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Hussain N, Muccee F. In-silico characterization of GABAT protein found in gut-brain axis associated bacteria of healthy individuals and multiple sclerosis patients. Saudi J Biol Sci 2024; 31:103939. [PMID: 38352114 PMCID: PMC10859293 DOI: 10.1016/j.sjbs.2024.103939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 01/10/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Background Multiple sclerosis (MS) is a neurodegenerative disease characterized by inflammation and demyelination of neurons. There is evidence to suggest that level of a neurotransmitter gamma-aminobutyric acid (GABA), due to the degradation by γ-aminobutyric acid transaminase (GABAT), is reduced in certain areas of the brain in MS patients. MS is always accompanied by gut bacteria dysbiosis. In healthy individuals, Faecalibacterium sp. while in MS patients A. calcoaceticus, Clostridium sp. and S. typhimurium are found abundantly. Although all these microbes produce GABAT but only in MS patients this enzyme significantly degrades GABA. Objective Present study is an attempt to characterize the GABAT protein sequences of these bacteria. Methodology Sequences of GABAT protein were retrieved from Uniprot database. Sequences were analyzed by Protparam, Gneg-mPLoc, SOSUI, PFP-FunDSeqE, Pepwheel program, PROTEUS and Alphafold and SAVES servers, MEME suite and HDOCK server. Results In healthy individuals gastrointestinal tract (GIT) bacteria, GABAT protein was present in inner-membrane with α helix content (61 and 62%) and β sheet content (5%), 4-helical cytokines functional domains. It has greater number of B-cell epitopes and more complex 3D configuration as compared to MS patients GIT bacterial enzymes. Conclusion Present study might enable us to modify the GABAT encoding gene and enzyme through site-directed mutagenesis in pathogenic bacteria thus reducing their potential of causing MS.
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Affiliation(s)
- Nadia Hussain
- Department of Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain Campus, Al Ain 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi Campus, Abu Dhabi P. O. Box 112612, United Arab Emirates
| | - Fatima Muccee
- School of Biochemistry and Biotechnology, University of Punjab, Lahore 52254, Pakistan
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2
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Chollet L, Heumel S, Deruyter L, Bouilloux F, Delval L, Robert V, Gevaert MH, Pichavant M, Sencio V, Robil C, Wolowczuk I, Sokol H, Auger S, Douablin A, Langella P, Chatel JM, Grangette C, Trottein F. Faecalibacterium duncaniae as a novel next generation probiotic against influenza. Front Immunol 2024; 15:1347676. [PMID: 38590519 PMCID: PMC11000806 DOI: 10.3389/fimmu.2024.1347676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/27/2024] [Indexed: 04/10/2024] Open
Abstract
The gut-lung axis is critical during viral respiratory infections such as influenza. Gut dysbiosis during infection translates into a massive drop of microbially produced short-chain fatty acids (SCFAs). Among them, butyrate is important during influenza suggesting that microbiome-based therapeutics targeting butyrate might hold promises. The butyrate-producing bacterium Faecalibacterium duncaniae (formerly referred to as F. prausnitzii) is an emerging probiotic with several health-promoting characteristics. To investigate the potential effects of F. duncaniae on influenza outcomes, mice were gavaged with live F. duncaniae (A2-165 or I-4574 strains) five days before infection. Supplementation of F. duncaniae was associated with less severe disease, a lower pulmonary viral load, and lower levels of lung inflammation. F. duncaniae supplementation impacted on gut dysbiosis induced by infection, as assessed by 16S rRNA sequencing. Interestingly, F. duncaniae administration was associated with a recovery in levels of SCFAs (including butyrate) in infected animals. The live form of F. duncaniae was more potent that the pasteurized form in improving influenza outcomes. Lastly, F. duncaniae partially protected against secondary (systemic) bacterial infection. We conclude that F. duncaniae might serve as a novel next generation probiotic against acute viral respiratory diseases.
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Affiliation(s)
- Loïc Chollet
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017 - CIIL – Centre d′Infection et d′Immunité de Lille, Lille, France
| | - Séverine Heumel
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017 - CIIL – Centre d′Infection et d′Immunité de Lille, Lille, France
| | - Lucie Deruyter
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017 - CIIL – Centre d′Infection et d′Immunité de Lille, Lille, France
| | | | - Lou Delval
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017 - CIIL – Centre d′Infection et d′Immunité de Lille, Lille, France
| | - Véronique Robert
- Unité Mixte de Recherche 1319 (UMR1319) Micalis, Université Paris-Saclay, Institut National de Recherche Pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), AgroParisTech, Jouy-en-Josas, France
| | - Marie-Hélène Gevaert
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Hospitalier Universitaire (CHU) Lille, Univ. Lille, Institut Pasteur de Lille, US 41-UAR 2014-PLBS, Lille, France
| | - Muriel Pichavant
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017 - CIIL – Centre d′Infection et d′Immunité de Lille, Lille, France
| | - Valentin Sencio
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017 - CIIL – Centre d′Infection et d′Immunité de Lille, Lille, France
| | - Cyril Robil
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017 - CIIL – Centre d′Infection et d′Immunité de Lille, Lille, France
| | - Isabelle Wolowczuk
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017 - CIIL – Centre d′Infection et d′Immunité de Lille, Lille, France
| | - Harry Sokol
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche Saint-Antoine, Centre de Recherche scientifique Saint-Antoine (CRSA), Assistance Public – Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, Gastroenterology Department, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM) Fédérations Hospitalo-Universitaires (FHU), Paris, France
| | - Sandrine Auger
- Unité Mixte de Recherche 1319 (UMR1319) Micalis, Université Paris-Saclay, Institut National de Recherche Pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), AgroParisTech, Jouy-en-Josas, France
| | | | - Philippe Langella
- Unité Mixte de Recherche 1319 (UMR1319) Micalis, Université Paris-Saclay, Institut National de Recherche Pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), AgroParisTech, Jouy-en-Josas, France
| | - Jean-Marc Chatel
- Unité Mixte de Recherche 1319 (UMR1319) Micalis, Université Paris-Saclay, Institut National de Recherche Pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), AgroParisTech, Jouy-en-Josas, France
| | - Corinne Grangette
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017 - CIIL – Centre d′Infection et d′Immunité de Lille, Lille, France
| | - François Trottein
- Univ. Lille, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Centre Hospitalier Universitaire (CHU) Lille, Institut Pasteur de Lille, U1019-Unité Mixte de Recherche (UMR) 9017 - CIIL – Centre d′Infection et d′Immunité de Lille, Lille, France
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3
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Gao Z, Zhang W, He L, Wang H, Li Y, Jiang X, D I S, Wang X, Zhang X, Han L, Liu Y, Gu C, Wu M, He X, Cheng L, Wang J, Tong X, Zhao L. Double-blinded, randomized clinical trial of Gegen Qinlian decoction pinpoints Faecalibacterium as key gut bacteria in alleviating hyperglycemia. Precis Clin Med 2024; 7:pbae003. [PMID: 38495337 PMCID: PMC10941319 DOI: 10.1093/pcmedi/pbae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
Background Accumulating evidence suggests that metabolic disorders, including type 2 diabetes mellitus (T2DM), can be treated with traditional Chinese medicine formulas, such as the Gegen Qinlian decoction (GQD). This study elucidates the mechanisms by which gut microbes mediate the anti-diabetic effects of GQD. Methods We conducted a double-blind randomized clinical trial involving 120 untreated participants with T2DM. During the 12-week intervention, anthropometric measurements and diabetic traits were recorded every 4 weeks. Fecal microbiota and serum metabolites were measured before and after the intervention using 16S rDNA sequencing, liquid chromatography-mass spectrometry, and Bio-Plex panels. Results Anti-diabetic effects were observed in the GQD group in the human trial. Specifically, glycated hemoglobin, fasting plasma glucose, and two-hour postprandial blood glucose levels were significantly lower in the GQD group than in the placebo group. Additionally, Faecalibacterium was significantly enriched in the GQD group, and the short-chain fatty acid levels were higher and the serum inflammation-associated marker levels were lower in the GQD group compared to the placebo group. Moreover, Faecalibacterium abundance negatively correlated with the levels of serum hemoglobin, fasting plasma glucose, and pro-inflammatory cytokines. Finally, the diabetes-alleviating effect of Faecalibacterium was confirmed by oral administration of Faecalibacterium prausnitzii (DSMZ 17677) in T2DM mouse model. Conclusions GQD improved type 2 diabetes primarily by modulating the abundance of Faecalibacterium in the gut microbiota, alleviating metabolic disorders and the inflammatory state. Trial registration Registry No. ChiCTR-IOR-15006626.
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Affiliation(s)
- Zezheng Gao
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
- Department of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Wenhui Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lisha He
- Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Han Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yufei Li
- Centre for Evidence-Based Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiaotian Jiang
- Department of Endocrinology, Affiliated Hospital of Changchun University of Chinese Medicine, Changchun 130000, China
| | - Sha D I
- Department of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Xinmiao Wang
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Xuan Zhang
- Biologicals Science and Technology Institute, Baotou Teacher's College, Baotou 014030, China
| | - Lin Han
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Yanwen Liu
- Department of Endocrinology, Zhengzhou T.C.M. Hospital, Zhengzhou 450007, China
| | - Chengjuan Gu
- Shenzhen Hospital, Guangzhou University of Chinese Medicine (Futian), Shenzhen 518000, China
| | - Mengyi Wu
- Department of Cardiology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510120, China
| | - Xinhui He
- Department of Cardiology, Yunnan Provincial Hospital of Traditional Chinese Medicine, Kunming 650000, China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolin Tong
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
| | - Linhua Zhao
- Institute of Metabolic Diseases, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China
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Ou Y, Belzer C, Smidt H, de Weerth C. Development of the gut microbiota in the first 14 years of life and its relations to internalizing and externalizing difficulties and social anxiety during puberty. Eur Child Adolesc Psychiatry 2024; 33:847-860. [PMID: 37071196 PMCID: PMC10894087 DOI: 10.1007/s00787-023-02205-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/03/2023] [Indexed: 04/19/2023]
Abstract
Relations between the gut microbiota and host mental health have been suggested by a growing number of case-control and cross-sectional studies, while supporting evidence is limited in large community samples followed during an extended period. Therefore, the current preregistered study ( https://osf.io/8ymav , September 7, 2022) described child gut microbiota development in the first 14 years of life and explored its relations to internalizing and externalizing difficulties and social anxiety in puberty, a period of high relevance for the development of mental health problems. Fecal microbiota composition was analysed by 16S ribosomal RNA gene amplicon sequencing in a total of 1003 samples from 193 children. Through a clustering method, four distinct microbial clusters were newly identified in puberty. Most children within three of these clusters remained in the same clusters from the age of 12 to 14 years, suggesting stability in microbial development and transition during this period. These three clusters were compositionally similar to enterotypes (i.e., a robust classification of the gut microbiota based on its composition across different populations) enriched in Bacteroides, Prevotella, and Ruminococcus, respectively. Two Prevotella 9-predominated clusters, including one reported by us earlier in middle childhood and the other one in puberty, were associated with more externalizing behavior at age 14. One Faecalibacterium-depleted pubertal cluster was related to more social anxiety at age 14. This finding was confirmed by a negative cross-sectional relation between Faecalibacterium and social anxiety in the 14-year-olds. The findings of this study continue to map gut microbiota development in a relatively large community sample followed from birth onwards, importantly extending our knowledge to puberty. Results indicate that Prevotella 9 and Faecalibacterium may be relevant microbial taxa in relation to externalizing behavior and social anxiety, respectively. These correlational findings need validations from other similar cohort studies, as well as well-designed mechanistic pre-clinical investigations before inferring cause and effect.
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Affiliation(s)
- Yangwenshan Ou
- Laboratory of Microbiology, Wageningen University and Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Center, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands.
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands
| | - Carolina de Weerth
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Medical Center, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands
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5
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Pepoyan E, Marotta F, Manvelyan A, Galstyan A, Stepanyan L, Grigoryan H, Grigoryan L, Mikayelyan M, Balayan M, Harutyunyan N, Mirzabekyan S, Tsaturyan V, Torok T, Pepoyan A. Placebo-resistant gut bacteria: Akkermansia muciniphila spp. and Familial Mediterranean fever disease. Front Cell Infect Microbiol 2024; 14:1336752. [PMID: 38465231 PMCID: PMC10920240 DOI: 10.3389/fcimb.2024.1336752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 12/19/2023] [Indexed: 03/12/2024] Open
Abstract
Introduction Despite numerous investigations into the impact of drugs/probiotics on the gut microbiota composition in Familial Mediterranean Fever (FMF) patients, the question as to whether there exists a significant bacterial diversity(ies) independent of the placebo effect that can be reliably considered in clinical and nutritional trials remains unresolved. Methods This study represents the in augural analysis of the placebo's influence on the gut microbiota of both healthy individuals and FMF afflicted men, utilizing previously collected data from PhyloChip™ DNA microarray experiments. A total of 15 healthy and 15 FMF male volunteers, aged 18 to 50, participated in this partially randomized placebo trial, which is accessible through the GEO Series accession number GSE111835. Results and Discussion Key findings from current investigations include i. the anticipated divergence in gut bacteria resistance to placebo between healthy and FMF individuals, ii. the minor impact of placebo on gut bacterial diversities in healthy individuals, with Enterobacteriaceae diversities identified as placebo-resistant among "healthy" gut bacteria, and iii. the comprehensive influence of placebo on all bacterial phyla in the gut microbiome of FMF patients, extending to nearly all bacterial genera, except for the resilience of gut Akkermansia muciniphila spp. to placebo in FMF patients. This study underscores the susceptibility of Faecalibacterium, Blautia, and Clostridium genera to placebo. Consequently, this investigation holds significance for the proper design of placebo-controlled trials and establishes a foundation for further exploration of the gut-brain axis. Furthermore, it contributes valuable insights to discussions regarding proposals for probiotic therapies, particularly focusing on Faecalibacterium spp., Blautia spp., and Clostridium spp.
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Affiliation(s)
- Elya Pepoyan
- Food Safety and Biotechnology Department, Scientific Research Institute of Food Science and Biotechnology, Armenian National Agrarian University, Yerevan, Armenia
- International Association for Human and Animals Health Improvement, Yerevan, Armenia
- Faculty of Military Medicine, Yerevan State Medical University, Yerevan, Armenia
| | | | - Anahit Manvelyan
- Food Safety and Biotechnology Department, Scientific Research Institute of Food Science and Biotechnology, Armenian National Agrarian University, Yerevan, Armenia
- International Association for Human and Animals Health Improvement, Yerevan, Armenia
| | - Artak Galstyan
- Faculty of Military Medicine, Yerevan State Medical University, Yerevan, Armenia
| | - Lena Stepanyan
- Food Safety and Biotechnology Department, Scientific Research Institute of Food Science and Biotechnology, Armenian National Agrarian University, Yerevan, Armenia
- International Association for Human and Animals Health Improvement, Yerevan, Armenia
| | - Hasmik Grigoryan
- Food Safety and Biotechnology Department, Scientific Research Institute of Food Science and Biotechnology, Armenian National Agrarian University, Yerevan, Armenia
- International Association for Human and Animals Health Improvement, Yerevan, Armenia
| | - Liana Grigoryan
- Food Safety and Biotechnology Department, Scientific Research Institute of Food Science and Biotechnology, Armenian National Agrarian University, Yerevan, Armenia
| | - Mikayel Mikayelyan
- Food Safety and Biotechnology Department, Scientific Research Institute of Food Science and Biotechnology, Armenian National Agrarian University, Yerevan, Armenia
- International Association for Human and Animals Health Improvement, Yerevan, Armenia
| | - Marine Balayan
- Food Safety and Biotechnology Department, Scientific Research Institute of Food Science and Biotechnology, Armenian National Agrarian University, Yerevan, Armenia
- International Association for Human and Animals Health Improvement, Yerevan, Armenia
| | - Natalya Harutyunyan
- Food Safety and Biotechnology Department, Scientific Research Institute of Food Science and Biotechnology, Armenian National Agrarian University, Yerevan, Armenia
- International Association for Human and Animals Health Improvement, Yerevan, Armenia
| | - Susanna Mirzabekyan
- Food Safety and Biotechnology Department, Scientific Research Institute of Food Science and Biotechnology, Armenian National Agrarian University, Yerevan, Armenia
- International Association for Human and Animals Health Improvement, Yerevan, Armenia
| | - Vardan Tsaturyan
- International Association for Human and Animals Health Improvement, Yerevan, Armenia
- Faculty of Military Medicine, Yerevan State Medical University, Yerevan, Armenia
| | - Tamas Torok
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Astghik Pepoyan
- Food Safety and Biotechnology Department, Scientific Research Institute of Food Science and Biotechnology, Armenian National Agrarian University, Yerevan, Armenia
- International Association for Human and Animals Health Improvement, Yerevan, Armenia
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Zhu La ALT, Li D, Cheng Z, Wen Q, Hu D, Jin X, Liu D, Feng Y, Guo Y, Cheng G, Hu Y. Enzymatically prepared neoagarooligosaccharides improve gut health and function through promoting the production of spermidine by Faecalibacterium in chickens. Sci Total Environ 2024; 912:169057. [PMID: 38056640 DOI: 10.1016/j.scitotenv.2023.169057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
Maintaining animal gut health through modulating the gut microbiota is a constant need when antibiotics are not used in animal feed during the food animal production process. Prebiotics is regarded as one of the most promising antibiotic alternatives for such purpose. As an attractive prebiotic, the role and mechanisms of neoagarooligosaccharides (NAOS) in promoting animal growth and gut health have not been elucidated. In this study, we first cloned and expressed marine bacterial β-agarase in yeast to optimize the NAOS preparation and then investigated the role and the underlying mechanisms of the prepared NAOS in improving chicken gut health and function. The marine bacterial β-agarase PDE13B was expressed in Pichia pastoris GS115 and generated even-numbered NAOS. Dietary the prepared NAOS promoted chicken growth and improved intestinal morphology, its barrier, and digestion capabilities, and absorption function. Metagenomic analysis indicated that NAOS modulated the chicken gut microbiota structure and function, and microbial interactions, and promoted the growth of spermidine-producing bacteria especially Faecalibacterium. Through integration of gut metagenome, gut content metabolome, and gut tissue transcriptome, we established connections among NAOS, gut microbes, spermidine, and chicken gut gene expression. The spermidine regulation of genes related to autophagy, immunity, and inflammation was further confirmed in chicken embryo intestinal epithelium cells. We also verified that NAOS can be utilized by Faecalibacterium prausnitzii to grow and produce spermidine in in vitro experiments. Collectively, we provide a systematic investigation of the role of NAOS in regulating gut health and demonstrate the microbial spermidine-mediated mechanism involved in prebiotic effects of NAOS, which lays foundation for future use of NAOS as a new antibiotic alternative in animal production.
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Affiliation(s)
- A La Teng Zhu La
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Depeng Li
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhiqian Cheng
- Huzhou Inspection & Quarantine Comprehensive Technology Center, Zhejiang 313000, China
| | - Qiu Wen
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Die Hu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaolu Jin
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Dan Liu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yuqing Feng
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gong Cheng
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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7
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Vestergaard MV, Allin KH, Eriksen C, Zakerska-Banaszak O, Arasaradnam RP, Alam MT, Kristiansen K, Brix S, Jess T. Gut microbiota signatures in inflammatory bowel disease. United European Gastroenterol J 2024; 12:22-33. [PMID: 38041519 PMCID: PMC10859715 DOI: 10.1002/ueg2.12485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/10/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of people worldwide with increasing incidence. OBJECTIVES Several studies have shown a link between gut microbiota composition and IBD, but results are often limited by small sample sizes. We aimed to re-analyze publicly available fecal microbiota data from IBD patients. METHODS We extracted original fecal 16S rRNA amplicon sequencing data from 45 cohorts of IBD patients and healthy individuals using the BioProject database at the National Center for Biotechnology Information. Unlike previous meta-analyses, we merged all study cohorts into a single dataset, including sex, age, geography, and disease information, based on which microbiota signatures were analyzed, while accounting for varying technical platforms. RESULTS Among 2518 individuals in the combined dataset, we discovered a hitherto unseen number of genera associated with IBD. A total of 77 genera associated with CD, of which 38 were novel associations, and a total of 64 genera associated with UC, of which 28 represented novel associations. Signatures were robust across different technical platforms and geographic locations. Reduced alpha diversity in IBD compared to healthy individuals, in CD compared to UC, and altered microbiota composition (beta diversity) in UC and especially in CD as compared to healthy individuals were found. CONCLUSIONS Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD. Identification of microbiota features robustly associated with CD and UC may pave the way for the identification of new treatment targets.
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Affiliation(s)
- Marie Vibeke Vestergaard
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Kristine H Allin
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
| | - Carsten Eriksen
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Ramesh P Arasaradnam
- Warwick Medical School & Cancer Research Centre, University of Leicester, Leicester, UK
| | - Mohammad T Alam
- Warwick Medical School & Cancer Research Centre, University of Leicester, Leicester, UK
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Karsten Kristiansen
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Brix
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
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8
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Fagundes RR, Bravo-Ruiseco G, Hu S, Kierans SJ, Weersma RK, Taylor CT, Dijkstra G, Harmsen HJM, Faber KN. Faecalibacterium prausnitzii promotes intestinal epithelial IL-18 production through activation of the HIF1α pathway. Front Microbiol 2023; 14:1298304. [PMID: 38163085 PMCID: PMC10755969 DOI: 10.3389/fmicb.2023.1298304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Intestinal epithelial cells produce interleukin-18 (IL-18), a key factor in promoting epithelial barrier integrity. Here, we analyzed the potential role of gut bacteria and the hypoxia-inducible factor 1α (HIF1α) pathway in regulating mucosal IL18 expression in inflammatory bowel disease (IBD). Methods Mucosal samples from patients with IBD (n = 760) were analyzed for bacterial composition, IL18 levels and HIF1α pathway activation. Wild-type Caco-2 and CRISPR/Cas9-engineered Caco-2-HIF1A-null cells were cocultured with Faecalibacterium prausnitzii in a "Human oxygen-Bacteria anaerobic" in vitro system and analyzed by RNA sequencing. Results Mucosal IL18 mRNA levels correlated positively with the abundance of mucosal-associated butyrate-producing bacteria, in particular F. prausnitzii, and with HIF1α pathway activation in patients with IBD. HIF1α-mediated expression of IL18, either by a pharmacological agonist (dimethyloxallyl glycine) or F. prausnitzii, was abrogated in Caco-2-HIF1A-null cells. Conclusion Butyrate-producing gut bacteria like F. prausnitzii regulate mucosal IL18 expression in a HIF1α-dependent manner that may aid in mucosal healing in IBD.
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Affiliation(s)
- Raphael R. Fagundes
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Gabriela Bravo-Ruiseco
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Sarah J. Kierans
- School of Medicine and Medical Science and the Conway Institute, University College Dublin, Dublin, Ireland
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Cormac T. Taylor
- School of Medicine and Medical Science and the Conway Institute, University College Dublin, Dublin, Ireland
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J. M. Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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9
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Abstract
Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human gut. Accumulating evidence suggests that dietary fiber plays a crucial role in host health, yet most studies have focused on how the dietary fiber affects health through gut Bacteroides. More recently, gut Firmicutes have been found to possess many genes responsible for fermenting dietary fiber, and could also interact with the intestinal mucosa and thereby contribute to homeostasis. Consequently, the relationship between dietary fiber and Firmicutes is of interest, as well as the role of Firmicutes in host health. In this review, we summarize the current knowledge regarding the molecular mechanism of dietary fiber degradation by gut Firmicutes and explain the communication pathway of the dietary fiber-Firmicutes-host axis, and the beneficial effects of dietary fiber-induced Firmicutes and their metabolites on health. A better understanding of the dialogue sustained by the dietary fiber-Firmicutes axis and the host could provide new insights into probiotic therapy and novel dietary interventions aimed at increasing the abundance of Firmicutes (such as Faecalibacterium, Lactobacillus, and Roseburia) to promote health.
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Affiliation(s)
- Yonggan Sun
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Shanshan Zhang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Qixing Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Huijun He
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Huizi Tan
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Fang Geng
- Key Laboratory of Coarse Cereal Processing (Ministry of Agriculture and Rural Affairs), School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Haihua Ji
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Jielun Hu
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Key laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
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10
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Ding XJ, Li HY, Wang H, Zhang XH, Song M, Jiang XH, Zhang X, Yue YX, Li XH. Altered gut microbiota and metabolites in untreated myasthenia gravis patients. Front Neurol 2023; 14:1248336. [PMID: 37789892 PMCID: PMC10542407 DOI: 10.3389/fneur.2023.1248336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/31/2023] [Indexed: 10/05/2023] Open
Abstract
Objective The homeostasis of the immune system is influenced by the gut microbiota. Previous studies have reported dysbiosis in the gut microbiota of myasthenia gravis (MG) patients. To investigate potential alterations in gut microbiota and metabolites in newly diagnosed and untreated MG patients, we conducted a case-control study. Methods Fecal samples were collected from 11 newly diagnosed and untreated MG patients as well as 11 age-and sex-matched healthy controls. These samples underwent analysis for gut microbiota using 16S ribosomal RNA (rRNA) gene sequencing, while fecal metabolome was analyzed using liquid chromatography-electrospray tandem mass spectrometry system (LC-ESI-MS/MS). Results The microbial community richness (observed species) and diversity (Shannon and Simpson indices) were significantly lower in the MG group compared to the control group. Microbiota composition analysis revealed significant differences between the MG and control groups at phylum, family, and genus levels. Linear discriminant analysis effect size (LEfSe) analysis showed a substantial decrease in abundance of the genus Faecalibacterium within the MG group. Fecal metabolome analysis identified three up-regulated metabolites involved in amino acid metabolism (taurine, creatinine, L-carnitine), one up-regulated metabolite involved in lipid metabolism (oleic acid), with correlation analysis indicating a positive association between Faecalibacterium abundance and creatinine levels. Conclusion Our findings suggest that dysbiosis already exists in newly diagnosed and untreated MG patients, implying that dysbiosis within the gut microbiota may be an initiating factor contributing to MG pathogenesis. Furthermore, F. prausnitzii may hold promise as a probiotic for treating MG.
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Affiliation(s)
- Xiao-Jun Ding
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Hong-Yan Li
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Huaiping Wang
- Department of Geriatric Medicine, Qingdao Fuwai Cardiovascular Hospital, Qingdao, China
| | - Xue-Hua Zhang
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Min Song
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xiao-Han Jiang
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xu Zhang
- Department of Clinical Psychology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yao-Xian Yue
- Department of Neurology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xiao-Hong Li
- Department of Neurology, Jinan Central Hospital, Shandong University, Jinan, China
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11
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Kubota S, Sugiura S, Takahashi M, Kadota Y, Takasato Y, Matsui T, Kitamura K, Tochio T, Ito K. Kestose Increases the Relative Abundance of Faecalibacterium spp. and Nominally Increases Cow Milk Tolerant Dose in Children with Cow's Milk Allergy - Preliminary Results. Pol J Microbiol 2023; 72:299-306. [PMID: 37725897 PMCID: PMC10508972 DOI: 10.33073/pjm-2023-030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/30/2023] [Indexed: 09/21/2023] Open
Abstract
A single-arm study was conducted with 10 children aged 2-12 years with severe cow's milk allergy (CMA) requiring complete allergen elimination. Subjects were administered kestose, a prebiotic, at 1 or 2 g/day for 12 weeks. Results of a subsequent oral food challenge (OFC) showed a statistically significant increase in the total dose of cow's milk ingestion (1.6 ml vs. 2.7 ml, p = 0.041). However, the overall evaluation of the OFC results, TS/Pro (total score of Anaphylaxis Scoring Aichi (ASCA)/cumulative dose of protein), showed no statistically significant improvement, although the values were nominally improved in seven out of 10 subjects. The 16S rDNA analysis of fecal samples collected from the subjects revealed a statistically significant increase in the proportion of Faecalibacterium spp. (3.8 % vs. 6.8%, p = 0.013), a type of intestinal bacterium that has been reported to be associated with food allergy. However, no statistically significant correlation was found between Faecalibacterium spp. abundance and the results of the OFC.
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Affiliation(s)
- Shohei Kubota
- Aichi Children's Health and Medical Center, Obu-shi, Japan
- Saiseikai Yokohamashi Tobu Hospital, Yokohama-shi, Japan
| | - Shiro Sugiura
- Aichi Children's Health and Medical Center, Obu-shi, Japan
| | | | | | | | - Teruaki Matsui
- Aichi Children's Health and Medical Center, Obu-shi, Japan
| | | | - Takumi Tochio
- B Food Science Co., Ltd., Chita-shi, Japan
- Fujita Health University, Toyoake-shi, Japan
| | - Komei Ito
- Aichi Children's Health and Medical Center, Obu-shi, Japan
- Nagoya University Graduate School of Medicine, Nagoya-shi, Japan
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12
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Raygoza Garay JA, Turpin W, Lee SH, Smith MI, Goethel A, Griffiths AM, Moayyedi P, Espin-Garcia O, Abreu M, Aumais GL, Bernstein CN, Biron IA, Cino M, Deslandres C, Dotan I, El-Matary W, Feagan B, Guttman DS, Huynh H, Dieleman LA, Hyams JS, Jacobson K, Mack D, Marshall JK, Otley A, Panaccione R, Ropeleski M, Silverberg MS, Steinhart AH, Turner D, Yerushalmi B, Paterson AD, Xu W, Croitoru K. Gut Microbiome Composition Is Associated With Future Onset of Crohn's Disease in Healthy First-Degree Relatives. Gastroenterology 2023; 165:670-681. [PMID: 37263307 DOI: 10.1053/j.gastro.2023.05.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND & AIMS The cause of Crohn's disease (CD) is unknown, but the current hypothesis is that microbial or environmental factors induce gut inflammation in genetically susceptible individuals, leading to chronic intestinal inflammation. Case-control studies of patients with CD have cataloged alterations in the gut microbiome composition; however, these studies fail to distinguish whether the altered gut microbiome composition is associated with initiation of CD or is the result of inflammation or drug treatment. METHODS In this prospective cohort study, 3483 healthy first-degree relatives (FDRs) of patients with CD were recruited to identify the gut microbiome composition that precedes the onset of CD and to what extent this composition predicts the risk of developing CD. We applied a machine learning approach to the analysis of the gut microbiome composition (based on 16S ribosomal RNA sequencing) to define a microbial signature that associates with future development of CD. The performance of the model was assessed in an independent validation cohort. RESULTS In the validation cohort, the microbiome risk score (MRS) model yielded a hazard ratio of 2.24 (95% confidence interval, 1.03-4.84; P = .04), using the median of the MRS from the discovery cohort as the threshold. The MRS demonstrated a temporal validity by capturing individuals that developed CD up to 5 years before disease onset (area under the curve > 0.65). The 5 most important taxa contributing to the MRS included Ruminococcus torques, Blautia, Colidextribacter, an uncultured genus-level group from Oscillospiraceae, and Roseburia. CONCLUSION This study is the first to demonstrate that gut microbiome composition is associated with future onset of CD and suggests that gut microbiome is a contributor in the pathogenesis of CD.
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Affiliation(s)
- Juan Antonio Raygoza Garay
- Division of Gastroenterology & Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Zane Cohen Center for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Williams Turpin
- Zane Cohen Center for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Sun-Ho Lee
- Division of Gastroenterology & Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Zane Cohen Center for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Michelle I Smith
- Zane Cohen Center for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ashleigh Goethel
- Zane Cohen Center for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anne M Griffiths
- Division of Gastroenterology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Paul Moayyedi
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Osvaldo Espin-Garcia
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada; Biostatistics Department, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Maria Abreu
- Division of Gastroenterology, Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida
| | - Guy L Aumais
- Hopital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | - Charles N Bernstein
- Inflammatory Bowel Disease Clinical and Research Center and Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Manitoba, Winnipeg, Canada
| | - Irit A Biron
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel
| | - Maria Cino
- Division of Gastroenterology & Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Colette Deslandres
- Department of Hepatology and Pediatric Nutrition, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Iris Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel
| | - Wael El-Matary
- Pediatric Gastroenterology, Max Rady College of Medicine, University of Manitoba, Manitoba, Winnipeg, Canada
| | - Brian Feagan
- Departments of Epidemiology and Biostatistics, University of Western Ontario, London, Ontario, Canada
| | - David S Guttman
- Center for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Hien Huynh
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Levinus A Dieleman
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, Connecticut
| | - Kevan Jacobson
- Research Institute, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - David Mack
- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, Ontario, Canada
| | - John K Marshall
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Anthony Otley
- Division of Gastroenterology, Izaak Walton Killam Hospital, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Remo Panaccione
- Inflammatory Bowel Disease Unit, University of Calgary, Calgary, Alberta, Canada
| | - Mark Ropeleski
- Gastrointestinal Diseases Research Unit, Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Mark S Silverberg
- Division of Gastroenterology & Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - A Hillary Steinhart
- Division of Gastroenterology & Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Dan Turner
- The Juliet Keidan Institute of Pediatric Gastroenterology and Nutrition, Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Baruch Yerushalmi
- Pediatric Gastroenterology Unit, Soroka University Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Andrew D Paterson
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada; Genetics and Genome Biology, The Hospital for Sick Children Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wei Xu
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada; Biostatistics Department, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.
| | - Kenneth Croitoru
- Division of Gastroenterology & Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Zane Cohen Center for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada.
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13
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Botin T, Ramirez-Chamorro L, Vidic J, Langella P, Martin-Verstraete I, Chatel JM, Auger S. The Tolerance of Gut Commensal Faecalibacterium to Oxidative Stress Is Strain Dependent and Relies on Detoxifying Enzymes. Appl Environ Microbiol 2023; 89:e0060623. [PMID: 37382539 PMCID: PMC10370306 DOI: 10.1128/aem.00606-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
Obligate anaerobic bacteria in genus Faecalibacterium are among the most dominant taxa in the colon of healthy individuals and contribute to intestinal homeostasis. A decline in the abundance of this genus is associated with the occurrence of various gastrointestinal disorders, including inflammatory bowel diseases. In the colon, these diseases are accompanied by an imbalance between the generation and elimination of reactive oxygen species (ROS), and oxidative stress is closely linked to disruptions in anaerobiosis. In this work, we explored the impact of oxidative stress on several strains of faecalibacteria. An in silico analysis of complete genomes of faecalibacteria revealed the presence of genes encoding O2- and/or ROS-detoxifying enzymes, including flavodiiron proteins, rubrerythrins, reverse rubrerythrins, superoxide reductases, and alkyl peroxidase. However, the presence and the number of these detoxification systems varied greatly among faecalibacteria. These results were confirmed by O2 stress survival tests, in which we found that strains differed widely in their sensitivity. We showed the protective role of cysteine, which limited the production of extracellular O2•- and improved the survival of Faecalibacterium longum L2-6 under high O2 tension. In the strain F. longum L2-6, we observed that the expression of genes encoding detoxifying enzymes was upregulated in the response to O2 or H2O2 stress but with different patterns of regulation. Based on these results, we propose a first model of the gene regulatory network involved in the response to oxidative stress in F. longum L2-6. IMPORTANCE Commensal bacteria in the genus Faecalibacterium have been proposed for use as next-generation probiotics, but efforts to cultivate and exploit the potential of these strains have been limited by their sensitivity to O2. More broadly, little is known about how commensal and health-associated bacterial species in the human microbiome respond to the oxidative stress that occurs as a result of inflammation in the colon. In this work, we provide insights regarding the genes that encode potential mechanisms of protection against O2 or ROS stress in faecalibacteria, which may facilitate future advances in work with these important bacteria.
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Affiliation(s)
- Tatiana Botin
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Luis Ramirez-Chamorro
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Jasmina Vidic
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Philippe Langella
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogénèse des Bactéries Anaérobies, Paris, France
- Institut Universitaire de France, Paris, France
| | - Jean-Marc Chatel
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Sandrine Auger
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
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14
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Sharma P, Singh S, Das K, Mahant S, Das R. Dysbiosis of gut microbiota due to diet, alcohol intake, body mass index, and gastrointestinal diseases in India. Appl Microbiol Biotechnol 2023; 107:2547-2560. [PMID: 36929191 DOI: 10.1007/s00253-023-12470-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/21/2023] [Accepted: 02/25/2023] [Indexed: 03/18/2023]
Abstract
The human gut is composed of diverse microflora which is influenced by dietary intake. Body mass index (BMI) and lifestyle patterns also play a vital role in human health to alter gut microbial composition. Our study aims to determine the impact of alcohol intake, BMI, and diet on gut microbiota and its relationship with gastrointestinal disorders. Thirty-nine gastric biopsies were taken from patients with various gastrointestinal (GI) diseases, and all the patient's lifestyle behavior were recorded in a written proforma. 16S rRNA metagenome analysis for V3-V4 regions was used to examine microbial compositions. The richness and diversity of gut microbiota were analyzed by PERMANOVA using the Bray-Curtis dissimilarity index and principal component analysis. The difference in relative abundance was calculated by ANOVA (p < 0.05). Alpha diversity indexes between vegetarians and non-vegetarians showed no significant difference based on BMI, alcohol status, and GI diseases. We found that in overweight vegetarian individuals Faecalibacterium and Rumicococcus might play a role in the control of Helicobacter pylori. Similarly, the increased abundance of Akkermansia muciniphila in non-vegetarian individuals with normal BMI might play a role to decrease the level of harmful bacteria like H. pylori, and Corynebacterium sp. Also, the relative abundance of Corynebacterium sp. among the vegetarians and Streptococcus sp. in the non-vegetarians was increased in alcoholics while H. pylori was increased in non-alcoholics irrespective of diet. There is an increased abundance of Faecalibacterium prausnitzii in vegetarians among all categories; however, we did not find any correlation between disease outcomes. Our study shows that alcohol intake and dietary habits have independent effects on gut microbial composition. The relative abundance of F. prausnitzii was high among vegetarians in all categories. KEY POINTS: • The presence of H. pylori is less among alcoholics. • Good bacteria help to maintain a normal body mass index. • Gut microbiota richness is high in vegetarians and diversity in non-vegetarians.
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Affiliation(s)
- Prateek Sharma
- Center for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, 201303, UP, India
| | - Sarika Singh
- Center for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, 201303, UP, India
| | - Kunal Das
- Department of Gastroenterology, Yashoda Super Specialty Hospital, Ghaziabad, UP, India.
| | - Shweta Mahant
- Center for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, 201303, UP, India
| | - Rajashree Das
- Center for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, 201303, UP, India.
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15
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Guo C, Che X, Briese T, Ranjan A, Allicock O, Yates RA, Cheng A, March D, Hornig M, Komaroff AL, Levine S, Bateman L, Vernon SD, Klimas NG, Montoya JG, Peterson DL, Lipkin WI, Williams BL. Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS. Cell Host Microbe 2023; 31:288-304.e8. [PMID: 36758522 PMCID: PMC10183837 DOI: 10.1016/j.chom.2023.01.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/10/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained debilitating fatigue, cognitive dysfunction, gastrointestinal disturbances, and orthostatic intolerance. Here, we report a multi-omic analysis of a geographically diverse cohort of 106 cases and 91 healthy controls that revealed differences in gut microbiome diversity, abundances, functional pathways, and interactions. Faecalibacterium prausnitzii and Eubacterium rectale, which are both recognized as abundant, health-promoting butyrate producers in the human gut, were reduced in ME/CFS. Functional metagenomics, qPCR, and metabolomics of fecal short-chain fatty acids confirmed a deficient microbial capacity for butyrate synthesis. Microbiome-based machine learning classifier models were robust to geographic variation and generalizable in a validation cohort. The abundance of Faecalibacterium prausnitzii was inversely associated with fatigue severity. These findings demonstrate the functional nature of gut dysbiosis and the underlying microbial network disturbance in ME/CFS, providing possible targets for disease classification and therapeutic trials.
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Affiliation(s)
- Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Amit Ranjan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Orchid Allicock
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Rachel A Yates
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Aaron Cheng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Dana March
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Mady Hornig
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Anthony L Komaroff
- Division of General Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Nancy G Klimas
- Institute for Neuro-Immune Medicine, College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314, USA; Miami VA Medical Center, Miami, FL 33125, USA
| | - Jose G Montoya
- Palo Alto Medical Foundation, Jack S. Remington Laboratory for Specialty Diagnostics of Toxoplasmosis, Palo Alto, CA 94301, USA
| | - Daniel L Peterson
- Sierra Internal Medicine at Incline Village, Incline Village, NV 89451, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Brent L Williams
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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16
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Gavin PG, Kim KW, Craig ME, Hill MM, Hamilton-Williams EE. Multi-omic interactions in the gut of children at the onset of islet autoimmunity. Microbiome 2022; 10:230. [PMID: 36527134 PMCID: PMC9756488 DOI: 10.1186/s40168-022-01425-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The gastrointestinal ecosystem is a highly complex environment with a profound influence on human health. Inflammation in the gut, linked to an altered gut microbiome, has been associated with the development of multiple human conditions including type 1 diabetes (T1D). Viruses infecting the gastrointestinal tract, especially enteroviruses, are also thought to play an important role in T1D pathogenesis possibly via overlapping mechanisms. However, it is not known whether the microbiome and virome act together or which risk factor may be of greater importance at the time when islet autoimmunity is initiated. RESULTS Here, we apply an integrative approach to combine comprehensive fecal virome, microbiome, and metaproteome data sampled before and at the onset of islet autoimmunity in 40 children at increased risk of T1D. We show strong age-related effects, with microbial and metaproteome diversity increasing with age while host antibody number and abundance declined with age. Mastadenovirus, which has been associated with a reduced risk of T1D, was associated with profound changes in the metaproteome indicating a functional shift in the microbiota. Multi-omic factor analysis modeling revealed a cluster of proteins associated with carbohydrate transport from the genus Faecalibacterium were associated with islet autoimmunity. CONCLUSIONS These findings demonstrate the interrelatedness of the gut microbiota, metaproteome and virome in young children. We show a functional remodeling of the gut microbiota accompanies both islet autoimmunity and viral infection with a switch in function in Faecalibacterium occurring at the onset of islet autoimmunity. Video Abstract.
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Affiliation(s)
- Patrick G Gavin
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, Australia
- Present Address: Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Present Address: Harvard Medical School, Boston, MA, USA
| | - Ki Wook Kim
- Virology Research Laboratory, Prince of Wales Hospital Randwick, Sydney, Australia
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Maria E Craig
- Virology Research Laboratory, Prince of Wales Hospital Randwick, Sydney, Australia
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
- Institute of Endocrinology and Diabetes, Children's Hospital at Westmead, Sydney, Australia
- Discipline of Child and Adolescent Health, University of Sydney, Sydney, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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17
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Li HB, Xu ML, Xu XD, Tang YY, Jiang HL, Li L, Xia WJ, Cui N, Bai J, Dai ZM, Han B, Li Y, Peng B, Dong YY, Aryal S, Manandhar I, Eladawi MA, Shukla R, Kang YM, Joe B, Yang T. Faecalibacterium prausnitzii Attenuates CKD via Butyrate-Renal GPR43 Axis. Circ Res 2022; 131:e120-e134. [PMID: 36164984 PMCID: PMC9588706 DOI: 10.1161/circresaha.122.320184] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/12/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND Despite available clinical management strategies, chronic kidney disease (CKD) is associated with severe morbidity and mortality worldwide, which beckons new solutions. Host-microbial interactions with a depletion of Faecalibacterium prausnitzii in CKD are reported. However, the mechanisms about if and how F prausnitzii can be used as a probiotic to treat CKD remains unknown. METHODS We evaluated the microbial compositions in 2 independent CKD populations for any potential probiotic. Next, we investigated if supplementation of such probiotic in a mouse CKD model can restore gut-renal homeostasis as monitored by its effects on suppression on renal inflammation, improvement in gut permeability and renal function. Last, we investigated the molecular mechanisms underlying the probiotic-induced beneficial outcomes. RESULTS We observed significant depletion of Faecalibacterium in the patients with CKD in both Western (n=283) and Eastern populations (n=75). Supplementation of F prausnitzii to CKD mice reduced renal dysfunction, renal inflammation, and lowered the serum levels of various uremic toxins. These are coupled with improved gut microbial ecology and intestinal integrity. Moreover, we demonstrated that the beneficial effects in kidney induced by F prausnitzii-derived butyrate were through the GPR (G protein-coupled receptor)-43. CONCLUSIONS Using a mouse CKD model, we uncovered a novel beneficial role of F prausnitzii in the restoration of renal function in CKD, which is, at least in part, attributed to the butyrate-mediated GPR-43 signaling in the kidney. Our study provides the necessary foundation to harness the therapeutic potential of F prausnitzii for ameliorating CKD.
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Affiliation(s)
- Hong-Bao Li
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Xi’an 710061, China
| | - Meng-Lu Xu
- Department of Nephrology, the First Affiliated Hospital of Xi’an Medical University, Xi’an 710077, China
| | - Xu-Dong Xu
- Department of Nephrology, Minhang Hospital, Fudan University, Shanghai 201199, China
| | - Yu-Yan Tang
- Department of Nephrology, Minhang Hospital, Fudan University, Shanghai 201199, China
| | - Hong-Li Jiang
- Department of Renal Dialysis, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, China
| | - Lu Li
- Department of Nephrology, the First Affiliated Hospital of Xi’an Medical University, Xi’an 710077, China
| | - Wen-Jie Xia
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Xi’an 710061, China
| | - Nan Cui
- Department of Reproductive Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, 710061 Xi’an, China
| | - Juan Bai
- Department of Anesthesiology, Center for Brain Science, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Zhi-Ming Dai
- Department of Anesthesiology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710004, China
| | - Bei Han
- School of Public Health, Health Science Center, Xi’an Jiaotong University, 710061 Xi’an, China
| | - Ying Li
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Xi’an 710061, China
| | - Bo Peng
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Xi’an 710061, China
| | - Yuan-Yuan Dong
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Xi’an 710061, China
| | - Sachin Aryal
- Department of Physiology and Pharmacology and Center for Hypertension and Precision Medicine, College of Medicine and Life Sciences, University of Toledo, OH 43614, USA
| | - Ishan Manandhar
- Department of Physiology and Pharmacology and Center for Hypertension and Precision Medicine, College of Medicine and Life Sciences, University of Toledo, OH 43614, USA
| | - Mahmoud Ali Eladawi
- Department of Neuroscience, College of Medicine and Life Sciences, University of Toledo, OH 43614, USA
| | - Rammohan Shukla
- Department of Neuroscience, College of Medicine and Life Sciences, University of Toledo, OH 43614, USA
| | - Yu-Ming Kang
- Department of Physiology and Pathophysiology, Xi’an Jiaotong University School of Basic Medical Sciences, Xi’an 710061, China
| | - Bina Joe
- Department of Physiology and Pharmacology and Center for Hypertension and Precision Medicine, College of Medicine and Life Sciences, University of Toledo, OH 43614, USA
| | - Tao Yang
- Department of Physiology and Pharmacology and Center for Hypertension and Precision Medicine, College of Medicine and Life Sciences, University of Toledo, OH 43614, USA
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18
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Lee SK, Jhun J, Lee SY, Choi S, Choi SS, Park MS, Lee SY, Cho KH, Lee AR, Ahn J, Choi HJ, You YK, Sung PS, Jang JW, Bae SH, Yoon SK, Cho ML, Choi JY. A decrease in functional microbiomes represented as Faecalibacterium affects immune homeostasis in long-term stable liver transplant patients. Gut Microbes 2022; 14:2102885. [PMID: 35951731 PMCID: PMC9377238 DOI: 10.1080/19490976.2022.2102885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
LT, liver transplantation; HCC, hepatocellular carcinoma; IS, immunosuppressants; DC, dendritic cells; Treg, regulatory T; Th17, T helper 17; AST, aspartate transaminase; ALT, alanine transaminase; OUT, operational taxonomic unit; LEfSe, linear discriminant analysis effect size; LDA, linear discriminant analysis; IL, interleukin; TGF, transforming growth factor; GM-CSF, granulocyte-macrophage colony-stimulating factor; IFN, interferon; TNF-α, tumor necrosis factor-α; MIP-1α, macrophage inflammatory protein-1α; IP-10, interferon γ-induced protein; MCP-1, monocyte chemoattractant protein-1; ACR, acute cellular rejection; NF-κB, nuclear factor κB; PT INR, prothrombin time; QC, quality check; PBMC, peripheral blood mononuclear cells; PBS, phosphate-buffered saline; ELISA, enzyme-linked immunosorbent assay.
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Affiliation(s)
- Soon Kyu Lee
- Division of gastroenterology and hepatology, Department of Internal Medicine, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - JooYeon Jhun
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Yoon Lee
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sukjung Choi
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, Korea
| | - Sun Shim Choi
- Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, Korea
| | | | - Seon-Young Lee
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Keun-Hyung Cho
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - A Ram Lee
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Joseph Ahn
- Department of Surgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ho Joong Choi
- Department of Surgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Young Kyoung You
- Department of Surgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Pil Soo Sung
- Division of gastroenterology and hepatology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong Won Jang
- Division of gastroenterology and hepatology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Si Hyun Bae
- Division of gastroenterology and hepatology, Department of Internal Medicine, Eunpyeong St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Kew Yoon
- Division of gastroenterology and hepatology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Mi-La Cho
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,Department of Medical Lifescience, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,CONTACT Mi-La Cho Rheumatism Research Center, Catholic Institutes of Medical Science, The Catholic University of Korea, 505 Banpo-dong, Seocho-gu, Seoul137-040, Korea
| | - Jong Young Choi
- Division of gastroenterology and hepatology, Department of Internal Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea,Jong Young Choi Division of Gastroenterology and Hepatology, Department of Internal Medicine, Seoul St. Mary’s Hospital, #222 Banpo-Daero, Seocho-gu, Seoul06591, Republic of Korea
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19
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Park J, Hosomi K, Kawashima H, Chen YA, Mohsen A, Ohno H, Konishi K, Tanisawa K, Kifushi M, Kogawa M, Takeyama H, Murakami H, Kubota T, Miyachi M, Kunisawa J, Mizuguchi K. Dietary Vitamin B1 Intake Influences Gut Microbial Community and the Consequent Production of Short-Chain Fatty Acids. Nutrients 2022; 14:nu14102078. [PMID: 35631219 PMCID: PMC9147846 DOI: 10.3390/nu14102078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota is closely related to good health; thus, there have been extensive efforts dedicated to improving health by controlling the gut microbial environment. Probiotics and prebiotics are being developed to support a healthier intestinal environment. However, much work remains to be performed to provide effective solutions to overcome individual differences in the gut microbial community. This study examined the importance of nutrients, other than dietary fiber, on the survival of gut bacteria in high-health-conscious populations. We found that vitamin B1, which is an essential nutrient for humans, had a significant effect on the survival and competition of bacteria in the symbiotic gut microbiota. In particular, sufficient dietary vitamin B1 intake affects the relative abundance of Ruminococcaceae, and these bacteria have proven to require dietary vitamin B1 because they lack the de novo vitamin B1 synthetic pathway. Moreover, we demonstrated that vitamin B1 is involved in the production of butyrate, along with the amount of acetate in the intestinal environment. We established the causality of possible associations and obtained mechanical insight, through in vivo murine experiments and in silico pathway analyses. These findings serve as a reference to support the development of methods to establish optimal intestinal environment conditions for healthy lifestyles.
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Affiliation(s)
- Jonguk Park
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Osaka 567-0085, Ibaraki, Japan; (H.K.); (Y.-A.C.); (A.M.)
- Correspondence: (J.P.); (J.K.); (K.M.)
| | - Koji Hosomi
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Osaka 567-0085, Ibaraki, Japan;
| | - Hitoshi Kawashima
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Osaka 567-0085, Ibaraki, Japan; (H.K.); (Y.-A.C.); (A.M.)
| | - Yi-An Chen
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Osaka 567-0085, Ibaraki, Japan; (H.K.); (Y.-A.C.); (A.M.)
| | - Attayeb Mohsen
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Osaka 567-0085, Ibaraki, Japan; (H.K.); (Y.-A.C.); (A.M.)
| | - Harumi Ohno
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 1-23-1 Toyama, Shinjuku 162-8636, Tokyo, Japan or (H.O.); (K.K.); (K.T.); (H.M.); (M.M.)
- Department of Nutrition, Kiryu University, 606-7 Azami, Kasakake-machi, Midori 379-2392, Gunma, Japan
| | - Kana Konishi
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 1-23-1 Toyama, Shinjuku 162-8636, Tokyo, Japan or (H.O.); (K.K.); (K.T.); (H.M.); (M.M.)
- Faculty of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura, Oura 374-0193, Gunma, Japan
| | - Kumpei Tanisawa
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 1-23-1 Toyama, Shinjuku 162-8636, Tokyo, Japan or (H.O.); (K.K.); (K.T.); (H.M.); (M.M.)
- School of Sport Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa 359-1192, Saitama, Japan
| | - Masako Kifushi
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku 162-8480, Tokyo, Japan; (M.K.); (H.T.)
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku 169-8555, Tokyo, Japan
| | - Masato Kogawa
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki, Shinjuku 162-0041, Tokyo, Japan;
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku 162-8480, Tokyo, Japan; (M.K.); (H.T.)
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku 169-8555, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki, Shinjuku 162-0041, Tokyo, Japan;
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku 169-8555, Tokyo, Japan
| | - Haruka Murakami
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 1-23-1 Toyama, Shinjuku 162-8636, Tokyo, Japan or (H.O.); (K.K.); (K.T.); (H.M.); (M.M.)
- Faculty of Sport and Health Science, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-0085, Shiga, Japan
| | - Tetsuya Kubota
- Department of Clinical Nutrition, National Institutes of Biomedical Innovation, Health and Nutrition, 1-23-1 Toyama, Shinjuku 162-8636, Tokyo, Japan;
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Kanagawa, Japan
- Division of Diabetes and Metabolism, The Institute for Medical Science, Asahi Life Foundation, 2-2-6 Nihonbashibakuro, Chuo 103-0002, Tokyo, Japan
| | - Motohiko Miyachi
- Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 1-23-1 Toyama, Shinjuku 162-8636, Tokyo, Japan or (H.O.); (K.K.); (K.T.); (H.M.); (M.M.)
- School of Sport Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa 359-1192, Saitama, Japan
| | - Jun Kunisawa
- Laboratory of Vaccine Materials, Center for Vaccine and Adjuvant Research and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Osaka 567-0085, Ibaraki, Japan;
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki, Shinjuku 162-0041, Tokyo, Japan;
- International Research and Development Center for Mucosal Vaccines, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato 108-8639, Tokyo, Japan
- Graduate School of Medicine, Graduate School of Pharmaceutical Sciences, Graduate School of Dentistry, Graduate School of Sciences, Osaka University, 1-1 Yamadaoka, Suita 565-0871, Osaka, Japan
- Department of Microbiology and Immunology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki, Chuo, Kobe 650-0017, Hyogo, Japan
- Correspondence: (J.P.); (J.K.); (K.M.)
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Osaka 567-0085, Ibaraki, Japan; (H.K.); (Y.-A.C.); (A.M.)
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Osaka, Japan
- Correspondence: (J.P.); (J.K.); (K.M.)
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20
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Vacca M, Raspini B, Calabrese FM, Porri D, De Giuseppe R, Chieppa M, Liso M, Cerbo RM, Civardi E, Garofoli F, Cena H, De Angelis M. The establishment of the gut microbiota in 1-year-aged infants: from birth to family food. Eur J Nutr 2022; 61:2517-2530. [PMID: 35211851 PMCID: PMC9279275 DOI: 10.1007/s00394-022-02822-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/25/2022] [Indexed: 12/14/2022]
Abstract
Purpose With the aim of characterizing the gastrointestinal (GI) microbiota and contextually determine how different prenatal, perinatal, and postnatal factors affected its composition in early childhood, infants were enrolled in a longitudinal-prospective study named “A.MA.MI.” (Alimentazione MAmma e bambino nei primi MIlle giorni; NCT04122612, October 2019). Methods Forty-five fecal samples were collected at 12 months of infants’ age, identified as the 3rd follow-up (T3). The evaluated variables were pre-gestational weight and weight gain during pregnancy, delivery mode, feeding, timing of weaning, and presence/absence of older siblings. Fecal alpha and beta-diversities were analyzed. Noteworthy, to determine the impact of the influencing factors, multivariate analyses were conducted. Results At T3, all prenatal and perinatal variables did not result to be significant whereas, among the postnatal variables, type of milk-feeding and weaning showed the greatest contribution in shaping the microbiota. Although aged 1 year, infants exclusively breastfed until 6 months were mainly colonized by Lactobacillaceae and Enterobacteriaceae. Differently, Bacteroidaceae characterized the microbiota of infants that were never breastfed in an exclusive way. Moreover, although an early introduction of solid foods determined higher values of Faith’s PD, high abundances of Ruminococcaceae and Faecalibacterium mainly associated with infants weaned after the 4th month of age. Conclusion The microbial colonization during the first year of life is likely affected by a simultaneous effect of multiple variables playing a significant role at different times. Therefore, these data contribute to add evidence concerning the complex multifactorial interaction between GI microbiota and various stimuli affecting infants during the early stages of life. Supplementary Information The online version contains supplementary material available at 10.1007/s00394-022-02822-1.
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Affiliation(s)
- Mirco Vacca
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Benedetta Raspini
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | | | - Debora Porri
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Rachele De Giuseppe
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Marcello Chieppa
- Institute of Research, National Institute of Gastroenterology "S. de Bellis", Castellana Grotte, Italy
| | - Marina Liso
- Institute of Research, National Institute of Gastroenterology "S. de Bellis", Castellana Grotte, Italy
| | - Rosa Maria Cerbo
- Neonatal Unit and Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elisa Civardi
- Neonatal Unit and Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Francesca Garofoli
- Neonatal Unit and Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Hellas Cena
- Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy. .,Unit of Internal Medicine and Endocrinology, Clinical Nutrition and Dietetics Service, ICS Maugeri IRCCS, Pavia, Italy.
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
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21
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Bellais S, Nehlich M, Ania M, Duquenoy A, Mazier W, van den Engh G, Baijer J, Treichel NS, Clavel T, Belotserkovsky I, Thomas V. Species-targeted sorting and cultivation of commensal bacteria from the gut microbiome using flow cytometry under anaerobic conditions. Microbiome 2022; 10:24. [PMID: 35115054 PMCID: PMC8812257 DOI: 10.1186/s40168-021-01206-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/04/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND There is a growing interest in using gut commensal bacteria as "next generation" probiotics. However, this approach is still hampered by the fact that there are few or no strains available for specific species that are difficult to cultivate. Our objective was to adapt flow cytometry and cell sorting to be able to detect, separate, isolate, and cultivate new strains of commensal species from fecal material. We focused on the extremely oxygen sensitive (EOS) species Faecalibacterium prausnitzii and the under-represented, health-associated keystone species Christensenella minuta as proof-of-concept. RESULTS A BD Influx® cell sorter was equipped with a glovebox that covered the sorting area. This box was flushed with nitrogen to deplete oxygen in the enclosure. Anaerobic conditions were maintained during the whole process, resulting in only minor viability loss during sorting and culture of unstained F. prausnitzii strains ATCC 27766, ATCC 27768, and DSM 17677. We then generated polyclonal antibodies against target species by immunizing rabbits with heat-inactivated bacteria. Two polyclonal antibodies were directed against F. prausnitzii type strains that belong to different phylogroups, whereas one was directed against C. minuta strain DSM 22607. The specificity of the antibodies was demonstrated by sorting and sequencing the stained bacterial fractions from fecal material. In addition, staining solutions including LIVE/DEAD™ BacLight™ Bacterial Viability staining and polyclonal antibodies did not severely impact bacterial viability while allowing discrimination between groups of strains. Finally, we combined these staining strategies as well as additional criteria based on bacterial shape for C. minuta and were able to detect, isolate, and cultivate new F. prausnitzii and C. minuta strains from healthy volunteer's fecal samples. CONCLUSIONS Targeted cell-sorting under anaerobic conditions is a promising tool for the study of fecal microbiota. It gives the opportunity to quickly analyze microbial populations, and can be used to sort EOS and/or under-represented strains of interest using specific antibodies, thus opening new avenues for culture experiments. Video abstract.
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Affiliation(s)
| | | | - Maryne Ania
- BIOASTER, 28 rue du Docteur Roux, 75015, Paris, France
| | | | | | | | - Jan Baijer
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Département de la Recherche Fondamentale, Institut de Biologie François Jacob, Institut de Radiobiologie Cellulaire et Moléculaire, Fontenay-aux-Roses, France
| | - Nicole Simone Treichel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
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22
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Abstract
Faecalibacterium and Roseburia are major producers of butyrate in the intestine. A reduced abundance of the organisms and a concurrent reduction in butyrate levels are associated with inflammatory bowel disease.
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Affiliation(s)
- Howard Faden
- Department of Pediatrics Division of Infectious Diseases, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, USA
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23
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Nolte Fong JV, Miketinas D, Moore LW, Nguyen DT, Graviss EA, Ajami N, Patterson MA. Precision Nutrition Model Predicts Glucose Control of Overweight Females Following the Consumption of Potatoes High in Resistant Starch. Nutrients 2022; 14:268. [PMID: 35057449 DOI: 10.3390/nu14020268] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 01/08/2023] Open
Abstract
Individual glycemic responses following dietary intake result from complex physiological processes, and can be influenced by physical properties of foods, such as increased resistant starch (RS) from starch retrogradation. Predictive equations are needed to provide personalized dietary recommendations to reduce chronic disease development. Therefore, a precision nutrition model predicting the postprandial glucose response (PPGR) in overweight women following the consumption of potatoes was formulated. Thirty overweight women participated in this randomized crossover trial. Participants consumed 250 g of hot (9.2 g RS) or cold (13.7 g RS) potatoes on two separate occasions. Baseline characteristics included demographics, 10-day dietary records, body composition, and the relative abundance (RA) and α-diversity of gut microbiota. Elastic net regression using 5-fold cross-validation predicted PPGR after potato intake. Most participants (70%) had a favorable PPGR to the cold potato. The model explained 32.2% of the variance in PPGR with the equation: 547.65 × (0 [if cold, high-RS potato], ×1, if hot, low-RS potato]) + (BMI [kg/m2] × 40.66)—(insoluble fiber [g] × 49.35) + (Bacteroides [RA] × 8.69)—(Faecalibacterium [RA] × 73.49)—(Parabacteroides [RA] × 42.08) + (α-diversity × 110.87) + 292.52. This model improves the understanding of baseline characteristics that explain interpersonal variation in PPGR following potato intake and offers a tool to optimize dietary recommendations for a commonly consumed food.
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24
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Li L, Chen L, Yang Y, Wang J, Guo L, An J, Ma X, Lu W, Xiao Y, Wang X, Dong Z. Characteristics of Gut Microbiome and Its Metabolites, Short-Chain Fatty Acids, in Children With Idiopathic Short Stature. Front Endocrinol (Lausanne) 2022; 13:890200. [PMID: 35757432 PMCID: PMC9226366 DOI: 10.3389/fendo.2022.890200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/12/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The gut microbiome is important for host nutrition and metabolism. Whether the gut microbiome under normal diet regulate human height remains to be addressed. Our study explored the possible relationship between gut microbiota, its metabolic products and the pathogenesis of idiopathic short stature disease (ISS) by comparing the gut microbiota between children with ISS and of normal height, and also the short-chain fatty acids (SCFAs) produced by the gut microbiota. METHODS The subjects of this study were 32 prepubescent children aged 4-8 years. The fecal microbial structure of the subjects was analyzed by 16S rRNA high-throughput sequencing technology. The concentrations of SCFAs in feces were determined by gas chromatography-mass spectrometry. RESULTS The richness of gut microbiota in ISS group was decreased, and the composition of gut microbiota was significantly different between ISS group and control group. The relative abundance of nine species including family Ruminococcaceae and genera Faecalibacterium and Eubacterium, in ISS group was significantly lower than that in control group (P<0.05). The relative abundance of 10 species, such as those belonging to genus Parabacteroides and genus Clostridium, in ISS group was significantly higher than that in control group (P<0.05). The concentration of total SCFAs and butyrate in ISS group was significantly lower than that in control group. The correlation analysis among different species, clinical indicators, and SCFAs showed that the relative abundance of family Ruminococcaceae and genera Faecalibacterium and Eubacterium was positively correlated with the standard deviation score of height. Furthermore, the concentrations of total SCFAs and butyrate were positively correlated with serum insulin-like growth factor 1 (IGF-1)-SDS. Disease prediction model constructed based on the bacteria who abundance differed between healthy children and ISS children exhibited high diagnostic value (AUC: 0.88). CONCLUSIONS The composition of gut microbiota and the change in its metabolite levels may be related to ISS pathogenesis. Strains with increased or decreased specificity could be used as biomarkers to diagnose ISS.
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Affiliation(s)
- Lin Li
- Department of Pediatrics, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lifen Chen
- Department of Pediatrics, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuanyan Yang
- Department of Pediatrics, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junqi Wang
- Department of Pediatrics, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li Guo
- Department of Molecular Medicine, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Jingjing An
- Department of Pediatrics, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyu Ma
- Department of Pediatrics, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenli Lu
- Department of Pediatrics, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan Xiao
- Department of Pediatrics, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xinqiong Wang
- Department of Pediatrics, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Zhiya Dong, ; Xinqiong Wang,
| | - Zhiya Dong
- Department of Pediatrics, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Zhiya Dong, ; Xinqiong Wang,
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25
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Di Pierro F. Gut Microbiota Parameters Potentially Useful in Clinical Perspective. Microorganisms 2021; 9:microorganisms9112402. [PMID: 34835527 PMCID: PMC8623243 DOI: 10.3390/microorganisms9112402] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
Interest in gut microbiota analyses is at an all-time high. Gut microbiota is thought to relate to an increasing range of diseases of interest to physicians and nutritionists. Overweight, obesity, response to diet, metabolic syndrome, low grade inflammation, diabetes and colon neoplasms could maybe be observed in microbiota if affordable markers were available. Possible biomarkers like the Firmicutes/Bacteroidetes ratio, the Gram-positive/Gram-negative ratio, the Prevotella/Bacteroides ratio, and the Fusobacterium nucleatum/Faecalibacterium prausnitzii ratio are here reviewed in a narrative way in the attempt to highlight their possible future role in routine practice and clinically relevant diagnostics.
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Affiliation(s)
- Francesco Di Pierro
- Digestive Endoscopy & Gastroenterology, Fondazione Poliambulanza, 25124 Brescia, Italy;
- UNICAM, Camerino University, 62032 Camerino, Italy
- Scientific Department, Velleja Research, 20124 Milan, Italy
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26
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Totzeck A, Ramakrishnan E, Schlag M, Stolte B, Kizina K, Bolz S, Thimm A, Stettner M, Marchesi JR, Buer J, Kleinschnitz C, Verhasselt HL, Hagenacker T. Gut bacterial microbiota in patients with myasthenia gravis: results from the MYBIOM study. Ther Adv Neurol Disord 2021; 14:17562864211035657. [PMID: 34394728 PMCID: PMC8361534 DOI: 10.1177/17562864211035657] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 07/08/2021] [Indexed: 11/23/2022] Open
Abstract
Background: Myasthenia gravis (MG) is an autoimmune neuromuscular disease, with gut microbiota considered to be a pathogenetic factor. Previous pilot studies have found differences in the gut microbiota of patients with MG and healthy individuals. To determine whether gut microbiota has a pathogenetic role in MG, we compared the gut microbiota of patients with MG with that of patients with non-inflammatory and inflammatory neurological disorders of the peripheral nervous system (primary endpoint) and healthy volunteers (secondary endpoint). Methods: Faecal samples were collected from patients with MG (n = 41), non-inflammatory neurological disorder (NIND, n = 18), chronic inflammatory demyelinating polyradiculoneuropathy (CIDP, n = 6) and healthy volunteers (n = 12). DNA was isolated from these samples, and the variable regions of the 16S rRNA gene were sequenced and statistically analysed. Results: No differences were found in alpha- and beta-diversity indices computed between the MG, NIND and CIDP groups, indicating an unaltered bacterial diversity and structure of the microbial community. However, the alpha-diversity indices, namely Shannon, Chao 1 and abundance-based coverage estimators, were significantly reduced between the MG group and healthy volunteers. Deltaproteobacteria and Faecalibacterium were abundant within the faecal microbiota of patients with MG compared with controls with non-inflammatory diseases. Conclusion: Although the overall diversity and structure of the gut microbiota did not differ between the MG, NIND and CIDP groups, the significant difference in the abundance of Deltaproteobacteria and Faecalibacterium supports the possible role of gut microbiota as a contributor to pathogenesis of MG. Further studies are needed to confirm these findings and to develop possible treatment strategies.
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Affiliation(s)
- Andreas Totzeck
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, Hufelandstr 55, Essen, 45147, Germany
| | - Elakiya Ramakrishnan
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Melina Schlag
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Benjamin Stolte
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kathrin Kizina
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Saskia Bolz
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Andreas Thimm
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Mark Stettner
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Julian R Marchesi
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christoph Kleinschnitz
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Hedda Luise Verhasselt
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Tim Hagenacker
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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27
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de Brito CBM, Menezes Souza CM, Bastos TS, Mesa D, Oliveira SG, Félix AP. Effect of dietary inclusion of dried apple pomace on faecal butyrate concentration and modulation of gut microbiota in dogs. Arch Anim Nutr 2021; 75:48-63. [PMID: 33475008 DOI: 10.1080/1745039x.2020.1867463] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
This research aimed to evaluate the apparent total tract digestibility (ATTD) of nutrients, metabolisable energy (ME) and palatability of the diet, as well as products of intestinal fermentation and faecal microbiota of dogs fed with dried apple. For this purpose, three experiments were performed. In Experiment I, digestibility and ME of four diets containing 0%, 3%, 6% and 9% dried apple were evaluated, in addition to the faecal characteristics of the dogs. The diets were offered to eight adult dogs, distributed in double Latin square (4 × 4), totalling eight repetitions per treatment. In Experiment II, products of intestinal fermentation and faecal microbiota from 16 adult dogs fed diets containing 0% and 9% dried apple for 30 d (n = 8) were evaluated. Finally, Experiment III compared the dietary preference of 0 vs. 9% dried apple using 15 adult dogs. The inclusion of dried apple in the diet (p < 0.05) showed a linear reduction in the ATTD of dry matter (DM), crude protein (CP), and acid hydrolysed ether extract (EEA), and a linear increase in the ATTD of total dietary fibre (TDF). Consumption of 9% of dried apple increased faecal butyrate and reduced propionate and ammonia (p < 0.05). With this diet, there was also an increase (p < 0.05) in the faecal concentration of Faecalibacterium, Erysipelatoclostridium, Blautia, and Bacteroides. No differences were found in the palatability of the diets. The inclusion of up to 9% of dried apple in the diet reduces the digestibility of nutrients and does not influence the dogs' food preference; however, it improves some indicators of dogs' intestinal functionality.
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Affiliation(s)
| | | | - Taís Silvino Bastos
- Department of Animal Sciences, Federal University of Paraná , Curitiba, Brazil
| | - Dany Mesa
- Department of Animal Sciences, Federal University of Paraná , Curitiba, Brazil
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28
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Ralli T, Neupane YR, Saifi Z, Kohli K. Gut microbiota as an emerging therapeutic avenue for the treatment of non-alcoholic fatty liver disease. Curr Pharm Des 2021; 27:4677-4685. [PMID: 34176456 DOI: 10.2174/1389201022666210625141526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/10/2021] [Indexed: 12/02/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is one of the leading causes of death related to liver diseases worldwide. Despite this, there is no specific treatment that is approved for the disease till now, which could be due to a poor understanding of the pathophysiology of this disease. In the past few decades, several scientists have speculated the root cause of NAFLD to be dysbalance in the gut microbiome resulting in a susceptibility totheinflammatory cascade in the liver. Herein, we hypothesize to fabricate a novel formulation containing prebiotic with probiotics, which, thereby would help in maintaining the gut homeostasis, and used for the treatment of NAFLD. The proposed novel formulation would contain a Bifidobacteriumsp. with Faecalibacteriumprausnitzii in the presence of a dietary fibre having hepatoprotective activity. These two strains of probiotics would help in increasing the concentration of butyrate in the gut, which in turn would inhibit intestinal inflammation and maintain gut integrity. The dietary fibre would serve a dual mechanism; firstly they would act as a prebiotic, which helps in the proliferation of administered probiotics and secondly, would protect the liver via own hepatoprotective action. This combinatorial approach would pave a new therapeutic avenue for the treatment of NAFLD.
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Affiliation(s)
- Tanya Ralli
- Department of Pharmaceutics, School of Pharmaceutical Education & Research, JamiaHamdard, New Delhi, India
| | - Yub Raj Neupane
- Department of Pharmacy, National University of Singapore, Singapore
| | - Zoya Saifi
- Department of Pharmaceutics, School of Pharmaceutical Education & Research, JamiaHamdard, New Delhi, India
| | - Kanchan Kohli
- Department of Pharmaceutics, School of Pharmaceutical Education & Research, JamiaHamdard, New Delhi, India
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29
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Yao Q, Tang M, Zeng L, Chu Z, Sheng H, Zhang Y, Zhou Y, Zhang H, Jiang H, Ye M. Potential of fecal microbiota for detection and postoperative surveillance of colorectal cancer. BMC Microbiol 2021; 21:156. [PMID: 34044781 PMCID: PMC8157663 DOI: 10.1186/s12866-021-02182-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/29/2021] [Indexed: 01/19/2023] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common cancers. In recent studies, the gut microbiota has been reported to be potentially involved in aggravating or favoring CRC development. However, little is known about the microbiota composition in CRC patients after treatment. In this study, we explored the fecal microbiota composition to obtain a periscopic view of gut microbial communities. We analyzed microbial 16S rRNA genes from 107 fecal samples of Chinese individuals from three groups, including 33 normal controls (NC), 38 CRC patients (Fa), and 36 CRC post-surgery patients (Fb). Results Species richness and diversity were decreased in the Fa and Fb groups compared with that of the NC group. Partial least squares discrimination analysis showed clustering of samples according to disease with an obvious separation between the Fa and NC, and Fb and NC groups, as well as a partial separation between the Fa and Fb groups. Based on linear discriminant analysis effect size analysis and a receiver operating characteristic model, Fusobacterium was suggested as a potential biomarker for CRC screening. Additionally, we found that surgery greatly reduced the bacterial diversity of microbiota in CRC patients. Some commensal beneficial bacteria of the intestinal canal, such as Faecalibacterium and Prevotella, were decreased, whereas the drug-resistant Enterococcus was visibly increased in CRC post-surgery group. Meanwhile, we observed a declining tendency of Fusobacterium in the majority of follow-up CRC patients who were still alive approximately 3 y after surgery. We also observed that beneficial bacteria dramatically decreased in CRC patients that recidivated or died after surgery. This revealed that important bacteria might be associated with prognosis. Conclusions The fecal bacterial diversity was diminished in CRC patients compared with that in NC. Enrichment and depletion of several bacterial strains associated with carcinomas and inflammation were detected in CRC samples. Fusobacterium might be a potential biomarker for early screening of CRC in Chinese or Asian populations. In summary, this study indicated that fecal microbiome-based approaches could be a feasible method for detecting CRC and monitoring prognosis post-surgery. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02182-6.
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Affiliation(s)
- Qiulin Yao
- Clinical laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China
| | - Meifang Tang
- Clinical laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
| | - Liuhong Zeng
- Clinical laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhonghua Chu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Gastrointestinal Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510060, China
| | - Hui Sheng
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Yuyu Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yuan Zhou
- Clinical laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongyun Zhang
- Clinical laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China
| | - Huayan Jiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Mingzhi Ye
- Clinical laboratory of BGI Health, BGI-Shenzhen, Shenzhen, 518083, China. .,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Zone B Room 401, Qinglan Street, Panyu District, Guangzhou, 510006, China.
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30
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Zhu L, Song Y, Liu H, Wu M, Gong H, Lan H, Zheng X. Gut microbiota regulation and anti-inflammatory effect of β-carotene in dextran sulfate sodium-stimulated ulcerative colitis in rats. J Food Sci 2021; 86:2118-2130. [PMID: 33884622 DOI: 10.1111/1750-3841.15684] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/14/2021] [Accepted: 02/17/2021] [Indexed: 12/21/2022]
Abstract
β-Carotene displays antioxidant and anti-inflammatory activities and prevents the development of cancer. Ulcerative colitis (UC) is a kind of inflammatory bowel disease that is accompanied by a certain risk of colon cancer. However, the role of β-carotene in the modulation of gut microbiota and UC improvement is unclear. In this research, the properties of β-carotene on anti-inflammatory and the composition of gut microbiota were evaluated in a rat model of UC induced by dextran sulfate sodium (DSS). The results revealed that β-carotene significantly (p < 0.05) decreased the severity of colitis in rats, as assessed using body weight (6.00 ± 1.73%), colon length (22.23 ± 0.53%), and disease activity index, and improved the structure of the colon damaged. Moreover, colonic levels of proinflammatory cytokines were significantly lower following β-carotene supplementation. β-Carotene intervention also lowered the expression levels of phosphorylated p65 (0.60 ± 0.02), p38 (0.57 ± 0.00), Erk (0.63 ± 0.04), and JNK (0.70 ± 0.00). The result of the relative abundance of gut microbiota showed that DSS administration significantly changed the microbial structure at the phylum and genus levels of rats. Furthermore, β-carotene treatment significantly increased the abundance of Faecalibacterium, the levels of which negatively correlated with the levels of inflammatory cytokines. Faecalibacterium may be a potential target in the alleviation of DSS-induced UC. β-Carotene can alleviate DSS-induced UC through the regulation of gut microbiota. This study provides a reference for the rational use of β-carotene in the treatment of UC. PRACTICAL APPLICATION: β-Carotene can relieve ulcerative colitis and regulate the gut microbiota; the nutritional intervention of β-carotene enhancing animal health.
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Affiliation(s)
- Lingyu Zhu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yang Song
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Huilin Liu
- School of Food Science and Technology, Dalian Polytechnic University, Liaoning, China
| | - Min Wu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Haizhou Gong
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Hainan Lan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xin Zheng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
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Climent E, Martinez-Blanch JF, Llobregat L, Ruzafa-Costas B, Carrión-Gutiérrez MÁ, Ramírez-Boscá A, Prieto-Merino D, Genovés S, Codoñer FM, Ramón D, Chenoll E, Navarro-López V. Changes in Gut Microbiota Correlates with Response to Treatment with Probiotics in Patients with Atopic Dermatitis. A Post Hoc Analysis of a Clinical Trial. Microorganisms 2021; 9:microorganisms9040854. [PMID: 33921166 PMCID: PMC8071520 DOI: 10.3390/microorganisms9040854] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022] Open
Abstract
Atopic dermatitis (AD) is a chronic recurrent inflammatory skin disease with a high impact on the comfort of those who are affected and long-term treated with corticosteroids with limited efficacy and a high prevalence of relapses. Because of the limited effectiveness of these treatments, new strategies for recovery from AD lesions are continually being explored. In this article, we describe the gut microbiome changes achieved in a recently published clinical trial with the probiotic formulation Bifidobacterium animalis subsp. lactis CECT 8145, Bifidobacterium longum CECT 7347, and Lacticaseibacillus casei CECT 9104 (formerly Lactobacillus casei CECT 9104), showing a significant improvement in SCORAD (scoring atopic dermatitis) index in children (4-17 years) with AD (Clinicaltrials.gov identifier: NCT02585986). The present gut microbiome post hoc study showed no significant changes in diversity (Shannon and Simpson indexes) after probiotic consumption. In the probiotic group, genera Bacteroides, Ruminococcus, and Bifidobacterium significantly increased their levels while Faecalibacterium decreased, compared to the placebo group. Faecalibacterium showed the highest presence and significant positive correlation with AD severity (SCORAD index), whereas Abyssivirga, Bifidobacterium, and Lactococcus were inversely correlated. The results suggest that the consumption of the probiotic formulation here assayed modulates the gut microbiome with significant changes in genera Bacteroides and Faecalibacterium. In turn, the improvement in SCORAD correlates with a decrease in Faecalibacterium and an increase in Bifidobacterium, among others.
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Affiliation(s)
- Eric Climent
- Biopolis S.L.-ADM, Catedrático Agustín Escardino Benlloch 9 Edif. 2, 46980 Paterna, Spain; (E.C.); (J.F.M.-B.); (L.L.); (S.G.); (F.M.C.); (D.R.)
| | - Juan Francisco Martinez-Blanch
- Biopolis S.L.-ADM, Catedrático Agustín Escardino Benlloch 9 Edif. 2, 46980 Paterna, Spain; (E.C.); (J.F.M.-B.); (L.L.); (S.G.); (F.M.C.); (D.R.)
| | - Laura Llobregat
- Biopolis S.L.-ADM, Catedrático Agustín Escardino Benlloch 9 Edif. 2, 46980 Paterna, Spain; (E.C.); (J.F.M.-B.); (L.L.); (S.G.); (F.M.C.); (D.R.)
| | - Beatriz Ruzafa-Costas
- Department of Clinical Medicine, Universidad Católica San Antonio de Murcia (UCAM), 30107 Murcia, Spain; (B.R.-C.); (A.R.-B.); (V.N.-L.)
| | | | - Ana Ramírez-Boscá
- Department of Clinical Medicine, Universidad Católica San Antonio de Murcia (UCAM), 30107 Murcia, Spain; (B.R.-C.); (A.R.-B.); (V.N.-L.)
- Department of Dermatology, Hospital Universitario Vinalopó, 03293 Elche, Spain
| | - David Prieto-Merino
- Applied Statistical Methods in Medical Research Group, Universidad Católica San Antonio de Murcia (UCAM), 30107 Murcia, Spain;
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London 400706, UK
| | - Salvador Genovés
- Biopolis S.L.-ADM, Catedrático Agustín Escardino Benlloch 9 Edif. 2, 46980 Paterna, Spain; (E.C.); (J.F.M.-B.); (L.L.); (S.G.); (F.M.C.); (D.R.)
| | - Francisco M. Codoñer
- Biopolis S.L.-ADM, Catedrático Agustín Escardino Benlloch 9 Edif. 2, 46980 Paterna, Spain; (E.C.); (J.F.M.-B.); (L.L.); (S.G.); (F.M.C.); (D.R.)
| | - Daniel Ramón
- Biopolis S.L.-ADM, Catedrático Agustín Escardino Benlloch 9 Edif. 2, 46980 Paterna, Spain; (E.C.); (J.F.M.-B.); (L.L.); (S.G.); (F.M.C.); (D.R.)
| | - Empar Chenoll
- Biopolis S.L.-ADM, Catedrático Agustín Escardino Benlloch 9 Edif. 2, 46980 Paterna, Spain; (E.C.); (J.F.M.-B.); (L.L.); (S.G.); (F.M.C.); (D.R.)
- Correspondence:
| | - Vicente Navarro-López
- Department of Clinical Medicine, Universidad Católica San Antonio de Murcia (UCAM), 30107 Murcia, Spain; (B.R.-C.); (A.R.-B.); (V.N.-L.)
- Clinical Microbiology and Infectious Disease Unit, Hospital Universitario Vinalopó, 03293 Elche, Spain
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32
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Wang X, Zhang D, Jiang H, Zhang S, Pang X, Gao S, Zhang H, Zhang S, Xiao Q, Chen L, Wang S, Qi D, Li Y. Gut Microbiota Variation With Short-Term Intake of Ginger Juice on Human Health. Front Microbiol 2021; 11:576061. [PMID: 33708178 PMCID: PMC7940200 DOI: 10.3389/fmicb.2020.576061] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/14/2020] [Indexed: 12/18/2022] Open
Abstract
Ginger, a widely used functional food and food additive, little is known about the effect of ginger juice, which is rich in many healthful agents, on healthy humans or on its relationship with gut microbiota composition variation. The aim of this study was to investigate the changes in the gut microbial communities that occur following the supplementation of fresh ginger-derived juice in healthy adults and its potential associations with function. A crossover intervention study in which 123 healthy subjects (63 men and 60 women) consumed fresh ginger juice from Zingiber officinale Rosc. or sterile 0.9% sodium chloride was conducted. 16S rRNA sequencing analyses were applied to characterize gut microbiota variation. We found that ginger juice intervention increased the species number of intestinal flora. A decreased relative abundance of the Prevotella-to-Bacteroides ratio and pro-inflammatory Ruminococcus_1 and Ruminococcus_2 while a tendency toward an increased Firmicutes-to-Bacteroidetes ratio, Proteobacteria and anti-inflammatory Faecalibacterium were found. When we did not consider gender, we found differences in bacterial diversity both in community evenness and in richness caused by ginger intervention. In fact, there were different changes in bacterial α-diversity induced by the ginger juice in men and women. We identified 19 bacterial genera with significant differences between the control group (women) and ginger group (women) and 15 significant differences between the control group (men) and ginger group (men) at the genus level. Our results showed that short-term intake of ginger juice had substantial effects on the composition and function of gut microbiota in healthy people. Moreover, our findings underscored the importance of analyzing both male and female individuals to investigate the effects of ginger on gut microbiota. Additional studies are necessary to confirm these findings.
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Affiliation(s)
- Xiaolong Wang
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China.,Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan, China.,Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Dan Zhang
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China.,Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan, China.,Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Haiqiang Jiang
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China.,Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan, China.,Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shuo Zhang
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaogang Pang
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China.,Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan, China.,Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shijie Gao
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China.,Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan, China.,Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Huimin Zhang
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shanyu Zhang
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Qiuyue Xiao
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Liyuan Chen
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shengqi Wang
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China.,Beijing Institute of Radiation Medicine, Beijing, China
| | - Dongmei Qi
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China.,Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan, China.,Shandong Provincial Key Laboratory of Traditional Chinese Medicine for Basic Research, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yunlun Li
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, China.,Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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33
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Ling Z, Zhu M, Yan X, Cheng Y, Shao L, Liu X, Jiang R, Wu S. Structural and Functional Dysbiosis of Fecal Microbiota in Chinese Patients With Alzheimer's Disease. Front Cell Dev Biol 2021; 8:634069. [PMID: 33614635 PMCID: PMC7889981 DOI: 10.3389/fcell.2020.634069] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Increasing evidence suggests that gut dysbiosis plays vital roles in a variety of gut–brain disorders, such as Alzheimer's disease (AD). However, alterations of the gut microbiota as well as their correlations with cognitive scores and host immunity have remained unclear in well-controlled trials on Chinese AD patients. In this study, samples from 100 AD patients, and 71 age- and gender-matched, cognitively normal controls were obtained to explore the structural and functional alterations of the fecal microbiota targeting the V3–V4 region of the 16S rRNA gene by MiSeq sequencing, and to analyze their associations with clinical characteristics. Our data demonstrated a remarkably reduction in the bacterial diversity and alterations in the taxonomic composition of the fecal microbiota of the AD patients. Interestingly, the abundant butyrate-producing genera such as Faecalibacterium decreased significantly, where this was positively correlated with such clinical indicators as the MMSE, WAIS, and Barthel scores in the AD patients. On the contrary, abundant lactate-producing genera, such as Bifidobacterium, increased prominently, and were inversely correlated with these indicators. This shift in the gut dysbiosis of the microbiota, from being butyrate producers to lactate producers, contributed to immune disturbances in the host that could be used as non-invasive biomarkers to distinguish the controls from the AD patients. Moreover, several predicted functional modules, including the biosynthesis and the metabolism of fatty acids, that were altered in the microbiota of the AD patients could be utilized by the bacteria to produce immunomodulatory metabolites. Our study established the structural and functional dysbiosis of fecal microbiota in AD patients, and the results suggest the potential for use of gut bacteria for the early, non-invasive diagnosis of AD, personalized treatment, and the development of tailor-made probiotics designed for Chinese AD patients.
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Affiliation(s)
- Zongxin Ling
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Manlian Zhu
- Department of Geriatrics, Lishui Second People's Hospital, Lishui, China
| | - Xiumei Yan
- Department of Geriatrics, Lishui Second People's Hospital, Lishui, China
| | - Yiwen Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Li Shao
- Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, Hangzhou, China.,Department of Liver Diseases, Institute of Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Xia Liu
- Department of Intensive Care Unit, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ruilai Jiang
- Department of Geriatrics, Lishui Second People's Hospital, Lishui, China
| | - Shaochang Wu
- Department of Geriatrics, Lishui Second People's Hospital, Lishui, China
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Fagundes RR, Bourgonje AR, Saeed A, Vich Vila A, Plomp N, Blokzijl T, Sadaghian Sadabad M, von Martels JZH, van Leeuwen SS, Weersma RK, Dijkstra G, Harmsen HJM, Faber KN. Inulin-grown Faecalibacterium prausnitzii cross-feeds fructose to the human intestinal epithelium. Gut Microbes 2021; 13:1993582. [PMID: 34793284 PMCID: PMC8604389 DOI: 10.1080/19490976.2021.1993582] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/08/2021] [Accepted: 10/06/2021] [Indexed: 02/04/2023] Open
Abstract
Many chronic diseases are associated with decreased abundance of the gut commensal Faecalibacterium prausnitzii. This strict anaerobe can grow on dietary fibers, e.g., prebiotics, and produce high levels of butyrate, often associated to epithelial metabolism and health. However, little is known about other F. prausnitzii metabolites that may affect the colonic epithelium. Here, we analyzed prebiotic cross-feeding between F. prausnitzii and intestinal epithelial (Caco-2) cells in a "Human-oxygen Bacteria-anaerobic" coculture system. Inulin-grown F. prausnitzii enhanced Caco-2 viability and suppressed inflammation- and oxidative stress-marker expression. Inulin-grown F. prausnitzii produced excess butyrate and fructose, but only fructose efficiently promoted Caco-2 growth. Finally, fecal microbial taxonomy analysis (16S sequencing) from healthy volunteers (n = 255) showed the strongest positive correlation for F. prausnitzii abundance and stool fructose levels. We show that fructose, produced and accumulated in a fiber-rich colonic environment, supports colonic epithelium growth, while butyrate does not.
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Affiliation(s)
- Raphael R. Fagundes
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arno R. Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ali Saeed
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Institute of Molecular Biology & Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Niels Plomp
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tjasso Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mehdi Sadaghian Sadabad
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Julius Z. H. von Martels
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sander S. van Leeuwen
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hermie J. M. Harmsen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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35
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Ling Z, Cheng Y, Yan X, Shao L, Liu X, Zhou D, Zhang L, Yu K, Zhao L. Alterations of the Fecal Microbiota in Chinese Patients With Multiple Sclerosis. Front Immunol 2020; 11:590783. [PMID: 33391265 PMCID: PMC7772405 DOI: 10.3389/fimmu.2020.590783] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
Mounting evidence indicates that alterations in the intestinal microbiota may be associated with neurological disorders such as multiple sclerosis (MS). MS is a putative autoimmune disease of the central nervous system. However, it has not been determined whether the intestinal microbiota and host immune status are altered in Chinese patients with stable MS. In our study, 22 Chinese patients with stable MS and 33 healthy controls were enrolled for fecal microbiota analysis and host immunity evaluation. The microbial diversity and composition, bacterial co-occurrence correlations, predictive functional profiles, and microbiota-cytokine correlations between the two groups were compared. We observed that while the overall structure of the fecal microbiota did not change significantly, the abundances of several key functional bacteria, primarily Faecalibacterium, decreased remarkably. Faecalibacterium and Granulicatella could be used to distinguish between patients with MS and healthy controls with an area under the curve of 0.832. PiCRUSt analysis revealed that genes associated with fructose, mannose, and fatty acid metabolism were significantly enriched in the MS microbiota. In addition, we also observed that the levels of several pro- and anti-inflammatory cytokines and chemokines, such as IL-1ra, IL-8, IL-17, and TNF-α changed observably, and the abundances of key functional bacteria like butyrate producers correlated with the changes in the cytokine levels. Our present study indicated that altered composition of the fecal microbiota might play vital roles in the etiopathogenesis of MS by regulating host immunity, which suggests that microbiota-targeting patient-tailored early intervention techniques might serve as novel therapeutic approaches for MS.
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Affiliation(s)
- Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiumei Yan
- Department of Laboratory Medicine, Lishui Second People's Hospital, Lishui, China
| | - Li Shao
- Hangzhou Normal University, Hangzhou, China.,Institute of Translational Medicine, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Xia Liu
- Department of Intensive Care Unit, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Dajin Zhou
- Department of Laboratory Medicine, Lishui Second People's Hospital, Lishui, China
| | - Lijuan Zhang
- Department of Laboratory Medicine, Lishui Second People's Hospital, Lishui, China
| | - Kunqiang Yu
- Department of Laboratory Medicine, Lishui Second People's Hospital, Lishui, China
| | - Longyou Zhao
- Department of Laboratory Medicine, Lishui Second People's Hospital, Lishui, China
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36
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Jin Y, Geng R, Liu Y, Liu L, Jin X, Zhao F, Feng J, Wei Y. Prediction of Postoperative Ileus in Patients With Colorectal Cancer by Preoperative Gut Microbiota. Front Oncol 2020; 10:526009. [PMID: 33324541 PMCID: PMC7724052 DOI: 10.3389/fonc.2020.526009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 09/21/2020] [Indexed: 12/16/2022] Open
Abstract
Background Ileus and postoperative ileus (POI) are common complications of colorectal cancer (CRC). However, little is known about the gut microbiota associated with ileus. Method Differences in gut microbiota were evaluated by 16S rRNA gene sequencing. We characterized the gut microbiota in 85 CRC patients (cohort 1) and detected differences, and an independent cohort composed of 38 CRC patients (cohort 2) was used to evaluate the results. Results The gut microbiota of CRC patients with and without ileus exhibited large differences in alpha- and beta-diversities and bacterial taxa. The Firmicutes-to-Bacteroidetes ratio and microbial dysbiosis index (MDI) showed greater dysbiosis among ileus patients than among those without ileus. According to the location of CRC, the difference in gut microbiota between patients with and without ileus was more obvious in those with distal CRC than in those with proximal CRC. Finally, Faecalibacterium was significantly reduced in the postoperative perioperative period in patients with ileus. Thus, we used Faecalibacterium as a biomarker for predicting perioperative or POI: the AUC value was 0.74 for perioperative ileus and 0.67 for POI that appeared at 6 months after hospital discharge. The predictive power was evaluated in Cohort 2, with an AUC value of 0.79. Conclusion These findings regarding difference of gut microbiota in postoperative CRC patients may provide a theoretical basis for the use of microbiota as biomarkers for the prediction of POI.
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Affiliation(s)
- Ye Jin
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Rui Geng
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Thyroid and Breast Surgery, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Yang Liu
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lujia Liu
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiangren Jin
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fuya Zhao
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jing Feng
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunwei Wei
- Department of Oncological and Laparoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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Ponziani FR, Scaldaferri F, De Siena M, Mangiola F, Matteo MV, Pecere S, Petito V, Sterbini FP, Lopetuso LR, Masucci L, Cammarota G, Sanguinetti M, Gasbarrini A. Increased Faecalibacterium abundance is associated with clinical improvement in patients receiving rifaximin treatment. Benef Microbes 2020; 11:519-525. [PMID: 32885687 DOI: 10.3920/bm2019.0171] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Compositional and functional alterations of the gut microbiota are involved in the pathogenesis of several gastrointestinal diseases. Rifaximin is often used to induce disease remission due to its eubiotic effects on the gut microbiota. To investigate the correlation between changes in the gut microbiota composition and symptoms improvement in patients who present a clinical response to rifaximin treatment. Patients with ulcerative colitis (UC), Crohn's disease (CD), irritable bowel syndrome (IBS) and diverticular disease (DD) undergoing rifaximin treatment for clinical indication were enrolled in the study. Rifaximin was administered at the dose of 1,200 mg/day for 10 days. Faecal samples were collected at baseline and at the end of treatment; clinical improvement was assessed by Mayo score for UC, CD Activity Index (CDAI) for CD, IBS severity scoring system (IBS-SSS) for IBS and global symptomatic score (GSS) for DD. Twenty-five patients were included in the analysis and a clinical improvement was recorded for 10/25 (40%) of them. Microbial alpha diversity showed a slight increase in clinical responders (P=0.271), while it decreased in patients who did not improved (P=0.05). A significant post-treatment increase in Faecalibacterium abundance was observed in patients with a positive response (log2FC 1.959, P=0.042). Roseburia abundance decreased in both groups, whereas Ruminococcus decreased only in patients who clinically improved. Clinical improvement consequent to rifaximin treatment is associated with an increase in Faecalibacterium abundance. Achieving a positive shift in the gut microbiota composition seems a key event to obtain a clinical benefit from treatment.
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Affiliation(s)
- F R Ponziani
- Internal Medicine, Gastroenterology and Hepatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy.,Institute of Special Medical Pathology and Medical Semeiotics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - F Scaldaferri
- Internal Medicine, Gastroenterology and Hepatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy.,Institute of Special Medical Pathology and Medical Semeiotics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - M De Siena
- Internal Medicine, Gastroenterology and Hepatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - F Mangiola
- Internal Medicine, Gastroenterology and Hepatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - M V Matteo
- Internal Medicine, Gastroenterology and Hepatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - S Pecere
- Internal Medicine, Gastroenterology and Hepatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - V Petito
- Internal Medicine, Gastroenterology and Hepatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - F Paroni Sterbini
- Microbiology Unit, Fondazione Policlinico A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy
| | - L R Lopetuso
- Internal Medicine, Gastroenterology and Hepatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - L Masucci
- Microbiology Unit, Fondazione Policlinico A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy.,Institute of Microbiology, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - G Cammarota
- Internal Medicine, Gastroenterology and Hepatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy.,Institute of Special Medical Pathology and Medical Semeiotics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - M Sanguinetti
- Microbiology Unit, Fondazione Policlinico A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy.,Institute of Microbiology, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - A Gasbarrini
- Internal Medicine, Gastroenterology and Hepatology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy.,Institute of Special Medical Pathology and Medical Semeiotics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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Thomas R, Wong WSW, Saadon R, Vilboux T, Deeken J, Niederhuber J, Hourigan SK, Yang E. Gut microbial composition difference between pediatric ALL survivors and siblings. Pediatr Hematol Oncol 2020; 37:475-488. [PMID: 32427521 PMCID: PMC7701956 DOI: 10.1080/08880018.2020.1759740] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer with high cure rates leading to rising numbers of long-term survivors. Adult survivors of childhood ALL are at increased risk of obesity, cardiovascular disease, and other chronic illnesses. We hypothesize that ALL therapy is associated with long-term gut microbiome alterations that contribute to predisposition to chronic medical conditions. We conducted a pilot study to test whether differences can be detected between stool microbiota of pediatric ALL survivors and their siblings. Stool samples were collected from 38 individuals under age 19 who were at least 1 year after completion of therapy for ALL. Stool samples collected from 16 healthy siblings served as controls. 16S ribosomal RNA gene sequencing was performed on the stool samples. Comparing microbiota of survivors to sibling controls, no statistically significant differences were found in alpha or beta diversity. However, among the top 10 operational taxonomic units (OTUs) from component 1 in sparse partial least squares discriminant analysis (sPLS-DA) with different relative abundance in survivors versus siblings, OTUs mapping to the genus Faecalibacterium were depleted in survivors. Differences in gut microbial composition were found between pediatric survivors of childhood ALL and their siblings. Specifically, the protective Faecalibacterium is depleted in survivors, which is reminiscent of gut microbiota alteration found in adult survivors of childhood ALL and reported in obesity, suggesting that microbiota alterations in pediatric ALL survivors start in childhood and may play a role in predisposition to chronic illness in later years of survivorship.
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Affiliation(s)
- Ronay Thomas
- Pediatric Hematology-Oncology, Pediatric Specialists of Virginia, Falls Church, Virginia, USA
| | - Wendy S. W. Wong
- Inova Translational Medicine Institute, Inova Health Systems, Falls Church, Virginia, USA
| | - Reem Saadon
- Pediatric Hematology-Oncology, Pediatric Specialists of Virginia, Falls Church, Virginia, USA
| | - Thierry Vilboux
- Inova Translational Medicine Institute, Inova Health Systems, Falls Church, Virginia, USA
| | - John Deeken
- Inova Schar Cancer Institute, Falls Church, Virginia, USA
| | - John Niederhuber
- Inova Translational Medicine Institute, Inova Health Systems, Falls Church, Virginia, USA;,Surgery and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Suchitra K. Hourigan
- Inova Translational Medicine Institute, Inova Health Systems, Falls Church, Virginia, USA;,Pediatric Gastroenterology, Pediatric Specialists of Virginia, Falls Church, Virginia, USA;,Pediatrics, Inova Children’s Hospital, Falls Church, Virginia, USA
| | - Elizabeth Yang
- Pediatric Hematology-Oncology, Pediatric Specialists of Virginia, Falls Church, Virginia, USA;,Pediatrics, George Washington University School of Medicine, Washington, DC, USA;,Pediatrics, Virginia Commonwealth University School of Medicine Inova Campus, Falls Church, Virginia, USA
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39
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Mesa D, Beirão BCB, Balsanelli E, Sesti L, Caron LF, Cruz LM, Souza EM. Cyclophosphamide Increases Lactobacillus in the Intestinal Microbiota in Chickens. mSystems 2020; 5:e00080-20. [PMID: 32817382 DOI: 10.1128/mSystems.00080-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Poultry production is a very intensive industry. Due to the substantial number of animals being raised by any one producer, even small variations in productivity lead to important economical outcomes. The intestinal microbiota of birds is under intense scrutiny by the immune system. Therefore, it is a factor that can influence the states of health and disease of the host. The body of knowledge on the interactions between these systems is gradually bringing practical guidance for poultry production. Recent data in humans indicate that immunosuppression is correlated with shifts in the intestinal microbiota. However, the relationship between immunosuppression and intestinal microbiota has not been studied in chickens. Thus, we investigated the correlations between immune cells and intestinal microbiota by massive parallel sequencing of the 16S rRNA bacterial gene in chickens immunosuppressed with cyclophosphamide. The results showed correlations between peripheral immune cells and intestinal microbiota. Surprisingly, an increase in the abundance of intestinal Lactobacillus in the immunosuppressed chickens was observed. These birds also had low intestinal IgA antibody levels among other alterations in the microbiota. These shifts indicate a role of the immunity system in controlling the microbiota of birds. IMPORTANCE Poultry production is a very intensive industry. Due to the substantial number of animals being raised by any one producer, even small variations in productivity lead to important economical outcomes. The intestinal microbiota of birds is under intense scrutiny by the immune system. Therefore, it is a factor that can influence the states of health and disease of the host. The body of knowledge on the interactions between these systems is gradually bringing practical guidance for poultry production.
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Zhang K, Sun D, Duan C, Chen H, Din AU, Kong X, Qin X, Zhang B. Application of a Faecalibacterium 16S rDNA genetic marker for species identification of dog fecal waste. Environ Sci Pollut Res Int 2020; 27:30615-30624. [PMID: 32472511 DOI: 10.1007/s11356-020-09369-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
A dog-associated 16S rDNA genetic marker (ED-1) was designed to detect dog fecal contamination in water through a comparative bioinformatics analysis of Faecalibacterium sequences. For the dog fecal samples, ED-1 had 100% specificity, a high positive rate (89% in dog feces and 92.3% in dog fecal-contaminated water samples), and a low detection limit (107 copies/100 mL) in dog-contaminated water samples. Detection of water samples from seven provinces or cities of China showed that ED-1 was stable enough to be applied in practice. Furthermore, the abundance and diversity of dog gut microbiota from two private house pets (PHP) and Third Military Medical University (TMMU) dogs were estimated by using operational taxonomic units, and the significant differences of dog feces were found, as the PHP dogs have a more diverse diet and closer contact with human than dogs in TMMU. However, ED-1 could detect the feces from the two regions, indicating that ED-1 has good reliability.
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Affiliation(s)
- Kun Zhang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400030, China
| | - Da Sun
- Institute of Life Sciences, Wenzhou University, Wenzhou, 325000, China.
| | - Chuanren Duan
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400030, China.
| | - Hang Chen
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400030, China
| | - Ahmad Ud Din
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400030, China
| | - Xiangjun Kong
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macau, 999078, China
| | - Xian Qin
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400030, China
| | - Baoyun Zhang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510000, China
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Furukawa M, Moriya K, Nakayama J, Inoue T, Momoda R, Kawaratani H, Namisaki T, Sato S, Douhara A, Kaji K, Kitade M, Shimozato N, Sawada Y, Saikawa S, Takaya H, Kitagawa K, Akahane T, Mitoro A, Yamao J, Tanaka Y, Yoshiji H. Gut dysbiosis associated with clinical prognosis of patients with primary biliary cholangitis. Hepatol Res 2020; 50:840-852. [PMID: 32346970 DOI: 10.1111/hepr.13509] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 03/26/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023]
Abstract
AIM Although some relationships between gut microbiota and liver diseases have been reported, it remains uncertain whether changes in gut microbiota owing to differences in race, food and living environment have similar effects. Response to ursodeoxycholic acid (UDCA) may predict the long-term prognosis of patients with primary biliary cholangitis (PBC); however, little is known about the significance of the gut microbiome in patients with PBC. We elucidated the relationships among clinical profiles, biochemical response to UDCA and gut microbiome composition in patients with PBC. METHODS Fecal samples from 76 patients with PBC treated at our hospital were collected; patients whose UDCA intake period was <1 year were excluded. The microbiome structures of patients were determined using 16S ribosomal RNA gene sequencing and were statistically compared with those of healthy subjects. The structures of patients in the UDCA responder (n = 43) and non-responder (n = 30) groups were compared according to the Nara criteria (reduction rate of gamma-glutamyl transpeptidase, ≥69%, after 1 year). RESULTS Compared with healthy subjects, bacterial diversity was lower in patients with PBC, with a decreased abundance of the order Clostridiales and increased abundance of Lactobacillales. The UDCA non-responder group had a significantly lower population of the genus Faecalibacterium, known as butyrate-producing beneficial bacteria (P < 0.05), although no significant differences in gender, body mass index, medicated drugs or other serological data were indicated between these two groups. CONCLUSIONS Gut dysbiosis with loss of beneficial Clostridiales commensals was observed in patients with PBC. Decrease in Faecalibacterium abundance might predict the long-term prognosis of patients with PBC.
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Affiliation(s)
| | - Kei Moriya
- Department of Gastroenterology, Nara Medical University
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University
| | - Takako Inoue
- Department of Clinical Laboratory Medicine, Nagoya City University Hospital
| | - Rie Momoda
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University
| | | | | | - Shinya Sato
- Department of Gastroenterology, Nara Medical University
| | | | - Kosuke Kaji
- Department of Gastroenterology, Nara Medical University
| | | | | | | | | | | | - Koh Kitagawa
- Department of Gastroenterology, Nara Medical University
| | | | - Akira Mitoro
- Department of Gastroenterology, Nara Medical University
| | - Junichi Yamao
- Department of Gastroenterology, Nara Medical University
| | - Yasuhito Tanaka
- Department of Clinical Laboratory Medicine, Nagoya City University Hospital.,Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Japan
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Okamoto T, Hatakeyama S, Imai A, Yamamoto H, Yoneyama T, Mori K, Yoneyama T, Hashimoto Y, Nakaji S, Ohyama C. Altered gut microbiome associated with overactive bladder and daily urinary urgency. World J Urol 2020; 39:847-853. [PMID: 32419054 DOI: 10.1007/s00345-020-03243-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/05/2020] [Indexed: 01/09/2023] Open
Abstract
PURPOSE To explore associations between the gut microbiome and overactive bladder (OAB) with daily urinary urgency among individuals reporting this diagnosis within a single community. METHODS This cross-sectional study surveyed 1113 individuals who participated in the Iwaki Health Promotion Project in Japan. OAB was defined as urinary urgency at least once per week and an Overactive Bladder Symptom Score (OABSS) of ≥ 3. OAB with urinary urgency at least once a day was defined as daily urgency. The gut microbiomes were assessed by next-generation sequencing of 16S rRNA genes extracted from fecal samples. The participants were divided into two groups: OAB-daily urgency and non-OAB. Cases were selected for inclusion on the basis of 1:1 propensity score matching; we assigned 58 individuals to each group (23 men and 35 women) for our analysis. RESULTS Individuals reporting OAB with daily urinary urgency demonstrated a lower bacterial diversity between individuals (Bray-Curtis distance 0.48 vs. 0.53, P < 0.001); the results cluster differently in the non-OAB groups. The relative abundance of genus Bifidobacterium was significantly lower among those reporting daily urgency (2.41% vs. 4.23%, P = 0.014). By contrast, the relative abundance of genus Faecalibacterium (9.25% vs. 6.26%, P = 0.006) was significantly higher in this group. CONCLUSION We observed significant differences in gut microbial contents and specific bacterial genera in association with OAB with daily urgency. Further study will be necessary to assess causal relationships between the gut microbiome and OAB.
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Affiliation(s)
- Teppei Okamoto
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Shingo Hatakeyama
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan.
| | - Atsushi Imai
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Hayato Yamamoto
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Tohru Yoneyama
- Department of Advanced Transplant and Regenerative Medicine, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Kazuyuki Mori
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Takahiro Yoneyama
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Yasuhiro Hashimoto
- Department of Advanced Transplant and Regenerative Medicine, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Shigeyuki Nakaji
- Department of Social Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifu-chou, Hirosaki, 036-8562, Japan
| | - Chikara Ohyama
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan.,Department of Advanced Transplant and Regenerative Medicine, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
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Wickramasinghe HKJP, Anast JM, Schmitz-Esser S, Serão NVL, Appuhamy JADRN. Beginning to offer drinking water at birth increases the species richness and the abundance of Faecalibacterium and Bifidobacterium in the gut of preweaned dairy calves. J Dairy Sci 2020; 103:4262-4274. [PMID: 32171510 DOI: 10.3168/jds.2019-17258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 01/21/2020] [Indexed: 12/14/2022]
Abstract
We previously demonstrated that dairy calves having access to drinking water since birth (W0) achieved greater body weight, fiber digestibility, and feed efficiency than those that first received drinking water at 17 d of age (W17). Since gut microbiota composition could be linked to growth and development of animals, the objective of this study was to examine the effect of offering drinking water to newborn calves on composition of bacteria in the gut using a fecal microbiota analysis. Fresh feces were collected directly from the rectum of calves in W0 (n = 14) and W17 (n = 15) at 2, 6, and 10 wk of age. All of the calves were fed pasteurized waste milk, weaned at 7 wk of age, and offered tap water according to the treatment. The DNA was sequenced using 16S rRNA gene-amplicon sequencing on an Illumina MiSeq system (Illumina Inc., San Diego, CA). The sequences were clustered into operational taxonomic units (OTU) with a 99% similarity threshold. Treatment effects on α-diversity indices and relative abundance of the 10 most abundant genera were analyzed using GLIMMIX procedure of SAS (SAS Institute Inc., Cary, NC). Statistical significance (q-value) of treatment effects on the 50 most abundant OTU was determined with a false discovery rate analysis. At 2 wk of age, W0 had a greater number of observed OTU (5,908 vs. 4,698) and species richness (Chao 1 index) than W17. The number of OTU and richness indices increased from wk 2 to 6, but the increment of W17 was greater than that of W0. The Shannon and inverse-Simpson indices increased linearly with age, but no difference was observed between W0 and W17 at any time point. The Firmicutes to Bacteroidetes ratios were also similar at every time point but decreased markedly when calves were weaned. The relative abundance of genera Faecalibacterium and Bacteroides was greater in W0 than W17 at 2 wk of age. The genus Faecalibacterium continued to be more abundant in W0 than W17 at 6 wk of age but had similar abundance 3 wk after weaning (10 wk of age). The abundance of Faecalibacterium at wk 6 was positively correlated with apparent total-tract digestibility of acid detergent fiber at 10 wk of age. Calves receiving water since birth had greater abundance of OTU related to Faecalibacterium prausnitzii, and Bifidobacterium breve at 6 wk of age (q < 0.085). These species are known to improve growth in preweaned calves. The abundance of none of the genera and OTU was different between W0 at W17 at 10 wk of age (q > 0.100). Overall, beginning to offer drinking water at birth has a potential to modulate gut microbiota composition and thereby positively affect performance of young dairy heifer calves (≤10 wk of age).
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Affiliation(s)
| | - J M Anast
- Department of Animal Science, Iowa State University, Ames 50011; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames 50011
| | - S Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames 50011; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames 50011
| | - N V L Serão
- Department of Animal Science, Iowa State University, Ames 50011
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Fehlbaum S, Chassard C, Schwab C, Voolaid M, Fourmestraux C, Derrien M, Lacroix C. In vitro Study of Lactobacillus paracasei CNCM I-1518 in Healthy and Clostridioides difficile Colonized Elderly Gut Microbiota. Front Nutr 2019; 6:184. [PMID: 31921877 PMCID: PMC6914822 DOI: 10.3389/fnut.2019.00184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/22/2019] [Indexed: 12/16/2022] Open
Abstract
Consumption of probiotic bacteria can result in a transient colonization of the human gut and thereby in potential interactions with the commensal microbiota. In this study, we used novel PolyFermS continuous fermentation models to investigate interactions of the candidate probiotic strain Lactobacillus paracasei CNCM I-1518 (L. paracasei) with colonic microbiota from healthy elderly subjects using 16S rRNA gene amplicon sequencing and metatranscriptomics, or with microbiota in vitro-colonized with Clostridioides difficile (C. difficile NCTC 13307 and C. difficile DSM 1296)—an enteropathogen prevalent in the elderly population. Small changes in microbiota composition were detected upon daily addition of L. paracasei, including increased abundances of closely related genera Lactobacillus and Enterococcus, and of the butyrate producer Faecalibacterium. Microbiota gene expression was also modulated by L. paracasei with distinct response of the Faecalibacterium transcriptome and an increase in carbohydrate utilization. However, no inhibitory effect of L. paracasei was observed on C. difficile colonization in the intestinal models under the tested conditions. Our data suggest that, in the in vitro experimental conditions tested and independent of the host, L. paracasei has modulatory effects on both the composition and function of elderly gut microbiota without affecting C. difficile growth and toxin production.
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Affiliation(s)
- Sophie Fehlbaum
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Christophe Chassard
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Maarja Voolaid
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | | | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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Renelies-Hamilton J, Noguera-Julian M, Parera M, Paredes R, Pacheco L, Dacal E, Saugar JM, Rubio JM, Poulsen M, Köster PC, Carmena D. Exploring interactions between Blastocystis sp., Strongyloides spp. and the gut microbiomes of wild chimpanzees in Senegal. Infect Genet Evol 2019; 74:104010. [PMID: 31442596 DOI: 10.1016/j.meegid.2019.104010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/02/2019] [Accepted: 08/18/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Gut parasites exert an important influence on the gut microbiome, with many studies focusing on the human gut microbiome. It has, however, undergone severe richness depletion. Hygienic lifestyle, antimicrobial treatments and altered gut homeostasis (e.g., chronic inflammation) reduce gut microbiome richness and also parasite prevalence; which may confound results. Studying species closely related to humans could help overcome this problem by providing insights into the ancestral relationship between humans, their gut microbiome and their gut parasites. Chimpanzees are a particularly promising model as they have similar gut microbiomes to humans and many parasites infect both species. AIMS We study the interaction between gut microbiome and enteric parasites in chimpanzees. Investigating what novel insights a closely related species can reveal when compared to studies on humans. METHODS Using eighty-seven faecal samples from wild western chimpanzees (Pan troglodytes verus) in Senegal, we combine 16S rRNA gene amplicon sequencing for gut microbiome characterization with PCR detection of parasite taxa (Blastocystis sp., Strongyloides spp., Giardia duodenalis, Cryptosporidium spp., Plasmodium spp., Filariae and Trypanosomatidae). We test for differences in gut microbiota ecosystem traits and taxonomical composition between Blastocystis and Strongyloides bearing and non-bearing samples. RESULTS For Blastocystis, twelve differentially abundant taxa (e.g., Methanobrevibacter), including Prevotella and Ruminococcus-Methanobrevibacter enterotype markers, replicate findings in humans. However, several richness indices are lower in Blastocystis carriers, contradicting human studies. This indicates Blastocystis, unlike Strongyloides, is associated to a "poor health" gut microbiome, as does the fact that Faecalibacterium, a bacterium with gut protective traits, is absent in Blastocystis-positive samples. Strongyloides was associated to Alloprevotella and five other taxonomic groups. Each parasite had its unique impact on the gut microbiota indicating parasite-specific niches. Our results suggest that studying the gut microbiomes of wild chimpanzees could help disentangle biological from artefactual associations between gut microbiomes and parasites.
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Affiliation(s)
- Justinn Renelies-Hamilton
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Jane Goodall Institute Spain, Station Biologique Fouta Djallon, Dindéfélo, Kédougou, Senegal.
| | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain; Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic - Central University of Catalonia (UVic - UCC), Vic, Spain
| | - Mariona Parera
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain; Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic - Central University of Catalonia (UVic - UCC), Vic, Spain
| | - Liliana Pacheco
- Jane Goodall Institute Spain, Station Biologique Fouta Djallon, Dindéfélo, Kédougou, Senegal
| | - Elena Dacal
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - José M Saugar
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - José M Rubio
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Pamela C Köster
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
| | - David Carmena
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III, Majadahonda, Spain
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Bjørkhaug ST, Aanes H, Neupane SP, Bramness JG, Malvik S, Henriksen C, Skar V, Medhus AW, Valeur J. Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption. Gut Microbes 2019; 10:663-675. [PMID: 30894059 PMCID: PMC6866679 DOI: 10.1080/19490976.2019.1580097] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Excessive alcohol intake can alter the gut microbiota, which may underlie the pathophysiology of alcohol-related diseases. We examined gut microbiota composition and functions in patients with alcohol overconsumption for >10 years, compared to a control group of patients with a history of no or low alcohol intake. Faecal microbiota composition was assessed by 16S rRNA sequencing. Gut microbiota functions were evaluated by quantification of short-chain fatty acids (SCFAs) and predictive metagenome profiling (PICRUSt). Twenty-four patients, mean age 64.8 years (19 males), with alcohol overconsumption, and 18 control patients, mean age 58.2 years (14 males) were included. The two groups were comparable regarding basic clinical variables. Nutritional assessment revealed lower total score on the screening tool Mini Nutritional Assessment, lower muscle mass as assessed by handgrip strength, and lower plasma vitamin C levels in the alcohol overconsumption group. Bacteria from phylum Proteobacteria were found in higher relative abundance, while bacteria from genus Faecalibacterium were found in lower relative abundance in the group of alcohol overconsumers. The group also had higher levels of the genera Sutterella, Holdemania and Clostridium, and lower concentration and percentage of butyric acid. When applying PICRUSt to predict the metagenomic composition, we found that genes related to invasion of epithelial cells were more common in the group of alcohol overconsumers. We conclude that gut microbiota composition and functions in patients with alcohol overconsumption differ from patients with low consumption of alcohol, and seem to be skewed into a putative pro-inflammatory direction.
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Affiliation(s)
| | | | - Sudan Prasad Neupane
- Norwegian National Advisory Unit on Concurrent Substance Abuse and Mental Health Disorders, Innlandet Hospital Trust, Brumunddal, Norway
| | - Jørgen G. Bramness
- Norwegian National Advisory Unit on Concurrent Substance Abuse and Mental Health Disorders, Innlandet Hospital Trust, Brumunddal, Norway,Institute of clinical medicine, UiT - Norway’s Arctic University, Tromsø, Norway
| | - Stine Malvik
- Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway,Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Christine Henriksen
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Viggo Skar
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway
| | - Asle W. Medhus
- Department of Gastroenterology, Oslo University Hospital, Oslo, Norway
| | - Jørgen Valeur
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo, Norway,CONTACT Jørgen Valeur Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, Oslo NO-0440, Norway
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Yoon HY, Kim HN, Lee SH, Kim SJ, Chang Y, Ryu S, Shin H, Kim HL, Lee JH. The Relationship between Platelet Count and Host Gut Microbiota: A Population-Based Retrospective Cross-Sectional Study. J Clin Med 2019; 8:E230. [PMID: 30744195 DOI: 10.3390/jcm8020230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 01/19/2023] Open
Abstract
Platelet count reflects the severity and prognosis of multiple diseases. Additionally, alterations in gut microbiota have been linked to several chronic diseases. The purpose of this study was to investigate the association between gut microbiota and platelet count. We selected 1268 subjects with fecal 16S RNA gene sequencing data from a Healthcare Screening Center cohort. Based on the third quartile of platelets (277 × 109/L), we compared the gut microbiota between the upper quartile (n = 321) and lower three quartiles groups (n = 947). The upper quartile group had lower alpha diversity based on observed amplicon sequence variants (q = 0.004) and phylogenetic index (q < 0.001) than the lower three quartiles group. Significant differences were also found in the weighted UniFrac distance (q = 0.001) and Jaccard dissimilarity (q = 0.047) beta diversity measures between the two groups. Compared with the lower three quartiles group, the upper quartile group exhibited decreased relative abundances of the genus Faecalibacterium, which was also inversely correlated with the platelet count. Increased platelet count was associated with reduced diversity in gut microbiota and lower abundances of Faecalibacterium with beneficial gut bacteria spices F. prausnitzii, suggesting that an increased platelet count, even within normal range, may adversely affect gut microbial diversity and composition.
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Abstract
BACKGROUND Gut dysbiosis associated with the use of proton-pump inhibitors (PPIs) has been found to lead to the occurrence of infectious and inflammatory adverse events. A longitudinal observational cohort study has demonstrated the heightened risk of death associated with PPI use. SUMMARY We evaluated meta-analyses to determine the association between PPI use and infectious and inflammatory diseases. Meta-analyses showed that PPI use is a potential risk for the development of enteric infections caused by Clostridium difficile, as well as small intestinal bacterial overgrowth, spontaneous bacterial peritonitis, community-acquired pneumonia, hepatic encephalopathy, and adverse outcomes in inflammatory bowel disease. We also examined changes in the composition and function of the gut microbiota with the use of PPIs. PPI use significantly increased the presence of Streptococcaceae and Enterococcaceae, which are risk factors for C. difficile infection, and decreased that of Faecalibacterium, a commensal anti-inflammatory microorganism. Key Message: High-throughput, microbial 16S rRNA gene sequencing has allowed us to investigate the association between the gut microbiome and PPI use. Future prospective comparison studies are necessary to confirm this association, and to develop new strategies to prevent complications of PPI use.
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Affiliation(s)
- Yuji Naito
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, Kyoto, Japan
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Mörkl S, Lackner S, Meinitzer A, Mangge H, Lehofer M, Halwachs B, Gorkiewicz G, Kashofer K, Painold A, Holl AK, Bengesser SA, Müller W, Holzer P, Holasek SJ. Gut microbiota, dietary intakes and intestinal permeability reflected by serum zonulin in women. Eur J Nutr 2018; 57:2985-97. [PMID: 30043185 DOI: 10.1007/s00394-018-1784-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/16/2018] [Indexed: 02/07/2023]
Abstract
PURPOSE Increased gut permeability causes the trespass of antigens into the blood stream which leads to inflammation. Gut permeability reflected by serum zonulin and diversity of the gut microbiome were investigated in this cross-sectional study involving female study participants with different activity and BMI levels. METHODS 102 women were included (BMI range 13.24-46.89 kg m-2): Anorexia nervosa patients (n = 17), athletes (n = 20), normal weight (n = 25), overweight (n = 21) and obese women (n = 19). DNA was extracted from stool samples and subjected to 16S rRNA gene analysis (V1-V2). Quantitative Insights Into Microbial Ecology (QIIME) was used to analyze data. Zonulin was measured with ELISA. Nutrient intake was assessed by repeated 24-h dietary recalls. We used the median of serum zonulin concentration to divide our participants into a "high-zonulin" (> 53.64 ng/ml) and "low-zonulin" (< 53.64 ng/ml) group. RESULTS The alpha-diversity (Shannon Index, Simpson Index, equitability) and beta-diversity (unweighted and weighted UniFrac distances) of the gut microbiome were not significantly different between the groups. Zonulin concentrations correlated significantly with total calorie-, protein-, carbohydrate-, sodium- and vitamin B12 intake. Linear discriminant analysis effect size (LEfSe) identified Ruminococcaceae (LDA = 4.163, p = 0.003) and Faecalibacterium (LDA = 4.151, p = 0.0002) as significantly more abundant in the low zonulin group. CONCLUSION Butyrate-producing gut bacteria such as Faecalibacteria could decrease gut permeability and lower inflammation. The diversity of the gut microbiota in women does not seem to be correlated with the serum zonulin concentration. Further interventional studies are needed to investigate gut mucosal permeability and the gut microbiome in the context of dietary factors.
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Prykhodko O, Sandberg J, Burleigh S, Björck I, Nilsson A, Fåk Hållenius F. Impact of Rye Kernel-Based Evening Meal on Microbiota Composition of Young Healthy Lean Volunteers With an Emphasis on Their Hormonal and Appetite Regulations, and Blood Levels of Brain-Derived Neurotrophic Factor. Front Nutr 2018; 5:45. [PMID: 29896479 PMCID: PMC5986961 DOI: 10.3389/fnut.2018.00045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/08/2018] [Indexed: 12/21/2022] Open
Abstract
Rye kernel bread (RKB) evening meals improve glucose tolerance, enhance appetite regulation and increase satiety in healthy volunteers. These beneficial effects on metabolic responses have been shown to be associated with increased gut fermentation. The present study aimed to elucidate if RKB evening meals may cause rapid alterations in microbiota composition that might be linked to metabolic-, immune-, and appetite- parameters. Gut-brain axis interaction was also studied by relating microbiota composition to amount of brain-derived neurotrophic factor (BDNF) in blood plasma. Nineteen healthy volunteers, ten women and nine men aged 22–29 years, BMI < 25 (NCT02093481) participated in the study performed in a crossover design. Each person was assigned to either white wheat bread (WWB) or RKB intake as a single evening meal or three consecutive evenings. Stool and blood samples as well as subjective appetite ratings were obtained the subsequent morning after each test occasion, resulting in four independent collections per participant (n = 76). DNA was extracted from the fecal samples and V4 hypervariable region of the bacterial 16S rRNA genes was sequenced using next generation sequencing technology. Higher abundance of Prevotella and Faecalibacterium with simultaneous reduction of Bacteroides spp. were observed after RKB meals compared to WWB. The associations between metabolic test variables and microbiota composition showed a positive correlation between Bacteroides and adiponectin levels, whereas only Prevotella genus was found to have positive association with plasma levels of BDNF. These novel findings in gut-brain interactions might be of importance, since decreased levels of BDNF, that plays an essential role in brain function, contribute to the pathogenesis of several major neurodisorders, including Alzheimer's. Thus, daily consumption of Faecalibacterium- and/or Prevotella-favoring meals should be investigated further for their potential to prevent neurodegenerative processes in the brain.
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Affiliation(s)
- Olena Prykhodko
- Food for Health Science Centre, Lund University, Lund, Sweden.,Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Jonna Sandberg
- Food for Health Science Centre, Lund University, Lund, Sweden.,Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Stephen Burleigh
- Food for Health Science Centre, Lund University, Lund, Sweden.,Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Inger Björck
- Food for Health Science Centre, Lund University, Lund, Sweden
| | - Anne Nilsson
- Food for Health Science Centre, Lund University, Lund, Sweden.,Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Frida Fåk Hållenius
- Food for Health Science Centre, Lund University, Lund, Sweden.,Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
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