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van Deuren T, Umanets A, Venema K, Moreno LL, Zoetendal EG, Canfora EE, Blaak EE. Specific dietary fibers steer toward distal colonic saccharolytic fermentation using the microbiota of individuals with overweight/obesity. Food Res Int 2025; 209:116271. [PMID: 40253188 DOI: 10.1016/j.foodres.2025.116271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 02/28/2025] [Accepted: 03/11/2025] [Indexed: 04/21/2025]
Abstract
BACKGROUND Evidence suggests that increased distal short-chain fatty acid (SCFA) production beneficially impacts metabolic health. However, indigestible carbohydrate availability is limited in the distal colon; consequently, microbes shift toward protein fermentation, often linked to adverse metabolic health effects. We aimed to identify specific fiber(s) that promote saccharolytic fermentation in the distal colon and thereby may (partially) inhibit proteolytic fermentation. METHODS Potato-fiber, pectin, and inulin were studied individually and in combination against a high (predigested) protein background using an in vitro model of the colon (TIM-2) inoculated with pooled, standardized fecal microbiota from individuals with overweight/obesity. Microbiota composition and activity were assessed at different timepoints to simulate the travel throughout the colon (proximal: 0-8 h, distal: 8-24 h) and compared to a high protein (HP)_control, receiving only proteins. RESULTS Fiber addition increased total SCFA production compared to HP_control (52.11 ± 1.49 vs 27.07 ± 0.26 mmol) whereas total branched-chain fatty acids (BCFA; a marker for protein fermentation) production only slightly decreased (3.31 ± 0.10 vs 4.18 ± 0.40 mmol). Combining potato-fiber and pectin led to the highest total and distal SCFA production and distal SCFA:BCFA. Fiber addition attenuated HP-induced increases in several bacterial taxa including Mogibacterium and Coprococcus, independent of fiber type. Additionally, time- and fiber-specific microbial signatures were identified: inulin increased Bifidobacterium (proximal) relative abundance and pectin and/or potato-fiber increased Prevotella 9 (distal) relative abundance. CONCLUSION The most marked increase in distal colonic SCFA production was induced by combining potato-fiber and pectin. Further research should elucidate whether this switch toward saccharolytic fermentation translates into beneficial metabolic health effects in humans.
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Affiliation(s)
- Thirza van Deuren
- Human Biology, Institute of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, the Netherlands'
| | - Alexander Umanets
- Chair Group Youth Food and Health, Faculty of Science and Engineering, Maastricht University-Campus Venlo, Venlo, the Netherlands; Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University-Campus Venlo, Venlo, the Netherlands
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University-Campus Venlo, Venlo, the Netherlands
| | - Luis L Moreno
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands; Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708, WE, Wageningen, the Netherlands
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708, WE, Wageningen, the Netherlands
| | - Emanuel E Canfora
- Human Biology, Institute of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, the Netherlands'
| | - Ellen E Blaak
- Human Biology, Institute of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, the Netherlands'.
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Budriesi R, Corazza I, Roncioni S, Scanferlato R, De Luca D, Marzetti C, Gotti R, Rizzardi N, Bergamini C, Micucci M, Roncarati D, Mattioli LB. Herbal Extracts Mixed with Essential Oils: A Network Approach for Gastric and Intestinal Motility Disorders. Nutrients 2024; 16:4357. [PMID: 39770978 PMCID: PMC11677010 DOI: 10.3390/nu16244357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 12/05/2024] [Accepted: 12/13/2024] [Indexed: 01/11/2025] Open
Abstract
BACKGROUND Three herbal extracts (Asparagus racemosus Willd., Tabebuia avellanedae Lorentz, and Glycyrrhiza glabra L.) were mixed with three essential oils (Foeniculum vulgare Mill., Mentha piperita L., and Pimpinella anisum L.) to formulate a product (HEMEO) whose active compounds include saponins and steroids in Asparagus racemosus, known for their anti-inflammatory properties; glycyrrhizin and flavonoids in Glycyrrhiza glabra, which exhibit gastroprotective and antispasmodic effects; menthol in Mentha piperita, contributing with antispasmodic and antimicrobial properties; and anethole and polyphenols in Pimpinella anisum, which modulate intestinal motility and offer antimicrobial activity. OBJECTIVE HEMEO was formulated for applications in intestinal motility disorders. METHODS HEMEO was evaluated for spontaneous and induced motility effects in isolated guinea pig ileum, colon, and stomach. Ex vivo experiments were conducted using LabChart software v7.0, and the product's antibacterial action against Helicobacter pylori and its antioxidant effects were assessed through disc diffusion and FRAP assays. The presence of the volatile compounds in the formulation was confirmed by GC-MS analysis; the TPC of HEMEO, determined using the Folin-Ciocalteu method, was 9.925 ± 0.42 mg GAE/g. CONCLUSIONS HEMEO showed a phenolic content correlated with its antioxidant potential and in addition inhibited H. pylori growth and demonstrated notable antioxidant properties, suggesting its role as a supportive agent in digestive processes and in managing motility disorders.
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Affiliation(s)
- Roberta Budriesi
- Food Chemistry and Nutraceutical Laboratory, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy;
| | - Ivan Corazza
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy;
| | - Simone Roncioni
- Valsambro S.r.l., 40121 Bologna, Italy; (S.R.); (R.S.); (D.D.L.); (C.M.)
| | | | - Dalila De Luca
- Valsambro S.r.l., 40121 Bologna, Italy; (S.R.); (R.S.); (D.D.L.); (C.M.)
| | - Carla Marzetti
- Valsambro S.r.l., 40121 Bologna, Italy; (S.R.); (R.S.); (D.D.L.); (C.M.)
| | - Roberto Gotti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Nicola Rizzardi
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy; (N.R.); (C.B.)
| | - Christian Bergamini
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy; (N.R.); (C.B.)
| | - Matteo Micucci
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, 61029 Urbino, Italy;
| | - Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Selmi 3, 40126 Bologna, Italy;
| | - Laura Beatrice Mattioli
- Food Chemistry and Nutraceutical Laboratory, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy;
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Mani AK, Parvathi VD, Ravindran S. The Anti-Elixir Triad: Non-Synced Circadian Rhythm, Gut Dysbiosis, and Telomeric Damage. Med Princ Pract 2024:1-14. [PMID: 39536739 DOI: 10.1159/000542557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 11/11/2024] [Indexed: 11/16/2024] Open
Abstract
Aging is an inevitable life process which is accelerated by lifestyle and environmental factors. It is an irreversible accretion of molecular and cellular damage associated with changes in the body composition and deterioration in physiological functions. Each cell (other than stem cells) reaches the limit of its ability to replicate, known as cellular or replicative senescence, and consequently, the organs lose their physiological functions, resulting in overall impairment. Other factors that promote aging include smoking, alcohol, UV rays, sleep habits, food, stress, sedentary lifestyle, and genetic abnormalities. These stress factors can alter our endogenous clock (the circadian rhythm) and the microbial commensals. As a result of the effect of these stressors, the microorganisms that generally support human physiological processes become baleful. The disturbance of natural physiology instigates many age-related pathologies, such as cardiovascular diseases, chronic obstructive pulmonary disorder, cerebrovascular diseases, opportunistic infections, high blood pressure, cancer, diabetes, kidney diseases, dementia, and Alzheimer's disease. The present review covers the three most essential processes of the circadian clock; the circadian gene mechanism and regulation, the mitotic clock (which plays a vital role in the telomere's attrition) and the gut microbiota and their metabolome that drive aging and lead to age-related pathologies. In conclusion, maintaining a synchronized circadian rhythm, a healthy gut microbiome, and telomere integrity is essential for mitigating the effects of aging and promoting longevity. The interplay among these factors underscores the importance of lifestyle choices in enhancing overall health and lifespan.
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Affiliation(s)
- Anup Kumar Mani
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Venkatachalam Deepa Parvathi
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Sumitha Ravindran
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
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Wang M, Song Z, Lai S, Tang F, Dou L, Yang F. Depression-associated gut microbes, metabolites and clinical trials. Front Microbiol 2024; 15:1292004. [PMID: 38357350 PMCID: PMC10864537 DOI: 10.3389/fmicb.2024.1292004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 01/16/2024] [Indexed: 02/16/2024] Open
Abstract
Depression is one of the most prevalent mental disorders today. Over the past decade, there has been considerable attention given to the field of gut microbiota associated with depression. A substantial body of research indicates a bidirectional communication pathway between gut microbiota and the brain. In this review, we extensively detail the correlation between gut microbiota, including Lactobacillus acidophilus and Bifidobacterium longum, and metabolites such as short-chain fatty acids (SCFAs) and 5-hydroxytryptamine (5-HT) concerning depression. Furthermore, we delve into the potential health benefits of microbiome-targeted therapies, encompassing probiotics, prebiotics, and synbiotics, in alleviating depression. Lastly, we underscore the importance of employing a constraint-based modeling framework in the era of systems medicine to contextualize metabolomic measurements and integrate multi-omics data. This approach can offer valuable insights into the complex metabolic host-microbiota interactions, enabling personalized recommendations for potential biomarkers, novel drugs, and treatments for depression.
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Affiliation(s)
- Meiling Wang
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Zhaoqi Song
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Shirong Lai
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Furong Tang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Lijun Dou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland, OH, United States
| | - Fenglong Yang
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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Peña-Juárez MC, Guadarrama-Escobar OR, Serrano-Castañeda P, Méndez-Albores A, Vázquez-Durán A, Vera-Graziano R, Rodríguez-Pérez B, Salgado-Machuca M, Anguiano-Almazán E, Morales-Florido MI, Rodríguez-Cruz IM, Escobar-Chávez JJ. Synergistic Effect of Retinoic Acid and Lactoferrin in the Maintenance of Gut Homeostasis. Biomolecules 2024; 14:78. [PMID: 38254678 PMCID: PMC10813542 DOI: 10.3390/biom14010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/26/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Lactoferrin (LF) is a glycoprotein that binds to iron ions (Fe2+) and other metallic ions, such as Mg2+, Zn2+, and Cu2+, and has antibacterial and immunomodulatory properties. The antibacterial properties of LF are due to its ability to sequester iron. The immunomodulatory capability of LF promotes homeostasis in the enteric environment, acting directly on the beneficial microbiota. LF can modulate antigen-presenting cell (APC) biology, including migration and cell activation. Nonetheless, some gut microbiota strains produce toxic metabolites, and APCs are responsible for initiating the process that inhibits the inflammatory response against them. Thus, eliminating harmful strains lowers the risk of inducing chronic inflammation, and consequently, metabolic disease, which can progress to type 2 diabetes mellitus (T2DM). LF and retinoic acid (RA) exhibit immunomodulatory properties such as decreasing cytokine production, thus modifying the inflammatory response. Their activities have been observed both in vitro and in vivo. The combined, simultaneous effect of these molecules has not been studied; however, the synergistic effect of LF and RA may be employed for enhancing the secretion of humoral factors, such as IgA. We speculate that the combination of LF and RA could be a potential prophylactic alternative for the treatment of metabolic dysregulations such as T2DM. The present review focuses on the importance of a healthy diet for a balanced gut and describes how probiotics and prebiotics with immunomodulatory activity as well as inductors of differentiation and cell proliferation could be acquired directly from the diet or indirectly through the oral administration of formulations aimed to maintain gut health or restore a eubiotic state in an intestinal environment that has been dysregulated by external factors such as stress and a high-fat diet.
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Affiliation(s)
- Ma. Concepción Peña-Juárez
- Unidad de Investigación Multidisciplinaria Lab-12 (Sistemas Transdérmicos y Materiales Nanoestructurados), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Carretera Cuautitlán Teoloyucan, Km 2.5, San Sebastián Xhala, Cuautitlán Izcalli 54714, Mexico; (M.C.P.-J.); (O.R.G.-E.); (P.S.-C.); (M.S.-M.); (E.A.-A.); (M.I.M.-F.)
| | - Omar Rodrigo Guadarrama-Escobar
- Unidad de Investigación Multidisciplinaria Lab-12 (Sistemas Transdérmicos y Materiales Nanoestructurados), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Carretera Cuautitlán Teoloyucan, Km 2.5, San Sebastián Xhala, Cuautitlán Izcalli 54714, Mexico; (M.C.P.-J.); (O.R.G.-E.); (P.S.-C.); (M.S.-M.); (E.A.-A.); (M.I.M.-F.)
| | - Pablo Serrano-Castañeda
- Unidad de Investigación Multidisciplinaria Lab-12 (Sistemas Transdérmicos y Materiales Nanoestructurados), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Carretera Cuautitlán Teoloyucan, Km 2.5, San Sebastián Xhala, Cuautitlán Izcalli 54714, Mexico; (M.C.P.-J.); (O.R.G.-E.); (P.S.-C.); (M.S.-M.); (E.A.-A.); (M.I.M.-F.)
| | - Abraham Méndez-Albores
- Unidad de Investigación Multidisciplinaria Lab-14 (Ciencia y Tecnología de los Materiales), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Carretera Cuautitlán Teoloyucan, Km 2.5, San Sebastián Xhala, Cuautitlán Izcalli 54714, Mexico; (A.M.-A.); (A.V.-D.)
| | - Alma Vázquez-Durán
- Unidad de Investigación Multidisciplinaria Lab-14 (Ciencia y Tecnología de los Materiales), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Carretera Cuautitlán Teoloyucan, Km 2.5, San Sebastián Xhala, Cuautitlán Izcalli 54714, Mexico; (A.M.-A.); (A.V.-D.)
| | - Ricardo Vera-Graziano
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Apartado Postal 70-360, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico;
| | - Betsabé Rodríguez-Pérez
- Laboratorio de Servicio de Análisis de Propóleos (LASAP), Unidad de Investigación Multidisciplinaria (UIM), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli 54714, Mexico;
| | - Mariana Salgado-Machuca
- Unidad de Investigación Multidisciplinaria Lab-12 (Sistemas Transdérmicos y Materiales Nanoestructurados), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Carretera Cuautitlán Teoloyucan, Km 2.5, San Sebastián Xhala, Cuautitlán Izcalli 54714, Mexico; (M.C.P.-J.); (O.R.G.-E.); (P.S.-C.); (M.S.-M.); (E.A.-A.); (M.I.M.-F.)
| | - Ericka Anguiano-Almazán
- Unidad de Investigación Multidisciplinaria Lab-12 (Sistemas Transdérmicos y Materiales Nanoestructurados), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Carretera Cuautitlán Teoloyucan, Km 2.5, San Sebastián Xhala, Cuautitlán Izcalli 54714, Mexico; (M.C.P.-J.); (O.R.G.-E.); (P.S.-C.); (M.S.-M.); (E.A.-A.); (M.I.M.-F.)
| | - Miriam Isabel Morales-Florido
- Unidad de Investigación Multidisciplinaria Lab-12 (Sistemas Transdérmicos y Materiales Nanoestructurados), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Carretera Cuautitlán Teoloyucan, Km 2.5, San Sebastián Xhala, Cuautitlán Izcalli 54714, Mexico; (M.C.P.-J.); (O.R.G.-E.); (P.S.-C.); (M.S.-M.); (E.A.-A.); (M.I.M.-F.)
- Laboratorio de Farmacia Molecular y Liberación Controlada, Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Mexico City 04960, Mexico
| | - Isabel Marlene Rodríguez-Cruz
- Unidad de Enseñanza e Investigación, Hospital Regional e Alta Especialidad de Sumpango, Carretera Zumpango-Jilotzingo #400, Barrio de Santiago, 2ª Sección, Zumpango 55600, Mexico;
| | - José Juan Escobar-Chávez
- Unidad de Investigación Multidisciplinaria Lab-12 (Sistemas Transdérmicos y Materiales Nanoestructurados), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Carretera Cuautitlán Teoloyucan, Km 2.5, San Sebastián Xhala, Cuautitlán Izcalli 54714, Mexico; (M.C.P.-J.); (O.R.G.-E.); (P.S.-C.); (M.S.-M.); (E.A.-A.); (M.I.M.-F.)
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Li Q. Bacterial infection and microbiota in carcinogenesis and tumor development. Front Cell Infect Microbiol 2023; 13:1294082. [PMID: 38035341 PMCID: PMC10684967 DOI: 10.3389/fcimb.2023.1294082] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Microbiota colonize exposed body tissues (e.g., gastrointestinal tract, skin, lungs, female genital tract, and urogenital tracts) and unexposed sites (e.g., breast). Persistent bacterial infection in the host lead to the development of multiple disease. They are implicated in the pathogenesis of various complex diseases, including diabetes, atherosclerosis, autoimmune diseases, Alzheimer's disease, and malignant diseases. Amounting studies have demonstrated the role of bacterial infection in carcinogenesis. The study of microbiota in tumorigenesis is primarily focused on lung cancer, colorectal cancer (CRC), breast cancer, gastric cancer, and gynecologic tumors, and so on. Infection of Helicobacter pylori in gastric cancer carcinogenesis is recognized as class I carcinogen by the World Health Organization (WHO) decades ago. The role of Fusobacterium nucleatum in the development of colorectal cancer is extensively investigated. Variable bacteria have been cultured from the tumor tissues. The identification of microbiota in multiple tumor tissues reveal that bacterial infection and microbiota are associated with tumor development. The microbiota affects multiple aspects of carcinogenesis and tumor development, including favoring epithelial cells proliferation, establishing inflammatory microenvironment, promoting metastasis, and causing resistance to therapy. On the other hand, microbiota can shape a tumor surveillance environment by enhancing cell activity, and sensitize the tumor cells to immune therapy. In the present review, the roles of microbiota in multiple malignancies are summarized, and unraveling the mechanisms of host-microbiota interactions can contribute to a better understanding of the interaction between microbiota and host cells, also the development of potential anti-tumor therapeutic strategies.
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Affiliation(s)
- Qiao Li
- Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, China
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Lv M, Zhang J, Deng J, Hu J, Zhong Q, Su M, Lin D, Xu T, Bai X, Li J, Guo X. Analysis of the relationship between the gut microbiota enterotypes and colorectal adenoma. Front Microbiol 2023; 14:1097892. [PMID: 37082183 PMCID: PMC10110881 DOI: 10.3389/fmicb.2023.1097892] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
IntroductionThe essence of enterotypes is to stratify the entire human gut microbiota, and dysregulation of gut microbiota is closely related to the development of colorectal adenoma. Enterotypes may therefore be a useful target for the prevention of colorectal adenoma. However, the relationship between gut microbiota and colorectal adenoma has not been fully elucidated. In this study, we aimed to analyze the differences in gut microbiome composition between adenoma and control populations.MethodsWe recruited 31 patients with colorectal adenoma and 71 non-adenoma controls. Patient demographics, risk factors, fecal samples from each subject were collected and metagenomic sequencing was performed. LEfSe analysis was used to reveal differences in intestinal microbiome composition. Multiple logistic regression analysis was used to determine the association between enterotypes and colorectal adenoma.ResultsThe results showed that Prevotella enterotype (enterotype 4) is only present in adenoma group. Logistic regression analysis showed that Prevotella enterotype was an independent risk factor for colorectal adenoma.DiscussionThe Prevotella enterotype may increase the occurrence of colorectal adenoma through inflammatory association and interference with glucose and lipid metabolism in human body. In conclusion, the differences we observed between different enterotypes add a new potential factor to the development of colorectal adenoma.
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Affiliation(s)
- Miwei Lv
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- School of Medicine, Xizang Minzu University, Xianyang, China
| | - Jiawei Zhang
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiaxin Deng
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiancong Hu
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qinghua Zhong
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mingli Su
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dezheng Lin
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tian Xu
- School of Medicine, Xizang Minzu University, Xianyang, China
| | - Xuhao Bai
- School of Medicine, Xizang Minzu University, Xianyang, China
| | - Juan Li
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Juan Li,
| | - Xuefeng Guo
- Department of Endoscopic Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Xuefeng Guo,
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Puri S, Shaheen M, Grover B. Nutrition and cognitive health: A life course approach. Front Public Health 2023; 11:1023907. [PMID: 37050953 PMCID: PMC10083484 DOI: 10.3389/fpubh.2023.1023907] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
Multiple factors affect cognitive health, such as age-related changes in the brain, injuries, mood disorders, substance abuse, and diseases. While some cannot be changed, evidence exists of many potentially possibly modifiable lifestyle factors: diet, physical activity, cognitive and social engagement, smoking and alcohol consumption which may stabilize or improve declining cognitive function. In nutrition, the focus has been mainly on its role in brain development in the early years. There is a strong emerging need to identify the role of diet and nutrition factors on age-related cognitive decline, which will open up the use of new approaches for prevention, treatment or management of age-related disorders and maintaining a good quality of life among older adults. While data on effect of high protein diets is not consistent, low-fat diets are protective against cognitive decline. Several micronutrients like B group vitamins and iron, as well as many polyphenols play a crucial role in cognitive health. Mediterranean, Nordic, DASH, and MIND diets are linked to a lower risk of cognitive decline and dementia. The relationship between the gut microbiome and brain function through the gut-brain axis has led to the emergence of data on the beneficial effects of dietary fibers and probiotics through the management of gut microbes. A “whole diet” approach as well as macro- and micro-nutrient intake levels that have protective effects against cardiovascular diseases are most likely to be effective against neurodegenerative disorders too. Young adulthood and middle age are crucial periods for determining cognitive health in old age. The importance of cardio metabolic risk factors such as obesity and hypertension, smoking and physical inactivity that develop in middle age suggest that preventive approaches are required for target populations in their 40s and 50s, much before they develop dementia. The commonality of dementia risk with cardiovascular and diabetes risk suggests that dementia could be added to present non-communicable disease management programs in primary healthcare and broader public health programs.
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Valles-Colomer M, Menni C, Berry SE, Valdes AM, Spector TD, Segata N. Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective. Nat Med 2023; 29:551-561. [PMID: 36932240 PMCID: PMC11258867 DOI: 10.1038/s41591-023-02260-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/16/2023] [Indexed: 03/19/2023]
Abstract
Cardiometabolic diseases have become a leading cause of morbidity and mortality globally. They have been tightly linked to microbiome taxonomic and functional composition, with diet possibly mediating some of the associations described. Both the microbiome and diet are modifiable, which opens the way for novel therapeutic strategies. High-throughput omics techniques applied on microbiome samples (meta-omics) hold the unprecedented potential to shed light on the intricate links between diet, the microbiome, the metabolome and cardiometabolic health, with a top-down approach. However, effective integration of complementary meta-omic techniques is an open challenge and their application on large cohorts is still limited. Here we review meta-omics techniques and discuss their potential in this context, highlighting recent large-scale efforts and the novel insights they provided. Finally, we look to the next decade of meta-omics research and discuss various translational and clinical pathways to improving cardiometabolic health.
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Affiliation(s)
- Mireia Valles-Colomer
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Cristina Menni
- Department of Twin Research, King's College London, London, UK
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Ana M Valdes
- School of Medicine, University of Nottingham, Nottingham, UK
- Nottingham National Institute for Health Research Biomedical Research Centre, Nottingham, UK
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
- European Institute of Oncology, Scientific Institute for Research, Hospitalization and Healthcare, Milan, Italy.
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10
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Manfredi M, Gismondi P, Iuliano S. Is Helicobacter pylori Anyway Pathogen in Children? INQUIRY : A JOURNAL OF MEDICAL CARE ORGANIZATION, PROVISION AND FINANCING 2023; 60:469580231154650. [PMID: 36803205 PMCID: PMC9940224 DOI: 10.1177/00469580231154650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Helicobacter pylori (H. pylori) infection is a continuous challenge for both gastroenterologists and pediatricians. The international guidelines regarding diagnostic and treatment pathways differ between adults and children. The pediatric guidelines are more restrictive because children are rarely affected by serious consequences, particularly in Western countries. Therefore, infected children should be treated only after a careful case-by-case evaluation by a pediatric gastroenterologist. In any case, recent studies are confirming an increasingly all-around pathological role of H. pylori even in asymptomatic children. For these reasons, following the current evidence, we feel that H. pylori-infected children could be treated starting in pre-adolescence, particularly in Eastern countries, because their stomachs have already begun to develop the biomarkers of gastric damage. Therefore, we believe that H. pylori is anyway pathogen in children. Nevertheless, the possible beneficial role of H. pylori in humans has not yet been conclusively disproved.
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Affiliation(s)
- Marco Manfredi
- Azienda USL-IRCCS di Reggio Emilia, Maternal and Child Department, Pediatric Unit, Sant’Anna Hospital, Castelnovo ne Monti, Reggio Emilia, Italy,Marco Manfredi, Azienda USL-IRCCS di Reggio Emilia, Maternal and Child Department, Pediatric Unit, Sant’Anna Hospital, via Roma, 2 - Castelnovo ne Monti, Reggio Emilia 42122, Italy.
| | - Pierpacifico Gismondi
- Week Hospital, Pietro Barilla Children’s Hospital, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Silvia Iuliano
- Pediatric Gastroenterology, Pietro Barilla Children’s Hospital, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
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11
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Kasarello K, Cudnoch-Jedrzejewska A, Czarzasta K. Communication of gut microbiota and brain via immune and neuroendocrine signaling. Front Microbiol 2023; 14:1118529. [PMID: 36760508 PMCID: PMC9907780 DOI: 10.3389/fmicb.2023.1118529] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/12/2023] [Indexed: 01/27/2023] Open
Abstract
The gastrointestinal tract of the human is inhabited by about 5 × 1013 bacteria (of about 1,000 species) as well as archaea, fungi, and viruses. Gut microbiota is known to influence the host organism, but the host may also affect the functioning of the microbiota. This bidirectional cooperation occurs in three main inter-organ signaling: immune, neural, and endocrine. Immune communication relies mostly on the cytokines released by the immune cells into circulation. Also, pathogen-associated or damage-associated molecular patterns (PAMPs or DAMPs) may enter circulation and affect the functioning of the internal organs and gut microbiota. Neural communication relies mostly on the direct anatomical connections made by the vagus nerve, or indirect connections via the enteric nervous system. The third pathway, endocrine communication, is the broadest one and includes the hypothalamic-pituitary-adrenal axis. This review focuses on presenting the latest data on the role of the gut microbiota in inter-organ communication with particular emphasis on the role of neurotransmitters (catecholamines, serotonin, gamma-aminobutyric acid), intestinal peptides (cholecystokinin, peptide YY, and glucagon-like peptide 1), and bacterial metabolites (short-chain fatty acids).
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12
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Lapidot Y, Reshef L, Cohen D, Muhsen K. Helicobacter pylori and the intestinal microbiome among healthy school-age children. Helicobacter 2021; 26:e12854. [PMID: 34617641 DOI: 10.1111/hel.12854] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND Helicobacter pylori (H. pylori) infection is acquired during childhood and causes chronic gastritis that remains asymptomatic in most infected people. H. pylori alters the gastric microbiota and causes peptic ulcer disease. Evidence on the relationship between asymptomatic H. pylori infection and children's gut microbiota remains elusive. AIM We characterized the relationship between H. pylori infection and the intestinal microbiome of healthy children, adjusting for known inter-personal and environmental exposures. MATERIALS AND METHODS This cross-sectional study included stool samples obtained from 163 Israeli Arab children aged 6-9 years from different socioeconomic strata. Sociodemographic information was collected through maternal interviews. H. pylori infection was determined using monoclonal antigen detection stool enzyme immunoassay. The gut microbiome was characterized by implementing 16S rRNA gene sequencing of the V4 region and a multivariate downstream analysis. RESULTS Overall, 57% of the participants were positive for H. pylori infection and it was significantly associated with low socioeconomic status. There was no significant association between H. pylori infection and bacterial richness of fecal microbiome. H. pylori infection was significantly associated with intestinal bacterial composition, including a strong association with Prevotella copri and Eubacterium biforme. Moreover, socioeconomic status was strongly associated with bacterial composition. DISCUSSION AND CONCLUSIONS H. pylori infection in healthy children was significantly associated with altered intestinal microbiome structure. Socioeconomic determinants exhibit a strong effect, related to both H. pylori infection and intestinal diversity and composition in childhood. These findings are clinically important to the understanding of the role of H. pylori infection and other intestinal microbes in health and disease.
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Affiliation(s)
- Yelena Lapidot
- The Sackler Faculty of Medicine, Department of Epidemiology and Preventive Medicine, School of Public Health, Tel Aviv University, Tel Aviv, Israel
| | - Leah Reshef
- Faculty of Life Sciences, The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Dani Cohen
- The Sackler Faculty of Medicine, Department of Epidemiology and Preventive Medicine, School of Public Health, Tel Aviv University, Tel Aviv, Israel
| | - Khitam Muhsen
- The Sackler Faculty of Medicine, Department of Epidemiology and Preventive Medicine, School of Public Health, Tel Aviv University, Tel Aviv, Israel
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13
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Hishida S, Iwasa Y. Spatial distribution of gut microbes along the intestinal duct. J Theor Biol 2021; 523:110725. [PMID: 33887297 DOI: 10.1016/j.jtbi.2021.110725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
We studied the spatial pattern of two microbial strains along the intestinal duct. Probiotic bacteria acidify the environment and suppress their competitors, non-probiotic bacteria. Food resources are supplied from the proximal end, and there exists a flow from the proximal end to the distal end. In the steady state, we observed three major patterns. In the "standard" pattern (ST), the abundance of probiotic bacteria was high in the proximal end, and it decreased toward the distal end; in contrast, the abundance of non-probiotic bacteria was low in the proximal end, and it increased toward the distal end. In the "proximal reversion" pattern (PR), non-probiotic bacteria were dominant and probiotic bacteria were suppressed in the proximal portion of the duct. Subsequently, the abundance values of the two competitors switched, followed by a spatial pattern similar to ST. In the "distal suppression" pattern (DS), the pattern was similar to ST in the proximal portion; however, toward the distal end, the abundance of probiotic bacteria remained at an intermediate level and suppressed the abundance of non-probiotic bacteria, resulting in a peak abundance of non-probiotic bacteria in the middle portion of the duct. We additionally discuss the nonmonotonic increase in the abundance of non-probiotic bacteria in ST and the transition of the spatial pattern from one type to another due to changes in the resource abundance in the influx.
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Affiliation(s)
- Shintaro Hishida
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan
| | - Yoh Iwasa
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo 669-1337, Japan.
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Nogal A, Valdes AM, Menni C. The role of short-chain fatty acids in the interplay between gut microbiota and diet in cardio-metabolic health. Gut Microbes 2021; 13:1-24. [PMID: 33764858 PMCID: PMC8007165 DOI: 10.1080/19490976.2021.1897212] [Citation(s) in RCA: 417] [Impact Index Per Article: 104.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/29/2021] [Accepted: 02/15/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiota plays an important role in cardio-metabolic diseases with diet being among the strongest modulators of gut microbiota composition and function. Resistant dietary carbohydrates are fermented to short-chain fatty acids (SCFAs) by the gut bacteria. Fiber and omega-3 rich diets increase SCFAs production and abundance of SCFA-producing bacteria. Likewise, SCFAs can improve gut barrier integrity, glucose, and lipid metabolism, regulate the immune system, the inflammatory response, and blood pressure. Therefore, targeting the gut microbiota with dietary strategies leading to increased SCFA production may benefit cardio-metabolic health. In this review, we provide an overview of the association between diet, SCFAs produced by the gut microbiota and cardio-metabolic diseases. We first discuss the association between the human gut microbiota and cardio-metabolic diseases, then investigate the role of SCFAs and finally explore the beneficial effects of specific dietary interventions that can improve cardio-metabolic outcomes through boosting the SCFA production.
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Affiliation(s)
- Ana Nogal
- Department of Twin Research, King’s College London, St Thomas’ Hospital Campus, London, UK
| | - Ana M. Valdes
- Department of Twin Research, King’s College London, St Thomas’ Hospital Campus, London, UK
- School of Medicine, Nottingham City Hospital, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham, UK
| | - Cristina Menni
- Department of Twin Research, King’s College London, St Thomas’ Hospital Campus, London, UK
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15
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Updated review of research on the gut microbiota and their relation to depression in animals and human beings. Mol Psychiatry 2020; 25:2759-2772. [PMID: 32332994 DOI: 10.1038/s41380-020-0729-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 02/06/2023]
Abstract
The gut microbiota are being called the human "second brain," as they play a key role in the regulation of the central nervous system (CNS). Recent findings provide strong evidence for the presence of bidirectional communication networks between the gut microbiota and the CNS, and such crosstalk has been correlated with alterations in major depressive disorder (MDD) and other psychiatric disorders. Further, germ-free animal models have been used to investigate the effect of the microbiota on MDD and other psychiatric disorders, which have greatly expanded our knowledge of the role of the microbiota in the etiology of MDD and promoted causality studies of this psychiatric disorder and others as well. In this review, we first introduce the methodological approaches used for microbiota research and then provide an overview of current research progress on the modulatory function and composition of the gut microbiota in MDD and the therapeutic effect of probiotics that has been gained using data from human studies as well as animal experiments. Future research should focus on identification and characterization of specific bacterial strains involved in MDD with the hope of applying these findings in the prevention and treatment of MDD.
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16
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Akimbekov NS, Digel I, Sherelkhan DK, Lutfor AB, Razzaque MS. Vitamin D and the Host-Gut Microbiome: A Brief Overview. Acta Histochem Cytochem 2020; 53:33-42. [PMID: 32624628 PMCID: PMC7322162 DOI: 10.1267/ahc.20011] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
There is a growing body of evidence for the effects of vitamin D on intestinal host-microbiome interactions related to gut dysbiosis and bowel inflammation. This brief review highlights the potential links between vitamin D and gut health, emphasizing the role of vitamin D in microbiological and immunological mechanisms of inflammatory bowel diseases. A comprehensive literature search was carried out in PubMed and Google Scholar using combinations of keywords "vitamin D," "intestines," "gut microflora," "bowel inflammation". Only articles published in English and related to the study topic are included in the review. We discuss how vitamin D (a) modulates intestinal microbiome function, (b) controls antimicrobial peptide expression, and (c) has a protective effect on epithelial barriers in the gut mucosa. Vitamin D and its nuclear receptor (VDR) regulate intestinal barrier integrity, and control innate and adaptive immunity in the gut. Metabolites from the gut microbiota may also regulate expression of VDR, while vitamin D may influence the gut microbiota and exert anti-inflammatory and immune-modulating effects. The underlying mechanism of vitamin D in the pathogenesis of bowel diseases is not fully understood, but maintaining an optimal vitamin D status appears to be beneficial for gut health. Future studies will shed light on the molecular mechanisms through which vitamin D and VDR interactions affect intestinal mucosal immunity, pathogen invasion, symbiont colonization, and antimicrobial peptide expression.
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Affiliation(s)
- Nuraly S. Akimbekov
- Department of Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Ilya Digel
- Institute for Bioengineering FH Aachen University of Applied Sciences, Jülich, Germany
| | - Dinara K. Sherelkhan
- Department of Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | - Mohammed S. Razzaque
- Department of Pathology, Lake Erie College of Osteopathic Medicine, Erie, PA, USA
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17
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Formiga F, Ferreira Teles CI, Chivite D. Impact of intestinal microbiota in patients with heart failure: A systematic review. Med Clin (Barc) 2019; 153:402-409. [PMID: 31416611 DOI: 10.1016/j.medcli.2019.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/21/2019] [Accepted: 06/22/2019] [Indexed: 10/26/2022]
Abstract
Heart failure (HF) is a chronic disease with significant morbidity and mortality. Substantial haemodynamic changes such as hypoperfusion and intestinal congestion can alter the composition of the intestinal microbiota in patients with HF. The aim of this systematic review is to evaluate the influence of bowel function in patients with HF and the possible role of the intestinal microbiota in the development and evolution of the latter. Eleven studies were included in the review. These studies seem to confirm that HF patients present with substantial abnormalities in the composition of their intestinal microbiota. Trimethylamine N-oxide is identified as a key mediator between the alterations in the intestinal microbiota and HF and correlates with worse prognosis in HF patients. In conclusion, patients with HF present with frequent abnormalities in the characteristics of their intestinal microbiota, which may play a role in the prognosis of the disease.
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Affiliation(s)
- Francesc Formiga
- Servicio de Medicina Interna, Hospital Universitario de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, España.
| | - Cristiana Isabel Ferreira Teles
- Servicio de Medicina Interna, Hospital Universitario de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, España
| | - David Chivite
- Servicio de Medicina Interna, Hospital Universitario de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, España
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18
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Germ-free animal experiments in the gut microbiota studies. Curr Opin Pharmacol 2019; 49:6-10. [PMID: 31051390 DOI: 10.1016/j.coph.2019.03.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 12/20/2022]
Abstract
Gut microbiota has a crucial role in the maintenance of health. Increasing evidence suggests that changes or disturbances in gut microbiota may be associated with various diseases. Therefore, preclinical and clinical studies related to gut microbiota are becoming increasingly important. Germ-free animal experimentation is one of the most important in vivo experimental models for preclinical studies on gut microbiota interactions. It represents a model to study effect of probiotic research and other experimental animal studies requiring careful control of outside contaminants that can affect the trial. Germ-free animals have defected immune systems, so they are used to model immune mediated metabolic, peripheral, and central diseases. In addition, gut-brain axis studies have recently increased. This minireview provides current information on this model and discusses the validity of its use in gut microbiota studies.
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19
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Shubitowski TB, Poll BG, Natarajan N, Pluznick JL. Short-chain fatty acid delivery: assessing exogenous administration of the microbiome metabolite acetate in mice. Physiol Rep 2019; 7:e14005. [PMID: 30810289 PMCID: PMC6391713 DOI: 10.14814/phy2.14005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 02/06/2023] Open
Abstract
Short-chain fatty acids (SCFAs) are fermentation by-products of gut microbes which have been linked to positive effects on host physiology; the most abundant SCFA is acetate. Exogenous administration of acetate alters host metabolism, immune function, and blood pressure, making it a biologic of interest. The effects of acetate have been attributed to activation of G-protein-coupled receptors and other proteins (i.e., HDACs), often occurring at locations distant from the gut such as the pancreas or the kidney. However, due to technical difficulties and costs, studies have often delivered exogenous acetate without determining if systemic plasma acetate levels are altered. Thus, it is unclear to what extent each method of acetate delivery may alter systemic plasma acetate levels. In this study, we aimed to determine if acetate is elevated after exogenous administration by drinking water (DW), oral gavage (OG), or intraperitoneal (IP) injection, and if so, over what timecourse, to best inform future studies. Using a commercially available kit, we demonstrated that sodium acetate delivered over 21 days in DW does not elicit a measurable change in systemic acetate over baseline. However, when acetate is delivered by OG or IP injection, there are rapid, reproducible, and dose-dependent changes in plasma acetate. These studies report, for the first time, the timecourse of changes in plasma acetate following acetate administration by three common methods, and thus inform the best practices for exogenous acetate delivery.
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Affiliation(s)
| | - Brian G. Poll
- Department of PhysiologyJohns Hopkins School of MedicineBaltimoreMaryland
| | - Niranjana Natarajan
- Department of Stem Cell and Regenerative BiologyHarvard Stem Cell InstituteHarvard UniversityCambridgeMassachusetts
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20
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De Almeida CV, de Camargo MR, Russo E, Amedei A. Role of diet and gut microbiota on colorectal cancer immunomodulation. World J Gastroenterol 2019; 25:151-162. [PMID: 30670906 PMCID: PMC6337022 DOI: 10.3748/wjg.v25.i2.151] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/20/2018] [Accepted: 12/27/2018] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers, and it is characterized by genetic and epigenetic alterations, as well as by inflammatory cell infiltration among malignant and stromal cells. However, this dynamic infiltration can be influenced by the microenvironment to promote tumor proliferation, survival and metastasis or cancer inhibition. In particular, the cancer microenvironment metabolites can regulate the inflammatory cells to induce a chronic inflammatory response that can be a predisposing condition for CRC retention. In addition, some nutritional components might contribute to a chronic inflammatory condition by regulating various immune and inflammatory pathways. Besides that, diet strongly modulates the gut microbiota composition, which has a key role in maintaining gut homeostasis and is associated with the modulation of host inflammatory and immune responses. Therefore, diet has a fundamental role in CRC initiation, progression and prevention. In particular, functional foods such as probiotics, prebiotics and symbiotics can have a potentially positive effect on health beyond basic nutrition and have anti-inflammatory effects. In this review, we discuss the influence of diet on gut microbiota composition, focusing on its role on gut inflammation and immunity. Finally, we describe the potential benefits of using probiotics and prebiotics to modulate the host inflammatory response, as well as its application in CRC prevention and treatment.
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Affiliation(s)
| | - Marcela Rodrigues de Camargo
- Department of Surgery, Stomatology, Pathology and Radiology, Bauru School of Dentistry, São Paulo University, Bauru-Sao Paulo 17012901, Brazil
| | - Edda Russo
- Department of Experimental and Clinical Medicine, University of Florence, Florence 50139, Italy
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence and Department of Biomedicine, Azienda Ospedaliera Universitaria Careggi (AOUC), Florence 50139, Italy
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21
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Mukherjee S, Joardar N, Sengupta S, Sinha Babu SP. Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings. J Nutr Biochem 2018; 61:111-128. [PMID: 30196243 PMCID: PMC7126101 DOI: 10.1016/j.jnutbio.2018.07.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/24/2018] [Accepted: 07/28/2018] [Indexed: 02/07/2023]
Abstract
The human gut microbiota has been the interest of extensive research in recent years and our knowledge on using the potential capacity of these microbes are growing rapidly. Microorganisms colonized throughout the gastrointestinal tract of human are coevolved through symbiotic relationship and can influence physiology, metabolism, nutrition and immune functions of an individual. The gut microbes are directly involved in conferring protection against pathogen colonization by inducing direct killing, competing with nutrients and enhancing the response of the gut-associated immune repertoire. Damage in the microbiome (dysbiosis) is linked with several life-threatening outcomes viz. inflammatory bowel disease, cancer, obesity, allergy, and auto-immune disorders. Therefore, the manipulation of human gut microbiota came out as a potential choice for therapeutic intervention of the several human diseases. Herein, we review significant studies emphasizing the influence of the gut microbiota on the regulation of host responses in combating infectious and inflammatory diseases alongside describing the promises of gut microbes as future therapeutics.
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Affiliation(s)
- Suprabhat Mukherjee
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Nikhilesh Joardar
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Subhasree Sengupta
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Santi P Sinha Babu
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India.
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22
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Sebastián Domingo JJ, Sánchez Sánchez C. From the intestinal flora to the microbiome. REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS 2018; 110:51-56. [PMID: 29271225 DOI: 10.17235/reed.2017.4947/2017] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this article, the history of the microbiota is reviewed and the related concepts of the microbiota, microbiome, metagenome, pathobiont, dysbiosis, holobiont, phylotype and enterotype are defined. The most precise and current knowledge about the microbiota is presented and the metabolic, nutritional and immunomodulatory functions are reviewed. Some gastrointestinal diseases whose pathogenesis is associated with the intestinal microbiota, including inflammatory bowel disease, irritable bowel syndrome and celiac disease, among others, are briefly discussed. Finally, some prominent and promising data with regard to the fecal microbiota transplantation in certain digestive illness are discussed.
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Rebuilding the Gut Microbiota Ecosystem. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15081679. [PMID: 30087270 PMCID: PMC6121872 DOI: 10.3390/ijerph15081679] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/04/2018] [Indexed: 11/17/2022]
Abstract
A microbial ecosystem in which bacteria no longer live in a mutualistic association is called dysbiotic. Gut microbiota dysbiosis is a condition related with the pathogenesis of intestinal illnesses (irritable bowel syndrome, celiac disease, and inflammatory bowel disease) and extra-intestinal illnesses (obesity, metabolic disorder, cardiovascular syndrome, allergy, and asthma). Dysbiosis status has been related to various important pathologies, and many therapeutic strategies aimed at restoring the balance of the intestinal ecosystem have been implemented. These strategies include the administration of probiotics, prebiotics, and synbiotics; phage therapy; fecal transplantation; bacterial consortium transplantation; and a still poorly investigated approach based on predatory bacteria. This review discusses the various aspects of these strategies to counteract intestinal dysbiosis.
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24
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Ghoddusi H, Thomas L. Microbiota of the Human Gut. PROBIOTIC DAIRY PRODUCTS 2017:1-15. [DOI: 10.1002/9781119214137.ch1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2025]
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25
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Wardhani, S., Ridho, M. R., Arinafril, Arita, S., Ngudiantoro. Consortium of heterotrophic nitrification bacteria Bacillus sp. and its application on urea fertilizer industrial wastewater treatment. MALAYSIAN JOURNAL OF MICROBIOLOGY 2017. [DOI: 10.1016/s1773-035x(15)72824-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Liang C, Tseng HC, Chen HM, Wang WC, Chiu CM, Chang JY, Lu KY, Weng SL, Chang TH, Chang CH, Weng CT, Wang HM, Huang HD. Diversity and enterotype in gut bacterial community of adults in Taiwan. BMC Genomics 2017; 18:932. [PMID: 28198673 PMCID: PMC5310273 DOI: 10.1186/s12864-016-3261-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background Gastrointestinal microbiota, particularly gut microbiota, is associated with human health. The biodiversity of gut microbiota is affected by ethnicities and environmental factors such as dietary habits or medicine intake, and three enterotypes of the human gut microbiome were announced in 2011. These enterotypes are not significantly correlated with gender, age, or body weight but are influenced by long-term dietary habits. However, to date, only two enterotypes (predominantly consisting of Bacteroides and Prevotella) have shown these characteristics in previous research; the third enterotype remains ambiguous. Understanding the enterotypes can improve the knowledge of the relationship between microbiota and human health. Results We obtained 181 human fecal samples from adults in Taiwan. Microbiota compositions were analyzed using next-generation sequencing (NGS) technology, which is a culture-independent method of constructing microbial community profiles by sequencing 16S ribosomal DNA (rDNA). In these samples, 17,675,898 sequencing reads were sequenced, and on average, 215 operational taxonomic units (OTUs) were identified for each sample. In this study, the major bacteria in the enterotypes identified from the fecal samples were Bacteroides, Prevotella, and Enterobacteriaceae, and their correlation with dietary habits was confirmed. A microbial interaction network in the gut was observed on the basis of the amount of short-chain fatty acids, pH value of the intestine, and composition of the bacterial community (enterotypes). Finally, a decision tree was derived to provide a predictive model for the three enterotypes. The accuracies of this model in training and independent testing sets were 97.2 and 84.0%, respectively. Conclusions We used NGS technology to characterize the microbiota and constructed a predictive model. The most significant finding was that Enterobacteriaceae, the predominant subtype, could be a new subtype of enterotypes in the Asian population. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3261-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao Liang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | | | - Hui-Mei Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan
| | | | | | | | - Kuan-Yi Lu
- Health GeneTech Corporation, Taoyuan, Taiwan
| | - Shun-Long Weng
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan.,Mackay Medicine, Nursing and Management College, Taipei, Taiwan.,Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
| | - Chao-Hsiang Chang
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | | | | | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan. .,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.
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Althani AA, Marei HE, Hamdi WS, Nasrallah GK, El Zowalaty ME, Al Khodor S, Al-Asmakh M, Abdel-Aziz H, Cenciarelli C. Human Microbiome and its Association With Health and Diseases. J Cell Physiol 2016; 231:1688-1694. [PMID: 26660761 DOI: 10.1002/jcp.25284] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/09/2015] [Indexed: 12/29/2022]
Abstract
Human microbiota are distinct communities of microorganisms that resides at different body niches. Exploration of the human microbiome has become a reality due to the availability of powerful metagenomics and metatranscriptomic analysis technologies. Recent advances in sequencing and bioinformatics over the past decade help provide a deep insight into the nature of the host-microbial interactions and identification of potential deriver genes and pathways associated with human health, well-being, and predisposition to different diseases. In the present review, we outline recent studies devoted to elucidate the possible link between the microbiota and various type of diseases. The present review also highlights the potential utilization of microbiota as a potential therapeutic option to treat a wide array of human diseases. J. Cell. Physiol. 231: 1688-1694, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Asmaa A Althani
- Biomedical Research Center, Qatar University, Doha, Qatar
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Hany E Marei
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Wedad S Hamdi
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Gheyath K Nasrallah
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | | | - Souhaila Al Khodor
- Infectious Disease Unit, Division of Translational Medicine, SIDRA Medical and Research Center, Qatar
| | - Maha Al-Asmakh
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Hassan Abdel-Aziz
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Carlo Cenciarelli
- CNR-Institute of Translational Pharmacology, Via Fosso del Cavaliere, Roma, Italy
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28
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Noto JM, Peek RM. Micronutrients: A double-edged sword in microbial-induced gastric carcinogenesis. Trends Cancer 2015; 1:136-144. [PMID: 26623443 DOI: 10.1016/j.trecan.2015.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/01/2015] [Accepted: 07/10/2015] [Indexed: 12/13/2022]
Abstract
Epidemiologic studies throughout the world have uniformly demonstrated significant relationships between the intake of dietary micronutrients and gastric cancer risk. An exciting concept that has gained considerable traction recently is that micronutrients modulate gene expression within Helicobacter pylori, the strongest identified risk factor for gastric carcinogenesis. We present evidence here that essential micronutrients have a direct effect on H. pylori virulence, which subsequently affects interactions at the host-pathogen interface, thereby facilitating the development of premalignant and malignant lesions in the stomach. Further, these fundamental concepts provide a framework for understanding mechanisms driving the development of other malignancies that arise from foci of gastrointestinal inflammation.
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Affiliation(s)
- Jennifer M Noto
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, MRB IV 1030C, Nashville, TN 37232-0252, , ,
| | - Richard M Peek
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue MRB IV 1030C, Nashville, TN 37232-0252, , ,
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Hunt RH, Camilleri M, Crowe SE, El-Omar EM, Fox JG, Kuipers EJ, Malfertheiner P, McColl KEL, Pritchard DM, Rugge M, Sonnenberg A, Sugano K, Tack J. The stomach in health and disease. Gut 2015; 64:1650-68. [PMID: 26342014 PMCID: PMC4835810 DOI: 10.1136/gutjnl-2014-307595] [Citation(s) in RCA: 241] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/14/2015] [Indexed: 12/12/2022]
Abstract
The stomach is traditionally regarded as a hollow muscular sac that initiates the second phase of digestion. Yet this simple view ignores the fact that it is the most sophisticated endocrine organ with unique physiology, biochemistry, immunology and microbiology. All ingested materials, including our nutrition, have to negotiate this organ first, and as such, the stomach is arguably the most important segment within the GI tract. The unique biological function of gastric acid secretion not only initiates the digestive process but also acts as a first line of defence against food-borne microbes. Normal gastric physiology and morphology may be disrupted by Helicobacter pylori infection, the most common chronic bacterial infection in the world and the aetiological agent for most peptic ulcers and gastric cancer. In this state-of-the-art review, the most relevant new aspects of the stomach in health and disease are addressed. Topics include gastric physiology and the role of gastric dysmotility in dyspepsia and gastroparesis; the stomach in appetite control and obesity; there is an update on the immunology of the stomach and the emerging field of the gastric microbiome. H. pylori-induced gastritis and its associated diseases including peptic ulcers and gastric cancer are addressed together with advances in diagnosis. The conclusions provide a future approach to gastric diseases underpinned by the concept that a healthy stomach is the gateway to a healthy and balanced host. This philosophy should reinforce any public health efforts designed to eradicate major gastric diseases, including stomach cancer.
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Affiliation(s)
- R H Hunt
- Division of Gastroenterology, Farncombe Family Digestive Health Research Institute, McMaster University Health Science Centre, Hamilton, Ontario, Canada
| | - M Camilleri
- Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - S E Crowe
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - E M El-Omar
- Division of Applied Medicine, Aberdeen University, Institute of Medical Sciences, Foresterhill, Aberdeen, UK
| | - J G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - E J Kuipers
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - P Malfertheiner
- Klinik für Gastroenterologie, Hepatologie und Infektiologi Universitätsklinikum Magdeburg A.ö.R.Leipziger Str. 44, Magdeburg, Germany
| | - K E L McColl
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - D M Pritchard
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - M Rugge
- Department of Medicine DIMED, Pathology & Cytopathology Unit, University of Padova, Padova, Italy
| | - A Sonnenberg
- Department of Gastroenterology, Oregon Health Science University, Portland, Oregon, USA
| | - K Sugano
- Department of Internal Medicine, Jichi Medical School, Shimotsuke, Japan
| | - J Tack
- Translational Research in GastroIntestinal Disorders, Leuven, Belgium
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Nisar M, Noureen N, Fazal S, Qadir MA. MCaVoH: A toolkit for mining, classification and visualization of human microbiota. J Microbiol Methods 2015; 117:28-35. [PMID: 26193336 DOI: 10.1016/j.mimet.2015.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022]
Abstract
Human body is the home for a large number of microbes. The complexity of enterotype depends on the body site. Microbial communities in various samples from different regions are being classified on the basis of 16S rRNA gene sequences. With the improvement in sequencing technologies various computational methods have been used for the analysis of microbiome data. Despite several available machine learning techniques there is no single platform available which could provide several techniques for clustering, multiclass classification, comparative analysis and the most significantly the identification of the subgroups present within larger groups of human microbial communities. We present a tool named MCaVoH for this purpose which performs clustering and classification of 16S rRNA sequence data and highlight various groups. Our tool has an added facility of biclustering which produces local group of communities present within larger groups (clusters). The core objective of our work was to identify the interaction between various bacterial species along with monitoring the composition and variations in microbial communities. MCaVoH also evaluates the performance and efficiency of different techniques using comparative analysis. The results are visualized through different plots and graphs. We implemented our tool in MATLAB. We tested our tool on several real and simulated 16S rRNA data sets and it outperforms several existing methods. Our tool provides a single platform for using multiple clustering, classification algorithms, local community identification along with their comparison which has not been done so far. Tool is available at https://sourceforge.net/projects/mcavoh/.
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Affiliation(s)
- Maryum Nisar
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Nighat Noureen
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan; Department of Bioinformatics and Biosciences, Faculty of Computing, Mohammad Ali Jinnah University, Islamabad, Pakistan.
| | - Sahar Fazal
- Department of Bioinformatics and Biosciences, Faculty of Computing, Mohammad Ali Jinnah University, Islamabad, Pakistan
| | - Muhammad Abdul Qadir
- Department of Bioinformatics and Biosciences, Faculty of Computing, Mohammad Ali Jinnah University, Islamabad, Pakistan; Department of Computer Science, Faculty of Computing, Mohammad Ali Jinnah University, Islamabad, Pakistan
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31
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Al-Asmakh M, Hedin L. Microbiota and the control of blood-tissue barriers. Tissue Barriers 2015; 3:e1039691. [PMID: 26451344 DOI: 10.1080/21688370.2015.1039691] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 12/24/2022] Open
Abstract
The gastro-intestinal tract is an ecosystem containing trillions of commensal bacteria living in symbiosis with the host. These microbiota modulate a variety of our physiological processes, including production of vitamins, absorption of nutrients and development of the immune system. One of their major functions is to fortify the intestinal barrier, thereby helping to prevent pathogens and harmful substances from crossing into the general circulation. Recently, effects of these microbiota on other blood-tissue barriers have also been reported. Here, we review the evidence indicating that gut bacteria play a role in regulating the blood-brain and blood-testis barriers. The underlying mechanisms include control of the expression of tight junction proteins by fermentation products such as butyrate, which also influences the activity of histone deacetylase.
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Affiliation(s)
- Maha Al-Asmakh
- Department of Health Sciences; College of Arts and Sciences; Qatar University ; Doha, Qatar
| | - Lars Hedin
- Sidra Medical and Research Center; Division of Clinical Epidemiology ; Doha, Qatar
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32
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Abstract
The gastro-intestinal tract is an ecosystem containing trillions of commensal bacteria living in symbiosis with the host. These microbiota modulate a variety of our physiological processes, including production of vitamins, absorption of nutrients and development of the immune system. One of their major functions is to fortify the intestinal barrier, thereby helping to prevent pathogens and harmful substances from crossing into the general circulation. Recently, effects of these microbiota on other blood-tissue barriers have also been reported. Here, we review the evidence indicating that gut bacteria play a role in regulating the blood-brain and blood-testis barriers. The underlying mechanisms include control of the expression of tight junction proteins by fermentation products such as butyrate, which also influences the activity of histone deacetylase.
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Affiliation(s)
- Maha Al-Asmakh
- Department of Health Sciences; College of Arts and Sciences; Qatar University ; Doha, Qatar
| | - Lars Hedin
- Sidra Medical and Research Center; Division of Clinical Epidemiology ; Doha, Qatar
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33
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Impact of nutrition on brain development and its neuroprotective implications following preterm birth. Pediatr Res 2015; 77:148-55. [PMID: 25314585 PMCID: PMC4291511 DOI: 10.1038/pr.2014.171] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/30/2014] [Indexed: 01/08/2023]
Abstract
The impact of nutrition on brain development in preterm infants has been increasingly appreciated. Early postnatal growth and nutrient intake have been demonstrated to influence brain growth and maturation with subsequent effects on neurodevelopment that persist into childhood and adolescence. Nutrition could also potentially protect against injury. Inflammation and perinatal infection play a crucial role in the pathogenesis of white matter injury, the most common pattern of brain injury in preterm infants. Therefore, nutritional components with immunomodulatory and/or anti-inflammatory effects may serve as neuroprotective agents. Moreover, growing evidence supports the existence of a microbiome-gut-brain axis. The microbiome is thought to interact with the brain through immunological, endocrine, and neural pathways. Consequently, nutritional components that may influence gut microbiota may also exert beneficial effects on the developing brain. Based on these properties, probiotics, prebiotic oligosaccharides, and certain amino acids are potential candidates for neuroprotection. In addition, the amino acid glutamine has been associated with a decrease in infectious morbidity in preterm infants. In conclusion, early postnatal nutrition is of major importance for brain growth and maturation. Additionally, certain nutritional components might play a neuroprotective role against white matter injury, through modulation of inflammation and infection, and may influence the microbiome-gut-brain axis.
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34
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Mao L, Franke J. Symbiosis, dysbiosis, and rebiosis-The value of metaproteomics in human microbiome monitoring. Proteomics 2014; 15:1142-51. [DOI: 10.1002/pmic.201400329] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/02/2014] [Accepted: 10/08/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Lei Mao
- Department of Life Science Engineering; HTW Berlin - University of Applied Sciences; Germany
| | - Jacqueline Franke
- Department of Life Science Engineering; HTW Berlin - University of Applied Sciences; Germany
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35
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Schippa S, Conte MP. Dysbiotic events in gut microbiota: impact on human health. Nutrients 2014; 6:5786-805. [PMID: 25514560 PMCID: PMC4276999 DOI: 10.3390/nu6125786] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/22/2014] [Accepted: 11/19/2014] [Indexed: 02/07/2023] Open
Abstract
The human body is colonized by a large number of microbes coexisting peacefully with their host. The most colonized site is the gastrointestinal tract (GIT). More than 70% of all the microbes in the human body are in the colon. The microorganism population is 10 times larger of the total number of our somatic and germ cells. Two bacterial phyla, accounting for more than 90% of the bacterial cells, dominate the healthy adult intestine: Firmicutes and Bacteroidetes. Considerable variability in the microbiota compositions between people is found when we look at the taxonomic level of species, and strains within species. It is possible to assert that the human microbiota could be compared to a fingerprint. The microbiota acts as a barrier from pathogens, exerts important metabolic functions, and regulates inflammatory response by stimulating the immune system. Gut microbial imbalance (dysbiosis), has been linked to important human diseases such as inflammation related disorders. The present review summarizes our knowledge on the gut microbiota in a healthy context, and examines intestinal dysbiosis in inflammatory bowel disease (IBD) patients; the most frequently reported disease proven to be associated with changes in the gut microbiota.
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Affiliation(s)
- Serena Schippa
- Public Health and Infectious Diseases Department, "Sapienza" University of Rome, Rome 00185, Italy.
| | - Maria Pia Conte
- Public Health and Infectious Diseases Department, "Sapienza" University of Rome, Rome 00185, Italy.
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36
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[Gut microbiota in health and disease]. REVISTA DE GASTROENTEROLOGÍA DE MÉXICO 2013; 78:240-8. [PMID: 24290319 DOI: 10.1016/j.rgmx.2013.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/13/2013] [Accepted: 04/16/2013] [Indexed: 12/26/2022]
Abstract
Gut microbiota is the community of live microorganisms residing in the digestive tract. There are many groups of researchers worldwide that are working at deciphering the collective genome of the human microbiota. Modern techniques for studying the microbiota have made us aware of an important number of nonculturable bacteria and of the relation between the microorganisms that live inside us and our homeostasis. The microbiota is essential for correct body growth, the development of immunity, and nutrition. Certain epidemics affecting humanity such as asthma and obesity may possibly be explained, at least partially, by alterations in the microbiota. Dysbiosis has been associated with a series of gastrointestinal disorders that include non-alcoholic fatty liver disease, celiac disease, and irritable bowel syndrome. The present article deals with the nomenclature, modern study techniques, and functions of gut microbiota, and its relation to health and disease.
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Abstract
The discovery of Helicobacter pylori overturned the conventional dogma that the stomach was a sterile organ and that pH values<4 were capable of sterilizing the stomach. H. pylori are an etiological agent associated with gastritis, hypochlorhydria, duodenal ulcers, and gastric cancer. It is now appreciated that the human stomach supports a bacterial community with possibly 100s of bacterial species that influence stomach homeostasis. Other bacteria colonizing the stomach may also influence H. pylori-associated gastric pathogenesis by creating reactive oxygen and nitrogen species and modulating inflammatory responses. In this review, we summarize the available literature concerning the gastric microbiota in humans, mice, and Mongolian gerbils. We also discuss the gastric perturbations, many involving H. pylori, that facilitate the colonization by bacteria from other compartments of the gastrointestinal tract, and identify risk factors known to affect gastric homeostasis that contribute to changes in the microbiota.
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Korecka A, de Wouters T, Cultrone A, Lapaque N, Pettersson S, Doré J, Blottière HM, Arulampalam V. ANGPTL4 expression induced by butyrate and rosiglitazone in human intestinal epithelial cells utilizes independent pathways. Am J Physiol Gastrointest Liver Physiol 2013; 304:G1025-37. [PMID: 23518684 DOI: 10.1152/ajpgi.00293.2012] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Short-chain fatty acids (SCFAs), such as butyrate and propionate, are metabolic products of carbohydrate fermentation by the microbiota and constitute the main source of energy for host colonocytes. SCFAs are also important for gastrointestinal health, immunity, and host metabolism. Intestinally produced angiopoietin-like protein 4 (ANGPTL4) is a secreted protein with metabolism-altering properties and may offer a route by which microbiota can regulate host metabolism. Peroxisome proliferator-activated receptor (PPAR)-γ has previously been shown to be involved in microbiota-induced expression of intestinal ANGPTL4, but the role of bacterial metabolites in this process has remained elusive. Here, we show that the SCFA butyrate regulates intestinal ANGPTL4 expression in a PPAR-γ-independent manner. Although PPAR-γ is not required for butyrate-driven intestinal ANGPTL4 expression, costimulating with PPAR-γ ligands and SCFAs leads to additive increases in ANGPTL4 levels. We suggest that PPAR-γ and butyrate rely on two separate regulatory sites, a PPAR-responsive element downstream the transcription start site and a butyrate-responsive element(s) within the promoter region, 0.5 kb upstream of the transcription start site. Furthermore, butyrate gavage and colonization with Clostridium tyrobutyricum, a SCFA producer, can independently induce expression of intestinal ANGPTL4 in germ-free mice. Thus, oral administration of SCFA or use of SCFA-producing bacteria may be additional routes to maintain intestinal ANGPTL4 levels for preventive nutrition or therapeutic purposes.
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Affiliation(s)
- Agata Korecka
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology (MTC), Stockholm, Sweden
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Gruss A, Borezée-Durant E, Lechardeur D. Environmental heme utilization by heme-auxotrophic bacteria. Adv Microb Physiol 2013; 61:69-124. [PMID: 23046952 DOI: 10.1016/b978-0-12-394423-8.00003-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Heme, an iron-containing porphyrin, is the prosthetic group for numerous key cellular enzymatic and regulatory processes. Many bacteria encode the biosynthetic enzymes needed for autonomous heme production. Remarkably, however, numerous other bacteria lack a complete heme biosynthesis pathway, yet encode heme-requiring functions. For such heme-auxotrophic bacteria (HAB), heme or porphyrins must be captured from the environment. Functional studies, aided by genomic analyses, provide insight into the HAB lifestyle, how they acquire and manage heme, and the uses of heme that make it worthwhile, and sometimes necessary, to capture this bioactive molecule.
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Affiliation(s)
- Alexandra Gruss
- INRA, UMR1319 Micalis and AgroParisTech, UMR Micalis, Jouy-en-Josas, France
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Abstract
Controversies have emerged regarding the beneficial v. detrimental effects of dietary n-6 PUFA. The alteration of the intestinal microbiota, a phenomenon termed dysbiosis, occurs during several chronic inflammatory diseases, but has not been well studied in an aged population. With present ‘Western’ diets predominantly composed of n-6 PUFA, we hypothesised that PUFA-rich diets cause intestinal dysbiosis in an aged population. C57BL/6 mice (aged 2 years) were fed a high-fat (40% energy), isoenergetic and isonitrogenous diet composed of rapeseed oil, maize oil or maize oil supplemented with fish oil. We examined ileal microbiota using fluorescence in situ hybridisation and stained tissues by immunofluorescence for the presence of immune cells and oxidative stress. We observed that feeding high-fat diets rich in n-6 PUFA promoted bacterial overgrowth but depleted microbes from the Bacteroidetes and Firmicutes phyla. This corresponded with increased body mass and infiltration of macrophages and neutrophils. Fish oil supplementation (rich in long-chain n-3 PUFA like DHA and EPA) restored the microbiota and inflammatory cell infiltration and promoted regulatory T-cell recruitment. However, fish oil supplementation was associated with increased oxidative stress, evident by the increased presence of 4-hydroxynonenal, a product of lipid peroxidation. These results suggest that an n-6 PUFA-rich diet can cause dysbiosis and intestinal inflammation in aged mice. However, while fish oil supplementation on an n-6 PUFA diet reverses dysbiosis, the combination of n-6 and n-3 PUFA, like DHA/EPA, leads to increased oxidative stress, which could exacerbate gastrointestinal disorders in the elderly.
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Abstract
The goal of this brief review is to address the role of the ageing gut in the genesis of malnutrition in the elderly. We assess the burden of malnutrition in the elderly, exploring the role of comorbid conditions and neurohumoral changes that take place to contribute towards the process of anorexia associated with ageing. Following this, the review assesses physiological changes that occur in each part of the gastrointestinal (GI) tract and what implication they may have in clinical practice. In the oropharynx and the oesophagus, changes in swallowing and oesophageal motility associated with ageing can be demonstrated using physiological testing. However, in the absence of comorbid disease, they often have little, if any, clinical significance. In the stomach, reduced fundal compliance may contribute to early satiety; however, the primary change is hypochlorhydria, which may predispose to malabsorption or bacterial overgrowth further along the GI tract. Almost uniquely, the small bowel, particularly its absorptive function, is unaffected by age and we review the literature demonstrating this. In the colon, there is evidence of a prolonged transit time related to a reduction in both neurotransmitters and receptors. Although this may cause symptoms, this aspect is unlikely to contribute to malnutrition. In addition, we assess the potential changes in the gut microbiome and how this may interact with the immune system in the process of 'inflamm-ageing'. We conclude by summarising the main changes and their impact for the clinician along with recommendations for future areas of research.
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Blumberg R, Powrie F. Microbiota, disease, and back to health: a metastable journey. Sci Transl Med 2012; 4:137rv7. [PMID: 22674557 PMCID: PMC5020897 DOI: 10.1126/scitranslmed.3004184] [Citation(s) in RCA: 220] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alterations in the composition of the commensal microbiota have been observed in many complex diseases. Understanding the basis for these changes, how they relate to disease risk or activity, and the mechanisms by which the symbiotic state of colonization resistance and host homeostasis is restored is critical for future therapies aimed at manipulating the microbiota.
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Affiliation(s)
- Richard Blumberg
- Gastroenterology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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Al-Asmakh M, Anuar F, Zadjali F, Rafter J, Pettersson S. Gut microbial communities modulating brain development and function. Gut Microbes 2012; 3:366-73. [PMID: 22743758 PMCID: PMC3463494 DOI: 10.4161/gmic.21287] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Mammalian brain development is initiated in utero and internal and external environmental signals can affect this process all the way until adulthood. Recent observations suggest that one such external cue is the indigenous microbiota which has been shown to affect developmental programming of the brain. This may have consequences for brain maturation and function that impact on cognitive functions later in life. This review discusses these recent findings from a developmental perspective.
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Affiliation(s)
- Maha Al-Asmakh
- Department of Microbiology; Tumor and Cell Biology; Karolinska Institutet; Huddinge, Sweden,Department of Biomedical Science; College of Arts and Sciences; Qatar University; Doha, Qatar·
| | - Farhana Anuar
- Institute of Molecular and Cell Biology; Singapore, Singapore
| | - Fahad Zadjali
- College of Medicine and Health Sciences; Sultan Qaboos University; Alkoudh, Oman
| | - Joseph Rafter
- Department of Biosciences and Nutrition; Karolinska Institutet; Huddinge, Sweden
| | - Sven Pettersson
- Department of Microbiology; Tumor and Cell Biology; Karolinska Institutet; Huddinge, Sweden,Laboratory of Inflammation Biology; National Cancer Centre Singapore; Singapore, Singapore,Correspondence to: Sven Pettersson,
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