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Bauset C, Carda-Diéguez M, Cejudo-Garcés A, Buetas E, Seco-Cervera M, Macias-Ceja DC, Navarro-Vicente F, Esplugues JV, Calatayud S, Mira Á, Ortiz-Masiá D, Barrachina MD, Cosín-Roger J. A disturbed metabolite-GPCR axis is associated with microbial dysbiosis in IBD patients: Potential role of GPR109A in macrophages. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167489. [PMID: 39233260 DOI: 10.1016/j.bbadis.2024.167489] [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: 01/31/2024] [Revised: 06/20/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024]
Abstract
Inflammatory Bowel Disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract characterized by disrupted immune function. Indeed, gut microbiota dysbiosis and metabolomic profile alterations, are hallmarks of IBD. In this scenario, metabolite-sensing G-protein coupled receptors (GPCRs), involved in several biological processes, have emerged as pivotal players in the pathophysiology of IBD. The aim of this study was to characterize the axis microbiota-metabolite-GPCR in intestinal surgical resections from IBD patients. Results showed that UC patients had a lower microbiota richness and bacterial load, with a higher proportion of the genus Cellulosimicrobium and a reduced proportion of Escherichia, whereas CD patients showed a decreased abundance of Enterococcus. Furthermore, metabolomic analysis revealed alterations in carboxylic acids, fatty acids, and amino acids in UC and CD samples. These patients also exhibited upregulated expression of most metabolite-sensing GPCRs analysed, which positively correlated with pro-inflammatory and pro-fibrotic markers. The role of GPR109A was studied in depth and increased expression of this receptor was detected in epithelial cells and cells from lamina propria, including CD68+ macrophages, in IBD patients. The treatment with β-hydroxybutyrate increased gene expression of GPR109A, CD86, IL1B and NOS2 in U937-derived macrophages. Besides, when GPR109A was transiently silenced, the mRNA expression and secretion of IL-1β, IL-6 and TNF-α were impaired in M1 macrophages. Finally, the secretome from siGPR109A M1 macrophages reduced the gene and protein expression of COL1A1 and COL3A1 in intestinal fibroblasts. A better understanding of metabolite-sensing GPCRs, such as GPR109A, could establish their potential as therapeutic targets for managing IBD.
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Affiliation(s)
- Cristina Bauset
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain
| | | | - Andrea Cejudo-Garcés
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain
| | - Elena Buetas
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain
| | | | | | | | - Juan Vicente Esplugues
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; CIBERehd (Centro de Investigaciones en Red Enfermedad Hepática y Digestiva), Madrid, Spain
| | - Sara Calatayud
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; CIBERehd (Centro de Investigaciones en Red Enfermedad Hepática y Digestiva), Madrid, Spain
| | - Álex Mira
- Genomics & Health Department, FISABIO Foundation, Valencia, Spain; CIBER Center for Epidemiology and Public Health, Madrid, Spain
| | - Dolores Ortiz-Masiá
- CIBERehd (Centro de Investigaciones en Red Enfermedad Hepática y Digestiva), Madrid, Spain; Departamento de Medicina, Facultad de Medicina, Universidad de Valencia, Valencia, Spain.
| | - María Dolores Barrachina
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; CIBERehd (Centro de Investigaciones en Red Enfermedad Hepática y Digestiva), Madrid, Spain.
| | - Jesús Cosín-Roger
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; CIBERehd (Centro de Investigaciones en Red Enfermedad Hepática y Digestiva), Madrid, Spain
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Ponce-de-Leon M, Wang-Sattler R, Peters A, Rathmann W, Grallert H, Artati A, Prehn C, Adamski J, Meisinger C, Linseisen J. Stool and blood metabolomics in the metabolic syndrome: a cross-sectional study. Metabolomics 2024; 20:105. [PMID: 39306637 PMCID: PMC11416374 DOI: 10.1007/s11306-024-02166-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 08/27/2024] [Indexed: 09/25/2024]
Abstract
INTRODUCTION/OBJECTIVES Changes in the stool metabolome have been poorly studied in the metabolic syndrome (MetS). Moreover, few studies have explored the relationship of stool metabolites with circulating metabolites. Here, we investigated the associations between stool and blood metabolites, the MetS and systemic inflammation. METHODS We analyzed data from 1,370 participants of the KORA FF4 study (Germany). Metabolites were measured by Metabolon, Inc. (untargeted) in stool, and using the AbsoluteIDQ® p180 kit (targeted) in blood. Multiple linear regression models, adjusted for dietary pattern, age, sex, physical activity, smoking status and alcohol intake, were used to estimate the associations of metabolites with the MetS, its components and high-sensitivity C-reactive protein (hsCRP) levels. Partial correlation and Multi-Omics Factor Analysis (MOFA) were used to investigate the relationship between stool and blood metabolites. RESULTS The MetS was significantly associated with 170 stool and 82 blood metabolites. The MetS components with the highest number of associations were triglyceride levels (stool) and HDL levels (blood). Additionally, 107 and 27 MetS-associated metabolites (in stool and blood, respectively) showed significant associations with hsCRP levels. We found low partial correlation coefficients between stool and blood metabolites. MOFA did not detect shared variation across the two datasets. CONCLUSIONS The MetS, particularly dyslipidemia, is associated with multiple stool and blood metabolites that are also associated with systemic inflammation. Further studies are necessary to validate our findings and to characterize metabolic alterations in the MetS. Although our analyses point to weak correlations between stool and blood metabolites, additional studies using integrative approaches are warranted.
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Affiliation(s)
- Mariana Ponce-de-Leon
- Institute for Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany.
- Epidemiology, Medical Faculty, Universität Augsburg, Augsburg, Germany.
| | - Rui Wang-Sattler
- Institute of Translational Genomics, Helmholtz Munich, Munich-Neuherberg, Germany
- German Center for Diabetes Research (DZD), Partner Neuherberg, Munich-Neuherberg, Germany
| | - Annette Peters
- Institute for Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Diabetes Research (DZD), Partner Neuherberg, Munich-Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Munich, Munich-Neuherberg, Germany
- Munich Heart Alliance, German Center for Cardiovascular Health (DZHK E.V), Munich, Germany
| | - Wolfgang Rathmann
- German Diabetes Center (DDZ), Leibniz Institute for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Düsseldorf, Munich-Neuherberg, Germany
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Partner Neuherberg, Munich-Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Munich, Munich-Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Munich, Munich-Neuherberg, Germany
| | - Anna Artati
- Metabolomics and Proteomics Core, Helmholtz Munich, Munich-Neuherberg, Germany
| | - Cornelia Prehn
- Metabolomics and Proteomics Core, Helmholtz Munich, Munich-Neuherberg, Germany
| | - Jerzy Adamski
- Institute of Experimental Genetics, Helmholtz Munich, Munich-Neuherberg, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Christa Meisinger
- Epidemiology, Medical Faculty, Universität Augsburg, Augsburg, Germany
| | - Jakob Linseisen
- Institute for Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Epidemiology, Medical Faculty, Universität Augsburg, Augsburg, Germany
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3
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Chen XL, Jiang MZ. [Research progress of metabolomics in children with irritable bowel syndrome]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2024; 26:989-994. [PMID: 39267517 PMCID: PMC11404471 DOI: 10.7499/j.issn.1008-8830.2404130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/17/2024]
Abstract
Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterized by symptoms such as abdominal pain, diarrhea, constipation, and indigestion. Given its unclear etiology and pathogenesis, and the absence of specific biomarkers, clinical diagnosis and treatment of IBS continue to pose significant challenges. In recent years, metabolomics technology, known for its non-invasive, high-throughput, high-precision, and highly reproducible features, has been widely applied in the diagnosis, treatment, and prognosis of various diseases. Therefore, metabolomics technology is expected to offer novel insights and methodologies for the biological mechanism research, diagnosis, and treatment of IBS. This article reviews recent advancements in the application of metabolomics to IBS, exploring its potential value in the clinical diagnosis and treatment of children with this condition.
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Affiliation(s)
- Xiao-Long Chen
- Department of Gastroenterology and Pediatric Endoscopy Center, Children's Hospital, Zhejiang University School of Medicine/National Clinical Research Center for Child Health/National Children's Regional Medical Center, Hangzhou 310052, China
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Archana, Gupta AK, Noumani A, Panday DK, Zaidi F, Sahu GK, Joshi G, Yadav M, Borah SJ, Susmitha V, Mohan A, Kumar A, Solanki PR. Gut microbiota derived short-chain fatty acids in physiology and pathology: An update. Cell Biochem Funct 2024; 42:e4108. [PMID: 39228159 DOI: 10.1002/cbf.4108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/28/2024] [Accepted: 08/09/2024] [Indexed: 09/05/2024]
Abstract
Short-chain fatty acids (SCFAs) are essential molecules produced by gut bacteria that fuel intestinal cells and may also influence overall health. An imbalance of SCFAs can result in various acute and chronic diseases, including diabetes, obesity and colorectal cancer (CRC). This review delves into the multifaceted roles of SCFAs, including a brief discussion on their source and various gut-residing bacteria. Primary techniques used for detection of SCFAs, including gas chromatography, high-performance gas chromatography, nuclear magnetic resonance and capillary electrophoresis are also discussed through this article. This review study also compiles various synthesis pathways of SCFAs from diverse substrates such as sugar, acetone, ethanol and amino acids. The different pathways through which SCFAs enter cells for immune response regulation are also highlighted. A major emphasis is the discussion on diseases associated with SCFA dysregulation, such as anaemia, brain development, CRC, depression, obesity and diabetes. This includes exploring the relationship between SCFA levels across ethnicities and their connection with blood pressure and CRC. In conclusion, this review highlights the critical role of SCFAs in maintaining gut health and their implications in various diseases, emphasizing the need for further research on SCFA detection, synthesis and their potential as diagnostic biomarkers. Future studies of SCFAs will pave the way for the development of novel diagnostic tools and therapeutic strategies for optimizing gut health and preventing diseases associated with SCFA dysregulation.
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Affiliation(s)
- Archana
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Abhijeet Kumar Gupta
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Ashab Noumani
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Dharmendra Kumar Panday
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Fareen Zaidi
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Gaurav Kumar Sahu
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Gunjan Joshi
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Manisha Yadav
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Shikha Jyoti Borah
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Vanne Susmitha
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
| | - Anand Mohan
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Anil Kumar
- National Institute of Immunology, New Delhi, India
| | - Pratima R Solanki
- Nano-Bio Laboratory, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi, India
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Zhang B, Magnaye KM, Stryker E, Moltzau-Anderson J, Porsche CE, Hertz S, McCauley KE, Smith BJ, Zydek M, Pollard KS, Ma A, El-Nachef N, Lynch SV. Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients. Sci Rep 2024; 14:18558. [PMID: 39122767 PMCID: PMC11316000 DOI: 10.1038/s41598-024-62463-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 05/16/2024] [Indexed: 08/12/2024] Open
Abstract
Fecal microbial transplantation (FMT) offers promise for treating ulcerative colitis (UC), though the mechanisms underlying treatment failure are unknown. This study harnessed longitudinally collected colonic biopsies (n = 38) and fecal samples (n = 179) from 19 adults with mild-to-moderate UC undergoing serial FMT in which antimicrobial pre-treatment and delivery mode (capsules versus enema) were assessed for clinical response (≥ 3 points decrease from the pre-treatment Mayo score). Colonic biopsies underwent dual RNA-Seq; fecal samples underwent parallel 16S rRNA and shotgun metagenomic sequencing as well as untargeted metabolomic analyses. Pre-FMT, the colonic mucosa of non-responsive (NR) patients harbored an increased burden of bacteria, including Bacteroides, that expressed more antimicrobial resistance genes compared to responsive (R) patients. NR patients also exhibited muted mucosal expression of innate immune antimicrobial response genes. Post-FMT, NR and R fecal microbiomes and metabolomes exhibited significant divergence. NR metabolomes had elevated concentrations of immunostimulatory compounds including sphingomyelins, lysophospholipids and taurine. NR fecal microbiomes were enriched for Bacteroides fragilis and Bacteroides salyersiae strains that encoded genes capable of taurine production. These findings suggest that both effective mucosal microbial clearance and reintroduction of bacteria that reshape luminal metabolism associate with FMT success and that persistent mucosal and fecal colonization by antimicrobial-resistant Bacteroides species may contribute to FMT failure.
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Affiliation(s)
- Bing Zhang
- Department of Medicine, Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Kevin M Magnaye
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
- The Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Emily Stryker
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Jacqueline Moltzau-Anderson
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
- The Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Cara E Porsche
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Sandra Hertz
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
| | - Kathryn E McCauley
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Byron J Smith
- The Gladstone Institutes, Data Science and Biotechnology, San Francisco, CA, 94158, USA
| | - Martin Zydek
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Katherine S Pollard
- The Gladstone Institutes, Data Science and Biotechnology, San Francisco, CA, 94158, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA University of California, San Francisco, CA, 94158, USA
| | - Averil Ma
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Najwa El-Nachef
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
- Division of Gastroenterology, Henry Ford Health System, Detroit, MI, 48208, USA
| | - Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA.
- The Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, CA, 94143, USA.
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6
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Mullins E, Bresson J, Dewhurst IC, Epstein MM, Firbank LG, Guerche P, Hejatko J, Moreno FJ, Naegeli H, Nogué F, Rostoks N, Sánchez Serrano JJ, Savoini G, Veromann E, Veronesi F, Cocconcelli PS, Glandorf D, Herman L, Jimenez Saiz R, Ruiz Garcia L, Aguilera Entrena J, Gennaro A, Schoonjans R, Kagkli DM, Dalmay T. New developments in biotechnology applied to microorganisms. EFSA J 2024; 22:e8895. [PMID: 39040572 PMCID: PMC11261303 DOI: 10.2903/j.efsa.2024.8895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024] Open
Abstract
EFSA was requested by the European Commission (in accordance with Article 29 of Regulation (EC) No 178/2002) to provide a scientific opinion on the application of new developments in biotechnology (new genomic techniques, NGTs) to viable microorganisms and products of category 4 to be released into the environment or placed on the market as or in food and feed, and to non-viable products of category 3 to be placed on the market as or in food and feed. A horizon scanning exercise identified a variety of products containing microorganisms obtained with NGTs (NGT-Ms), falling within the remit of EFSA, that are expected to be placed on the (EU) market in the next 10 years. No novel potential hazards/risks from NGT-Ms were identified as compared to those obtained by established genomic techniques (EGTs), or by conventional mutagenesis. Due to the higher efficiency, specificity and predictability of NGTs, the hazards related to the changes in the genome are likely to be less frequent in NGT-Ms than those modified by EGTs and conventional mutagenesis. It is concluded that EFSA guidances are 'partially applicable', therefore on a case-by-case basis for specific NGT-Ms, fewer requirements may be needed. Some of the EFSA guidances are 'not sufficient' and updates are recommended. Because possible hazards relate to genotypic and phenotypic changes introduced and not to the method used for the modification, it is recommended that any new guidance should take a consistent risk assessment approach for strains/products derived from or produced with microorganisms obtained with conventional mutagenesis, EGTs or NGTs.
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7
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Raba G, Luis AS, Schneider H, Morell I, Jin C, Adamberg S, Hansson GC, Adamberg K, Arike L. Metaproteomics reveals parallel utilization of colonic mucin glycans and dietary fibers by the human gut microbiota. iScience 2024; 27:110093. [PMID: 38947523 PMCID: PMC11214529 DOI: 10.1016/j.isci.2024.110093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/29/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
A diet lacking dietary fibers promotes the expansion of gut microbiota members that can degrade host glycans, such as those on mucins. The microbial foraging on mucin has been associated with disruptions of the gut-protective mucus layer and colonic inflammation. Yet, it remains unclear how the co-utilization of mucin and dietary fibers affects the microbiota composition and metabolic activity. Here, we used 14 dietary fibers and porcine colonic and gastric mucins to study the dynamics of mucin and dietary fiber utilization by the human fecal microbiota in vitro. Combining metaproteome and metabolites analyses revealed the central role of the Bacteroides genus in the utilization of complex fibers together with mucin while Akkermansia muciniphila was the main utilizer of sole porcine colonic mucin but not gastric mucin. This study gives a broad overview of the colonic environment in response to dietary and host glycan availability.
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Affiliation(s)
- Grete Raba
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Ana S. Luis
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
- SciLifeLab, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Hannah Schneider
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Indrek Morell
- Center of Food and Fermentation Technologies, 12618 Tallinn, Estonia
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Signe Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Gunnar C. Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Kaarel Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
- Center of Food and Fermentation Technologies, 12618 Tallinn, Estonia
| | - Liisa Arike
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
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Park Y, Ahn JB, Kim DH, Park IS, Son M, Kim JH, Ma HW, Kim SW, Cheon JH. Integrated Analysis of Microbiome and Metabolome Reveals Disease-Specific Profiles in Inflammatory Bowel Diseases and Intestinal Behçet's Disease. Int J Mol Sci 2024; 25:6697. [PMID: 38928402 PMCID: PMC11203907 DOI: 10.3390/ijms25126697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/09/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
The gut microbial and metabolic characteristics of intestinal Behçet's disease (BD), a condition sharing many clinical similarities with ulcerative colitis (UC) and Crohn's disease (CD), are largely unexplored. This study investigated the gut microbial and metabolic characteristics of intestinal BD as well as potential biomarkers, comparing them with those in UC, CD, and healthy controls. Colon tissue and stool samples from 100 patients (35 UC, 30 CD, and 35 intestinal BD) and 41 healthy volunteers were analyzed using 16S ribosomal RNA sequencing to assess microbial diversity, taxonomic composition, and functional profiling. Plasma metabolomic analyses were performed using gas chromatography and ultra-performance liquid chromatography-mass spectrometry. Results indicated reduced microbial diversity in CD but not in intestinal BD, with intestinal BD showing fewer changes compared to controls yet distinct taxonomic features from UC, CD, and controls. Common alterations across all diseases included a reduction in beneficial bacteria producing short-chain fatty acids. Intestinal BD-specific changes featured a decreased abundance of Bacteroides fragilis. Metabolomic profiles in intestinal BD were similar to those in CD but distinct from those in UC, displaying significant changes in energy metabolism and genetic information processing. This integrative analysis revealed both shared and unique profiles in intestinal BD compared with UC, CD, and controls, advancing our understanding of the distinctive features of these diseases.
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Affiliation(s)
- Yehyun Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Department of Internal Medicine, Ewha Womans University Seoul Hospital, Seoul 03760, Republic of Korea
| | - Jae Bum Ahn
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
| | - Da Hye Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
| | - I Seul Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Mijeong Son
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ji Hyung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyun Woo Ma
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Seung Won Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jae Hee Cheon
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (Y.P.); (J.B.A.); (D.H.K.)
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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9
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Vakili O, Adibi Sedeh P, Pourfarzam M. Metabolic biomarkers in irritable bowel syndrome diagnosis. Clin Chim Acta 2024; 560:119753. [PMID: 38821336 DOI: 10.1016/j.cca.2024.119753] [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: 04/14/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Irritable bowel syndrome (IBS) is a chronic gastrointestinal (GI) disorder characterized by altered bowel habits and abdominal discomfort during defecation. It significantly impacts life quality and work productivity for those affected. Global data suggests a slightly higher prevalence in females than in males. Today, unambiguous diagnosis of IBS remains challenging due to the absence of a specific biochemical, histopathological, or radiological test. Current diagnosis relies heavily on thorough symptom evaluation. Efforts by the Rome committees have established standardized diagnostic criteria (Rome I-IV), improving consistency and clinical applicability. Recent studies in this framework, seem to have successfully employed metabolomics techniques to identify distinct metabolite profiles in breath and stool samples of IBS patients, differentiating them from healthy controls and those with other functional GI disorders, such as inflammatory bowel disease (IBD). Building on this success, researchers are investigating the presence of similar metabolites in easily accessible biofluids such as urine, potentially offering a less invasive diagnostic approach. Accordingly, this review focuses on key metabolites specifically detected in IBS patients' biological specimens, with a focus on urinary metabolites, using various methods, particularly mass spectrometry (MS)-based techniques, including gas chromatography-MS (GC-MS), liquid chromatography-tandem MS (LC-MS/MS), and capillary electrophoresis-MS (CE-MS) metabolomics assays. These findings may make provision for a new set of non-invasive biomarkers for IBS diagnosis and management.
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Affiliation(s)
- Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Peyman Adibi Sedeh
- Gastroenterology and Hepatology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Morteza Pourfarzam
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
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10
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Luo S, Lou F, Yan L, Dong Y, Zhang Y, Liu Y, Ji P, Jin X. Comprehensive analysis of the oral microbiota and metabolome change in patients of burning mouth syndrome with psychiatric symptoms. J Oral Microbiol 2024; 16:2362313. [PMID: 38835338 PMCID: PMC11149574 DOI: 10.1080/20002297.2024.2362313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 05/27/2024] [Indexed: 06/06/2024] Open
Abstract
Background Burning mouth syndrome (BMS) is a chronic idiopathic facial pain with intraoral burning or dysesthesia. BMS patients regularly suffer from anxiety/depression, and the association of psychiatric symptoms with BMS has received considerable attention in recent years. The aims of this study were to investigate the potential interplay between psychiatric symptoms and BMS. Methods Using 16S rRNA sequencing and liquid chromatography-mass spectrometry (LC/MS) to evaluate the oral microbiota and saliva metabolism of 40 BMS patients [including 29 BMS patients with depression or anxiety symptoms (DBMS)] and 40 age matched healthy control (HC). Results The oral microbiota composition in BMS exhibited no significant differences from HC, although DBMS manifested decreased α-diversity relative to HC. Noteworthy was the discernible elevation in the abundance of proinflammatory microorganisms within the oral microbiome of individuals with DBMS. Parallel findings in LC/MS analyses revealed discernible disparities in metabolites between DBMS and HC groups. Principal differential metabolites were notably enriched in amino acid metabolism and lipid metabolism, exhibiting associations with infectious and immunological diseases. Furthermore, the integrated analysis underscores a definitive association between the oral microbiome and metabolism in DBMS. Conclusions This study suggests possible future modalities for better understanding the pathogenesis and personalized treatment plans of BMS.
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Affiliation(s)
- Shihong Luo
- College of Stomatology, Chongqing Medical University, Chongqing, China
- Department of Oral Implantology, The Affiliated Stomatology Hospital of Southwest Medical University, Luzhou, China
| | - Fangzhi Lou
- College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Li Yan
- College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Yunmei Dong
- College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Yingying Zhang
- College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Yang Liu
- College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Ping Ji
- College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Xin Jin
- College of Stomatology, Chongqing Medical University, Chongqing, China
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11
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Ju X, Jiang Z, Ma J, Yang D. Changes in Fecal Short-Chain Fatty Acids in IBS Patients and Effects of Different Interventions: A Systematic Review and Meta-Analysis. Nutrients 2024; 16:1727. [PMID: 38892659 PMCID: PMC11174707 DOI: 10.3390/nu16111727] [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: 05/06/2024] [Revised: 05/20/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
CONTEXT Short-chain fatty acids (SCFAs) have been reported to be associated with the pathogenesis of irritable bowel syndrome (IBS), but the results are conflicting. OBJECTIVE Here, a systematic review of case-control studies detecting fecal SCFAs in IBS patients compared with healthy controls (HCs) and self-controlled studies or randomized controlled trials (RCTs) investigating fecal SCFA alterations after interventions were identified from several databases. DATA SOURCES A systematic search of databases (PubMed, Web of Science, and Embase) identified 21 studies published before 24 February 2023. Data extractions: Three independent reviewers completed the relevant data extraction. DATA ANALYSIS It was found that the fecal propionate concentration in IBS patients was significantly higher than that in HCs, while the acetate proportion was significantly lower. Low-FODMAP diets significantly reduced the fecal propionate concentration in the IBS patients while fecal microbiota transplantation and probiotic administration did not significantly change the fecal propionate concentration or acetate proportion. CONCLUSIONS The results suggested that the fecal propionate concentration and acetate proportion could be used as biomarkers for IBS diagnosis. A low-FODMAP diet intervention could potentially serve as a treatment for IBS while FMT and probiotic administration need more robust trials.
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Affiliation(s)
| | | | | | - Dong Yang
- Beijing Key Laboratory of Functional Food from Plant Resources, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (X.J.); (Z.J.); (J.M.)
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12
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Lin Z, Luo W, Zhang K, Dai S. Environmental and Microbial Factors in Inflammatory Bowel Disease Model Establishment: A Review Partly through Mendelian Randomization. Gut Liver 2024; 18:370-390. [PMID: 37814898 PMCID: PMC11096900 DOI: 10.5009/gnl230179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/09/2023] [Accepted: 07/24/2023] [Indexed: 10/11/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a complex condition resulting from environmental, microbial, immunologic, and genetic factors. With the advancement of Mendelian randomization research in IBD, we have gained new insights into the relationship between these factors and IBD. Many animal models of IBD have been developed using different methods, but few studies have attempted to model IBD by combining environmental factors and microbial factors. In this review, we examine how environmental factors and microbial factors affect the development and progression of IBD, and how they interact with each other and with the intestinal microbiota. We also summarize the current methods for creating animal models of IBD and compare their advantages and disadvantages. Based on the latest findings from Mendelian randomization studies on the role of environmental factors in IBD, we discuss which environmental and microbial factors could be used to construct a more realistic and reliable IBD experimental model. We propose that animal models of IBD should consider both environmental and microbial factors to better mimic human IBD pathogenesis and to reveal the underlying mechanisms of IBD at the immune and genetic levels. We highlight the importance of environmental and microbial factors in IBD pathogenesis and offer new perspectives and suggestions for improving experimental animal modeling. Our goal is to create a model that closely resembles the clinical picture of IBD.
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Affiliation(s)
- Zesheng Lin
- The First Clinical Medical School, Southern Medical University, Guangzhou, China
| | - Wenjing Luo
- The Second Clinical Medical School, Southern Medical University, Guangzhou, China
| | - Kaijun Zhang
- Department of Gastroenterology, Guangdong Provincial Geriatrics Institute, Guangzhou, ChinaNational Key Clinical Specialty, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Shixue Dai
- Department of Gastroenterology, Guangdong Provincial Geriatrics Institute, Guangzhou, ChinaNational Key Clinical Specialty, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Department of Gastroenterology, Geriatric Center, National Regional Medical Center, Ganzhou Hospital Affiliated to Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Ganzhou, China
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13
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Liu M, Zhang Y, Liu J, Xiang C, Lu Q, Lu H, Yang T, Wang X, Zhang Q, Fan C, Feng C, Zou D, Li H, Tang W. Revisiting the Role of Valeric Acid in Manipulating Ulcerative Colitis. Inflamm Bowel Dis 2024; 30:617-628. [PMID: 38206334 DOI: 10.1093/ibd/izad187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND Ulcerative colitis (UC) is characterized by a complicated interaction between mucosal inflammation, epithelial dysfunction, abnormal activation of innate immune responses, and gut microbiota dysbiosis. Though valeric acid (VA), one type of short-chain fatty acids (SCFAs), has been identified in other inflammatory disorders and cancer development, the pathological role of VA and underlying mechanism of VA in UC remain under further investigation. METHODS Studies of human clinical specimens and experimental colitis models were conducted to confirm the pathological manifestations of the level of SCFAs from human fecal samples and murine colonic homogenates. Valeric acid-intervened murine colitis and a macrophage adoptive transfer were applied to identify the underlying mechanisms. RESULTS In line with gut microbiota dysfunction in UC, alteration of SCFAs from gut microbes were identified in human UC patients and dextran sodium sulfate -induced murine colitis models. Notably, VA was consistently negatively related to the disease severity of UC, the population of monocytes, and the level of interluekin-6. Moreover, VA treatment showed direct suppressive effects on lipopolysaccharides (LPS)-activated human peripheral blood mononuclear cells and murine macrophages in the dependent manner of upregulation of GPR41 and GPR43. Therapeutically, replenishment of VA or adoptive transfer with VA-modulated macrophages showed resistance to dextran sodium sulfate-driven murine colitis though modulating the production of inflammatory cytokine interleukin-6. CONCLUSIONS In summary, the research uncovered the pathological role of VA in modulating the activation of macrophages in UC and suggested that VA might be a potential effective agent for UC patients.
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Affiliation(s)
- Moting Liu
- Laboratory of Anti-inflammation and Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Zhang
- Department of Gastroenterology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jia Liu
- Institutional Technology Service Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Caigui Xiang
- Laboratory of Anti-inflammation and Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiukai Lu
- Laboratory of Anti-inflammation and Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huimin Lu
- Laboratory of Anti-inflammation and Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Yang
- Laboratory of Anti-inflammation and Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohan Wang
- Laboratory of Anti-inflammation and Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingli Zhang
- Institutional Technology Service Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chen Fan
- Laboratory of Anti-inflammation and Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chunlan Feng
- Laboratory of Anti-inflammation and Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Duowu Zou
- Department of Gastroenterology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Heng Li
- Laboratory of Anti-inflammation and Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wei Tang
- Laboratory of Anti-inflammation and Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Wang H, Zhao D, Wang S, Liu H, Zhao S, Li Z, Qin X, Liu X. Gastrointestinal Characteristics of Constipation from the Perspectives of Microbiome and Metabolome. Dig Dis Sci 2024; 69:1318-1335. [PMID: 38446304 DOI: 10.1007/s10620-024-08334-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Constipation is one of the most common gastrointestinal complaints. Yet, the underlying mechanisms of constipation remain to be explored deeply. Integration of microbiome and metabolome is powerful and promising to demonstrate characteristics of constipation. AIM OF STUDY This study aimed to characterize intestinal microbiome and metabolome of constipation. In addition, this study revealed the correlations among behaviors, intestinal microbiota, and metabolites interrupted by constipation. METHODS Firstly, the constipation model was successfully applied. At the macro level, the ability of learning, memory, locomotor activity, and the defecation index of rats with constipation-like phenotype were characterized. At the micro-level, 16S rRNA sequencing was applied to analyze the intestinal microbiota in rats with constipation-like phenotype. 1H nuclear magnetic resonance (NMR)-based metabolomics was employed to investigate the metabolic phenotype of constipation. In addition, we constructed a correlation network, intuitively showing the correlations among behaviors, intestinal microbiota, and metabolites. RESULTS Constipation significantly attenuated the locomotor activity, memory recognition, and frequency of defecation of rats, while increased the time of defecation. Constipation significantly changed the diversity of intestinal microbial communities, which correspondingly involved in 5 functional pathways. Besides, 28 fecal metabolites were found to be associated with constipation, among which 14 metabolites were further screened that can be used to diagnose constipation. On top of this, associated networks intuitively showed the correlations among behaviors, intestinal microbiota, and metabolites. CONCLUSIONS The current findings are significant in terms of not only laying a foundation for understanding characteristics of constipation, but also providing accurate diagnosis and treatments of constipation clinically.
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Affiliation(s)
- Huimin Wang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- Institute of Biomedicine and Health, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
| | - Di Zhao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- Institute of Biomedicine and Health, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
| | - Senyan Wang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- Institute of Biomedicine and Health, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
| | - Huanle Liu
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- Institute of Biomedicine and Health, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
| | - Sijun Zhao
- Department of Pharmacology, Shanxi Institute for Food and Drug Control, No. 12, Taiyuan South Rd., Yingze Dist, Taiyuan, 030001, Shanxi, China
| | - Zhenyu Li
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- Institute of Biomedicine and Health, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
- Institute of Biomedicine and Health, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China
| | - Xiaojie Liu
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China.
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China.
- Institute of Biomedicine and Health, Shanxi University, No. 92, Wucheng Rd. Xiaodian Dist., Taiyuan, 030006, Shanxi, China.
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15
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Liu M, Guo S, Wang L. Systematic review of metabolomic alterations in ulcerative colitis: unveiling key metabolic signatures and pathways. Therap Adv Gastroenterol 2024; 17:17562848241239580. [PMID: 38560428 PMCID: PMC10981261 DOI: 10.1177/17562848241239580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/28/2024] [Indexed: 04/04/2024] Open
Abstract
Background Despite numerous metabolomic studies on ulcerative colitis (UC), the results have been highly variable, making it challenging to identify key metabolic abnormalities in UC. Objectives This study aims to uncover key metabolites and metabolic pathways in UC by analyzing existing metabolomics data. Design A systematic review. Data sources and methods We conducted a comprehensive search in databases (PubMed, Cochrane Library, Embase, and Web of Science) and relevant study references for metabolomic research on UC up to 28 December 2022. Significant metabolite differences between UC patients and controls were identified, followed by an analysis of relevant metabolic pathways. Results This review incorporated 78 studies, identifying 2868 differentially expressed metabolites between UC patients and controls. The metabolites were predominantly from 'lipids and lipid-like molecules' and 'organic acids and derivatives' superclasses. We found 101 metabolites consistently altered in multiple datasets within the same sample type and 78 metabolites common across different sample types. Of these, 62 metabolites exhibited consistent regulatory trends across various datasets or sample types. Pathway analysis revealed 22 significantly altered metabolic pathways, with 6 pathways being recurrently enriched across different sample types. Conclusion This study elucidates key metabolic characteristics in UC, offering insights into molecular mechanisms and biomarker discovery for the disease. Future research could focus on validating these findings and exploring their clinical applications.
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Affiliation(s)
- Meiling Liu
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Siyi Guo
- Chongqing Medical University, Chongqing, China
| | - Liang Wang
- Chongqing Medical University, Chongqing, China
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16
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Colosimo R, Harris HC, Ahn-Jarvis J, Troncoso-Rey P, Finnigan TJA, Wilde PJ, Warren FJ. Colonic in vitro fermentation of mycoprotein promotes shifts in gut microbiota, with enrichment of Bacteroides species. Commun Biol 2024; 7:272. [PMID: 38443511 PMCID: PMC10915147 DOI: 10.1038/s42003-024-05893-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024] Open
Abstract
Mycoprotein is a fungal-derived ingredient used for meat alternative products whose fungal cell walls are rich in dietary fibre (β-glucans and chitin) and defines its structure. Several health benefits have been reported after mycoprotein consumption, however, little is known about the impact of mycoprotein fermentation on the gut microbiota. This study aims to identify changes in microbiome composition and microbial metabolites during colonic fermentation of mycoprotein following simulated upper gastrointestinal digestion. Changes in microbial populations and metabolites produced by the fermentation of mycoprotein fibre were investigated and compared to a plant (oat bran) and an animal (chicken) comparator. In this model fermentation system, mycoprotein and oat showed different but marked changes in the microbial population compared to chicken, which showed minimal differentiation. In particular, Bacteroides species known for degrading β-glucans were found in abundance following fermentation of mycoprotein fibre. Mycoprotein fermentation resulted in short-chain fatty acid production comparable with oat and chicken at 72 h. Significantly higher branched-chain amino acids were observed following chicken fermentation. This study suggests that the colonic fermentation of mycoprotein can promote changes in the colonic microbial profile. These results highlight the impact that the unique structure of mycoprotein can have on digestive processes and the gut microbiota.
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Affiliation(s)
- Raffaele Colosimo
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Elsevier B.V, Radarweg 29a, 1043, NX, Amsterdam, Netherlands
| | - Hannah C Harris
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Jennifer Ahn-Jarvis
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Perla Troncoso-Rey
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Tim J A Finnigan
- Marlow Foods Ltd, Station Road, Stokesley, North Yorkshire, TS9 7AB, UK
| | - Pete J Wilde
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Frederick J Warren
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
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17
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Mao L, Gao B, Chang H, Shen H. Interaction and Metabolic Pathways: Elucidating the Role of Gut Microbiota in Gestational Diabetes Mellitus Pathogenesis. Metabolites 2024; 14:43. [PMID: 38248846 PMCID: PMC10819307 DOI: 10.3390/metabo14010043] [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: 11/28/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Gestational diabetes mellitus (GDM) is a complex metabolic condition during pregnancy with an intricate link to gut microbiota alterations. Throughout gestation, notable shifts in the gut microbial component occur. GDM is marked by significant dysbiosis, with a decline in beneficial taxa like Bifidobacterium and Lactobacillus and a surge in opportunistic taxa such as Enterococcus. These changes, detectable in the first trimester, hint as the potential early markers for GDM risk. Alongside these taxa shifts, microbial metabolic outputs, especially short-chain fatty acids and bile acids, are perturbed in GDM. These metabolites play pivotal roles in host glucose regulation, insulin responsiveness, and inflammation modulation, which are the key pathways disrupted in GDM. Moreover, maternal GDM status influences neonatal gut microbiota, indicating potential intergenerational health implications. With the advance of multi-omics approaches, a deeper understanding of the nuanced microbiota-host interactions via metabolites in GDM is emerging. The reviewed knowledge offers avenues for targeted microbiota-based interventions, holding promise for innovative strategies in GDM diagnosis, management, and prevention.
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Affiliation(s)
- Lindong Mao
- State Key Laboratory of Infectious Disease Vaccine Development, Xiang An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China; (L.M.); (B.G.); (H.C.)
| | - Biling Gao
- State Key Laboratory of Infectious Disease Vaccine Development, Xiang An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China; (L.M.); (B.G.); (H.C.)
| | - Hao Chang
- State Key Laboratory of Infectious Disease Vaccine Development, Xiang An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China; (L.M.); (B.G.); (H.C.)
| | - Heqing Shen
- State Key Laboratory of Infectious Disease Vaccine Development, Xiang An Biomedicine Laboratory & State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China; (L.M.); (B.G.); (H.C.)
- Department of Obstetrics, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361003, China
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18
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Connell E, Blokker B, Kellingray L, Le Gall G, Philo M, Pontifex MG, Narbad A, Müller M, Vauzour D. Refined diet consumption increases neuroinflammatory signalling through bile acid dysmetabolism. Nutr Neurosci 2024:1-14. [PMID: 38170169 DOI: 10.1080/1028415x.2023.2301165] [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] [Indexed: 01/05/2024]
Abstract
Over recent decades, dietary patterns have changed significantly due to the increasing availability of convenient, ultra-processed refined foods. Refined foods are commonly depleted of key bioactive compounds, which have been associated with several deleterious health conditions. As the gut microbiome can influence the brain through a bidirectional communication system known as the 'microbiota-gut-brain axis', the consumption of refined foods has the potential to affect cognitive health. In this study, multi-omics approaches were employed to assess the effect of a refined diet on the microbiota-gut-brain axis, with a particular focus on bile acid metabolism. Mice maintained on a refined low-fat diet (rLFD), consisting of high sucrose, processed carbohydrates and low fibre content, for eight weeks displayed significant gut microbial dysbiosis, as indicated by diminished alpha diversity metrics (p < 0.05) and altered beta diversity (p < 0.05) when compared to mice receiving a chow diet. Changes in gut microbiota composition paralleled modulation of the metabolome, including a significant reduction in short-chain fatty acids (acetate, propionate and n-butyrate; p < 0.001) and alterations in bile acid concentrations. Interestingly, the rLFD led to dysregulated bile acid concentrations across both the colon (p < 0.05) and the brain (p < 0.05) which coincided with altered neuroinflammatory gene expression. In particular, the concentration of TCA, TDCA and T-α-MCA was inversely correlated with the expression of NF-κB1, a key transcription factor in neuroinflammation. Overall, our results suggest a novel link between a refined low-fat diet and detrimental neuronal processes, likely in part through modulation of the microbiota-gut-brain axis and bile acid dysmetabolism.
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Affiliation(s)
- Emily Connell
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Britt Blokker
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Lee Kellingray
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Mark Philo
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Arjan Narbad
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Michael Müller
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - David Vauzour
- Norwich Medical School, University of East Anglia, Norwich, UK
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19
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Zhu J, Yin J, Chen J, Hu M, Lu W, Wang H, Zhang H, Chen W. Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis. Gut Microbes 2024; 16:2336877. [PMID: 38563656 PMCID: PMC10989691 DOI: 10.1080/19490976.2024.2336877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Ulcerative colitis (UC) is a challenging form of inflammatory bowel disease, and its etiology is intricately linked to disturbances in the gut microbiome. To identify the potential alleviators of UC, we employed an integrative analysis combining microbial community modeling with advanced machine learning techniques. Using metagenomics data sourced from the Integrated Human Microbiome Project, we constructed individualized microbiome community models for each participant. Our analysis highlighted a significant decline in both α and β-diversity of strain-level microbial populations in UC subjects compared to controls. Distinct differences were also observed in the predicted fecal metabolite profiles and strain-to-metabolite contributions between the two groups. Using tree-based machine learning models, we successfully identified specific microbial strains and their associated metabolites as potential alleviators of UC. Notably, our experimental validation using a dextran sulfate sodium-induced UC mouse model demonstrated that the administration of Parabacteroides merdae ATCC 43,184 and N-acetyl-D-mannosamine provided notable relief from colitis symptoms. In summary, our study underscores the potential of an integrative approach to identify novel therapeutic avenues for UC, paving the way for future targeted interventions.
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Affiliation(s)
- Jinlin Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jialin Yin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jing Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mingyi Hu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi People’s Hospital, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
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20
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Pandey H, Jain D, Tang DWT, Wong SH, Lal D. Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease. Intest Res 2024; 22:15-43. [PMID: 37935653 PMCID: PMC10850697 DOI: 10.5217/ir.2023.00080] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 11/09/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a multifactorial disease, which is thought to be an interplay between genetic, environment, microbiota, and immune-mediated factors. Dysbiosis in the gut microbial composition, caused by antibiotics and diet, is closely related to the initiation and progression of IBD. Differences in gut microbiota composition between IBD patients and healthy individuals have been found, with reduced biodiversity of commensal microbes and colonization of opportunistic microbes in IBD patients. Gut microbiota can, therefore, potentially be used for diagnosing and prognosticating IBD, and predicting its treatment response. Currently, there are no curative therapies for IBD. Microbiota-based interventions, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, have been recognized as promising therapeutic strategies. Clinical studies and studies done in animal models have provided sufficient evidence that microbiota-based interventions may improve inflammation, the remission rate, and microscopic aspects of IBD. Further studies are required to better understand the mechanisms of action of such interventions. This will help in enhancing their effectiveness and developing personalized therapies. The present review summarizes the relationship between gut microbiota and IBD immunopathogenesis. It also discusses the use of gut microbiota as a noninvasive biomarker and potential therapeutic option.
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Affiliation(s)
| | | | - Daryl W. T. Tang
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Sunny H. Wong
- Centre for Microbiome Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Devi Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
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21
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An R, Wilms E, Gerritsen J, Kim HK, Pérez CS, Besseling-van der Vaart I, Jonkers DM, Rijkers GT, de Vos WM, Masclee AA, Zoetendal EG, Troost FJ, Smidt H. Spatio-temporal dynamics of the human small intestinal microbiome and its response to a synbiotic. Gut Microbes 2024; 16:2350173. [PMID: 38738780 PMCID: PMC11093041 DOI: 10.1080/19490976.2024.2350173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
Although fecal microbiota composition is considered to preserve relevant and representative information for distal colonic content, it is evident that it does not represent microbial communities inhabiting the small intestine. Nevertheless, studies investigating the human small intestinal microbiome and its response to dietary intervention are still scarce. The current study investigated the spatio-temporal dynamics of the small intestinal microbiome within a day and over 20 days, as well as its responses to a 14-day synbiotic or placebo control supplementation in 20 healthy subjects. Microbial composition and metabolome of luminal content of duodenum, jejunum, proximal ileum and feces differed significantly from each other. Additionally, differences in microbiota composition along the small intestine were most pronounced in the morning after overnight fasting, whereas differences in composition were not always measurable around noon or in the afternoon. Although overall small intestinal microbiota composition did not change significantly within 1 day and during 20 days, remarkable, individual-specific temporal dynamics were observed in individual subjects. In response to the synbiotic supplementation, only the microbial diversity in jejunum changed significantly. Increased metabolic activity of probiotic strains during intestinal passage, as assessed by metatranscriptome analysis, was not observed. Nevertheless, synbiotic supplementation led to a short-term spike in the relative abundance of genera included in the product in the small intestine approximately 2 hours post-ingestion. Collectively, small intestinal microbiota are highly dynamic. Ingested probiotic bacteria could lead to a transient spike in the relative abundance of corresponding genera and ASVs, suggesting their passage through the entire gastrointestinal tract. This study was registered to http://www.clinicaltrials.gov, NCT02018900.
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Affiliation(s)
- Ran An
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Department of Food science and Technology, Shanghai Jiao Tong University, Shanghai, China
| | - Ellen Wilms
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Jacoline Gerritsen
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Winclove Probiotics, Amsterdam, The Netherlands
| | - Hye Kyong Kim
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Celia Seguí Pérez
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Winclove Probiotics, Amsterdam, The Netherlands
- Infectious Diseases & Immunology, University of Utrecht, Utrecht, The Netherland
| | | | - Daisy M.A.E. Jonkers
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Ger T. Rijkers
- Science Department, University College Roosevelt, Middelburg, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Human Microbiomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ad A.M. Masclee
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Erwin G. Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Freddy J. Troost
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
- Food Innovation and Health, Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Venlo, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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22
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Chalifour B, Holzhausen EA, Lim JJ, Yeo EN, Shen N, Jones DP, Peterson BS, Goran MI, Liang D, Alderete TL. The potential role of early life feeding patterns in shaping the infant fecal metabolome: implications for neurodevelopmental outcomes. NPJ METABOLIC HEALTH AND DISEASE 2023; 1:2. [PMID: 38299034 PMCID: PMC10828959 DOI: 10.1038/s44324-023-00001-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/24/2023] [Indexed: 02/02/2024]
Abstract
Infant fecal metabolomics can provide valuable insights into the associations of nutrition, dietary patterns, and health outcomes in early life. Breastmilk is typically classified as the best source of nutrition for nearly all infants. However, exclusive breastfeeding may not always be possible for all infants. This study aimed to characterize associations between levels of mixed breastfeeding and formula feeding, along with solid food consumption and the infant fecal metabolome at 1- and 6-months of age. As a secondary aim, we examined how feeding-associated metabolites may be associated with early life neurodevelopmental outcomes. Fecal samples were collected at 1- and 6-months, and metabolic features were assessed via untargeted liquid chromatography/high-resolution mass spectrometry. Feeding groups were defined at 1-month as 1) exclusively breastfed, 2) breastfed >50% of feedings, or 3) formula fed ≥50% of feedings. Six-month groups were defined as majority breastmilk (>50%) or majority formula fed (≥50%) complemented by solid foods. Neurodevelopmental outcomes were assessed using the Bayley Scales of Infant Development at 2 years. Changes in the infant fecal metabolome were associated with feeding patterns at 1- and 6-months. Feeding patterns were associated with the intensities of a total of 57 fecal metabolites at 1-month and 25 metabolites at 6-months, which were either associated with increased breastmilk or increased formula feeding. Most breastmilk-associated metabolites, which are involved in lipid metabolism and cellular processes like cell signaling, were associated with higher neurodevelopmental scores, while formula-associated metabolites were associated with lower neurodevelopmental scores. These findings offer preliminary evidence that feeding patterns are associated with altered infant fecal metabolomes, which may be associated with cognitive development later in life.
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Affiliation(s)
- Bridget Chalifour
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO USA
| | | | - Joseph J. Lim
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO USA
| | - Emily N. Yeo
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO USA
| | - Natalie Shen
- Rollins School of Public Health, Emory University, Atlanta, GA USA
| | - Dean P. Jones
- School of Medicine, Emory University, Atlanta, GA USA
| | | | | | - Donghai Liang
- Rollins School of Public Health, Emory University, Atlanta, GA USA
| | - Tanya L. Alderete
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO USA
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23
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Lee BL, Rout M, Mandal R, Wishart DS. Automated identification and quantification of metabolites in human fecal extracts by nuclear magnetic resonance spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:705-717. [PMID: 37265043 DOI: 10.1002/mrc.5372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 06/03/2023]
Abstract
We report the development of a software program, called MagMet-F, that automates the processing and quantification of 1D 1 H NMR of human fecal extracts. To optimize the program, we identified 82 potential fecal metabolites using 1D 1 H NMR of six human fecal extracts using manual profiling and a literature review of known fecal metabolites. We acquired pure versions of those metabolites and then acquired their 1D 1 H NMR spectra at 700 MHz to generate a fecal metabolite spectral library for MagMet-F. The fitting of these metabolites by MagMet-F was iteratively optimized to replicate manual profiling. We validated MagMet-F's automated profiling using a test set of six fecal extracts. It correctly identified 80% of the compounds and quantified those within <20% of the values determined by manual profiling using Chenomx. We also compared MagMet-F's profiling performance to two other open-access NMR profiling tools, Bayesil and Batman. MagMet-F outperformed both. Bayesil repeatedly overestimated metabolite concentrations by 10% to 40% while Batman was unable to properly quantify any compounds and took 10-20× longer. We have implemented MagMet-F as a freely accessible web server to enable automated, fast and convenient 1D 1 H NMR spectral profiling of fecal samples. MagMet-F is available at https://www.magmet.ca.
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Affiliation(s)
- Brian L Lee
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Manoj Rout
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
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24
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Sánchez-Terrón G, Martínez R, Ruiz J, Luna C, Estévez M. Impact of Sustained Fructose Consumption on Gastrointestinal Function and Health in Wistar Rats: Glycoxidative Stress, Impaired Protein Digestion, and Shifted Fecal Microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16270-16285. [PMID: 37859404 PMCID: PMC10623553 DOI: 10.1021/acs.jafc.3c04515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
The gastrointestinal tract (GIT) is the target of assorted pathological conditions, and dietary components are known to affect its functionality and health. In previous in vitro studies, we observed that reducing sugars induced protein glycoxidation and impaired protein digestibility. To gain further insights into the pathophysiological effects of dietary sugars, Wistar rats were provided with a 30% (w/v) fructose water solution for 10 weeks. Upon slaughter, in vivo protein digestibility was assessed, and the entire GIT (digests and tissues) was analyzed for markers of oxidative stress and untargeted metabolomics. Additionally, the impact of sustained fructose intake on colonic microbiota was also evaluated. High fructose intake for 10 weeks decreased protein digestibility and promoted changes in the physiological digestion of proteins, enhancing intestinal digestion rather than stomach digestion. Moreover, at colonic stages, the oxidative stress was harmfully increased, and both the microbiota and the intraluminal colonic metabolome were modified.
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Affiliation(s)
- Guadalupe Sánchez-Terrón
- TECAL Research Group, Meat and Meat Products Research Institute (IPROCAR), Universidad de Extremadura (UEX), Cáceres 10003, Spain
| | - Remigio Martínez
- TECAL Research Group, Meat and Meat Products Research Institute (IPROCAR), Universidad de Extremadura (UEX), Cáceres 10003, Spain
- Animal Health Department, Universidad of Extremadura (UEX), Cáceres 10003, Spain
- Animal Health Department, GISAZ Research Group, ENZOEM Competitive Research Unit, Universidad of Córdoba (UCO), Córdoba 14014, Spain
| | - Jorge Ruiz
- TECAL Research Group, Meat and Meat Products Research Institute (IPROCAR), Universidad de Extremadura (UEX), Cáceres 10003, Spain
| | - Carolina Luna
- Emergency Unit, Servicio Extremeño de Salud, SES, Junta de Extremadura, Cáceres 10003, Spain
| | - Mario Estévez
- TECAL Research Group, Meat and Meat Products Research Institute (IPROCAR), Universidad de Extremadura (UEX), Cáceres 10003, Spain
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25
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Qin J, Ling X, Wang Q, Huang Z, Guo B, Zhang C, Meng M, Feng S, Guo Y, Zheng H, Liang Y, Su Z. Integrated Gut Microbiota and Urine Metabolite Analyses of T2DM with NAFLD Rat Model. Appl Biochem Biotechnol 2023; 195:6478-6494. [PMID: 36870027 DOI: 10.1007/s12010-023-04419-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/05/2023]
Abstract
Globally 80% type 2 diabetes mellitus (T2DM) patients suffer nonalcoholic fatty liver disease (NAFLD). The interplay of gut microbiota and endogenous metabolic networks has not yet been reported in the setting of T2DM with NAFLD. As such, this study utilized 16S rRNA gene sequencing to assess the changes in intestinal flora and nuclear magnetic resonance spectroscopy (1H NMR) to identify potential metabolites in a T2DM with NAFLD rat model. Spearman correlation analysis was performed to explore the relationship between gut microbiota and metabolites. Results revealed that among T2DM with NAFLD rats, diversity indexes of intestinal microbiota were distinctly decreased while levels of 18 bacterial genera within the intestinal tract were significantly altered. In addition, levels of eight metabolites mainly involved in the synthesis and degradation of ketone bodies, the TCA cycle, and butanoate metabolism were altered. Correlation analysis revealed that gut bacteria such as Blautia, Ruminococcus torques group, Allobaculum, and Lachnoclostridium strongly associate with 3-hydroxybutyrate, acetone, acetoacetate, 2-oxoglutarate, citrate, creatinine, hippurate, and allantoin. Our findings can provide a basis for future development of targeted treatments.
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Affiliation(s)
- Jinghua Qin
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Xue Ling
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Qianyi Wang
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Zheng Huang
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Bingjian Guo
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Chi Zhang
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Mingwei Meng
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Shisui Feng
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
| | - Yue Guo
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Traditional Medical and Pharmaceutical Sciences, Nanning, 530022, People's Republic of China
| | - Hua Zheng
- Life Sciences Institute, Guangxi Medical University, Nanning, 530021, China.
| | - Yonghong Liang
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China.
| | - Zhiheng Su
- Pharmaceutical College, Guangxi Medical University, Nanning, 530021, China.
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation, Nanning, 530021, China.
- Guangxi Engineering Research Center for Beibu Gulf Marine Biomedicine Precision Development and High-Value Utilization, Nanning, 530021, China.
- Guangxi Health Commission Key Laboratory of Basic Research On Antigeriatric Drugs, Nanning, 530021, China.
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26
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Almalki AH. Recent Analytical Advances for Decoding Metabolic Reprogramming in Lung Cancer. Metabolites 2023; 13:1037. [PMID: 37887362 PMCID: PMC10609104 DOI: 10.3390/metabo13101037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Metabolic reprogramming is a fundamental trait associated with lung cancer development that fuels tumor proliferation and survival. Monitoring such metabolic pathways and their intermediate metabolites can provide new avenues concerning treatment strategies, and the identification of prognostic biomarkers that could be utilized to monitor drug responses in clinical practice. In this review, recent trends in the analytical techniques used for metabolome mapping of lung cancer are capitalized. These techniques include nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and imaging mass spectrometry (MSI). The advantages and limitations of the application of each technique for monitoring the metabolite class or type are also highlighted. Moreover, their potential applications in the analysis of many biological samples will be evaluated.
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Affiliation(s)
- Atiah H. Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
- Addiction and Neuroscience Research Unit, Health Science Campus, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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27
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Nikolaki MD, Kasti AN, Katsas K, Petsis K, Lambrinou S, Patsalidou V, Stamatopoulou S, Karlatira K, Kapolos J, Papadimitriou K, Triantafyllou K. The Low-FODMAP Diet, IBS, and BCFAs: Exploring the Positive, Negative, and Less Desirable Aspects-A Literature Review. Microorganisms 2023; 11:2387. [PMID: 37894045 PMCID: PMC10609264 DOI: 10.3390/microorganisms11102387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The literature about the association of branched short-chain fatty acids (BCFAs) and irritable bowel syndrome (IBS) is limited. BCFAs, the bacterial products of the catabolism of branched-chain amino acids, are proposed as markers for colonic protein fermentation. IBS is a gastrointestinal disorder characterized by low-grade inflammation and intestinal dysbiosis. The low-FODMAP diet (LFD) has increasingly been applied as first-line therapy for managing IBS symptoms, although it decreases the production of short-chain fatty acids (SCFA), well known for their anti-inflammatory action. In parallel, high protein consumption increases BCFAs. Protein fermentation alters the colonic microbiome through nitrogenous metabolites production, known for their detrimental effects on the intestinal barrier promoting inflammation. Purpose: This review aims to explore the role of BCFAs on gut inflammation in patients with IBS and the impact of LFD in BCFAs production. Methods: A literature search was carried out using a combination of terms in scientific databases. Results: The included studies have contradictory findings about how BCFAs affect the intestinal health of IBS patients. Conclusions: Although evidence suggests that BCFAs may play a protective role in gut inflammation, other metabolites of protein fermentation are associated with gut inflammation. Further research is needed in order to clarify how diet protein composition and, consequently, the BCFAs are implicated in IBS pathogenesis or in symptoms management with LFD+.
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Affiliation(s)
- Maroulla D. Nikolaki
- Department of Nutrition and Dietetics, ATTIKON University General Hospital, 12462 Athens, Greece; (M.D.N.); (A.N.K.); (K.K.); (K.P.); (V.P.); (S.S.); (K.K.)
- Department of Nutrition and Dietetics Sciences, Hellenic Mediterranean University, 72300 Crete, Greece
| | - Arezina N. Kasti
- Department of Nutrition and Dietetics, ATTIKON University General Hospital, 12462 Athens, Greece; (M.D.N.); (A.N.K.); (K.K.); (K.P.); (V.P.); (S.S.); (K.K.)
| | - Konstantinos Katsas
- Department of Nutrition and Dietetics, ATTIKON University General Hospital, 12462 Athens, Greece; (M.D.N.); (A.N.K.); (K.K.); (K.P.); (V.P.); (S.S.); (K.K.)
- Institute of Preventive Medicine Environmental and Occupational Health Prolepsis, 15125 Athens, Greece
| | - Konstantinos Petsis
- Department of Nutrition and Dietetics, ATTIKON University General Hospital, 12462 Athens, Greece; (M.D.N.); (A.N.K.); (K.K.); (K.P.); (V.P.); (S.S.); (K.K.)
| | - Sophia Lambrinou
- Department of Clinical Nutrition & Dietetics, General Hospital of Karpathos “Aghios Ioannis o Karpathios”, 85700 Karpathos, Greece;
| | - Vasiliki Patsalidou
- Department of Nutrition and Dietetics, ATTIKON University General Hospital, 12462 Athens, Greece; (M.D.N.); (A.N.K.); (K.K.); (K.P.); (V.P.); (S.S.); (K.K.)
| | - Sophia Stamatopoulou
- Department of Nutrition and Dietetics, ATTIKON University General Hospital, 12462 Athens, Greece; (M.D.N.); (A.N.K.); (K.K.); (K.P.); (V.P.); (S.S.); (K.K.)
| | - Katerina Karlatira
- Department of Nutrition and Dietetics, ATTIKON University General Hospital, 12462 Athens, Greece; (M.D.N.); (A.N.K.); (K.K.); (K.P.); (V.P.); (S.S.); (K.K.)
| | - John Kapolos
- Department of Food Science and Technology, University of Peloponnese, 24100 Kalamata, Greece;
| | - Konstantinos Papadimitriou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, 11855 Athens, Greece;
| | - Konstantinos Triantafyllou
- Hepatogastroenterology Unit, 2nd Department of Internal Propaedeutic Medicine, Medical School, National and Kapodistrian University of Athens, ATTIKON University General Hospital, 12462 Athens, Greece
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28
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Meiller L, Sauvinet V, Breyton AE, Ranaivo H, Machon C, Mialon A, Meynier A, Bischoff SC, Walter J, Neyrinck AM, Laville M, Delzenne NM, Vinoy S, Nazare JA. Metabolic signature of 13C-labeled wheat bran consumption related to gut fermentation in humans: a pilot study. Eur J Nutr 2023; 62:2633-2648. [PMID: 37222787 DOI: 10.1007/s00394-023-03161-5] [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: 11/07/2022] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
PURPOSE The aim of this pilot study was to analyze concomitantly the kinetics of production of 13C-labeled gut-derived metabolites from 13C-labeled wheat bran in three biological matrices (breath, plasma, stools), in order to assess differential fermentation profiles among subjects. METHODS Six healthy women consumed a controlled breakfast containing 13C-labeled wheat bran biscuits. H2, CH4 and 13CO2, 13CH4 24 h-concentrations in breath were measured, respectively, by gas chromatography (GC) and GC-isotope ratio mass spectrometry (GC-IRMS). Plasma and fecal concentrations of 13C-short-chain fatty acids (linear SCFAs: acetate, propionate, butyrate, valerate; branched SCFAs: isobutyrate, isovalerate) were quantified using GC-combustion-IRMS. Gut microbiota composition was assessed by16S rRNA gene sequencing analysis. RESULTS H2 and CH4 24 h-kinetics distinguished two groups in terms of fermentation-related gas excretion: high-CH4 producers vs low-CH4 producers (fasting concentrations: 45.3 ± 13.6 ppm vs 6.5 ± 3.6 ppm). Expired 13CH4 was enhanced and prolonged in high-CH4 producers compared to low-CH4 producers. The proportion of plasma and stool 13C-butyrate tended to be higher in low-CH4 producers, and inversely for 13C-acetate. Plasma branched SCFAs revealed different kinetics of apparition compared to linear SCFAs. CONCLUSION This pilot study allowed to consider novel procedures for the development of biomarkers revealing dietary fiber-gut microbiota interactions. The non-invasive assessment of exhaled gas following 13C-labeled fibers ingestion enabled to decipher distinct fermentation profiles: high-CH4 producers vs low-CH4 producers. The isotope labeling permits a specific in vivo characterisation of the dietary fiber impact consumption on microbiota metabolite production. CLINICAL TRIAL REGISTRATION The study has been registered under the number NCT03717311 at ClinicalTrials.gov on October 24, 2018.
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Affiliation(s)
- Laure Meiller
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | - Valérie Sauvinet
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | - Anne-Esther Breyton
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
- CarMeN Laboratory, INSERM, INRAe, Claude Bernard Lyon1 University, Pierre Bénite, France
| | - Harimalala Ranaivo
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
- CarMeN Laboratory, INSERM, INRAe, Claude Bernard Lyon1 University, Pierre Bénite, France
| | - Christelle Machon
- Service de Biochimie et Biologie Moléculaire, Hospices Civils de Lyon, Pierre Bénite, France
| | - Anne Mialon
- Service de Biochimie et Biologie Moléculaire, Hospices Civils de Lyon, Pierre Bénite, France
| | | | - Stephan C Bischoff
- Institute of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany
| | - Jens Walter
- Department of Medicine, School of Microbiology, APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Audrey M Neyrinck
- Metabolism and Nutrition Research Group, UCLouvain, Brussels, Belgium
| | - Martine Laville
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
- CarMeN Laboratory, INSERM, INRAe, Claude Bernard Lyon1 University, Pierre Bénite, France
- Service d'Endocrinologie Diabète Nutrition, Hospices Civils de Lyon, Pierre Bénite, France
| | | | - Sophie Vinoy
- Nutrition Research, Mondelez International, Saclay, France
| | - Julie-Anne Nazare
- Centre de Recherche en Nutrition Humaine Rhône-Alpes, Univ-Lyon, INSERM, INRAe, Claude Bernard Lyon1 University, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France.
- CarMeN Laboratory, INSERM, INRAe, Claude Bernard Lyon1 University, Pierre Bénite, France.
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Calzadilla N, Qazi A, Sharma A, Mongan K, Comiskey S, Manne J, Youkhana AG, Khanna S, Saksena S, Dudeja PK, Alrefai WA, Gill RK. Mucosal Metabolomic Signatures in Chronic Colitis: Novel Insights into the Pathophysiology of Inflammatory Bowel Disease. Metabolites 2023; 13:873. [PMID: 37512580 PMCID: PMC10386370 DOI: 10.3390/metabo13070873] [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: 06/11/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Inflammatory bowel diseases (IBD) involve complex interactions among genetic factors, aberrant immune activation, and gut microbial dysbiosis. While metabolomic studies have focused on feces and serum, fewer investigations have examined the intestinal mucosa despite its crucial role in metabolite absorption and transport. The goals of this study were twofold: to test the hypothesis that gut microbial dysbiosis from chronic intestinal inflammation leads to mucosal metabolic alterations suitable for therapeutic targeting, and to address gaps in metabolomic studies of intestinal inflammation that have overlooked the mucosal metabolome. The chronic DSS colitis was induced for five weeks in 7-9-week-old wild-type C57BL/6J male mice followed by microbial profiling with targeted 16srRNA sequencing service. Mucosal metabolite measurements were performed by Metabolon (Morrisville, NC). The data were analyzed using the bioinformatic tools Pathview, MetOrigin, and Metaboanalyst. The novel findings demonstrated increases in several host- and microbe-derived purine, pyrimidine, endocannabinoid, and ceramide metabolites in colitis. Origin analysis revealed that microbial-related tryptophan metabolites kynurenine, anthranilate, 5-hydroxyindoleacetate, and C-glycosyltryptophan were significantly increased in colon mucosa during chronic inflammation and strongly correlated with disease activity. These findings offer new insights into the pathophysiology of IBD and provide novel potential targets for microbial-based therapeutics.
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Affiliation(s)
- Nathan Calzadilla
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Aisha Qazi
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Anchal Sharma
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Kai Mongan
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Shane Comiskey
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Jahnavi Manne
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Alvin G Youkhana
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Sonam Khanna
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Seema Saksena
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Pradeep K Dudeja
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Waddah A Alrefai
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Ravinder K Gill
- Division of Gastroenterology & Hepatology, University of Illinois Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
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Lai J, Zhuo X, Yin K, Jiang F, Liu L, Xu X, Liu H, Wang J, Zhao J, Xu W, Yang S, Guo H, Yuan X, Lin X, Qi F, Fu G. Potential mechanism of pyrotinib-induced diarrhea was explored by gut microbiome and ileum metabolomics. Anticancer Drugs 2023; 34:747-762. [PMID: 36378136 DOI: 10.1097/cad.0000000000001440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pyrotinib is a novel epidermal growth factor receptor/human epidermal growth factor receptor-2 (HER2) tyrosine kinase inhibitor that exhibited clinical efficacy in patients with HER2-positive breast cancer and HER2-mutant/amplified lung cancer. However, severe diarrhea adverse responses preclude its practical use. At present, the mechanism of pyrotinib-induced diarrhea is unknown and needs further study. First, to develop a suitable and reproducible animal model, we compared the effects of different doses of pyrotinib (20, 40, 60 and 80 mg/kg) in Wistar rats. Second, we used this model to examine the intestinal toxicity of pyrotinib. Finally, the mechanism underlying pyrotinib-induced diarrhea was fully studied using gut microbiome and host intestinal tissue metabolomics profiling. Reproducible diarrhea occurred in rats when they were given an 80 mg/kg daily dose of pyrotinib. Using the pyrotinib-induced model, we observed that Lachnospiraceae and Acidaminococcaceae decreased in the pyrotinib groups, whereas Enterobacteriaceae, Helicobacteraceae and Clostridiaceae increased at the family level by 16S rRNA gene sequence. Multiple bioinformatics methods revealed that glycocholic acid, ursodeoxycholic acid and cyclic AMP increased in the pyrotinib groups, whereas kynurenic acid decreased, which may be related to the pathogenesis of pyrotinib-induced diarrhea. Additionally, pyrotinib-induced diarrhea may be associated with a number of metabolic changes mediated by the gut microbiome, such as Primary bile acid biosynthesis. We reported the establishment of a reproducible pyrotinib-induced animal model for the first time. Furthermore, we concluded from this experiment that gut microbiome imbalance and changes in related metabolites are significant contributors to pyrotinib-induced diarrhea.
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Affiliation(s)
- Jingjiang Lai
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University
- The Second Clinical Medical College, Shandong University of Traditional Chinese Medicine
| | - Xiaoli Zhuo
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University
- The Clinical Medical College, Shandong First Medical University (Shandong Academy of Medicine)
| | - Ke Yin
- Department of Pathology, Shandong Provincial Hospital, Cheeloo College of Medicine
| | - Fengxian Jiang
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University
- The Second Clinical Medical College, Shandong University of Traditional Chinese Medicine
| | - Lei Liu
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University
- The Clinical Medical College, Shandong First Medical University (Shandong Academy of Medicine)
| | - Xiaoying Xu
- Department of Pathology, Shandong Provincial Hospital, Cheeloo College of Medicine
| | - Hongjing Liu
- The Second Clinical Medical College, Shandong University of Traditional Chinese Medicine
| | - Jingliang Wang
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University
- The Second Clinical Medical College, Shandong University of Traditional Chinese Medicine
| | - Jing Zhao
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University
- The Clinical Medical College, Shandong First Medical University (Shandong Academy of Medicine)
| | | | - Shuping Yang
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University
| | - Honglin Guo
- Department of Central Laboratory, Shandong Provincial Hospital
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University
| | | | - Xiaoyan Lin
- Department of Pathology, Shandong Provincial Hospital, Cheeloo College of Medicine
- Department of Pathology
| | - Fanghua Qi
- Traditional Chinese Medicine, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Guobin Fu
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University
- Department of Oncology
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Sun R, Jin D, Fei F, Xu Z, Cao B, Li J. Mushroom polysaccharides from Grifola frondosa (Dicks.) Gray and Inonotus obliquus (Fr.) Pilat ameliorated dextran sulfate sodium-induced colitis in mice by global modulation of systemic metabolism and the gut microbiota. Front Pharmacol 2023; 14:1172963. [PMID: 37351508 PMCID: PMC10282762 DOI: 10.3389/fphar.2023.1172963] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/09/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction: Polysaccharides from Grifola frondosa (Dicks.) Gray (HSH) and Inonotus obliquus (Fr.) Pilat (BHR) showed noticeable effects on dextran sulfate sodium (DSS)-induced colitis, but their systemic modulation effects have not been fully revealed. This study aimed to investigate the regulation of the gut microbiota and systemic metabolism by HSH and BHR in DSS-induced colitis. Methods: C57BL/6J mice were given DSS (2.5%) in water and were treated with HSH and BHR (200 mg/kg/day) by gavage. Body weight and colon length were recorded, and H&E and AB-PAS staining of the colon were conducted to evaluate the model and the protective effect of the polysaccharides. Additionally, an LC-QTOF/MS-based untargeted metabolomic platform was used to identify the metabolites in the serum, colon tissue, gut contents, and faeces and investigate differential metabolites and metabolic pathways. 16S rDNA gene sequencing was used to measure the composition of bacterial communities. Results: The results showed that the mouse colitis model was established successfully, as evidenced by an increased disease activity index score [2.83 ± 0.62 vs. 0.06 ± 0.14 (p < 0.001)] and shortened colon length [5.43 ± 0.64 cm vs. 7.04 ± 0.29 cm (p < 0.001)], and HSH and BHR ameliorated DSS-induced colitis by improving the disease activity index (2.17 ± 0.28 and 1.83 ± 0.29, respectively) and restoring the colon length (6.12 ± 0.30 cm and 6.62 ± 0.35 cm, respectively). HSH and BHR significantly modulated metabolites involved in aromatic amino acid metabolism, the citrate cycle, purine metabolism, pyrimidine metabolism, etc. HSH and BHR increased the Chao1 index by 64.25% and 60.25%, respectively, and they increased the Shannon index by 13.02% and 10.23%, respectively. They both reversed the increase in the abundances of g_Odoribacter, g_Clostridium, g_AF12, g_Parabacteroides and g_Turicibacter and reversed the decrease in the abundance of g_unclassified_Bacteria induced by DSS. Specifically, HSH reversed the reductions in g_unclassified_Lactobacillales and g_Ruminococcus, and BHR reversed the decreases in g_unidentified_Coriobacteriaceae and g_unclassified_Firmicutes. Discussion: These results suggested that HSH and BHR may ameliorate DSS-induced colitis by global modulation of systemic metabolism and the gut microbiota. Targeting the gut microbiota may be a potentially effective strategy to modulate systemic metabolism and treat colitis.
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Affiliation(s)
- Runbin Sun
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Dandan Jin
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Fei Fei
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhi Xu
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Bei Cao
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Juan Li
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
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Arroyo-Manzanares N, García-Nicolás M, Abellán-Alfocea F, Prieto-Baeza L, Campillo N, Del Val Oliver B, Zarauz-García J, Sáenz L, Viñas P. Application of untargeted volatile profiling in inflammatory bowel disease research. Anal Bioanal Chem 2023:10.1007/s00216-023-04748-x. [PMID: 37233766 DOI: 10.1007/s00216-023-04748-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Inflammatory bowel disease (IBD) diagnosis depends on criteria based on histological, endoscopic, radiological, and clinical results. These studies show drawbacks as being expensive, invasive, and time-consuming. In this work, an untargeted metabolomic strategy based on the monitoring of volatile compounds in serum by headspace gas chromatography-mass spectrometry is proposed as a complementary, fast, and efficient test for IBD patient diagnosis. To develop the method and build a chemometric model that allows the IBD diagnosis, serum samples including IBD patients and healthy volunteers were collected. Analyses were performed by incubating 400 µL of serum for 10 min at 90 °C. For data processing, an untargeted metabolomic strategy was used. A total of 96 features were detected, of which a total of 10 volatile compounds could be identified and confirmed by means of the analysis of real standards. The chemometric treatment consisted of a discriminant analysis of orthogonal partial least squares (OPLS-DA) obtaining a 100% of classification rate, since all the analyzed samples were correctly classified.
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Affiliation(s)
- Natalia Arroyo-Manzanares
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain
| | - María García-Nicolás
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain
| | - Fuensanta Abellán-Alfocea
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain
| | - Laura Prieto-Baeza
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain
| | - Natalia Campillo
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain
| | - Blanca Del Val Oliver
- Internal Medicine Service - Gastroenterology and Hepatology Section, Hospital General Universitario Rafael Méndez, Lorca, Spain
| | - José Zarauz-García
- Laboratory Medicine Department, Hospital General Universitario Rafael Méndez, Lorca, Spain
| | - Luis Sáenz
- Laboratory Medicine Department, Hospital General Universitario Rafael Méndez, Lorca, Spain
| | - Pilar Viñas
- Department of Analytical Chemistry, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", E-30100, Murcia, Spain.
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Song Z, Ohnishi Y, Osada S, Gan L, Jiang J, Hu Z, Kumeta H, Kumaki Y, Yokoi Y, Nakamura K, Ayabe T, Yamauchi K, Aizawa T. Application of Benchtop NMR for Metabolomics Study Using Feces of Mice with DSS-Induced Colitis. Metabolites 2023; 13:metabo13050611. [PMID: 37233652 DOI: 10.3390/metabo13050611] [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: 03/24/2023] [Revised: 04/22/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Nuclear magnetic resonance (NMR)-based metabolomics, which comprehensively measures metabolites in biological systems and investigates their response to various perturbations, is widely used in research to identify biomarkers and investigate the pathogenesis of underlying diseases. However, further applications of high-field superconducting NMR for medical purposes and field research are restricted by its high cost and low accessibility. In this study, we applied a low-field, benchtop NMR spectrometer (60 MHz) employing a permanent magnet to characterize the alterations in the metabolic profile of fecal extracts obtained from dextran sodium sulfate (DSS)-induced ulcerative colitis model mice and compared them with the data acquired from high-field NMR (800 MHz). Nineteen metabolites were assigned to the 60 MHz 1H NMR spectra. Non-targeted multivariate analysis successfully discriminated the DSS-induced group from the healthy control group and showed high comparability with high-field NMR. In addition, the concentration of acetate, identified as a metabolite with characteristic behavior, could be accurately quantified using a generalized Lorentzian curve fitting method based on the 60 MHz NMR spectra.
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Affiliation(s)
- Zihao Song
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Yuki Ohnishi
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | | | - Li Gan
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Jiaxi Jiang
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Zhiyan Hu
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Hiroyuki Kumeta
- Advanced NMR Facility, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Yasuhiro Kumaki
- High-Resolution NMR Laboratory, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yuki Yokoi
- Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Kiminori Nakamura
- Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Tokiyoshi Ayabe
- Innate Immunity Laboratory, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
| | - Kazuo Yamauchi
- Instrumental Analysis Section, Okinawa Institute of Science and Technology, Onna 904-0495, Japan
| | - Tomoyasu Aizawa
- Laboratory of Protein Science, Graduate School of Life Science, Hokkaido University, Sapporo 060-0808, Japan
- Advanced NMR Facility, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0808, Japan
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Cedeno M, Murillo-Saich J, Coras R, Cedola F, Brandy A, Prior A, Pedersen A, Mateo L, Martinez-Morillo M, Guma M. Serum metabolomic profiling identifies potential biomarkers in arthritis in older adults: an exploratory study. Metabolomics 2023; 19:37. [PMID: 37022535 DOI: 10.1007/s11306-023-02004-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 03/29/2023] [Indexed: 04/07/2023]
Abstract
BACKGROUND Seronegative elderly-onset rheumatoid arthritis (EORA)neg and polymyalgia rheumatica (PMR) have similar clinical characteristics making them difficult to distinguish based on clinical features. We hypothesized that the study of serum metabolome could identify potential biomarkers of PMR vs. EORAneg. METHODS Arthritis in older adults (ARTIEL) is an observational prospective cohort with patients older than 60 years of age with newly diagnosed arthritis. Patients' blood samples were compared at baseline with 18 controls. A thorough clinical examination was conducted. A Bruker Avance 600 MHz spectrometer was used to acquire Nuclear Magnetic Resonance (NMR) spectra of serum samples. Chenomx NMR suite 8.5 was used for metabolite identification and quantification.Student t-test, one-way ANOVA, binary linear regression and ROC curve, Pearson's correlation along with pathway analyses were conducted. RESULTS Twenty-eight patients were diagnosed with EORAneg and 20 with PMR. EORAneg patients had a mean disease activity score (DAS)-Erythrocyte Sedimentation Rate (ESR) of 6.21 ± 1.00. All PMR patients reported shoulder pain, and 90% reported pelvic pain. Fifty-eight polar metabolites were identified. Of these, 3-hydroxybutyrate, acetate, glucose, glycine, lactate, and o-acetylcholine (o-ACh), were significantly different between groups. Of interest, IL-6 correlated with different metabolites in PMR and EORAneg suggesting different inflammatory activated pathways. Finally, lactate, o-ACh, taurine, and sex (female) were identified as distinguishable factors of PMR from EORAneg with a sensitivity of 90%, specificity of 92.3%, and an AUC of 0.925 (p < 0.001). CONCLUSION These results suggest that EORAneg and PMR have different serum metabolomic profiles that might be related to their pathobiology and can be used as biomarker to discriminate between both diseases.
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Affiliation(s)
- Martha Cedeno
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jessica Murillo-Saich
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Roxana Coras
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, Autonomous University of Barcelona, Plaça Cívica, Bellaterra, Barcelona, 08193, Spain
| | - Francesca Cedola
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Anahy Brandy
- Department of Rheumatology, Germans Trias i Pujol, University Hospital, Carretera de Canyet, Badalona, 08916, Spain
| | - Agueda Prior
- Department of Rheumatology, Germans Trias i Pujol, University Hospital, Carretera de Canyet, Badalona, 08916, Spain
| | - Anders Pedersen
- Swedish NMR Centre, University of Gothenburg, Gothenburg, 41390, Sweden
| | - Lourdes Mateo
- Department of Rheumatology, Germans Trias i Pujol, University Hospital, Carretera de Canyet, Badalona, 08916, Spain
| | - Melania Martinez-Morillo
- Department of Rheumatology, Germans Trias i Pujol, University Hospital, Carretera de Canyet, Badalona, 08916, Spain.
| | - Monica Guma
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, Autonomous University of Barcelona, Plaça Cívica, Bellaterra, Barcelona, 08193, Spain.
- VA Healthcare Service, San Diego, CA, 92161, USA.
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Cong J, Wang P, Gai H, Zhou S, Zhang Y, Zhao T. Effects of compound prebiotics as prophylactic and therapeutic supplementation in a mouse model of acute colitis. Appl Microbiol Biotechnol 2023; 107:2597-2609. [PMID: 36869880 DOI: 10.1007/s00253-023-12453-z] [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: 12/16/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 03/05/2023]
Abstract
Compound prebiotics (CP) have been explored in modulation of intestinal microbiota and remission of inflammatory responses in the acute colitis (AC). Yet, research on the roles of simultaneous prophylactic and therapeutic CP intervention in relation to AC remains lacking. Here, CP were pre-fed to examine preventive effects. CP, CP combined with mesalazine (5-aminosalicylic acid) (CPM), and mesalazine were used to evaluate therapeutic effects on the dextran sulfate sodium (DSS)-induced AC. Results showed that prophylactic CP and therapeutic CPM alleviated AC, evidenced by variations of body weight, colon length, spleen index, disease activity index score, histological score, and intestinal mucosa. Ruminococcus and Bifidobacterium were detected in significant abundance in the prophylactic CP and therapeutic CPM groups, respectively. Phylogenetic ecological network analysis revealed that therapeutic CPM probably had the strongest coupling between microbes in changing intestinal microbiota to influence treatment. However, changes in short-chain fatty acids (SCFAs) seemed to have no persuasive results, probably due to reduced SCFA level in feces and variability in transit, absorption, and utilization. Furthermore, therapeutic CP exerted higher value in terms of observed species and Shannon diversity, as well as a more concentrated distribution by principal coordinates analysis. Together, the favorable roles of CP in colitis provide directions for prebiotics in designing effective prophylactic functional diets and treatment strategies. KEY POINTS: • Prebiotics as prophylactic intervention effectively inhibited acute colitis. • Prebiotics as prophylactic and therapeutic interventions had distinct effects on gut microbiota. • Prebiotics combined with drug intervention had higher efficacy in treating acute colitis.
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Affiliation(s)
- Jing Cong
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266000, China.
| | - Peng Wang
- Department of Radiology, Shanghai 411 Hospital, China RongTong Medical Healthcare Group Co. Ltd., Shanghai, 200080, China
| | - Huirong Gai
- Department of Oncology, Affiliated Qingdao Central Hospital of Qingdao University, Qingdao Cancer Hospital, Qingdao, 266000, China
| | - Siyu Zhou
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266000, China
| | - Yun Zhang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266000, China
| | - Tianyu Zhao
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266000, China
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Ng QX, Yau CE, Yaow CYL, Chong RIH, Chong NZY, Teoh SE, Lim YL, Soh AYS, Ng WK, Thumboo J. What Has Longitudinal ‘Omics’ Studies Taught Us about Irritable Bowel Syndrome? A Systematic Review. Metabolites 2023; 13:metabo13040484. [PMID: 37110143 PMCID: PMC10142038 DOI: 10.3390/metabo13040484] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
Irritable bowel syndrome is a prototypical disorder of the brain–gut–microbiome axis, although the underlying pathogenesis and mechanisms remain incompletely understood. With the recent advances in ‘omics’ technologies, studies have attempted to uncover IBS-specific variations in the host–microbiome profile and function. However, no biomarker has been identified to date. Given the high inter-individual and day-to-day variability of the gut microbiota, and a lack of agreement across the large number of microbiome studies, this review focused on omics studies that had sampling at more than one time point. A systematic literature search was performed using various combinations of the search terms “Irritable Bowel Syndrome” and “Omics” in the Medline, EMBASE, and Cochrane Library up to 1 December 2022. A total of 16 original studies were reviewed. These multi-omics studies have implicated Bacteroides, Faecalibacterium prausnitzii, Ruminococcus spp., and Bifidobacteria in IBS and treatment response, found altered metabolite profiles in serum, faecal, or urinary samples taken from IBS patients compared to the healthy controls, and revealed enrichment in the immune and inflammation-related pathways. They also demonstrated the possible therapeutic mechanisms of diet interventions, for example, synbiotics and low fermentable oligosaccharides, disaccharides, monosaccharides, and polyol (FODMAP) diets on microbial metabolites. However, there was significant heterogeneity among the studies and no uniform characteristics of IBS-related gut microbiota. There is a need to further study these putative mechanisms and also ensure that they can be translated to therapeutic benefits for patients with IBS.
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Altered Gut Microbic Flora and Haemorrhoids: Could They Have a Possible Relationship? J Clin Med 2023; 12:jcm12062198. [PMID: 36983199 PMCID: PMC10054427 DOI: 10.3390/jcm12062198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
To date, the exact pathophysiology of haemorrhoids is poorly understood. The different philosophies on haemorrhoids aetiology may lead to different approaches of treatment. A pathogenic theory involving a correlation between altered anal canal microflora, local inflammation, and muscular dyssynergia is proposed through an extensive review of the literature. Since the middle of the twentieth century, three main theories exist: (1) the varicose vein theory, (2) the vascular hyperplasia theory, and (3) the concept of a sliding anal lining. These phenomena determine changes in the connective tissue (linked to inflammation), including loss of organization, muscular hypertrophy, fragmentation of the anal subepithelial muscle and the elastin component, and vascular changes, including abnormal venous dilatation and vascular thrombosis. Recent studies have reported a possible involvement of gut microbiota in gut motility alteration. Furthermore, dysbiosis seems to represent the leading cause of bowel mucosa inflammation in any intestinal district. The alteration of the gut microbioma in the anorectal district could be responsible for haemorrhoids and other anorectal disorders. A deeper knowledge of the gut microbiota in anorectal disorders lays the basis for unveiling the roles of these various gut microbiota components in anorectal disorder pathogenesis and being conductive to instructing future therapeutics. The therapeutic strategy of antibiotics, prebiotics, probiotics, and fecal microbiota transplantation will benefit the effective application of precision microbiome manipulation in anorectal disorders.
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Wu W, Li Q, Chen H, Fang X, Niu B, Liu R, Mu H, Gao H. In vitro fermentation characteristics of the dietary fiber in bamboo (Phyllostachys edulis) shoots and its regulatory effects on the intestinal microbiota and metabolites. Food Chem 2023; 404:134707. [DOI: 10.1016/j.foodchem.2022.134707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
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Zhu C, Zhang Q, Zhao X, Yang Z, Yang F, Yang Y, Tang J, Laghi L. Metabolomic Analysis of Multiple Biological Specimens (Feces, Serum, and Urine) by 1H-NMR Spectroscopy from Dairy Cows with Clinical Mastitis. Animals (Basel) 2023; 13:ani13040741. [PMID: 36830529 PMCID: PMC9952568 DOI: 10.3390/ani13040741] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Due to huge economic losses to the dairy industry worldwide, mastitis can be considered as one of the most common diseases in dairy cows. This work aimed to study this disease by comparing multiple biological specimens (feces, serum, and urine) from individuals with or without clinical mastitis. This was performed by a single analytical platform, namely 1H-NMR, through a multi-matrix strategy. Thanks to the high reproducibility of 1H-NMR, we could characterize 120 molecules across dairy cow feces, serum, and urine. Among them, 23 molecules were in common across the three biofluids. By integrating the results of multi-matrix metabolomics, several pathways pertaining to energy metabolism and amino acid metabolism appeared to be affected by clinical mastitis. The present work wished to deepen the understanding of dairy cow mastitis in its clinical form. Simultaneous analysis of metabolome changes across several key biofluids could facilitate knowledge discovery and the reliable identification of potential biomarkers, which could be, in turn, used to shed light on the early diagnosis of dairy cow mastitis in its subclinical form.
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Affiliation(s)
- Chenglin Zhu
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, China
| | - Qian Zhang
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, China
| | - Xin Zhao
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, China
| | - Zhibo Yang
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, China
| | - Falong Yang
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Yang Yang
- Farming and Animal Husbandry Bureau of Ganzi County, Ganzi 626700, China
| | - Junni Tang
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, China
- Correspondence: (J.T.); (L.L.); Tel.: +86-028-85928243 (J.T.); +39-0547-338106 (L.L.)
| | - Luca Laghi
- Department of Agricultural and Food Sciences, University of Bologna, 47521 Cesena, Italy
- Correspondence: (J.T.); (L.L.); Tel.: +86-028-85928243 (J.T.); +39-0547-338106 (L.L.)
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Waseem MR, Shin A, Siwiec R, James-Stevenson T, Bohm M, Rogers N, Wo J, Waseem L, Gupta A, Jarrett M, Kadariya J, Xu H. Associations of Fecal Short Chain Fatty Acids With Colonic Transit, Fecal Bile Acid, and Food Intake in Irritable Bowel Syndrome. Clin Transl Gastroenterol 2023; 14:e00541. [PMID: 36227781 PMCID: PMC9875959 DOI: 10.14309/ctg.0000000000000541] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/23/2022] [Accepted: 10/03/2022] [Indexed: 01/31/2023] Open
Abstract
INTRODUCTION Short-chain fatty acids (SCFAs) correlate with colonic transit time (CTT) and may influence irritable bowel syndrome (IBS) pathophysiology. However, the clinical significance of fecal SCFAs, relationships between SCFAs and other metabolites (bile acids [BAs]), and real-time diet effects on SCFAs in IBS are uncertain. The aim was to evaluate fecal SCFA associations with IBS phenotype and mechanisms and explore effects of real-time diet. METHODS We conducted a prospective observational study of fecal SCFA, BAs, and CTT in healthy controls (HCs) and participants with IBS. We compared study end points across groups, analyzed relationships between end points, and evaluated the discriminative ability of SCFAs. Diet effects were explored in participants with dietary data. RESULTS Among 21 HCs and 43 participants with IBS, fecal SCFAs (total, individual) were inversely correlated with overall (all P < 0.01) and segmental (all P < 0.05) CTT; similar associations were observed within HC and IBS groups. The acetate-to-butyrate ratio correlated with slower overall and left CTT in all and in HCs (both P < 0.01). SCFAs (total, acetate) correlated with BAs (total, % primary) in all participants and in those with IBS with diarrhea. Logistic regression analyses demonstrated associations of acetate with slower transit (odds ratio = 0.988, P = 0.002) and BA diarrhea (BAD; odds ratio = 1.014, P = 0.001). Acetate accurately predicted delayed CTT (area under the receiving operating characteristic curve = 0.84) and BAD (area under the receiver operating characteristic curve = 0.79). Adjusting for diet strengthened correlations of total SCFAs with overall CTT ( R = [-0.46], P = 0.04) and SCFAs with transverse CTT (all P < 0.05). DISCUSSION Fecal SCFAs correlate with CTT and fecal BAs and reliably exclude delayed CTT and BAD. Accounting for diet strengthens SCFA associations with transit.
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Affiliation(s)
- Mohammed Rayyan Waseem
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Andrea Shin
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Robert Siwiec
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Toyia James-Stevenson
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Matthew Bohm
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nicholas Rogers
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - John Wo
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Lina Waseem
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Anita Gupta
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Megan Jarrett
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jhalka Kadariya
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Huiping Xu
- Department of Biostatistics and Health Data Sciences, Indiana University School of Medicine, Indianapolis, Indiana, USA
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You HJ, Si J, Kim J, Yoon S, Cha KH, Yoon HS, Lee G, Yu J, Choi JS, Jung M, Kim DJ, Lee Y, Kim M, Vázquez-Castellanos JF, Sung J, Park JM, Ko G. Bacteroides vulgatus SNUG 40005 Restores Akkermansia Depletion by Metabolite Modulation. Gastroenterology 2023; 164:103-116. [PMID: 36240952 DOI: 10.1053/j.gastro.2022.09.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND & AIMS Weight loss and exercise intervention have been reported to increase the interaction between Bacteroides spp and Akkermansiamuciniphila (Am), although the underlying mechanisms and consequences of the interaction remain unknown. METHODS Using a healthy Korean twin cohort (n = 582), we analyzed taxonomic associations with host body mass index. B vulgatus strains were isolated from mice and human subjects to investigate the strain-specific effect of B vulgatus SNUG 40005 (Bvul) on obesity. The mechanisms underlying Am enrichment by Bvul administration were investigated by multiple experiments: (1) in vitro cross-feeding experiments, (2) construction of Bvul mutants with the N-acetylglucosaminidase gene knocked out, and (3) in vivo validation cohorts with different metabolites. Finally, metabolite profiling in mouse and human fecal samples was performed. RESULTS An interaction between Bvul and Am was observed in lean subjects but was disrupted in obese subjects. The administration of Bvul to mice fed a high-fat diet decreased body weight, insulin resistance, and gut permeability. In particular, Bvul restored the abundance of Am, which decreased significantly after a long-term high-fat diet. A cross-feeding analysis of Am with cecal contents or Bvul revealed that Am enrichment was attributed to metabolites produced during mucus degradation by Bvul. The metabolome profile of mouse fecal samples identified N-acetylglucosamine as contributing to Am enrichment, which was confirmed by in vitro and in vivo experiments. Metabolite network analysis of the twin cohort found that lysine serves as a bridge between N-acetylglucosamine, Bvul, and Am. CONCLUSIONS Strain-specific microbe-microbe interactions modulate the mucosal environment via metabolites produced during mucin degradation in the gut.
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Affiliation(s)
- Hyun Ju You
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Institute of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Center for Human and Environmental Microbiome, Seoul National University, Seoul, Korea; N-Bio, Seoul National University, Seoul, Korea; KoBioLabs, Seoul, Korea
| | - Jiyeon Si
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Institute of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Center for Human and Environmental Microbiome, Seoul National University, Seoul, Korea; Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Korea
| | - Jinwook Kim
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Sunghyun Yoon
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Kwang Hyun Cha
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Korea
| | - Hyo Shin Yoon
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Korea
| | - Giljae Lee
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Junsun Yu
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Joon-Sun Choi
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Minkyung Jung
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Do June Kim
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Yujin Lee
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Minyoung Kim
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Jorge F Vázquez-Castellanos
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Joohon Sung
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Jin Mo Park
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts
| | - GwangPyo Ko
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Center for Human and Environmental Microbiome, Seoul National University, Seoul, Korea; N-Bio, Seoul National University, Seoul, Korea; KoBioLabs, Seoul, Korea.
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Cronobacter sakazakii Cue for the Attraction and Its Impact on the Immunity of Caenorhabditis elegans. Infect Immun 2022; 90:e0028122. [PMID: 36377894 PMCID: PMC9753658 DOI: 10.1128/iai.00281-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cronobacter sakazakii, an opportunistic foodborne pathogen prevalently detected in contaminated powdered infant formula, is associated with different diseases, including meningitis. It can cross the blood-brain barrier and affects the CNS. The impact of C. sakazakii on host neuronal cells and behavior is largely unknown. Hence, detailed molecular data are required to understand its severity. Caenorhabditis elegans is a unique model for studying chemical communication, as it relies on chemosensation for searching nutritional supplements. Although, C. sakazakii is pathogenic to C. elegans, our analysis indicated that C. elegans was highly attracted toward C. sakazakii compared to its food source, E. coli OP50. To study the cue for the attraction, bioactive components (RNA/Protein/Lipopolysaccharides/Metabolites) of C. sakazakii were isolated and used for observing the chemotaxis behavior of C. elegans. The results signified that C. elegans was more attracted toward acid extracted metabolites than those of the other extraction methods. The combined action of acid extracted metabolites of C. sakazakii and a candidate pathogen drastically reduced the survival of C. elegans. In addition, qPCR analysis suggested that the exposure of isolated metabolites through acid extraction to C. elegans for 24 h modified the candidate immune regulatory genes involved in pathogen recognition and kinase activity such as clec-60, clec-87, lys-7, akt-2, pkc-1, and jnk-1.
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Holst LM, Iribarren C, Sapnara M, Savolainen O, Törnblom H, Wettergren Y, Strid H, Simrén M, Magnusson MK, Öhman L. Fecal Luminal Factors from Patients with Gastrointestinal Diseases Alter Gene Expression Profiles in Caco-2 Cells and Colonoids. Int J Mol Sci 2022; 23:ijms232415505. [PMID: 36555145 PMCID: PMC9779506 DOI: 10.3390/ijms232415505] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Previous in vitro studies have shown that the intestinal luminal content, including metabolites, possibly regulates epithelial layer responses to harmful stimuli and promotes disease. Therefore, we aimed to test the hypothesis that fecal supernatants from patients with colon cancer (CC), ulcerative colitis (UC) and irritable bowel syndrome (IBS) contain distinct metabolite profiles and establish their effects on Caco-2 cells and human-derived colon organoids (colonoids). The metabolite profiles of fecal supernatants were analyzed by liquid chromatography-mass spectrometry and distinguished patients with CC (n = 6), UC (n = 6), IBS (n = 6) and healthy subjects (n = 6). Caco-2 monolayers and human apical-out colonoids underwent stimulation with fecal supernatants from different patient groups and healthy subjects. Their addition did not impair monolayer integrity, as measured by transepithelial electrical resistance; however, fecal supernatants from different patient groups and healthy subjects altered the gene expression of Caco-2 monolayers, as well as colonoid cultures. In conclusion, the stimulation of Caco-2 cells and colonoids with fecal supernatants derived from CC, UC and IBS patients altered gene expression profiles, potentially reflecting the luminal microenvironment of the fecal sample donor. This experimental approach allows for investigating the crosstalk at the gut barrier and the effects of the gut microenvironment in the pathogenesis of intestinal diseases.
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Affiliation(s)
- Luiza Moraes Holst
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Cristina Iribarren
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Maria Sapnara
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, 70210 Kuopio, Finland
| | - Hans Törnblom
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Yvonne Wettergren
- Department of Surgery, Institute of Clinical Sciences, Sahlgrenska University Hospital, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Hans Strid
- Department of Internal Medicine, Södra Älvsborgs Hospital, 501 82 Borås, Sweden
| | - Magnus Simrén
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Maria K. Magnusson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Lena Öhman
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence:
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Taladrid D, Zorraquín‐Peña I, Molinero N, Silva M, Manceñido N, Pajares R, Bartolomé B, Moreno‐Arribas MV. Polyphenols and Ulcerative Colitis: An Exploratory Study of the Effects of Red Wine Consumption on Gut and Oral Microbiome in Active-Phase Patients. Mol Nutr Food Res 2022; 66:e2101073. [PMID: 35633101 PMCID: PMC9787944 DOI: 10.1002/mnfr.202101073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/09/2022] [Indexed: 12/30/2022]
Abstract
SCOPE This paper explores the effects of moderate red wine consumption on the clinical status and symptomatology of patients with ulcerative colitis (UC), including the study of the oral and intestinal microbiome. METHODS AND RESULTS A case control intervention study in UC patients is designed. Intervention patients (n = 5) consume red wine (250 mL day-1 ) for 4 weeks whereas control patients (n = 5) do not. Moderate wine consumption significantly (p < 0.05) improves some clinical parameters related to serum iron, and alleviates intestinal symptoms as evaluated by the IBDQ-32 questionnaire. 16S rRNA gene sequencing indicate a non-significant (p > 0.05) increase in bacterial alpha diversity after wine intervention in both saliva and fecal microbiota. Additional comparison of taxonomic data between UC patients (n = 10) and healthy subjects (n = 8) confirm intestinal dysbiosis for the UC patients. Finally, analysis of fecal metabolites (i.e., phenolic acids and SCFAs) indicates a non-significant increase (p > 0.05) for the UC patients that consumed wine. CONCLUSIONS Moderate and regular red wine intake seems to improve the clinical status and symptoms of UC patients in the active phase of the disease. However, studies with a greater sample size are required to achieve conclusive results.
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Affiliation(s)
- Diego Taladrid
- Institute of Food Science Research (CIAL)CSIC‐UAM, c/Nicolás Cabrera 9Madrid28049Spain
| | - Irene Zorraquín‐Peña
- Institute of Food Science Research (CIAL)CSIC‐UAM, c/Nicolás Cabrera 9Madrid28049Spain
| | - Natalia Molinero
- Institute of Food Science Research (CIAL)CSIC‐UAM, c/Nicolás Cabrera 9Madrid28049Spain
| | - Mariana Silva
- Institute of Food Science Research (CIAL)CSIC‐UAM, c/Nicolás Cabrera 9Madrid28049Spain
| | - Noemi Manceñido
- Hospital Universitario “Infanta Sofia”, P.° de Europa34, 28703 San Sebastián de los ReyesMadridSpain
| | - Ramón Pajares
- Hospital Universitario “Infanta Sofia”, P.° de Europa34, 28703 San Sebastián de los ReyesMadridSpain
| | - Begoña Bartolomé
- Institute of Food Science Research (CIAL)CSIC‐UAM, c/Nicolás Cabrera 9Madrid28049Spain
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Churcheward B, Millet M, Bihouée A, Fertin G, Chaffron S. MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics. mSystems 2022; 7:e0043222. [PMID: 35703559 PMCID: PMC9426564 DOI: 10.1128/msystems.00432-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 12/24/2022] Open
Abstract
Metagenome-assembled genomes (MAGs) represent individual genomes recovered from metagenomic data. MAGs are extremely useful to analyze uncultured microbial genomic diversity, as well as to characterize associated functional and metabolic potential in natural environments. Recent computational developments have considerably improved MAG reconstruction but also emphasized several limitations, such as the nonbinning of sequence regions with repetitions or distinct nucleotidic composition. Different assembly and binning strategies are often used; however, it still remains unclear which assembly strategy, in combination with which binning approach, offers the best performance for MAG recovery. Several workflows have been proposed in order to reconstruct MAGs, but users are usually limited to single-metagenome assembly or need to manually define sets of metagenomes to coassemble prior to genome binning. Here, we present MAGNETO, an automated workflow dedicated to MAG reconstruction, which includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery. MAGNETO is implemented as a Snakemake workflow and is available at: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto. IMPORTANCE Genome-resolved metagenomics has led to the discovery of previously untapped biodiversity within the microbial world. As the development of computational methods for the recovery of genomes from metagenomes continues, existing strategies need to be evaluated and compared to eventually lead to standardized computational workflows. In this study, we compared commonly used assembly and binning strategies and assessed their performance using both simulated and real metagenomic data sets. We propose a novel approach to automate coassembly, avoiding the requirement for a priori knowledge to combine metagenomic information. The comparison against a previous coassembly approach demonstrates a strong impact of this step on genome binning results, but also the benefits of informing coassembly for improving the quality of recovered genomes. MAGNETO integrates complementary assembly-binning strategies to optimize genome reconstruction and provides a complete reads-to-genomes workflow for the growing microbiome research community.
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Affiliation(s)
| | - Maxime Millet
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, Nantes, France
| | - Audrey Bihouée
- Nantes Université, CNRS, INSERM, l’institut du thorax, F-44000 Nantes, France
- Nantes Université, CHU Nantes, SFR Bonamy, F-44000 Nantes, France
| | - Guillaume Fertin
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, Nantes, France
| | - Samuel Chaffron
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
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Koev TT, Harris HC, Kiamehr S, Khimyak YZ, Warren FJ. Starch hydrogels as targeted colonic drug delivery vehicles. Carbohydr Polym 2022; 289:119413. [DOI: 10.1016/j.carbpol.2022.119413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 01/22/2023]
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Cao C, Wang L, Ai C, Gong G, Wang Z, Huang L, Song S, Zhu B. Impact of Lycium barbarum arabinogalactan on the fecal metabolome in a DSS-induced chronic colitis mouse model. Food Funct 2022; 13:8703-8716. [PMID: 35912853 DOI: 10.1039/d2fo01283a] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ulcerative colitis (UC) is often accompanied by the dysbiosis of gut microbiota and metabolism. Our previous study indicated that arabinogalactan from Lycium barbarum (LBP-3) could markedly attenuate the symptoms of chronic UC in mice by modulating the structure of gut microbiota. This study explored the impact of LBP-3 on the fecal metabolomic profiling of the same cohort of mice by HPLC-TripleTOF/MS. Untargeted metabolomic analyses indicated that supplementation with LBP-3 markedly reversed 18 of the 48 differential metabolites (mainly belonging to amino acids and organic acids) disturbed by DSS. Targeted metabolomics revealed that the lower levels of tryptophan, lysine, diiodothyronine, kynurenine, and betaine and higher levels of phenylalanine, leucine, glutamine, isoleucine, homoserine, (S)-2-hydroxyglutarate, 2-isopropylmalic acid, ascorbic acid, gluconic acid, and taurine, which were caused by DSS induction, were reversed by LBP-3 treatment. In addition, pathway analysis showed that the pentose phosphate pathway, phenylalanine metabolism, ascorbate and aldarate metabolism, and phenylalanine, tyrosine and tryptophan biosynthesis were strongly affected by LBP-3. More importantly, the above amino acids, organic acids, and metabolic pathways changed by LBP-3 were correlated with the abundance of gut microbiota such as Turicibacter, Lactobacillus, Parasutterella, Odoribacter, Veillonella, Faecalibacterium, and Ruminococcaceae. This study advances our understanding of the interaction between the microbiome and metabolomics in DSS-induced chronic colitis after LBP-3 treatment.
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Affiliation(s)
- Cui Cao
- Collaborative Innovation Center of Seafood Deep Processing, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China. .,National and Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, P. R. China.,Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, P. R. China.
| | - Linlin Wang
- Collaborative Innovation Center of Seafood Deep Processing, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China. .,National and Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Chunqing Ai
- Collaborative Innovation Center of Seafood Deep Processing, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China. .,National and Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Guiping Gong
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, P. R. China.
| | - Zhongfu Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, P. R. China.
| | - Linjuan Huang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, P. R. China.
| | - Shuang Song
- Collaborative Innovation Center of Seafood Deep Processing, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China. .,National and Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Beiwei Zhu
- Collaborative Innovation Center of Seafood Deep Processing, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, P. R. China. .,National and Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, P. R. China
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48
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Deutsch L, Debevec T, Millet GP, Osredkar D, Opara S, Šket R, Murovec B, Mramor M, Plavec J, Stres B. Urine and Fecal 1H-NMR Metabolomes Differ Significantly between Pre-Term and Full-Term Born Physically Fit Healthy Adult Males. Metabolites 2022; 12:metabo12060536. [PMID: 35736470 PMCID: PMC9228004 DOI: 10.3390/metabo12060536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
Preterm birth (before 37 weeks gestation) accounts for ~10% of births worldwide and remains one of the leading causes of death in children under 5 years of age. Preterm born adults have been consistently shown to be at an increased risk for chronic disorders including cardiovascular, endocrine/metabolic, respiratory, renal, neurologic, and psychiatric disorders that result in increased death risk. Oxidative stress was shown to be an important risk factor for hypertension, metabolic syndrome and lung disease (reduced pulmonary function, long-term obstructive pulmonary disease, respiratory infections, and sleep disturbances). The aim of this study was to explore the differences between preterm and full-term male participants' levels of urine and fecal proton nuclear magnetic resonance (1H-NMR) metabolomes, during rest and exercise in normoxia and hypoxia and to assess general differences in human gut-microbiomes through metagenomics at the level of taxonomy, diversity, functional genes, enzymatic reactions, metabolic pathways and predicted gut metabolites. Significant differences existed between the two groups based on the analysis of 1H-NMR urine and fecal metabolomes and their respective metabolic pathways, enabling the elucidation of a complex set of microbiome related metabolic biomarkers, supporting the idea of distinct host-microbiome interactions between the two groups and enabling the efficient classification of samples; however, this could not be directed to specific taxonomic characteristics.
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Affiliation(s)
- Leon Deutsch
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (L.D.); (S.O.)
| | - Tadej Debevec
- Faculty of Sports, University of Ljubljana, SI-1000 Ljubljana, Slovenia;
- Department of Automation, Biocybernetics and Robotics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Gregoire P. Millet
- Institute of Sport Sciences, University of Lausanne, CH-1015 Lausanne, Switzerland;
| | - Damjan Osredkar
- Department of Pediatric Neurology, University Children’s Hospital, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia;
- Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Simona Opara
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (L.D.); (S.O.)
| | - Robert Šket
- Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia;
| | - Boštjan Murovec
- Faculty of Electrical Engineering, University of Ljubljana, Jamova 2, SI-1000 Ljubljana, Slovenia;
| | - Minca Mramor
- Department of Infectious Diseases, University Medical Centre Ljubljana, SI-1000 Ljubljana, Slovenia;
| | - Janez Plavec
- National Institute of Chemistry, NMR Center, SI-1000 Ljubljana, Slovenia;
| | - Blaz Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (L.D.); (S.O.)
- Department of Automation, Biocybernetics and Robotics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
- Institute of Sanitary Engineering, Faculty of Civil and Geodetic Engineering, University of Ljubljana, SI-1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-4156-7633
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49
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Yang L, Xiang Z, Zou J, Zhang Y, Ni Y, Yang J. Comprehensive Analysis of the Relationships Between the Gut Microbiota and Fecal Metabolome in Individuals With Primary Sjogren's Syndrome by 16S rRNA Sequencing and LC-MS-Based Metabolomics. Front Immunol 2022; 13:874021. [PMID: 35634334 PMCID: PMC9130595 DOI: 10.3389/fimmu.2022.874021] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota has been associated with primary Sjogren’s syndrome (pSS), yet the biological implications of these associations are often elusive. We analyzed the fecal microbiota through 16S rRNA gene amplification and sequencing in 30 patients with pSS and 20 healthy controls (HCs); At the same time, the fecal metabolome was characterized by ultrahigh-performance liquid chromatography–mass spectrometry. In addition, correlation analyses of microbiota and metabolome data were performed to identify meaningful associations. We found that the microbiota composition of pSS patients was significantly different from that of HCs. The pSS gut microbiota is characterized by increased abundances of proinflammatory microbes, especially Escherichia-Shigella, and decreased abundances of anti-inflammatory microbes. Concerning the metabolome, a multivariate model with 33 metabolites efficiently distinguished cases from controls. Through KEGG enrichment analysis, we found that these metabolites were mainly involved in amino acid metabolism and lipid metabolism. The correlation analysis indicated that there were certain correlations between the microbiota and metabolism in pSS patients. In addition, an abundance of Escherichia-Shigella was found to be correlated with high levels of four metabolites (aflatoxin M1, glycocholic acid, L-histidine and phenylglyoxylic acid). Our research suggests that in pSS patients, the gut microbiota is characterized by a specific combination of proinflammatory changes and metabolic states. Escherichia-Shigella is a factor related to gut dysbiosis, which may promote intestinal damage and affect amino acid metabolism.
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Affiliation(s)
- Li Yang
- Department of Rheumatology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Zhao Xiang
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, China
| | - Jinmei Zou
- Department of Rheumatology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Yu Zhang
- Department of Rheumatology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Yuanpiao Ni
- Department of Rheumatology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Jing Yang
- Department of Rheumatology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
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50
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Metwaly A, Reitmeier S, Haller D. Microbiome risk profiles as biomarkers for inflammatory and metabolic disorders. Nat Rev Gastroenterol Hepatol 2022; 19:383-397. [PMID: 35190727 DOI: 10.1038/s41575-022-00581-2] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 12/12/2022]
Abstract
The intestine harbours a complex array of microorganisms collectively known as the gut microbiota. The past two decades have witnessed increasing interest in studying the gut microbiota in health and disease, largely driven by rapid innovation in high-throughput multi-omics technologies. As a result, microbial dysbiosis has been linked to many human pathologies, including type 2 diabetes mellitus and inflammatory bowel disease. Integrated analyses of multi-omics data, including metagenomics and metabolomics along with measurements of host response and cataloguing of bacterial isolates, have identified many bacteria and bacterial products that are correlated with disease. Nevertheless, insight into the mechanisms through which microbes affect intestinal health requires going beyond correlation to causation. Current understanding of the contribution of the gut microbiota to disease causality remains limited, largely owing to the heterogeneity of microbial community structures, interindividual differences in disease evolution and incomplete understanding of the mechanisms that integrate microbiota-derived signals into host signalling pathways. In this Review, we provide a broad insight into the microbiome signatures linked to inflammatory and metabolic disorders, discuss outstanding challenges in this field and propose applications of multi-omics technologies that could lead to an improved mechanistic understanding of microorganism-host interactions.
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Affiliation(s)
- Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Sandra Reitmeier
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany. .,ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany.
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