. The targeted metabolomics data showed a high level of correlation between different types of biological fluids from the same individual, indicating that mucus metabolite composition could be used for fish health monitoring and research.
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Affiliation(s)
- Lada Ivanova
- Norwegian Veterinary Institute, P.O. Box 64, N-1431 Ås, Norway; (O.D.R.-H.); (H.T.); (M.C.G.); (M.K.D.); (S.U.)
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