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Dong T, Zhu W, Yang Z, Matos Pires NM, Lin Q, Jing W, Zhao L, Wei X, Jiang Z. Advances in heart failure monitoring: Biosensors targeting molecular markers in peripheral bio-fluids. Biosens Bioelectron 2024; 255:116090. [PMID: 38569250 DOI: 10.1016/j.bios.2024.116090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/10/2024] [Accepted: 01/28/2024] [Indexed: 04/05/2024]
Abstract
Cardiovascular diseases (CVDs), especially chronic heart failure, threaten many patients' lives worldwide. Because of its slow course and complex causes, its clinical screening, diagnosis, and prognosis are essential challenges. Clinical biomarkers and biosensor technologies can rapidly screen and diagnose. Multiple types of biomarkers are employed for screening purposes, precise diagnosis, and treatment follow-up. This article provides an up-to-date overview of the biomarkers associated with the six main heart failure etiology pathways. Plasma natriuretic peptides (BNP and NT-proBNP) and cardiac troponins (cTnT, cTnl) are still analyzed as gold-standard markers for heart failure. Other complementary biomarkers include growth differentiation factor 15 (GDF-15), circulating Galactose Lectin 3 (Gal-3), soluble interleukin (sST2), C-reactive protein (CRP), and tumor necrosis factor-alpha (TNF-α). For these biomarkers, the electrochemical biosensors have exhibited sufficient sensitivity, detection limit, and specificity. This review systematically summarizes the latest molecular biomarkers and sensors for heart failure, which will provide comprehensive and cutting-edge authoritative scientific information for biomedical and electronic-sensing researchers in the field of heart failure, as well as patients. In addition, our proposed future outlook may provide new research ideas for researchers.
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Affiliation(s)
- Tao Dong
- Chongqing Key Laboratory of Micro-Nano Systems and Intelligent Transduction, Collaborative Innovation Center on Micro-Nano Transduction and Intelligent Eco-Internet of Things, Chongqing Key Laboratory of Colleges and Universities on Micro-Nano Systems Technology and Smart Transducing, National Research Base of Intelligent Manufacturing Service, School of Mechanical Engincering, Chongqing Technology and Business University, Nan'an District, Chongqing, 400067, China; X Multidisciplinary Research Institute, Faculty of Instrumentation Science and Technology, State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Xi'an Jiaotong University, Xi'an, 710049, China; Department of Microsystems- IMS, Faculty of Technology, Natural Sciences and Maritime Sciences, University of South-Eastern Norway-USN, P.O. Box 235, Kongsberg, 3603, Norway
| | - Wangang Zhu
- Chongqing Key Laboratory of Micro-Nano Systems and Intelligent Transduction, Collaborative Innovation Center on Micro-Nano Transduction and Intelligent Eco-Internet of Things, Chongqing Key Laboratory of Colleges and Universities on Micro-Nano Systems Technology and Smart Transducing, National Research Base of Intelligent Manufacturing Service, School of Mechanical Engincering, Chongqing Technology and Business University, Nan'an District, Chongqing, 400067, China; X Multidisciplinary Research Institute, Faculty of Instrumentation Science and Technology, State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Zhaochu Yang
- Chongqing Key Laboratory of Micro-Nano Systems and Intelligent Transduction, Collaborative Innovation Center on Micro-Nano Transduction and Intelligent Eco-Internet of Things, Chongqing Key Laboratory of Colleges and Universities on Micro-Nano Systems Technology and Smart Transducing, National Research Base of Intelligent Manufacturing Service, School of Mechanical Engincering, Chongqing Technology and Business University, Nan'an District, Chongqing, 400067, China
| | - Nuno Miguel Matos Pires
- Chongqing Key Laboratory of Micro-Nano Systems and Intelligent Transduction, Collaborative Innovation Center on Micro-Nano Transduction and Intelligent Eco-Internet of Things, Chongqing Key Laboratory of Colleges and Universities on Micro-Nano Systems Technology and Smart Transducing, National Research Base of Intelligent Manufacturing Service, School of Mechanical Engincering, Chongqing Technology and Business University, Nan'an District, Chongqing, 400067, China
| | - Qijing Lin
- X Multidisciplinary Research Institute, Faculty of Instrumentation Science and Technology, State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Weixuan Jing
- X Multidisciplinary Research Institute, Faculty of Instrumentation Science and Technology, State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Libo Zhao
- X Multidisciplinary Research Institute, Faculty of Instrumentation Science and Technology, State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xueyong Wei
- X Multidisciplinary Research Institute, Faculty of Instrumentation Science and Technology, State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Zhuangde Jiang
- X Multidisciplinary Research Institute, Faculty of Instrumentation Science and Technology, State Key Laboratory for Manufacturing Systems Engineering, International Joint Laboratory for Micro/Nano Manufacturing and Measurement Technologies, Xi'an Jiaotong University, Xi'an, 710049, China
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Bishehsari F, Drees M, Adnan D, Sharma D, Green S, Koshy J, Giron LB, Goldman A, Abdel-Mohsen M, Rasmussen HE, Miller GE, Keshavarzian A. Multi-omics approach to socioeconomic disparity in metabolic syndrome reveals roles of diet and microbiome. Proteomics 2023; 23:e2300023. [PMID: 37525324 DOI: 10.1002/pmic.202300023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/23/2023] [Accepted: 07/10/2023] [Indexed: 08/02/2023]
Abstract
The epidemy of metabolic syndrome (MetS) is typically preceded by adoption of a "risky" lifestyle (e.g., dietary habit) among populations. Evidence shows that those with low socioeconomic status (SES) are at an increased risk for MetS. To investigate this, we recruited 123 obese subjects (body mass index [BMI] ≥ 30) from Chicago. Multi-omic data were collected to interrogate fecal microbiota, systemic markers of inflammation and immune activation, plasma metabolites, and plasma glycans. Intestinal permeability was measured using the sugar permeability testing. Our results suggest a heterogenous metabolic dysregulation among obese populations who are at risk of MetS. Systemic inflammation, linked to poor diet, intestinal microbiome dysbiosis, and gut barrier dysfunction may explain the development of MetS in these individuals. Our analysis revealed 37 key features associated with increased numbers of MetS features. These features were used to construct a composite metabolic-inflammatory (MI) score that was able to predict progression of MetS among at-risk individuals. The MI score was correlated with several markers of poor diet quality as well as lower levels of gut microbial diversity and abnormalities in several species of bacteria. This study reveals novel targets to reduce the burden of MetS and suggests access to healthy food options as a practical intervention.
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Affiliation(s)
- Faraz Bishehsari
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
| | - Michael Drees
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
| | - Darbaz Adnan
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
| | - Deepak Sharma
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
| | - Stefan Green
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
| | - Jane Koshy
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Leila B Giron
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Aaron Goldman
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | | | - Gregory E Miller
- Institute for Policy Research and Dept of Psychology, Northwestern Univ, Evanston, Illinois, USA
| | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
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Boktor JC, Sharon G, Verhagen Metman LA, Hall DA, Engen PA, Zreloff Z, Hakim DJ, Bostick JW, Ousey J, Lange D, Humphrey G, Ackermann G, Carlin M, Knight R, Keshavarzian A, Mazmanian SK. Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome. Mov Disord 2023; 38:399-409. [PMID: 36691982 DOI: 10.1002/mds.29300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The gut microbiome is altered in several neurologic disorders, including Parkinson's disease (PD). OBJECTIVES The aim is to profile the fecal gut metagenome in PD for alterations in microbial composition, taxon abundance, metabolic pathways, and microbial gene products, and their relationship with disease progression. METHODS Shotgun metagenomic sequencing was conducted on 244 stool donors from two independent cohorts in the United States, including individuals with PD (n = 48, n = 47, respectively), environmental household controls (HC, n = 29, n = 30), and community population controls (PC, n = 41, n = 49). Microbial features consistently altered in PD compared to HC and PC subjects were identified. Data were cross-referenced to public metagenomic data sets from two previous studies in Germany and China to determine generalizable microbiome features. RESULTS We find several significantly altered taxa between PD and controls within the two cohorts sequenced in this study. Analysis across global cohorts returns consistent changes only in Intestinimonas butyriciproducens. Pathway enrichment analysis reveals disruptions in microbial carbohydrate and lipid metabolism and increased amino acid and nucleotide metabolism in PD. Global gene-level signatures indicate an increased response to oxidative stress, decreased cellular growth and microbial motility, and disrupted intercommunity signaling. CONCLUSIONS A metagenomic meta-analysis of PD shows consistent and novel alterations in functional metabolic potential and microbial gene abundance across four independent studies from three continents. These data reveal that stereotypic changes in the functional potential of the gut microbiome are a consistent feature of PD, highlighting potential diagnostic and therapeutic avenues for future research. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Joseph C Boktor
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Gil Sharon
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Leo A Verhagen Metman
- Department of Neurology Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Deborah A Hall
- Department of Neurology Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Phillip A Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
| | - Zoe Zreloff
- The BioCollective, LLC, Denver, Colorado, USA
| | - Daniel J Hakim
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - John W Bostick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
| | - James Ousey
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | | | - Gregory Humphrey
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
| | | | - Rob Knight
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
- Departments of Internal Medicine, Anatomy & Cell Biology, Rush University Medical Center, Chicago, Illinois, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
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Liu C, Gan RY, Chen D, Zheng L, Ng SB, Rietjens IMCM. Gut microbiota-mediated metabolism of green tea catechins and the biological consequences: An updated review. Crit Rev Food Sci Nutr 2023. [DOI: 10.1080/10408398.2023.2180478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Chen Liu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
- Division of Toxicology, Wageningen University and Research, Wageningen, the Netherlands
- Tea Refining and Innovation Key Laboratory of Sichuan Province, College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ren-You Gan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Liang Zheng
- Division of Toxicology, Wageningen University and Research, Wageningen, the Netherlands
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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Barbosa JMG, de Mendonça DR, David LC, E Silva TC, Fortuna Lima DA, de Oliveira AE, Lopes WDZ, Fioravanti MCS, da Cunha PHJ, Antoniosi Filho NR. A cerumenolomic approach to bovine trypanosomosis diagnosis. Metabolomics 2022; 18:42. [PMID: 35739279 DOI: 10.1007/s11306-022-01901-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/25/2022] [Indexed: 10/17/2022]
Abstract
INTRODUCTION Trypanosomiasis caused by Trypanosoma vivax (T. vivax, subgenus Duttonella) is a burden disease in bovines that induces losses of billions of dollars in livestock activity worldwide. To control the disease, the first step is identifying the infected animals at early stages. However, convention tools for animal infection detection by T. vivax present some challenges, facilitating the spread of the pathogenesis. OBJECTIVES This work aims to develop a new procedure to identify infected bovines by T. vivax using cerumen (earwax) in a volatilomic approach, here named cerumenolomic, which is performed in an easy, quick, accurate, and non-invasive manner. METHODS Seventy-eight earwax samples from Brazilian Curraleiro Pé-Duro calves were collected in a longitudinal study protocol during health and inoculated stages. The samples were analyzed using Headspace/Gas Chromatography-Mass Spectrometry followed by multivariate analysis approaches. RESULTS The cerumen analyses lead to the identification of a broad spectrum of volatile organic metabolites (VOMs), of which 20 VOMs can discriminate between healthy and infected calves (AUC = 0.991, sensitivity = 0.967, specificity = 1.000). Furthermore, 13 VOMs can indicate a pattern of discrimination between the acute and chronic phases of the T. vivax infection in the animals (AUC = 0.989, sensitivity = 0.944, specificity = 1.000). CONCLUSION The cerumen volatile metabolites present alterations in their occurrence during the T.vivax infection, which may lead to identifying the infection in the first weeks of inoculation and discriminating between the acute and chronic phases of the illness. These results may be a breakthrough to avoid the T. vivax outbreak and provide a faster clinical approach to the animal.
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Affiliation(s)
- João Marcos G Barbosa
- Laboratório de Métodos de Extração e Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus II - Samambaia, Goiânia, GO, 74690-900, Brazil.
| | - Débora Ribeiro de Mendonça
- Escola de Veterinária e Zootecnia (EVZ), Universidade Federal de Goiás (UFG), Rodovia Goiânia - Nova Veneza, Km 8, Campus II - Samambaia, Goiânia, GO, CEP, 74001-970, Brazil
| | - Lurian C David
- Laboratório de Métodos de Extração e Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus II - Samambaia, Goiânia, GO, 74690-900, Brazil
| | - Taynara C E Silva
- Laboratório de Métodos de Extração e Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus II - Samambaia, Goiânia, GO, 74690-900, Brazil
| | - Danielly A Fortuna Lima
- Laboratório de Métodos de Extração e Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus II - Samambaia, Goiânia, GO, 74690-900, Brazil
| | - Anselmo E de Oliveira
- Laboratory of Theoretical and Computational Chemistry, Instituto de Química, UFG, Goiânia, GO, 74690-970, Brazil
| | - Welber Daniel Zanetti Lopes
- Centro de Parasitologia Veterinária, Escola de Veterinária e Zootecnia (EVZ), Universidade Federal de Goiás (UFG), Rodovia Goiânia - Nova Veneza, Km 8, Campus II - Samambaia, Goiânia, Goiás, CEP, 74001-970, Brazil
| | - Maria Clorinda S Fioravanti
- Escola de Veterinária e Zootecnia (EVZ), Universidade Federal de Goiás (UFG), Rodovia Goiânia - Nova Veneza, Km 8, Campus II - Samambaia, Goiânia, GO, CEP, 74001-970, Brazil
| | - Paulo H Jorge da Cunha
- Escola de Veterinária e Zootecnia (EVZ), Universidade Federal de Goiás (UFG), Rodovia Goiânia - Nova Veneza, Km 8, Campus II - Samambaia, Goiânia, GO, CEP, 74001-970, Brazil
| | - Nelson R Antoniosi Filho
- Laboratório de Métodos de Extração e Separação (LAMES), Instituto de Química (IQ), Universidade Federal de Goiás (UFG), Campus II - Samambaia, Goiânia, GO, 74690-900, Brazil.
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Hofman D, Kudla U, Miqdady M, Nguyen TVH, Morán-Ramos S, Vandenplas Y. Faecal Microbiota in Infants and Young Children with Functional Gastrointestinal Disorders: A Systematic Review. Nutrients 2022; 14:nu14050974. [PMID: 35267949 PMCID: PMC8912645 DOI: 10.3390/nu14050974] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 01/27/2023] Open
Abstract
Functional gastrointestinal disorders (FGIDs) refer to gastrointestinal tract issues that lack clear structural or biochemical causes. Their pathophysiology is still unclear, but gut microbiota alterations are thought to play an important role. This systematic review aimed to provide a comprehensive overview of the faecal microbiota of infants and young children with FGIDs compared to healthy controls. A systematic search and screening of the literature resulted in the inclusion of thirteen full texts. Most papers reported on infantile colic, only one studied functional constipation. Despite methodological limitations, data show alterations in microbial diversity, stability, and colonisation patterns in colicky infants compared to healthy controls. Several studies (eight) reported increases in species of (pathogenic) Proteobacteria, and some studies (six) reported a decrease in (beneficial) bacteria such as Lactobacilli and Bifidobacteria. In addition, accumulation of related metabolites, as well as low-grade inflammation, might play a role in the pathophysiology of infantile colic. Infants and toddlers with functional constipation had significantly lower levels of Lactobacilli in their stools compared to controls. Microbial dysbiosis and related changes in metabolites may be inherent to FGIDs. There is a need for more standardised methods within research of faecal microbiota in FGIDs to obtain a more comprehensive picture and understanding of infant and childhood FGIDs.
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Affiliation(s)
- Denise Hofman
- FrieslandCampina, Stationsplein 1, 3818 LE Amersfoort, The Netherlands;
- Correspondence:
| | - Urszula Kudla
- FrieslandCampina, Stationsplein 1, 3818 LE Amersfoort, The Netherlands;
| | - Mohamad Miqdady
- Ped. GI, Hepatology & Nutrition Division, Sheikh Khalifa Medical City, P.O. Box 51900, Abu Dhabi 51133, United Arab Emirates;
| | - Thi Viet Ha Nguyen
- Department of Pediatrics, Hanoi Medical University, Hanoi 116001, Vietnam;
| | - Sofía Morán-Ramos
- Unidad de Genomica de Poblaciones, Instituto Nacional de Medicina Genomica, Mexico City 14610, Mexico;
| | - Yvan Vandenplas
- Paediatric Gastro-Enterology and Nutrition, Vrije Universiteit Brussel, UZ Brussel, KidZ Health Castle, 1050 Brussels, Belgium;
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Jones J, Reinke SN, Ali A, Palmer DJ, Christophersen CT. Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations. Sci Rep 2021; 11:13964. [PMID: 34234185 PMCID: PMC8263620 DOI: 10.1038/s41598-021-93031-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Associations between the human gut microbiome and health outcomes continues to be of great interest, although fecal sample collection methods which impact microbiome studies are sometimes neglected. Here, we expand on previous work in sample optimization, to promote high quality microbiome data. To compare fecal sample collection methods, amplicons from the bacterial 16S rRNA gene (V4) and fungal (ITS2) region, as well as short chain fatty acid (SCFA) concentrations were determined in fecal material over three timepoints. We demonstrated that spot sampling of stool results in variable detection of some microbial members, and inconsistent levels of SCFA; therefore, sample homogenization prior to subsequent analysis or subsampling is recommended. We also identify a trend in microbial and metabolite composition that shifts over two consecutive stool collections less than 25 h apart. Lastly, we show significant differences in bacterial composition that result from collecting stool samples in OMNIgene·Gut tube (DNA Genotec) or Stool Nucleic Acid Collection and Preservation Tube (NORGEN) compared to immediate freezing. To assist with planning fecal sample collection and storage procedures for microbiome investigations with multiple analyses, we recommend participants to collect the first full bowel movement of the day and freeze the sample immediately after collection.
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Affiliation(s)
- Jacquelyn Jones
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.
- The Western Australian Human Microbiome Collaboration Centre, Curtin University, Bentley, WA, Australia.
| | - Stacey N Reinke
- Centre for Integrative Metabolomics and Computational Biology, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Alishum Ali
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- The Western Australian Human Microbiome Collaboration Centre, Curtin University, Bentley, WA, Australia
| | - Debra J Palmer
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
- School of Medicine, University of Western Australia, Crawley, WA, Australia
| | - Claus T Christophersen
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
- The Western Australian Human Microbiome Collaboration Centre, Curtin University, Bentley, WA, Australia
- Centre for Integrative Metabolomics and Computational Biology, School of Science, Edith Cowan University, Joondalup, WA, Australia
- School of Medical & Health Sciences, Edith Cowan University, Joondalup, WA, Australia
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Utembe W, Kamng'ona AW. Gut microbiota-mediated pesticide toxicity in humans: Methodological issues and challenges in the risk assessment of pesticides. CHEMOSPHERE 2021; 271:129817. [PMID: 33736210 DOI: 10.1016/j.chemosphere.2021.129817] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Many in vivo and in vitro studies have shown that pesticides can disrupt the functioning of gut microbiota (GM), which can lead to many diseases in humans. While the tests developed by the Organization of Economic Cooperation and Development (OECD) are expected to capture most apical effects resulting from GM disruptions, exclusion of GM in the risk assessment might mischaracterize hazards or overestimate/underestimate risks, especially when extrapolating results from one species to another species or population with a substantially different GM. On the other hand, direct assessment of GM-mediated effects may face challenges in identifying hazards, since not all GM perturbations will lead to human adverse effects. In this regard, reliable and validated biomarkers for common GM-mediated adverse effects may be very useful in the identification of GM-mediated pesticide toxicity. Nevertheless, proving causality of GM-mediated effects will need modifications of Bradford Hill criteria as well as Koch's postulates, which are more suitable for the "one-pathogen" paradigm. Furthermore, risk assessment of GM-mediated effects may require pesticide toxicokinetics along the gut, possibly through modeling, and the establishment of the involvement of GM in the mechanism of action (MOA) of the pesticide. Risk assessment of GM mediated effects also requires the standardization of experimental approaches as well as the establishment of microbial reference communities, since variations exist among GM in human populations.
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Affiliation(s)
- Wells Utembe
- Toxicology Department, National Institute for Occupational Health (a division of the National Health Laboratory Service), Johannesburg, 2000, South Africa; Department of Environmental Heath, Faculty of Health Sciences, University of Johannesburg, Johannesburg, 2000, South Africa.
| | - Arox Wadson Kamng'ona
- Department of Biomedical Sciences, College of Medicine, University Of Malawi, Blantyre, Malawi; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
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Abstract
The field of pharmacogenetic testing was hailed as one of the early successful clinical applications arising from the personalized (or precision) medicine revolution. Substantial progress has been made to identify genes and genetic variants involved in drug response and establish clinical implementation programs. Yet, drug response is a complex trait and recent work has highlighted the key role played by the gut microbiome. As the study of the gut microbiome and pharmacogenetics converge, it may be possible to generate more precise predictions of drug response and improve health outcomes to treatments. Substantial effort will be needed to understand the dynamic impact of the microbiome and the interplay with host genetics and how to implement expanded pharmacogenetic testing.
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Affiliation(s)
- Susanne B Haga
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, 101 Science Drive, Box 3382, Durham, NC 27708, USA
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10
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VOC fingerprints: metabolomic signatures of biothreat agents with and without antibiotic resistance. Sci Rep 2020; 10:11746. [PMID: 32678173 PMCID: PMC7367350 DOI: 10.1038/s41598-020-68622-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/30/2020] [Indexed: 12/21/2022] Open
Abstract
Category A and B biothreat agents are deemed to be of great concern by the US Centers for Disease Control and Prevention (CDC) and include the bacteria Francisella tularensis, Yersinia pestis, Burkholderia mallei, and Brucella species. Underscored by the impact of the 2020 SARS-CoV-2 outbreak, 2016 Zika pandemic, 2014 Ebola outbreak, 2001 anthrax letter attacks, and 1984 Rajneeshee Salmonella attacks, the threat of future epidemics/pandemics and/or terrorist/criminal use of pathogenic organisms warrants continued exploration and development of both classic and alternative methods of detecting biothreat agents. Volatile organic compounds (VOCs) comprise a large and highly diverse group of carbon-based molecules, generally related by their volatility at ambient temperature. Recently, the diagnostic potential of VOCs has been realized, as correlations between the microbial VOC metabolome and specific bacterial pathogens have been identified. Herein, we describe the use of microbial VOC profiles as fingerprints for the identification of biothreat-relevant microbes, and for differentiating between a kanamycin susceptible and resistant strain. Additionally, we demonstrate microbial VOC profiling using a rapid-throughput VOC metabolomics method we refer to as ‘simultaneous multifiber headspace solid-phase microextraction’ (simulti-hSPME). Finally, through VOC analysis, we illustrate a rapid non-invasive approach to the diagnosis of BALB/c mice infected with either F. tularensis SCHU S4 or Y. pestis CO92.
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11
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Manzoor SS, Doedens A, Burns MB. The promise and challenge of cancer microbiome research. Genome Biol 2020; 21:131. [PMID: 32487228 PMCID: PMC7265652 DOI: 10.1186/s13059-020-02037-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 05/07/2020] [Indexed: 02/06/2023] Open
Abstract
Many microbial agents have been implicated as contributors to cancer genesis and development, and the search to identify and characterize new cancer-related organisms is ongoing. Modern developments in methodologies, especially culture-independent approaches, have accelerated and driven this research. Recent work has shed light on the multifaceted role that the community of organisms in and on the human body plays in cancer onset, development, detection, treatment, and outcome. Much remains to be discovered, however, as methodological variation and functional testing of statistical correlations need to be addressed for the field to advance.
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Affiliation(s)
| | - Annemiek Doedens
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Michael B Burns
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA.
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12
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Van Malderen K, De Winter BY, De Man JG, De Schepper HU, Lamote K. Volatomics in inflammatory bowel disease and irritable bowel syndrome. EBioMedicine 2020; 54:102725. [PMID: 32330874 PMCID: PMC7177032 DOI: 10.1016/j.ebiom.2020.102725] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 02/07/2023] Open
Abstract
Volatile organic compounds (VOCs) are produced by the human metabolism, inflammation and gut microbiota and form the basis of innovative volatomics research. VOCs detected through breath and faecal analysis hence serve as attractive, non-invasive biomarkers for diagnosing and monitoring irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). This review describes the clinical applicability of volatomics in discriminating between IBS, IBD and healthy volunteers with acceptable accuracy in breath (70%-100%) and faecal (58%-85%) samples. Promising compounds are propan-1-ol for diagnosing and monitoring of IBD patients, and 1-methyl-4-propan-2-ylcyclohexa-1,4-diene as biomarker for IBS diagnosis. However, these VOCs often seem to be related to inflammation and probably will need to be used in conjunction with other clinical evidence. Furthermore, three interventional studies underlined the potential of VOCs in predicting treatment outcome and patient follow-up. This shows great promise for future use of VOCs as non-invasive breath and faecal biomarkers in personalised medicine. However, properly designed studies that correlate VOCs to IBD/IBS pathogenesis, while taking microbial influences into account, are still key before clinical implementation can be expected.
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Affiliation(s)
- Kathleen Van Malderen
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium
| | - Benedicte Y De Winter
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium
| | - Joris G De Man
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium
| | - Heiko U De Schepper
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium; Antwerp University Hospital, Edegem, Belgium
| | - Kevin Lamote
- Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Infla-Med Research Consortium of Excellence, University of Antwerp, Antwerp, Belgium; Internal Medicine and Paediatrics, Ghent University, Ghent, Belgium.
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13
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Dailey A, Couch R. Rapid Diagnosis of Bacterial Pneumonia Using Volatile Organic Compounds (VOCs). FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Zhgun ES, Ilina EN. Fecal Metabolites As Non-Invasive Biomarkers of Gut Diseases. Acta Naturae 2020; 12:4-14. [PMID: 32742723 PMCID: PMC7385093 DOI: 10.32607/actanaturae.10954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/04/2020] [Indexed: 12/14/2022] Open
Abstract
Recent studies have shown the importance of the human intestinal microbiome in maintaining a healthy gastrointestinal tract, as well as in the development of pathological processes. The intestinal microbiome manifests itself primarily as fecal metabolites. In the past decade, there has been growing interest in studying its composition, which for the most part had to do with the possibility of using the metabolomic analysis in clinical diagnosis. In contrast to the comprehensive description of blood serum, urine, saliva, and cerebrospinal fluid metabolites, data on fecal metabolites is sparse. Despite the instrumental and methodological achievements in the metabolomic analysis in general, the analysis of fecal metabolome remains less well developed, mainly because of the inhomogeneity of its composition and the lack of standardized methods for collecting, processing, and analyzing fecal samples. This review summarizes data on methods for studying and describing various groups of fecal metabolites. It also assesses their potential as tools in the diagnosis of gastrointestinal diseases.
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Affiliation(s)
- E. S. Zhgun
- Federal Research and Clinical Center of Physical-chemical Medicine of Federal Medical Biological Agency, Moscow, 119435 Russia
| | - E. N. Ilina
- Federal Research and Clinical Center of Physical-chemical Medicine of Federal Medical Biological Agency, Moscow, 119435 Russia
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15
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Important Considerations for Sample Collection in Metabolomics Studies with a Special Focus on Applications to Liver Functions. Metabolites 2020; 10:metabo10030104. [PMID: 32178364 PMCID: PMC7142637 DOI: 10.3390/metabo10030104] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 12/16/2022] Open
Abstract
Metabolomics has found numerous applications in the study of liver metabolism in health and disease. Metabolomics studies can be conducted in a variety of biological matrices ranging from easily accessible biofluids such as urine, blood or feces, to organs, tissues or even cells. Sample collection and storage are critical steps for which standard operating procedures must be followed. Inappropriate sample collection or storage can indeed result in high variability, interferences with instrumentation or degradation of metabolites. In this review, we will first highlight important general factors that should be considered when planning sample collection in the study design of metabolomic studies, such as nutritional status and circadian rhythm. Then, we will discuss in more detail the specific procedures that have been described for optimal pre-analytical handling of the most commonly used matrices (urine, blood, feces, tissues and cells).
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16
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Shah RM, McKenzie EJ, Rosin MT, Jadhav SR, Gondalia SV, Rosendale D, Beale DJ. An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome. Metabolites 2020; 10:E94. [PMID: 32155792 PMCID: PMC7143645 DOI: 10.3390/metabo10030094] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/18/2020] [Accepted: 02/27/2020] [Indexed: 02/06/2023] Open
Abstract
Our understanding of the human gut microbiome has grown exponentially. Advances in genome sequencing technologies and metagenomics analysis have enabled researchers to study microbial communities and their potential function within the context of a range of human gut related diseases and disorders. However, up until recently, much of this research has focused on characterizing the gut microbiological community structure and understanding its potential through system wide (meta) genomic and transcriptomic-based studies. Thus far, the functional output of these microbiomes, in terms of protein and metabolite expression, and within the broader context of host-gut microbiome interactions, has been limited. Furthermore, these studies highlight our need to address the issues of individual variation, and of samples as proxies. Here we provide a perspective review of the recent literature that focuses on the challenges of exploring the human gut microbiome, with a strong focus on an integrated perspective applied to these themes. In doing so, we contextualize the experimental and technical challenges of undertaking such studies and provide a framework for capitalizing on the breadth of insight such approaches afford. An integrated perspective of the human gut microbiome and the linkages to human health will pave the way forward for delivering against the objectives of precision medicine, which is targeted to specific individuals and addresses the issues and mechanisms in situ.
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Affiliation(s)
- Rohan M. Shah
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia;
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Dutton Park, QLD 4102, Australia
| | - Elizabeth J. McKenzie
- Liggins Institute, The University of Auckland, Grafton, Auckland 1142, New Zealand; (E.J.M.); (M.T.R.)
| | - Magda T. Rosin
- Liggins Institute, The University of Auckland, Grafton, Auckland 1142, New Zealand; (E.J.M.); (M.T.R.)
| | - Snehal R. Jadhav
- Centre for Advanced Sensory Science, School of Exercise and Nutrition Sciences, Deakin University, Burwood, VIC 3125, Australia;
| | - Shakuntla V. Gondalia
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia;
| | | | - David J. Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Dutton Park, QLD 4102, Australia
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Nasykhova YA, Barbitoff YA, Serebryakova EA, Katserov DS, Glotov AS. Recent advances and perspectives in next generation sequencing application to the genetic research of type 2 diabetes. World J Diabetes 2019; 10:376-395. [PMID: 31363385 PMCID: PMC6656706 DOI: 10.4239/wjd.v10.i7.376] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/23/2019] [Accepted: 06/11/2019] [Indexed: 02/05/2023] Open
Abstract
Type 2 diabetes (T2D) mellitus is a common complex disease that currently affects more than 400 million people worldwide and has become a global health problem. High-throughput sequencing technologies such as whole-genome and whole-exome sequencing approaches have provided numerous new insights into the molecular bases of T2D. Recent advances in the application of sequencing technologies to T2D research include, but are not limited to: (1) Fine mapping of causal rare and common genetic variants; (2) Identification of confident gene-level associations; (3) Identification of novel candidate genes by specific scoring approaches; (4) Interrogation of disease-relevant genes and pathways by transcriptional profiling and epigenome mapping techniques; and (5) Investigation of microbial community alterations in patients with T2D. In this work we review these advances in application of next-generation sequencing methods for elucidation of T2D pathogenesis, as well as progress and challenges in implementation of this new knowledge about T2D genetics in diagnosis, prevention, and treatment of the disease.
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Affiliation(s)
- Yulia A Nasykhova
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg 199034, Russia
| | - Yury A Barbitoff
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
- Bioinformatics Institute, St. Petersburg 194021, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Elena A Serebryakova
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg 199034, Russia
- Department of Genetics, City Hospital No. 40, St. Petersburg 197706, Russia
| | - Dmitry S Katserov
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad 236016, Russia
| | - Andrey S Glotov
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology and Reproductology, St. Petersburg 199034, Russia
- Department of Genetics, City Hospital No. 40, St. Petersburg 197706, Russia
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad 236016, Russia
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18
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Effect of Daily Intake of Lactobacillus casei on Microbial Diversity and Dynamics in a Healthy Pediatric Population. Curr Microbiol 2019; 76:1020-1027. [PMID: 31187207 PMCID: PMC6663929 DOI: 10.1007/s00284-019-01713-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 06/03/2019] [Indexed: 12/26/2022]
Abstract
Emerging evidence exists that an altered gut microbiota is a key factor in the pathophysiology of a variety of diseases. Consequently, microbiota-targeted interventions, including administration of probiotics, have increasingly been evaluated. Mechanisms on how probiotics contribute to homeostasis or reverse (effects of) dysbiosis remain yet to be elucidated. In the current study, we assessed the effects of daily Lactobacillus casei strain Shirota (LcS) ingestion in healthy children aged from 12–18 years on gut microbiota compositional diversity and stability. Results were compared to healthy children without LcS exposure. For a period of 6 weeks, fecal samples were collected weekly by both groups. In total, 18 children were included (6 probiotics; 12 non-probiotics). At 1-week intervals, no differences in diversity and stability were observed in children exposed to LcS versus controls. LcS ingestion by healthy children does not result in a more diverse and stable gut microbiota composition. Large double-blind placebo-controlled randomized clinical trials in children should be performed to gain more insight on potential beneficial health consequences.
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19
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Huang S, Chen G, Ye N, Kou X, Zhu F, Shen J, Ouyang G. Solid-phase microextraction: An appealing alternative for the determination of endogenous substances - A review. Anal Chim Acta 2019; 1077:67-86. [PMID: 31307724 DOI: 10.1016/j.aca.2019.05.054] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 02/07/2023]
Abstract
The determination of endogenous substances is of great significance for obtaining important biotic information such as biological components, metabolic pathways and disease biomarkers in different living organisms (e.g. plants, insects, animals and humans). However, due to the complex matrix and the trace concentrations of target analytes, the sample preparation procedure is an essential step before the analytes of interest are introduced into a detection instrument. Solid-phase microextraction (SPME), an emerging sample preparation technique that integrates sampling, extraction, concentration, and sample introduction into one step, has gained wide acceptance in various research fields, including in the determination of endogenous compounds. In this review, recent developments and applications of SPME for the determination of endogenous substances over the past five years are summarized. Several aspects, including the design of SPME devices (sampling configuration and coating), applications (in vitro and in vivo sampling), and coupling with emerging instruments (comprehensive two-dimensional gas chromatography (GC × GC), ambient mass spectrometry (AMS) and surface enhanced Raman scattering (SERS)) are involved. Finally, the challenges and opportunities of SPME methods in endogenous substances analysis are also discussed.
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Affiliation(s)
- Siming Huang
- Department of Radiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No. 107 Yanjiang Road West, Guangzhou, 510120, China
| | - Guosheng Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Niru Ye
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiaoxue Kou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fang Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jun Shen
- Department of Radiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No. 107 Yanjiang Road West, Guangzhou, 510120, China.
| | - Gangfeng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China; College of Chemistry & Molecular Engineering, Center of Advanced Analysis and Computational Science, Zhengzhou University, Kexue Avenue 100, Zhengzhou, 450001, PR China.
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20
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Faecal volatile biomarkers of Clostridium difficile infection. PLoS One 2019; 14:e0215256. [PMID: 30986230 PMCID: PMC6464219 DOI: 10.1371/journal.pone.0215256] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 03/19/2019] [Indexed: 12/17/2022] Open
Abstract
Care of patients with potential CDI can involve isolation and use of antibiotics, often before a definitive diagnosis is available, impacting healthcare resource and contributing to antibiotic resistance. There is anecdotal evidence that the faeces of CDI patients have a distinctive odour, while it is well-established that changes in the gut microbiota are associated with changes in the volatile organic compounds (VOC) produced. A total of twenty-four candidate volatile biomarkers were identified from a review of the literature including in vitro, animal and human studies. Using thermal desorption-gas chromatography-time-of flight mass spectrometry (TD-GC-ToFMS), VOC emission rates were determined on stored frozen stool samples from 53 CDI-positive and 53 CDI-negative patients with unexplained diarrhoea which had previously been diagnosed using enzymatic and nucleic acid amplification tests. Sample preparation was limited to placement of a subsample in an appropriate container. Compounds exhibiting a statistically significant difference (p < 0.05) in emission rate between the CDI-positive and-negative groups and a corresponding area under the receiver-operator characteristic curve (ROC) >0.7 were considered potentially indicative of CDI. Seven compounds were so identified: propan-1-ol (ROC 0.75), 3-methylbutanal (ROC 0.84), ethyl propionate (ROC 0.81), hexanoic acid (ROC 0.73), 4-methylphenol (ROC 0.81), dodecane (ROC 0.80) and indole (ROC 0.85). A number of potential volatile biomarkers of CDI can be sampled rapidly and with little prior preparation from faecal samples of patients with diarrhoea. Of these 4-methylphenol (p-cresol) is of particular interest as it has been anecdotally linked to CDI and is closely related to the biology and virulence of Clostridium difficile. This approach shows promise for the rapid, point-of-care diagnosis of CDI with good sensitivity and specificity.
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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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Wilson AD. Application of Electronic-Nose Technologies and VOC-Biomarkers for the Noninvasive Early Diagnosis of Gastrointestinal Diseases †. SENSORS (BASEL, SWITZERLAND) 2018; 18:E2613. [PMID: 30096939 PMCID: PMC6111575 DOI: 10.3390/s18082613] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/13/2022]
Abstract
Conventional methods utilized for clinical diagnosis of gastrointestinal (GI) diseases have employed invasive medical procedures that cause stress, anxiety and pain to patients. These methods are often expensive, time-consuming, and require sophisticated chemical-analysis instruments and advanced modeling procedures to achieve diagnostic interpretations. This paper reviews recent applications of simpler, electronic-nose (e-nose) devices for the noninvasive early diagnosis of a wide range of GI diseases by collective analysis of headspace volatile organic compound (VOC)-metabolites from clinical samples to produce disease-specific aroma signatures (VOC profiles). A different "metabolomics" approach to GI disease diagnostics, involving identifications and quantifications of disease VOC-metabolites, are compared to the electronic-nose approach based on diagnostic costs, accuracy, advantages and disadvantages. The importance of changes in gut microbiome composition that result from disease are discussed relative to effects on disease detection. A new diagnostic approach, which combines the use of e-nose instruments for early rapid prophylactic disease-screenings with targeted identification of known disease biomarkers, is proposed to yield cheaper, quicker and more dependable diagnostic results. Some priority future research needs and coordination for bringing e-nose instruments into routine clinical practice are summarized.
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Affiliation(s)
- Alphus Dan Wilson
- Pathology Department, Southern Hardwoods Laboratory, Center for Bottomland Hardwoods Research, Southern Research Station, USDA Forest Service, 432 Stoneville Road, Stoneville, MS 38776, USA.
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Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe. Methods 2018; 149:3-12. [PMID: 29715508 DOI: 10.1016/j.ymeth.2018.04.029] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/06/2018] [Accepted: 04/22/2018] [Indexed: 02/06/2023] Open
Abstract
It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted.
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Hough R, Archer D, Probert C. A comparison of sample preparation methods for extracting volatile organic compounds (VOCs) from equine faeces using HS-SPME. Metabolomics 2018; 14:19. [PMID: 29367839 PMCID: PMC5754382 DOI: 10.1007/s11306-017-1315-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/22/2017] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Disturbance to the hindgut microbiota can be detrimental to equine health. Metabolomics provides a robust approach to studying the functional aspect of hindgut microorganisms. Sample preparation is an important step towards achieving optimal results in the later stages of analysis. The preparation of samples is unique depending on the technique employed and the sample matrix to be analysed. Gas chromatography mass spectrometry (GCMS) is one of the most widely used platforms for the study of metabolomics and until now an optimised method has not been developed for equine faeces. OBJECTIVES To compare a sample preparation method for extracting volatile organic compounds (VOCs) from equine faeces. METHODS Volatile organic compounds were determined by headspace solid phase microextraction gas chromatography mass spectrometry (HS-SPME-GCMS). Factors investigated were the mass of equine faeces, type of SPME fibre coating, vial volume and storage conditions. RESULTS The resultant method was unique to those developed for other species. Aliquots of 1000 or 2000 mg in 10 ml or 20 ml SPME headspace were optimal. From those tested, the extraction of VOCs should ideally be performed using a divinylbenzene-carboxen-polydimethysiloxane (DVB-CAR-PDMS) SPME fibre. Storage of faeces for up to 12 months at - 80 °C shared a greater percentage of VOCs with a fresh sample than the equivalent stored at - 20 °C. CONCLUSIONS An optimised method for extracting VOCs from equine faeces using HS-SPME-GCMS has been developed and will act as a standard to enable comparisons between studies. This work has also highlighted storage conditions as an important factor to consider in experimental design for faecal metabolomics studies.
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Affiliation(s)
- Rachael Hough
- Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK.
| | - Debra Archer
- Department of Epidemiology and Population Health, University of Liverpool, Liverpool, UK
| | - Christopher Probert
- Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK
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Rojo D, Méndez-García C, Raczkowska BA, Bargiela R, Moya A, Ferrer M, Barbas C. Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiol Rev 2017; 41:453-478. [PMID: 28333226 PMCID: PMC5812509 DOI: 10.1093/femsre/fuw046] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023] Open
Abstract
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.
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Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
| | | | - Beata Anna Raczkowska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), 46020 Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Paterna, 46980 Valencia, Spain
- These authors contributed equally to this work
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Corresponding author: Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain. Tel: (+34) 915854872; E-mail:
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
- These authors contributed equally to this work
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Sniffing Out Paediatric Gastrointestinal Diseases: The Potential of Volatile Organic Compounds as Biomarkers for Disease. J Pediatr Gastroenterol Nutr 2016; 63:585-591. [PMID: 27875502 DOI: 10.1097/mpg.0000000000001250] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The diagnostic work-up and follow-up of paediatric functional gastrointestinal disorders and organic conditions usually includes invasive tests, carrying a high burden on patients. There is a place, therefore, for novel, noninvasive disease-specific biomarkers. Volatile organic compounds (VOCs), originating from (patho)physiological metabolic processes in the human body, are excreted as waste products through all conceivable bodily excrements. The spectrum of VOCs harbours a magnificent source of information, with the potential to serve as noninvasive diagnostic biomarkers and to monitor disease activity. VOC analysis has been studied in children and infants with a variety of gastrointestinal diseases, including inflammatory bowel disease, liver diseases, irritable bowel syndrome, necrotizing enterocolitis and infectious diarrhoea. Most of these studies, although limited in sample size, show that patients can be discriminated from controls based on their VOC profiles, underscoring the potential of VOC analysis in diagnosis and follow-up. Currently, however, the application of VOC analysis in clinical practice is limited; substantial challenges, including methodological, biological, and analytical problems, still need to be met. In this review we provide an overview of the available literature on the potential of VOCs as biomarkers for paediatric gastrointestinal diseases. We discuss the available techniques to analyse VOCs and provide topics for VOC-related research, which need to be addressed before VOC diagnostics can be implemented in daily clinical practice.
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Ultra-high performance liquid chromatographic determination of levofloxacin in human plasma and prostate tissue with use of experimental design optimization procedures. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1029-1030:48-59. [DOI: 10.1016/j.jchromb.2016.06.051] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 06/25/2016] [Accepted: 06/28/2016] [Indexed: 11/21/2022]
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Castillo-Peinado LS, Luque de Castro MD. Present and foreseeable future of metabolomics in forensic analysis. Anal Chim Acta 2016; 925:1-15. [PMID: 27188312 DOI: 10.1016/j.aca.2016.04.040] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/12/2016] [Accepted: 04/17/2016] [Indexed: 01/24/2023]
Abstract
The revulsive publications during the last years on the precariousness of forensic sciences worldwide have promoted the move of major steps towards improvement of this science. One of the steps (viz. a higher involvement of metabolomics in the new era of forensic analysis) deserves to be discussed under different angles. Thus, the characteristics of metabolomics that make it a useful tool in forensic analysis, the aspects in which this omics is so far implicit, but not mentioned in forensic analyses, and how typical forensic parameters such as the post-mortem interval or fingerprints take benefits from metabolomics are critically discussed in this review. The way in which the metabolomics-forensic binomial succeeds when either conventional or less frequent samples are used is highlighted here. Finally, the pillars that should support future developments involving metabolomics and forensic analysis, and the research required for a fruitful in-depth involvement of metabolomics in forensic analysis are critically discussed.
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Affiliation(s)
- L S Castillo-Peinado
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; University of Córdoba, Agrifood Excellence Campus, ceiA3, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, E-14071, Córdoba, Spain
| | - M D Luque de Castro
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; University of Córdoba, Agrifood Excellence Campus, ceiA3, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, E-14071, Córdoba, Spain.
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Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults. PLoS One 2016; 11:e0148952. [PMID: 26859894 PMCID: PMC4747579 DOI: 10.1371/journal.pone.0148952] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 12/22/2015] [Indexed: 12/14/2022] Open
Abstract
In the United States, there are persistent and widening socioeconomic gaps in morbidity and mortality from chronic diseases. Although most disparities research focuses on person-level socioeconomic-status, mounting evidence suggest that chronic diseases also pattern by the demographic characteristics of neighborhoods. Yet the biological mechanisms underlying these associations are poorly understood. There is increasing recognition that chronic diseases share common pathogenic features, some of which involve alterations in the composition, diversity, and functioning of the gut microbiota. This study examined whether socioeconomic-status was associated with alpha-diversity of the colonic microbiota. Forty-four healthy adults underwent un-prepped sigmoidoscopy, during which mucosal biopsies and fecal samples were collected. Subjects’ zip codes were geocoded, and census data was used to form a composite indicator of neighborhood socioeconomic-status, reflecting household income, educational attainment, employment status, and home value. In unadjusted analyses, neighborhood socioeconomic-status explained 12–18 percent of the variability in alpha-diversity of colonic microbiota. The direction of these associations was positive, meaning that as neighborhood socioeconomic-status increased, so did alpha-diversity of both the colonic sigmoid mucosa and fecal microbiota. The strength of these associations persisted when models were expanded to include covariates reflecting potential demographic (age, gender, race/ethnicity) and lifestyle (adiposity, alcohol use, smoking) confounds. In these models neighborhood socioeconomic-status continued to explain 11–22 percent of the variability in diversity indicators. Further analyses suggested these patterns reflected socioeconomic variations in evenness, but not richness, of microbial communities residing in the sigmoid. We also found indications that residence in neighborhoods of higher socioeconomic-status was associated with a greater abundance of Bacteroides and a lower abundance of Prevotella, suggesting that diet potentially underlies differences in microbiota composition. These findings suggest the presence of socioeconomic variations in colonic microbiota diversity. Future research should explore whether these variations contribute to disparities in chronic disease outcomes.
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Mathay C, Hamot G, Henry E, Georges L, Bellora C, Lebrun L, de Witt B, Ammerlaan W, Buschart A, Wilmes P, Betsou F. Method optimization for fecal sample collection and fecal DNA extraction. Biopreserv Biobank 2016; 13:79-93. [PMID: 25880472 DOI: 10.1089/bio.2014.0031] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND This is the third in a series of publications presenting formal method validation for biospecimen processing in the context of accreditation in laboratories and biobanks. We report here optimization of a stool processing protocol validated for fitness-for-purpose in terms of downstream DNA-based analyses. METHODS Stool collection was initially optimized in terms of sample input quantity and supernatant volume using canine stool. Three DNA extraction methods (PerkinElmer MSM I®, Norgen Biotek All-In-One®, MoBio PowerMag®) and six collection container types were evaluated with human stool in terms of DNA quantity and quality, DNA yield, and its reproducibility by spectrophotometry, spectrofluorometry, and quantitative PCR, DNA purity, SPUD assay, and 16S rRNA gene sequence-based taxonomic signatures. RESULTS The optimal MSM I protocol involves a 0.2 g stool sample and 1000 μL supernatant. The MSM I extraction was superior in terms of DNA quantity and quality when compared to the other two methods tested. Optimal results were obtained with plain Sarstedt tubes (without stabilizer, requiring immediate freezing and storage at -20°C or -80°C) and Genotek tubes (with stabilizer and RT storage) in terms of DNA yields (total, human, bacterial, and double-stranded) according to spectrophotometry and spectrofluorometry, with low yield variability and good DNA purity. No inhibitors were identified at 25 ng/μL. The protocol was reproducible in terms of DNA yield among different stool aliquots. CONCLUSIONS We validated a stool collection method suitable for downstream DNA metagenomic analysis. DNA extraction with the MSM I method using Genotek tubes was considered optimal, with simple logistics in terms of collection and shipment and offers the possibility of automation. Laboratories and biobanks should ensure protocol conditions are systematically recorded in the scope of accreditation.
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Affiliation(s)
- Conny Mathay
- 1 Integrated BioBank of Luxemburg (IBBL) , Luxembourg
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31
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Thomas V, Clark J, Doré J. Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies. Future Microbiol 2015; 10:1485-504. [PMID: 26347019 DOI: 10.2217/fmb.15.87] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Despite huge interest, there are still no universally accepted standards to conduct clinical studies in the field of gut microbiota analysis. Stool material is frequently used as a proxy of gut microbiota, but many different protocols can be used for collection and DNA extraction. Whereas 16S rRNA encoding gene amplification and sequencing has been widely used to study the composition of bacterial populations, it is now being challenged by the random, shotgun approach that brings far more information, although at a higher cost. In this review we give an overview of existing methods and important points to consider when conducting gut microbiota studies, with the objective to provide recommendations to those who would like to conduct such research.
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Affiliation(s)
- Vincent Thomas
- Enterome Biosciences, 94-96 Avenue Ledru Rollin, 75011 Paris, France
| | - James Clark
- Enterome Biosciences, 94-96 Avenue Ledru Rollin, 75011 Paris, France
| | - Joël Doré
- INRA, MetaGenoPolis & Micalis Research Units 1319 & 1367, Jouy-en-Josas, France
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Couch RD, Dailey A, Zaidi F, Navarro K, Forsyth CB, Mutlu E, Engen PA, Keshavarzian A. Alcohol induced alterations to the human fecal VOC metabolome. PLoS One 2015; 10:e0119362. [PMID: 25751150 PMCID: PMC4353727 DOI: 10.1371/journal.pone.0119362] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/13/2015] [Indexed: 12/15/2022] Open
Abstract
Studies have shown that excessive alcohol consumption impacts the intestinal microbiota composition, causing disruption of homeostasis (dysbiosis). However, this observed change is not indicative of the dysbiotic intestinal microbiota function that could result in the production of injurious and toxic products. Thus, knowledge of the effects of alcohol on the intestinal microbiota function and their metabolites is warranted, in order to better understand the role of the intestinal microbiota in alcohol associated organ failure. Here, we report the results of a differential metabolomic analysis comparing volatile organic compounds (VOC) detected in the stool of alcoholics and non-alcoholic healthy controls. We performed the analysis with fecal samples collected after passage as well as with samples collected directly from the sigmoid lumen. Regardless of the approach to fecal collection, we found a stool VOC metabolomic signature in alcoholics that is different from healthy controls. The most notable metabolite alterations in the alcoholic samples include: (1) an elevation in the oxidative stress biomarker tetradecane; (2) a decrease in five fatty alcohols with anti-oxidant property; (3) a decrease in the short chain fatty acids propionate and isobutyrate, important in maintaining intestinal epithelial cell health and barrier integrity; (4) a decrease in alcohol consumption natural suppressant caryophyllene; (5) a decrease in natural product and hepatic steatosis attenuator camphene; and (6) decreased dimethyl disulfide and dimethyl trisulfide, microbial products of decomposition. Our results showed that intestinal microbiota function is altered in alcoholics which might promote alcohol associated pathologies.
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Affiliation(s)
- Robin D. Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
- * E-mail:
| | - Allyson Dailey
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Fatima Zaidi
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Karl Navarro
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Christopher B. Forsyth
- Department of Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Biochemistry, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Ece Mutlu
- Department of Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Phillip A. Engen
- Department of Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Ali Keshavarzian
- Department of Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Pharmacology, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, Illinois, United States of America
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
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Amann A, Costello BDL, Miekisch W, Schubert J, Buszewski B, Pleil J, Ratcliffe N, Risby T. The human volatilome: volatile organic compounds (VOCs) in exhaled breath, skin emanations, urine, feces and saliva. J Breath Res 2014; 8:034001. [PMID: 24946087 DOI: 10.1088/1752-7155/8/3/034001] [Citation(s) in RCA: 358] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Breath analysis is a young field of research with its roots in antiquity. Antoine Lavoisier discovered carbon dioxide in exhaled breath during the period 1777-1783, Wilhelm (Vilém) Petters discovered acetone in breath in 1857 and Johannes Müller reported the first quantitative measurements of acetone in 1898. A recent review reported 1765 volatile compounds appearing in exhaled breath, skin emanations, urine, saliva, human breast milk, blood and feces. For a large number of compounds, real-time analysis of exhaled breath or skin emanations has been performed, e.g., during exertion of effort on a stationary bicycle or during sleep. Volatile compounds in exhaled breath, which record historical exposure, are called the 'exposome'. Changes in biogenic volatile organic compound concentrations can be used to mirror metabolic or (patho)physiological processes in the whole body or blood concentrations of drugs (e.g. propofol) in clinical settings-even during artificial ventilation or during surgery. Also compounds released by bacterial strains like Pseudomonas aeruginosa or Streptococcus pneumonia could be very interesting. Methyl methacrylate (CAS 80-62-6), for example, was observed in the headspace of Streptococcus pneumonia in concentrations up to 1420 ppb. Fecal volatiles have been implicated in differentiating certain infectious bowel diseases such as Clostridium difficile, Campylobacter, Salmonella and Cholera. They have also been used to differentiate other non-infectious conditions such as irritable bowel syndrome and inflammatory bowel disease. In addition, alterations in urine volatiles have been used to detect urinary tract infections, bladder, prostate and other cancers. Peroxidation of lipids and other biomolecules by reactive oxygen species produce volatile compounds like ethane and 1-pentane. Noninvasive detection and therapeutic monitoring of oxidative stress would be highly desirable in autoimmunological, neurological, inflammatory diseases and cancer, but also during surgery and in intensive care units. The investigation of cell cultures opens up new possibilities for elucidation of the biochemical background of volatile compounds. In future studies, combined investigations of a particular compound with regard to human matrices such as breath, urine, saliva and cell culture investigations will lead to novel scientific progress in the field.
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Affiliation(s)
- Anton Amann
- Univ-Clinic for Anesthesia and Intensive Care, Innsbruck Medical University, Anichstr, 35, A-6020 Innsbruck, Austria. Breath Research Institute of the University of Innsbruck, Rathausplatz 4, A-6850 Dornbirn, Austria
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