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Zhou L, Yu D, Zheng S, Ouyang R, Wang Y, Xu G. Gut microbiota-related metabolome analysis based on chromatography-mass spectrometry. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Cui M, Trimigno A, Aru V, Khakimov B, Engelsen SB. Human Faecal 1H NMR Metabolomics: Evaluation of Solvent and Sample Processing on Coverage and Reproducibility of Signature Metabolites. Anal Chem 2020; 92:9546-9555. [DOI: 10.1021/acs.analchem.0c00606] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mengni Cui
- Chemometrics and Analytical Technology, Department of Food Science, Faculty of Science, University of Copenhagen Rolighedsvej 26, Frederiksberg 1958, Denmark
| | - Alessia Trimigno
- Chemometrics and Analytical Technology, Department of Food Science, Faculty of Science, University of Copenhagen Rolighedsvej 26, Frederiksberg 1958, Denmark
| | - Violetta Aru
- Chemometrics and Analytical Technology, Department of Food Science, Faculty of Science, University of Copenhagen Rolighedsvej 26, Frederiksberg 1958, Denmark
| | - Bekzod Khakimov
- Chemometrics and Analytical Technology, Department of Food Science, Faculty of Science, University of Copenhagen Rolighedsvej 26, Frederiksberg 1958, Denmark
| | - Søren Balling Engelsen
- Chemometrics and Analytical Technology, Department of Food Science, Faculty of Science, University of Copenhagen Rolighedsvej 26, Frederiksberg 1958, Denmark
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3
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Karu N, Deng L, Slae M, Guo AC, Sajed T, Huynh H, Wine E, Wishart DS. A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database. Anal Chim Acta 2018; 1030:1-24. [DOI: 10.1016/j.aca.2018.05.031] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/05/2018] [Accepted: 05/09/2018] [Indexed: 12/19/2022]
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Federici E, Prete R, Lazzi C, Pellegrini N, Moretti M, Corsetti A, Cenci G. Bacterial Composition, Genotoxicity, and Cytotoxicity of Fecal Samples from Individuals Consuming Omnivorous or Vegetarian Diets. Front Microbiol 2017; 8:300. [PMID: 28293225 PMCID: PMC5328950 DOI: 10.3389/fmicb.2017.00300] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/14/2017] [Indexed: 12/16/2022] Open
Abstract
This study analyzes the composition of viable fecal bacteria and gut toxicology biomarkers of 29 healthy volunteers, who followed omnivorous, lacto-ovo-vegetarian, or vegan diets. In particular, the research was focused on the prevalence of some representative viable bacteria from the four dominant phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria) commonly present in human feces, in order to evaluate the relationship between microorganisms selected by the habitual dietary patterns and the potential risk due to fecal water (FW) genotoxicity and cytotoxicity, considered as biomarkers for cancer risk and protective food activity. The relative differences of viable bacteria among dietary groups were generally not statistically significant. However, compared to omnivores, lacto-ovo-vegetarians showed low levels of total anaerobes. Otherwise, vegans showed total anaerobes counts similar to those of omnivores, but with lower number of bifidobacteria and the highest levels of bacteria from the Bacteroides–Prevotella genera. FW genotoxicity of lacto-ovo-vegetarians resulted significantly lower either in relation to that of omnivores and vegans. Lacto-ovo-vegetarians also showed the lowest levels of cytotoxicity, while the highest were found for vegans. These results highlighted that lacto-ovo-vegetarian diet was particularly effective in a favorable modulation of microbial activity, thus contributing to a significant reduction of the genotoxic and cytotoxic risk in the gut.
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Affiliation(s)
- Ermanno Federici
- Laboratory of Microbiology, Department of Chemistry, Biology and Biotechnology, University of Perugia Perugia, Italy
| | - Roberta Prete
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo Teramo, Italy
| | - Camilla Lazzi
- Department of Food Science, University of Parma Parma, Italy
| | | | - Massimo Moretti
- Department of Pharmaceutical Sciences, University of Perugia Perugia, Italy
| | - Aldo Corsetti
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo Teramo, Italy
| | - Giovanni Cenci
- Laboratory of Microbiology, Department of Chemistry, Biology and Biotechnology, University of Perugia Perugia, Italy
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Del Chierico F, Vernocchi P, Petrucca A, Paci P, Fuentes S, Praticò G, Capuani G, Masotti A, Reddel S, Russo A, Vallone C, Salvatori G, Buffone E, Signore F, Rigon G, Dotta A, Miccheli A, de Vos WM, Dallapiccola B, Putignani L. Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development. PLoS One 2015; 10:e0137347. [PMID: 26332837 PMCID: PMC4557834 DOI: 10.1371/journal.pone.0137347] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/14/2015] [Indexed: 12/28/2022] Open
Abstract
The colonization and development of gut microbiota immediately after birth is highly variable and depends on several factors, such as delivery mode and modality of feeding during the first months of life. A cohort of 31 mother and neonate pairs, including 25 at-term caesarean (CS) and 6 vaginally (V) delivered neonates (DNs), were included in this study and 121 meconium/faecal samples were collected at days 1 through 30 following birth. Operational taxonomic units (OTUs) were assessed in 69 stool samples by phylogenetic microarray HITChip and inter- and intra-individual distributions were established by inter-OTUs correlation matrices and OTUs co-occurrence or co-exclusion networks. 1H-NMR metabolites were determined in 70 stool samples, PCA analysis was performed on 55 CS DNs samples, and metabolome/OTUs co-correlations were assessed in 45 CS samples, providing an integrated map of the early microbiota OTUs-metabolome. A microbiota "core" of OTUs was identified that was independent of delivery mode and lactation stage, suggesting highly specialized communities that act as seminal colonizers of microbial networks. Correlations among OTUs, metabolites, and OTUs-metabolites revealed metabolic profiles associated with early microbial ecological dynamics, maturation of milk components, and host physiology.
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Affiliation(s)
| | - Pamela Vernocchi
- Unit of Metagenomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Andrea Petrucca
- Unit of Metagenomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Diagnostic Science, Sant’Andrea Hospital, Rome, Italy
| | - Paola Paci
- CNR, Institute of Systems Analysis and Informatics Antonio Ruberti, Rome, Italy
| | - Susana Fuentes
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Giulia Praticò
- Department of Chemistry, Sapienza University, Rome, Italy
| | | | | | - Sofia Reddel
- Unit of Metagenomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Alessandra Russo
- Unit of Metagenomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Cristina Vallone
- Department of Obstetrics and Gyneacology, San Camillo Hospital, Rome, Italy
| | - Guglielmo Salvatori
- Department of Neonatology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Elsa Buffone
- Department of Neonatology, San Camillo Hospital, Rome, Italy
| | - Fabrizio Signore
- Department of Obstetrics and Gyneacology, San Camillo Hospital, Rome, Italy
| | - Giuliano Rigon
- Department of Obstetrics and Gyneacology, San Camillo Hospital, Rome, Italy
| | - Andrea Dotta
- Department of Neonatology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | | | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Departments of Veterinary Biosciences and Bacteriology & Immunology, Helsinki University, Helsinki, Finland
| | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Metagenomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Unit of Parasitology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- * E-mail:
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Deda O, Gika HG, Wilson ID, Theodoridis GA. An overview of fecal sample preparation for global metabolic profiling. J Pharm Biomed Anal 2015; 113:137-50. [DOI: 10.1016/j.jpba.2015.02.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 02/05/2015] [Indexed: 01/25/2023]
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Lamichhane S, Yde CC, Schmedes MS, Jensen HM, Meier S, Bertram HC. Strategy for Nuclear-Magnetic-Resonance-Based Metabolomics of Human Feces. Anal Chem 2015; 87:5930-7. [DOI: 10.1021/acs.analchem.5b00977] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Santosh Lamichhane
- Department
of Food Science, Aarhus University, Kirstinebjergvej 10, DK-5792 Aarslev, Denmark
| | - Christian C. Yde
- Department
of Food Science, Aarhus University, Kirstinebjergvej 10, DK-5792 Aarslev, Denmark
| | - Mette S. Schmedes
- Department
of Food Science, Aarhus University, Kirstinebjergvej 10, DK-5792 Aarslev, Denmark
| | - Henrik Max Jensen
- DuPont Nutrition
Biosciences ApS, Edwin Rahrsvej 38, 8220 Brabrand, Aarhus, Denmark
| | - Sebastian Meier
- Department
of Chemistry, Technical University of Denmark, Kemitorvet, Building 201, DK-2800 Kongens Lyngby, Denmark
| | - Hanne Christine Bertram
- Department
of Food Science, Aarhus University, Kirstinebjergvej 10, DK-5792 Aarslev, Denmark
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Nutritional modulation of the metabonome: applications of metabolic phenotyping in translational nutritional research. Curr Opin Gastroenterol 2014; 30:196-207. [PMID: 24468802 DOI: 10.1097/mog.0000000000000036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Metabolic profiling technologies provide a global overview of complex dietary processes. Metabonomic analytical approaches have now been translated into multiple areas of clinical nutritional research based on the widespread adoption of high-throughput mass spectrometry and proton nuclear magnetic resonance spectroscopy. This has generated novel insights into the molecular mechanisms that shape the microbiome-dietary-chronic disease axis. RECENT FINDINGS Metabolome-wide association studies have created a new paradigm in nutritional molecular epidemiology and they have highlighted the importance of gut microbial cometabolic processes in the development of cardiovascular disease and diabetes. Targeted analyses are helping to explain the mechanisms by which high-risk diets (such as red meat) modulate disease risk and they are generating novel biomarkers that will serve to re-define how the efficacy of nutritional interventions is assessed. Nutritional metabonome-microbiome interactions have also been defined in extreme dietary states such as obesity and starvation, and they also serve as important models for understanding how the gut microbiome modifies disease risk. Finally, nutritional systems medicine approaches are creating novel insights into the functional components of our diet, and the mechanisms by which they cause disease. SUMMARY Diet is an important modulator of the human metabolic phenotype and the analysis of the nutritional metabolome will drive future development of personalized nutritional interventions.
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Bordonaro M, Venema K, Putri AK, Lazarova D. Approaches that ascertain the role of dietary compounds in colonic cancer cells. World J Gastrointest Oncol 2014; 6:1-10. [PMID: 24578783 PMCID: PMC3936191 DOI: 10.4251/wjgo.v6.i1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/26/2013] [Accepted: 12/17/2013] [Indexed: 02/05/2023] Open
Abstract
Preventive approaches against cancer have not been fully developed and applied. For example, the incidence of some types of cancer, including colon cancer, is highly dependent upon lifestyle, and therefore, amenable to prevention. Among the lifestyle factors, diet strongly affects the incidence of colon cancer; however, there are no definitive dietary recommendations that protect against this malignancy. The association between diet-derived bioactives and development of colonic neoplasms will remain ill defined if we do not take into account: (1) the identity of the metabolites present in the colonic lumen; (2) their concentrations in the colon; and (3) the effect of the colonic contents on the function of individual bioactives. We review two approaches that address these questions: the use of fecal water and in vitro models of the human colon. Compared to treatment with individual diet-derived compounds, the exposure of colon cancer cells to samples from fecal water or human colon simulators mimics closer the in vitro conditions and allows for more reliable studies on the effects of diet on colon cancer development. The rationale and the advantages of these strategies are discussed from the perspective of a specific question on how to analyze the combined effect of two types of bioactives, butyrate and polyphenol metabolites, on colon cancer cells.
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Strömstedt AA, Felth J, Bohlin L. Bioassays in natural product research - strategies and methods in the search for anti-inflammatory and antimicrobial activity. PHYTOCHEMICAL ANALYSIS : PCA 2014; 25:13-28. [PMID: 24019222 DOI: 10.1002/pca.2468] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 06/24/2013] [Accepted: 06/24/2013] [Indexed: 06/02/2023]
Abstract
INTRODUCTION Identifying bioactive molecules from complex biomasses requires careful selection and execution of relevant bioassays in the various stages of the discovery process of potential leads and targets. OBJECTIVE The aim of this review is to share our long-term experience in bioassay-guided isolation, and mechanistic studies, of bioactive compounds from different organisms in nature with emphasis on anti-inflammatory and antimicrobial activity. METHODS In the search for anti-inflammatory activity, in vivo and in vitro model combinations with enzymes and cells involved in the inflammatory process have been used, such as cyclooxygenases, human neutrophils and human cancer cell lines. Methods concerning adsorption and perforation of bacteria, fungi, human cells and model membranes, have been developed and optimised, with emphasis on antimicrobial peptides and their interaction with the membrane target, in particular their ability to distinguish host from pathogen. RESULTS A long-term research has provided experience of selection and combination of bioassay models, which has led to an increased understanding of ethnopharmacological and ecological observations, together with in-depth knowledge of mode of action of isolated compounds. CONCLUSION A more multidisciplinary approach and a higher degree of fundamental research in development of bioassays are often necessary to identify and to fully understand the mode of action of bioactive molecules with novel structure-activity relationships from natural sources.
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Affiliation(s)
- Adam A Strömstedt
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Center, Uppsala University, Box 574, 751 23, Uppsala, Sweden
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11
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Global gas chromatography/time-of-flight mass spectrometry (GC/TOFMS)-based metabonomic profiling of lyophilized human feces. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 937:103-13. [PMID: 24029555 DOI: 10.1016/j.jchromb.2013.08.025] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 08/14/2013] [Accepted: 08/18/2013] [Indexed: 02/08/2023]
Abstract
Gas chromatography mass spectrometry (GC/MS)-based fecal metabonomics represents a powerful systems biology approach for elucidating metabolic biomarkers of lower gastrointestinal tract (GIT) diseases. Unlike metabolic profiling of fecal water, the profiling of complete fecal material remains under-explored. Here, a gas chromatography/time-of-flight mass spectrometry (GC/TOFMS) method was developed and validated for the global metabonomic profiling of human feces. Fecal and fecal water metabotypes were also profiled and compared. Additionally, the unclear influence of blood in stool on the fecal metabotype was investigated unprecedentedly. Eighty milligram of lyophilized feces was ultrasonicated with 1mL of methanol:water (8:2) for 30min, followed by centrifugation, drying of supernatant, oximation and trimethylsilylation for 45min. Lyophilized feces demonstrated a more comprehensive metabolic coverage than fecal water, based on the number of chromatographic peaks. Principal component analysis (PCA) indicated occult blood (1mgHb/g feces) exerted a negligible effect on the fecal metabotype. Conversely, a unique metabotype related to feces spiked with gross blood (100mgHb/g feces) was revealed (PCA, R(2)X=0.837, Q(2)=0.794), confirming the potential confounding effect of gross GIT bleeding on the fecal metabotype. This pertinent finding highlights the importance of prudent interpretation of fecal metabonomic data, particularly in GIT diseases where bleeding is prevalent.
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12
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Ryan EP, Heuberger AL, Broeckling CD, Borresen EC, Tillotson C, Prenni JE. Advances in Nutritional Metabolomics. ACTA ACUST UNITED AC 2013; 1:109-120. [PMID: 29682447 DOI: 10.2174/2213235x11301020001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Metabolomics is maturing as an experimental approach in nutrition science, and it is a useful analysis for revealing systems biology outcomes associated with changes in diet. A major goal of this review is to present the rapidly evolving body of scientific literature that seeks to reveal connections between an individual's metabolic profile and experimentally manipulated or naturally varied dietary intakes. Metabolite profiles in tissue, serum, urine, or stool reflect changes in metabolic pathways that respond to dietary intervention which makes them accessible samples for revealing metabolic effects of diet. Three broadly defined areas of investigation related to dietary-metabolomic strategies include: (1) describing the metabolite variation within and between dietary exposures or interventions; (2) characterizing the metabolic response to dietary interventions with respect to time; and (3) assessing individual variation in baseline nutritional health and/or disease status. An overview of metabolites that were responsive to dietary interventions as reported from original research in human or animal studies is provided and illustrates the breadth of metabolites affected by dietary intervention. Advantages and drawbacks for assessing metabolic changes are discussed in relation to types of metabolite analysis platforms. A combination of targeted and non-targeted global profiling studies as a component of future dietary intervention trials will increase our understanding of nutrition in a systems context.
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Affiliation(s)
- Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins CO 80523
| | - Adam L Heuberger
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins CO 80523
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins CO 80523
| | - Erica C Borresen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins CO 80523
| | - Cadie Tillotson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins CO 80523
| | - Jessica E Prenni
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins CO 80523.,Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins CO 80523
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Ahn Y, Jung JY, Chung YH, Chae M, Jeon CO, Cerniglia CE. In vitro Analysis of the Impact of Enrofloxacin Residues on the Human Intestinal Microbiota Using 1H-NMR Spectroscopy. J Mol Microbiol Biotechnol 2012; 22:317-25. [DOI: 10.1159/000345147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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14
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Gill CIR, McDougall GJ, Glidewell S, Stewart D, Shen Q, Tuohy K, Dobbin A, Boyd A, Brown E, Haldar S, Rowland IR. Profiling of phenols in human fecal water after raspberry supplementation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:10389-10395. [PMID: 20809621 DOI: 10.1021/jf1017143] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The phenolic compositions of fecal water samples from ten free-living human subjects without marked dietary restrictions were monitored before and after intake of raspberry puree (200 g/day, 4 days) using gas chromatography-mass spectrometry. No single phenolic component was increased in all subjects after intake, but a majority of subjects had significant elevations in phenylacetic acid (7/10), 4-hydroxyphenylacetic acid (6/10), 3-hydroxyphenylacetic acid (5/10), 3-phenylpropionic acid and 3-(4-hydroxyphenyl)propionic acid. The levels of 3,4-dihydroxbenzoic acid were elevated in 8/10 subjects, significantly for 6 subjects (p < 0.05), and not significantly reduced in the other 2 subjects. In addition, unlike most other fecal metabolites, the increase was always >2-fold. This metabolite may be representative of the increased colonic dose of cyanidin anthocyanins. The colonic microbiota varied greatly between individuals, and supplementation with raspberries did not produce any statistically significant alterations in the profile of colonic bacteria, nor was a common pattern revealed to account for the interindividual variations observed in the fecal water phenolic profiles.
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Affiliation(s)
- Chris I R Gill
- Northern Ireland Centre for Food and Health, Centre for Molecular Biosciences, University of Ulster, Cromore Road, Coleraine, N Ireland BT52 1SA, UK.
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Bohlin L, Göransson U, Alsmark C, Wedén C, Backlund A. Natural products in modern life science. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2010; 9:279-301. [PMID: 20700376 PMCID: PMC2912726 DOI: 10.1007/s11101-009-9160-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Accepted: 11/17/2009] [Indexed: 05/02/2023]
Abstract
With a realistic threat against biodiversity in rain forests and in the sea, a sustainable use of natural products is becoming more and more important. Basic research directed against different organisms in Nature could reveal unexpected insights into fundamental biological mechanisms but also new pharmaceutical or biotechnological possibilities of more immediate use. Many different strategies have been used prospecting the biodiversity of Earth in the search for novel structure-activity relationships, which has resulted in important discoveries in drug development. However, we believe that the development of multidisciplinary incentives will be necessary for a future successful exploration of Nature. With this aim, one way would be a modernization and renewal of a venerable proven interdisciplinary science, Pharmacognosy, which represents an integrated way of studying biological systems. This has been demonstrated based on an explanatory model where the different parts of the model are explained by our ongoing research. Anti-inflammatory natural products have been discovered based on ethnopharmacological observations, marine sponges in cold water have resulted in substances with ecological impact, combinatory strategy of ecology and chemistry has revealed new insights into the biodiversity of fungi, in depth studies of cyclic peptides (cyclotides) has created new possibilities for engineering of bioactive peptides, development of new strategies using phylogeny and chemography has resulted in new possibilities for navigating chemical and biological space, and using bioinformatic tools for understanding of lateral gene transfer could provide potential drug targets. A multidisciplinary subject like Pharmacognosy, one of several scientific disciplines bridging biology and chemistry with medicine, has a strategic position for studies of complex scientific questions based on observations in Nature. Furthermore, natural product research based on intriguing scientific questions in Nature can be of value to increase the attraction for young students in modern life science.
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Affiliation(s)
- Lars Bohlin
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Box 574, 751 23 Uppsala, Sweden
| | - Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Box 574, 751 23 Uppsala, Sweden
| | - Cecilia Alsmark
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Box 574, 751 23 Uppsala, Sweden
| | - Christina Wedén
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Box 574, 751 23 Uppsala, Sweden
| | - Anders Backlund
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, Box 574, 751 23 Uppsala, Sweden
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Wu J, An Y, Yao J, Wang Y, Tang H. An optimised sample preparation method for NMR-based faecal metabonomic analysis. Analyst 2010; 135:1023-30. [PMID: 20419252 DOI: 10.1039/b927543f] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Faecal metabonomic NMR analysis plays an essential role in investigating the interactions between mammalian metabolism and symbiotic gut microbiota. However, the faecal metabolite extraction method remains to be optimised and standardised to take into consideration signal-to-noise ratios, pH and chemical shift consistency. In the current investigation, we compared extraction consistency of three homogenisation methods including manual ultrasonication, automatic homogenization with tissuelyser and their combination, and systematically optimised faecal metabolite extraction parameters, including the faeces-to-buffer ratio (W(f) : V(b)), extraction repetition times and duration. We found that automatic homogenisation with tissuelyser was the choice of extraction method owning to its good metabolite extraction consistency and high throughput. We also recommend W(f) : V(b) of 1 : 10 (mg microl(-1)) and use of the combined first two extracts as the resultant samples to represent faecal metabolite composition. Such recommendation is based on considerations of maximisation of the spectral signal-to-noise ratio, pH and chemical shift consistency, completeness of metabolite extraction and sample preparation throughput so that the method is suitable for analysing a large number of samples especially in human population studies.
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Affiliation(s)
- Junfang Wu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
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Bezabeh T, Somorjai RL, Smith ICP. MR metabolomics of fecal extracts: applications in the study of bowel diseases. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47 Suppl 1:S54-S61. [PMID: 19842159 DOI: 10.1002/mrc.2530] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
NMR-based metabolomics is becoming a useful tool in the study of body fluids and has a strong potential to contribute to disease diagnosis. While applications on urine and serum have been the focus to date, there are a number of other body fluids that are readily available and could potentially be used for metabolomics-based disease diagnosis. One such body fluid is stool or fecal extract. Given its contact with and transient stay in the colon and rectum, stool carries a lot of useful information regarding the health/disease status of both the colon and the rectum. This could be particularly useful for the non-invasive diagnosis of colorectal cancer and inflammatory bowel disease--the two bowel diseases that are very common and pose significant public health problems. Different methodological considerations including the collection of sample, the storage of sample, the preparation of sample, NMR acquisition parameters, experimental conditions and data analysis methods are discussed. Results obtained in the detection of colorectal cancer and in the differentiation of the two major forms of inflammatory bowel disease (i.e. ulcerative colitis and Crohn's disease) are presented. This is concluded with a brief discussion on the future of MR metabolomics of fecal extracts.
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Affiliation(s)
- Tedros Bezabeh
- National Research Council, Institute for Biodiagnostics, Winnipeg, Manitoba, Canada.
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Joosen AM, Kuhnle GG, Aspinall SM, Barrow TM, Lecommandeur E, Azqueta A, Collins AR, Bingham SA. Effect of processed and red meat on endogenous nitrosation and DNA damage. Carcinogenesis 2009; 30:1402-7. [PMID: 19498009 PMCID: PMC2718076 DOI: 10.1093/carcin/bgp130] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 05/08/2009] [Accepted: 05/19/2009] [Indexed: 01/22/2023] Open
Abstract
Haem in red meat (RM) stimulates the endogenous production of mutagenic nitroso compounds (NOC). Processed (nitrite-preserved red) meat additionally contains high concentrations of preformed NOC. In two studies, of a fresh RM versus a vegetarian (VEG) diet (six males and six females) and of a nitrite-preserved red meat (PM) versus a VEG diet (5 males and 11 females), we investigated whether processing of meat might increase colorectal cancer risk by stimulating nitrosation and DNA damage. Meat diets contained 420 g (males) or 366 g (females) meat/per day. Faecal homogenates from day 10 onwards were analysed for haem and NOC and associated supernatants for genotoxicity. Means are adjusted for differences in male to female ratios between studies. Faecal NOC concentrations on VEG diets were low (2.6 and 3.5 mmol/g) but significantly higher on meat diets (PM 175 +/- 19 nmol/g versus RM 185 +/- 22 nmol/g; P = 0.75). The RM diet resulted in a larger proportion of nitrosyl iron (RM 78% versus PM 54%; P < 0.0001) and less nitrosothiols (RM 12% versus PM 19%; P < 0.01) and other NOC (RM 10% versus PM 27%; P < 0.0001). There was no statistically significant difference in DNA breaks induced by faecal water (FW) following PM and RM diets (P = 0.80). However, PM resulted in higher levels of oxidized pyrimidines (P < 0.05). Surprisingly, VEG diets resulted in significantly more FW-induced DNA strand breaks than the meat diets (P < 0.05), which needs to be clarified in further studies. Meats cured with nitrite have the same effect as fresh RM on endogenous nitrosation but show increased FW-induced oxidative DNA damage.
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Affiliation(s)
- Annemiek M.C.P. Joosen
- To whom correspondence should be addressed. Tel: +44 1223 252 762; Fax: +44 1223 252 765;
| | | | | | | | | | - Amaya Azqueta
- Department of Nutrition, Faculty of Medicine, University of Oslo, 0316 Oslo, Norway
| | - Andrew R. Collins
- Department of Nutrition, Faculty of Medicine, University of Oslo, 0316 Oslo, Norway
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Metabolite analysis of human fecal water by gas chromatography/mass spectrometry with ethyl chloroformate derivatization. Anal Biochem 2009; 393:163-75. [PMID: 19573517 DOI: 10.1016/j.ab.2009.06.036] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 06/25/2009] [Accepted: 06/25/2009] [Indexed: 01/30/2023]
Abstract
Fecal water is a complex mixture of various metabolites with a wide range of physicochemical properties and boiling points. The analytical method developed here provides a qualitative and quantitative gas chromatography/mass spectrometry (GC/MS) analysis, with high sensitivity and efficiency, coupled with derivatization of ethyl chloroformate in aqueous medium. The water/ethanol/pyridine ratio was optimized to 12:6:1, and a two-step derivatization with an initial pH regulation of 0.1M sodium bicarbonate was developed. The deionized water exhibited better extraction efficiency for fecal water compounds than did acidified and alkalized water. Furthermore, more amino acids were extracted from frozen fecal samples than from fresh samples based on multivariate statistical analysis and univariate statistical validation on GC/MS data. Method validation by 34 reference standards and fecal water samples showed a correlation coefficient higher than 0.99 for each of the standards, and the limit of detection (LOD) was from 10 to 500pg on-column for most of the standards. The analytical equipment exhibited excellent repeatability, with the relative standard deviation (RSD) lower than 4% for standards and lower than 7% for fecal water. The derivatization method also demonstrated good repeatability, with the RSD lower than 6.4% for standards (except 3,4-dihydroxyphenylacetic acid) and lower than 10% for fecal water (except dicarboxylic acids). The qualitative means by searching the electron impact (EI) mass spectral database, chemical ionization (CI) mass spectra validation, and reference standards comparison totally identified and structurally confirmed 73 compounds, and the fecal water compounds of healthy humans were also quantified. This protocol shows a promising application in metabolome analysis based on human fecal water samples.
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