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Lammi C, Ottaviano E, Fiore G, Bollati C, d'Adduzio L, Fanzaga M, Ceccarani C, Vizzuso S, Zuccotti G, Borghi E, Verduci E. Effect of docosahexaenoic acid as an anti-inflammatory for Caco-2 cells and modulating agent for gut microbiota in children with obesity (the DAMOCLE study). J Endocrinol Invest 2024:10.1007/s40618-024-02444-w. [PMID: 39186221 DOI: 10.1007/s40618-024-02444-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
PURPOSE Docosahexaenoic acid (DHA) is a long-chain omega-3 polyunsaturated fatty acid. We investigated the dual health ability of DHA to modulate gut microbiota in children with obesity and to exert anti-inflammatory activity on human intestinal Caco-2 cells. METHODS In a pilot study involving 18 obese children (8-14 years), participants received a daily DHA supplement (500 mg/day) and dietary intervention from baseline (T0) to 4 months (T1), followed by dietary intervention alone from 4 months (T1) to 8 months (T2). Fecal samples, anthropometry, biochemicals and dietary assessment were collected at each timepoint. At preclinical level, we evaluated DHA's antioxidant and anti-inflammatory effects on Caco-2 cells stimulated with Hydrogen peroxide (H2O2) and Lipopolysaccharides (LPS), by measuring also Inducible nitric oxide synthase (iNOS) levels and cytokines, respectively. RESULTS Ten children were included in final analysis. No major changes were observed for anthropometric and biochemical parameters, and participants showed a low dietary compliance at T1 and T2. DHA supplementation restored the Firmicutes/Bacteroidetes ratio that was conserved also after the DHA discontinuation at T2. DHA supplementation drove a depletion in Ruminococcaceae and Dialisteraceae, and enrichment in Bacteroidaceae, Oscillospiraceae, and Akkermansiaceae. At genus level, Allisonella was the most decreased by DHA supplementation. In Caco-2 cells, DHA decreased H2O2-induced reactive oxygen species (ROS) and nitric oxide (NO) production via iNOS pathway modulation. Additionally, DHA modulated proinflammatory (IL-1β, IL-6, IFN-γ, TNF-α) and anti-inflammatory (IL-10) cytokine production in LPS-stimulated Caco-2 cells. CONCLUSION An improvement in gut dysbiosis of children with obesity seems to be triggered by DHA and to continue after discontinuation. The ability to modulate gut microbiota, matches also with an anti-inflammatory effect of DHA on Caco-2 cells.
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Affiliation(s)
- C Lammi
- Department of Pharmaceutical Sciences, University of Milan, 20133, Milan, Italy
| | - E Ottaviano
- Department of Health Sciences, University of Milan, 20142, Milan, Italy
| | - G Fiore
- Department of Health Sciences, University of Milan, 20142, Milan, Italy.
- Department of Pediatrics, Vittore Buzzi Children's Hospital, University of Milan, Via Lodovico Castelvetro 32, 20154, Milan, Italy.
| | - C Bollati
- Department of Pharmaceutical Sciences, University of Milan, 20133, Milan, Italy
| | - L d'Adduzio
- Department of Pharmaceutical Sciences, University of Milan, 20133, Milan, Italy
| | - M Fanzaga
- Department of Pharmaceutical Sciences, University of Milan, 20133, Milan, Italy
| | - C Ceccarani
- Institute for Biomedical Technologies, CNR, Segrate, Italy
| | - S Vizzuso
- Department of Pediatrics, Vittore Buzzi Children's Hospital, University of Milan, Via Lodovico Castelvetro 32, 20154, Milan, Italy
| | - G Zuccotti
- Department of Pediatrics, Vittore Buzzi Children's Hospital, University of Milan, Via Lodovico Castelvetro 32, 20154, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, 20157, Milan, Italy
| | - E Borghi
- Department of Health Sciences, University of Milan, 20142, Milan, Italy
| | - E Verduci
- Department of Health Sciences, University of Milan, 20142, Milan, Italy
- Metabolic Diseases Unit, Department of Paediatrics, Vittore Buzzi Children's Hospital, University of Milan, 20157, Milan, Italy
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Furci F, Cicero N, Allegra A, Gangemi S. Microbiota, Diet and Acute Leukaemia: Tips and Tricks on Their Possible Connections. Nutrients 2023; 15:4253. [PMID: 37836537 PMCID: PMC10574113 DOI: 10.3390/nu15194253] [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: 08/24/2023] [Revised: 09/15/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Acute leukaemia is probably one of the most recurrent cancers in children and younger adults, with an incidence of acute lymphoblastic leukaemia in 80% of cases and an incidence of acute myeloid leukaemia in 15% of cases. Yet, while incidence is common in children and adolescents, acute leukaemia is a rare disease whose aetiology still requires further analysis. Many studies have investigated the aetiology of acute leukaemia, reporting that the formation of gut microbiota may be modified by the start and development of many diseases. Considering that in patients affected by acute lymphoblastic leukaemia, there is an inherent disequilibrium in the gut microbiota before treatment compared with healthy patients, increasing evidence shows how dysbiosis of the gut microbiota provokes an inflammatory immune response, contributing to the development of cancer. Our analysis suggeststhe key role of gut microbiota in the modulation of the efficacy of leukaemia treatment as well as in the progress of many cancers, such as acute leukaemia. Therefore, in this paper, we present an examination of information found in literature regarding the role of dietary factors and gut microbiota alterations in the development of leukaemia and suggest possible future preventive and therapeutic strategies.
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Affiliation(s)
- Fabiana Furci
- Provincial Healthcare Unit, Section of Allergy, 89900 Vibo Valentia, Italy;
| | - Nicola Cicero
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Via Consolare Valeria, 98125 Messina, Italy
| | - Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy;
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria, 98125 Messina, Italy;
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Qian W, Li M, Yu L, Tian F, Zhao J, Zhai Q. Effects of Taurine on Gut Microbiota Homeostasis: An Evaluation Based on Two Models of Gut Dysbiosis. Biomedicines 2023; 11:biomedicines11041048. [PMID: 37189666 DOI: 10.3390/biomedicines11041048] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/16/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Taurine, an abundant free amino acid, plays multiple roles in the body, including bile acid conjugation, osmoregulation, oxidative stress, and inflammation prevention. Although the relationship between taurine and the gut has been briefly described, the effects of taurine on the reconstitution of intestinal flora homeostasis under conditions of gut dysbiosis and underlying mechanisms remain unclear. This study examined the effects of taurine on the intestinal flora and homeostasis of healthy mice and mice with dysbiosis caused by antibiotic treatment and pathogenic bacterial infections. The results showed that taurine supplementation could significantly regulate intestinal microflora, alter fecal bile acid composition, reverse the decrease in Lactobacillus abundance, boost intestinal immunity in response to antibiotic exposure, resist colonization by Citrobacter rodentium, and enhance the diversity of flora during infection. Our results indicate that taurine has the potential to shape the gut microbiota of mice and positively affect the restoration of intestinal homeostasis. Thus, taurine can be utilized as a targeted regulator to re-establish a normal microenvironment and to treat or prevent gut dysbiosis.
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4
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Roager HM, Stanton C, Hall LJ. Microbial metabolites as modulators of the infant gut microbiome and host-microbial interactions in early life. Gut Microbes 2023; 15:2192151. [PMID: 36942883 PMCID: PMC10038037 DOI: 10.1080/19490976.2023.2192151] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
The development of infant gut microbiome is a pivotal process affecting the ecology and function of the microbiome, as well as host health. While the establishment of the infant microbiome has been of interest for decades, the focus on gut microbial metabolism and the resulting small molecules (metabolites) has been rather limited. However, technological and computational advances are now enabling researchers to profile the plethora of metabolites in the infant gut, allowing for improved understanding of how gut microbial-derived metabolites drive microbiome community structuring and host-microbial interactions. Here, we review the current knowledge on development of the infant gut microbiota and metabolism within the first year of life, and discuss how these microbial metabolites are key for enhancing our basic understanding of interactions during the early life developmental window.
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Affiliation(s)
- Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Catherine Stanton
- APC Microbiome Ireland, Teagasc Moorepark Food Research Centre, Fermoy, Co. Cork, Ireland
| | - Lindsay J. Hall
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich, UK
- Intestinal Microbiome, School of Life Sciences, ZIEL – Institute for Food & Health, Technical University of Munich, Freising, Germany
- Norwich Medical School, University of East Anglia, Norwich, UK
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5
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Okeke ES, Chukwudozie KI, Nyaruaba R, Ita RE, Oladipo A, Ejeromedoghene O, Atakpa EO, Agu CV, Okoye CO. Antibiotic resistance in aquaculture and aquatic organisms: a review of current nanotechnology applications for sustainable management. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:69241-69274. [PMID: 35969340 PMCID: PMC9376131 DOI: 10.1007/s11356-022-22319-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/27/2022] [Indexed: 05/13/2023]
Abstract
Aquaculture has emerged as one of the world's fastest-growing food industries in recent years, helping food security and boosting global economic status. The indiscriminate disposal of untreated or improperly managed waste and effluents from different sources including production plants, food processing sectors, and healthcare sectors release various contaminants such as bioactive compounds and unmetabolized antibiotics, and antibiotic-resistant organisms into the environment. These emerging contaminants (ECs), especially antibiotics, have the potential to pollute the environment, particularly the aquatic ecosystem due to their widespread use in aquaculture, leading to various toxicological effects on aquatic organisms as well as long-term persistence in the environment. However, various forms of nanotechnology-based technologies are now being explored to assist other remediation technologies to boost productivity, efficiency, and sustainability. In this review, we critically highlighted several ecofriendly nanotechnological methods including nanodrug and vaccine delivery, nanoformulations, and nanosensor for their antimicrobial effects in aquaculture and aquatic organisms, potential public health risks associated with nanoparticles, and their mitigation measures for sustainable management.
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Affiliation(s)
- Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, 41000, Enugu State, Nigeria
- Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, 41000, Enugu State, Nigeria
- Institute of Environmental Health and Ecological Security, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
| | - Kingsley Ikechukwu Chukwudozie
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Nigeria
- Department of Clinical Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Raphael Nyaruaba
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- Center for Biosafety Megascience, Wuhan Institute of Virology, CAS, Wuhan, China
| | - Richard Ekeng Ita
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- Ritman University, Ikot Ekpene, Akwa Ibom State, Nigeria
| | - Abiodun Oladipo
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, Jiangsu, People's Republic of China
| | - Onome Ejeromedoghene
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- School of Chemistry and Chemical Engineering, Southeast University, Jiangning District, Nanjing, Jiangsu Province, 211189, People's Republic of China
| | - Edidiong Okokon Atakpa
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya
- Institute of Marine Biology & Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
- Department of Animal & Environmental Biology, University of Uyo, Uyo, 1017, Akwa Ibom State, Nigeria
| | | | - Charles Obinwanne Okoye
- Organisation of African Academic Doctors (OAAD), Off Kamiti Road, Nairobi, Kenya.
- Department of Zoology & Environmental Biology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410001, Nigeria.
- School of Environment & Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, China.
- Key Laboratory of Intelligent Agricultural Machinery Equipment, Jiangsu University, Zhenjiang, 212013, China.
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6
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Qiu H, Ma QG, Chen XT, Wen X, Zhang N, Liu WM, Wang TT, Zhang LZ. Different classes of antibiotics exhibit disparate negative impacts on the therapeutic efficacy of immune checkpoint inhibitors in advanced non-small cell lung cancer patients. Am J Cancer Res 2022; 12:3175-3184. [PMID: 35968357 PMCID: PMC9360237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023] Open
Abstract
It has been reported that antibiotics (ATBs) have adverse effect on the efficacy of treatment with immune checkpoint inhibitors (ICIs) in cancer patients. Since different classes of ATBs have different antibacterial spectrum, we aimed to study whether all ATBs had similar or different negative effects on the clinical outcomes of ICIs in patients with advanced non-small cell lung cancer (NSCLC). Patients with advanced NSCLC who received ICIs were included in this retrospective study and grouped by the class of ATBs they had used around the ICIs treatment time. The overall survival (OS) and the progression free survival (PFS) of patients among these groups were compared using Kaplan-Meier method and Cox proportional hazards model. A total of 148 eligible patients were enrolled, and 80 patients used ATBs. The results indicated that quinolones had no significant negative consequence on the clinical outcomes, while β-lactams significantly shortened the OS and PFS of patients. Furthermore, patients exposed to the combination of β-lactams and quinolones suffered the worst OS and PFS. Moreover, the subgroup analysis of β-lactams revealed that only penicillins, but not carbapenems and cephalosporins, markedly reduced both OS and PFS. In addition to the class of ATBs used, the time frame of ATBs used also affected the clinical outcomes of ICIs therapy. Patients receiving ATBs within 60 days prior to and 30 days after the initiation of ICI treatment had significantly shorter OS and PFS compared with those who did not use ATBs. This study demonstrated that different classes of ATBs had disparate negative impacts on the clinical outcomes, and the use of β-lactams, especially penicillins, should be avoided in advanced NSCLC patients who are receiving or scheduled to receive ICIs within 60 days.
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Affiliation(s)
- Hui Qiu
- Cancer Institute, Xuzhou Medical UniversityXuzhou 221000, Jiangsu, China
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical UniversityXuzhou 221000, Jiangsu, China
| | - Qing-Gong Ma
- Cancer Institute, Xuzhou Medical UniversityXuzhou 221000, Jiangsu, China
| | - Xue-Ting Chen
- Cancer Institute, Xuzhou Medical UniversityXuzhou 221000, Jiangsu, China
| | - Xin Wen
- Cancer Institute, Xuzhou Medical UniversityXuzhou 221000, Jiangsu, China
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical UniversityXuzhou 221000, Jiangsu, China
| | - Nie Zhang
- Cancer Institute, Xuzhou Medical UniversityXuzhou 221000, Jiangsu, China
| | - Wan-Ming Liu
- Cancer Institute, Xuzhou Medical UniversityXuzhou 221000, Jiangsu, China
| | - Ting-Ting Wang
- Cancer Institute, Xuzhou Medical UniversityXuzhou 221000, Jiangsu, China
| | - Long-Zhen Zhang
- Cancer Institute, Xuzhou Medical UniversityXuzhou 221000, Jiangsu, China
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical UniversityXuzhou 221000, Jiangsu, China
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7
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Gough EK. The impact of mass drug administration of antibiotics on the gut microbiota of target populations. Infect Dis Poverty 2022; 11:76. [PMID: 35773678 PMCID: PMC9245274 DOI: 10.1186/s40249-022-00999-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/09/2022] [Indexed: 12/15/2022] Open
Abstract
Antibiotics have become a mainstay of healthcare in the past century due to their activity against pathogens. This manuscript reviews the impact of antibiotic use on the intestinal microbiota in the context of mass drug administration (MDA). The importance of the gut microbiota to human metabolism and physiology is now well established, and antibiotic exposure may impact host health via collateral effects on the microbiota and its functions. To gain further insight into how gut microbiota respond to antibiotic perturbation and the implications for public health, factors that influence the impact of antibiotic exposure on the microbiota, potential health outcomes of antibiotic-induced microbiota alterations, and strategies that have the potential to ameliorate these wider antibiotic-associated microbiota perturbations are also reviewed.
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Affiliation(s)
- Ethan K Gough
- Department of International Health, Human Nutrition Program, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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Gao J, He S, Nag A, Zeng X. Physicochemical and rheological properties of interacted protein hydrolysates derived from tuna processing by‐products with sodium alginate. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jingrong Gao
- School of Chemistry and Chemical Engineering Guangzhou University Guangzhou 510006 China
| | - Shan He
- School of Chemistry and Chemical Engineering Guangzhou University Guangzhou 510006 China
- Institute for NanoScale Science and Technology College of Science and Engineering Flinders University Bedford Park 5042 Australia
| | - Anindya Nag
- Faculty of Electrical and Computer Engineering Technische Universität Dresden Dresden 01062 Germany
- Centre for Tactile Internet with Human‐in‐the‐Loop (CeTI) Technische Universität Dresden Dresden 01069 Germany
| | - Xin‐An Zeng
- School of Food Science and Engineering South China University of Technology Guangzhou 510640 China
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9
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Hou K, Wu ZX, Chen XY, Wang JQ, Zhang D, Xiao C, Zhu D, Koya JB, Wei L, Li J, Chen ZS. Microbiota in health and diseases. Signal Transduct Target Ther 2022; 7:135. [PMID: 35461318 PMCID: PMC9034083 DOI: 10.1038/s41392-022-00974-4] [Citation(s) in RCA: 650] [Impact Index Per Article: 325.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 02/07/2023] Open
Abstract
The role of microbiota in health and diseases is being highlighted by numerous studies since its discovery. Depending on the localized regions, microbiota can be classified into gut, oral, respiratory, and skin microbiota. The microbial communities are in symbiosis with the host, contributing to homeostasis and regulating immune function. However, microbiota dysbiosis can lead to dysregulation of bodily functions and diseases including cardiovascular diseases (CVDs), cancers, respiratory diseases, etc. In this review, we discuss the current knowledge of how microbiota links to host health or pathogenesis. We first summarize the research of microbiota in healthy conditions, including the gut-brain axis, colonization resistance and immune modulation. Then, we highlight the pathogenesis of microbiota dysbiosis in disease development and progression, primarily associated with dysregulation of community composition, modulation of host immune response, and induction of chronic inflammation. Finally, we introduce the clinical approaches that utilize microbiota for disease treatment, such as microbiota modulation and fecal microbial transplantation.
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Affiliation(s)
- Kaijian Hou
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, The First Affiliated Hospital of Medical College of Shantou University, Shantou, Guangdong, 515000, China
| | - Zhuo-Xun Wu
- Department of Pharmaceutical Sciences, Institute for Biotechnology, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Xuan-Yu Chen
- Department of Pharmaceutical Sciences, Institute for Biotechnology, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Jing-Quan Wang
- Department of Pharmaceutical Sciences, Institute for Biotechnology, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Dongya Zhang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd, Guangzhou, 510535, China
| | - Chuanxing Xiao
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, The First Affiliated Hospital of Medical College of Shantou University, Shantou, Guangdong, 515000, China
| | - Dan Zhu
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, The First Affiliated Hospital of Medical College of Shantou University, Shantou, Guangdong, 515000, China
| | - Jagadish B Koya
- Department of Pharmaceutical Sciences, Institute for Biotechnology, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Liuya Wei
- School of Pharmacy, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Jilin Li
- Department of Cardiovascular, The Second Affiliated Hospital of Medical College of Shantou University, Shantou, Guangdong, 515000, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, Institute for Biotechnology, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
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Solans M, Barceló MA, Morales-Suárez-Varela M, Moya A, Saez M. Prenatal exposure to antibiotics and risk of childhood overweight or obesity: A systematic review and meta-analysis. Obes Rev 2022; 23 Suppl 1:e13382. [PMID: 34859947 DOI: 10.1111/obr.13382] [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: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 10/19/2022]
Abstract
Infant antibiotic use has been modestly associated with childhood overweight, while evidence on prenatal exposures remains less clear. A systematic review and meta-analysis were conducted to examine associations between maternal antibiotic exposure and subsequent risk of childhood overweight/obesity. Publications were retrieved from PubMed and Web of Science databases up to December 2019. A random effects model was used to summarize risk estimates, overall, and by period and frequency of exposure. Ten observational studies were included in the narrative synthesis. We did not observe a clear pattern of association between prenatal antibiotic use and childhood overweight/obesity. There were suggestive associations for repeated exposures (≥3 courses) and those taking place during the second trimester of gestation, which were also pointed out in our meta-analysis (relative risk, RR2T = 1.15 (95% CI 1.04; 1.28, I2 = 18%), and RR3courses = 1.31 (95% CI 1.03; 1.67, I2 = 65%), respectively). In most studies, however, confounding by underlying infections cannot be ruled out. Overall, current data do not conclusively support the hypothesis that prenatal exposure to antibiotics is a risk factor for childhood obesity/overweight. Further studies, controlling for underlying infections and exploring the association according to frequency, period (both prenatal and intrapartum) and type of antibiotic, are needed to clarify this association.
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Affiliation(s)
- Marta Solans
- Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP), Girona, Spain.,Research Group on Statistics, Econometrics and Health (GRECS), University of Girona, Girona, Spain
| | - Maria A Barceló
- Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP), Girona, Spain.,Research Group on Statistics, Econometrics and Health (GRECS), University of Girona, Girona, Spain
| | - Maria Morales-Suárez-Varela
- Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP), Girona, Spain.,Department of Preventive Medicine and Public Health, Food Sciences, Toxicology, and Legal Medicine, School of Pharmacy, University of Valencia, Valencia, Spain
| | - Andrés Moya
- Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP), Girona, Spain.,Instituto de Biología Integrativa de Sistemas, Universitat de València and Spanish Research Council (CSIC), Valencia, Spain.,Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Valencia, Spain
| | - Marc Saez
- Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP), Girona, Spain.,Research Group on Statistics, Econometrics and Health (GRECS), University of Girona, Girona, Spain
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11
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Metaproteomics Approach and Pathway Modulation in Obesity and Diabetes: A Narrative Review. Nutrients 2021; 14:nu14010047. [PMID: 35010920 PMCID: PMC8746330 DOI: 10.3390/nu14010047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
Low-grade inflammatory diseases revealed metabolic perturbations that have been linked to various phenotypes, including gut microbiota dysbiosis. In the last decade, metaproteomics has been used to investigate protein composition profiles at specific steps and in specific healthy/pathologic conditions. We applied a rigorous protocol that relied on PRISMA guidelines and filtering criteria to obtain an exhaustive study selection that finally resulted in a group of 10 studies, based on metaproteomics and that aim at investigating obesity and diabetes. This batch of studies was used to discuss specific microbial and human metaproteome alterations and metabolic patterns in subjects affected by diabetes (T1D and T2D) and obesity. We provided the main up- and down-regulated protein patterns in the inspected pathologies. Despite the available results, the evident paucity of metaproteomic data is to be considered as a limiting factor in drawing objective considerations. To date, ad hoc prepared metaproteomic databases collecting pathologic data and related metadata, together with standardized analysis protocols, are required to increase our knowledge on these widespread pathologies.
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12
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Goh YQ, Cheam G, Wang Y. Understanding Choline Bioavailability and Utilization: First Step Toward Personalizing Choline Nutrition. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10774-10789. [PMID: 34392687 DOI: 10.1021/acs.jafc.1c03077] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Choline is an essential macronutrient involved in neurotransmitter synthesis, cell-membrane signaling, lipid transport, and methyl-group metabolism. Nevertheless, the vast majority are not meeting the recommended intake requirement. Choline deficiency is linked to nonalcoholic fatty liver disease, skeletal muscle atrophy, and neurodegenerative diseases. The conversion of dietary choline to trimethylamine by gut microbiota is known for its association with atherosclerosis and may contribute to choline deficiency. Choline-utilizing bacteria constitutes less than 1% of the gut community and is modulated by lifestyle interventions such as dietary patterns, antibiotics, and probiotics. In addition, choline utilization is also affected by genetic factors, further complicating the impact of choline on health. This review overviews the complex interplay between dietary intakes of choline, gut microbiota and genetic factors, and the subsequent impact on health. Understanding of gut microbiota metabolism of choline substrates and interindividual variability is warranted in the development of personalized choline nutrition.
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Affiliation(s)
- Ying Qi Goh
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921
| | - Guoxiang Cheam
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921
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13
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Wang S, Yong H, He XD. Multi-omics: Opportunities for research on mechanism of type 2 diabetes mellitus. World J Diabetes 2021; 12:1070-1080. [PMID: 34326955 PMCID: PMC8311486 DOI: 10.4239/wjd.v12.i7.1070] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/22/2021] [Accepted: 05/22/2021] [Indexed: 02/06/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a burdensome global disease. In-depth understanding of its mechanism will help to optimize diagnosis and treatment, which reduces the burden. Multi-omics research has unparalleled advantages in contributing to the overall understanding of the mechanism of this chronic metabolic disease. In the past two decades, the study of multi-omics on T2DM-related intestinal flora perturbation and plasma dyslipidemia has shown tremendous potential and is expected to achieve major breakthroughs. The regulation of intestinal flora in diabetic patients has been confirmed by multiple studies. The use of metagenomics, 16S RNA sequencing, and metabolomics has comprehensively identified the overall changes in the intestinal flora and the metabolic disturbances that could directly or indirectly participate in the intestinal flora-host interactions. Lipidomics combined with other “omics” has characterized lipid metabolism disorders in T2DM. The combined application and cross-validation of multi-omics can screen for dysregulation in T2DM, which will provide immense opportunities to understand the mechanisms behind T2DM.
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Affiliation(s)
- Shuai Wang
- Institute of Toxicology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong Province, China
| | - Hui Yong
- Institute of Toxicology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong Province, China
| | - Xiao-Dong He
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong Province, China
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14
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Pernica JM, Harman S, Kam AJ, Carciumaru R, Vanniyasingam T, Crawford T, Dalgleish D, Khan S, Slinger RS, Fulford M, Main C, Smieja M, Thabane L, Loeb M. Short-Course Antimicrobial Therapy for Pediatric Community-Acquired Pneumonia: The SAFER Randomized Clinical Trial. JAMA Pediatr 2021; 175:475-482. [PMID: 33683325 PMCID: PMC7941245 DOI: 10.1001/jamapediatrics.2020.6735] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
IMPORTANCE Community-acquired pneumonia (CAP) is a common occurrence in childhood; consequently, evidence-based recommendations for its treatment are required. OBJECTIVE To determine whether 5 days of high-dose amoxicillin for CAP was associated with noninferior rates of clinical cure compared with 10 days of high-dose amoxicillin. DESIGN, SETTING, AND PARTICIPANTS The SAFER (Short-Course Antimicrobial Therapy for Pediatric Respiratory Infections) study was a 2-center, parallel-group, noninferiority randomized clinical trial consisting of a single-center pilot study from December 1, 2012, to March 31, 2014, and the follow-up main study from August 1, 2016, to December 31, 2019 at the emergency departments of McMaster Children's Hospital and the Children's Hospital of Eastern Ontario. Research staff, participants, and outcome assessors were blinded to treatment allocation. Eligible children were aged 6 months to 10 years and had fever within 48 hours, respiratory symptoms, chest radiography findings consistent with pneumonia as per the emergency department physician, and a primary diagnosis of pneumonia. Children were excluded if they required hospitalization, had comorbidities that would predispose them to severe disease and/or pneumonia of unusual origin, or had previous β-lactam antibiotic therapy. Data were analyzed from March 1 to July 8, 2020. INTERVENTIONS Five days of high-dose amoxicillin therapy followed by 5 days of placebo (intervention group) vs 5 days of high-dose amoxicillin followed by a different formulation of 5 days of high-dose amoxicillin (control group). MAIN OUTCOMES AND MEASURES Clinical cure at 14 to 21 days. RESULTS Among the 281 participants, the median age was 2.6 (interquartile range, 1.6-4.9) years (160 boys [57.7%] of 279 with sex listed). Clinical cure was observed in 101 of 114 children (88.6%) in the intervention group and in 99 of 109 (90.8%) in the control group in per-protocol analysis (risk difference, -0.016; 97.5% confidence limit, -0.087). Clinical cure at 14 to 21 days was observed in 108 of 126 (85.7%) in the intervention group and in 106 of 126 (84.1%) in the control group in the intention-to-treat analysis (risk difference, 0.023; 97.5% confidence limit, -0.061). CONCLUSIONS AND RELEVANCE Short-course antibiotic therapy appeared to be comparable to standard care for the treatment of previously healthy children with CAP not requiring hospitalization. Clinical practice guidelines should consider recommending 5 days of amoxicillin for pediatric pneumonia management in accordance with antimicrobial stewardship principles. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02380352.
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Affiliation(s)
- Jeffrey M. Pernica
- Division of Infectious Diseases, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada,Pediatric Emergency Research Canada, Calgary, Alberta, Canada
| | - Stuart Harman
- Pediatric Emergency Research Canada, Calgary, Alberta, Canada,Division of Emergency Medicine, Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - April J. Kam
- Pediatric Emergency Research Canada, Calgary, Alberta, Canada,Division of Emergency Medicine, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Redjana Carciumaru
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Thuva Vanniyasingam
- Biostiatistics Unit, St Joseph’s Healthcare Hamilton, Hamilton, Ontario, Canada
| | - Tyrus Crawford
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Dale Dalgleish
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Sarah Khan
- Division of Infectious Diseases, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Robert S. Slinger
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Martha Fulford
- Division of Infectious Diseases, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Cheryl Main
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Marek Smieja
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Lehana Thabane
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Mark Loeb
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
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15
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Abstract
We are in the midst of “the microbiome revolution”—not a day goes by without some new revelation on the potential role of the gut microbiome in some disease or disorder. From an ever-increasing recognition of the many roles of the gut microbiome in health and disease comes the expectation that its modulation could treat or prevent these very same diseases. A variety of interventions could, at least in theory, be employed to alter the composition or functional capacity of the microbiome, ranging from diet to fecal microbiota transplantation (FMT). For some, such as antibiotics, prebiotics, and probiotics, an extensive, albeit far from consistent, literature already exists; for others, such as other dietary supplements and FMT, high-quality clinical studies are still relatively few in number. Not surprisingly, researchers have turned to the microbiome itself as a source for new entities that could be used therapeutically to manipulate the microbiome; for example, some probiotic strains currently in use were sourced from the gastrointestinal tract of healthy humans. From all of the extant studies of interventions targeted at the gut microbiome, a number of important themes have emerged. First, with relatively few exceptions, we are still a long way from a precise definition of the role of the gut microbiome in many of the diseases where a disturbed microbiome has been described—association does not prove causation. Second, while animal models can provide fascinating insights into microbiota–host interactions, they rarely recapitulate the complete human phenotype. Third, studies of several interventions have been difficult to interpret because of variations in study population, test product, and outcome measures, not to mention limitations in study design. The goal of microbiome modulation is a laudable one, but we need to define our targets, refine our interventions, and agree on outcomes.
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Affiliation(s)
- Eamonn M M Quigley
- Lynda K and David M Underwood Center for Digestive Disorders, Division of Gastroenterology and Hepatology, Houston Methodist Hospital, Houston, Texas, 77030, USA
| | - Prianka Gajula
- Department of Medicine, Houston Methodist Hospital, Houston, Texas, 77030, USA
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16
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Zhou ZY, Xu X, Zhou Y. [Research progress on carbohydrate active enzymes of human microbiome]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2019; 37:666-670. [PMID: 31875448 DOI: 10.7518/hxkq.2019.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A massive variety of microorganisms live in and on the human body, especially at oral, skin, vaginal, gastroin-testinal, and respiratory sites. The complicated metabolic activities of microorganisms assist human digestive function and participate in a series of physiological and pathogenetic processes. Carbohydrate-active enzymes (CAZymes) are a series of enzymes that function in degradation, modification, and formation of glycoside bonds. Microbes regulate the physiological and pathogenetic processes of human body by producing various CAZymes to degrade and modify complex carbohydrates and generate signal molecules for further utilization in human cells. Here, we reviewed the mechanisms of complex carbohy-drate metabolism and related microbial CAZymes, especially in digestive tract and oral cavity. We also summarized the rela-tionship between microbial CAZymes and human health, and proposed potential applications.
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Affiliation(s)
- Zhi-Yan Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Conservative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xin Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Conservative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yuan Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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17
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Keerthisinghe TP, Wang M, Zhang Y, Dong W, Fang M. Low-dose tetracycline exposure alters gut bacterial metabolism and host-immune response: "Personalized" effect? ENVIRONMENT INTERNATIONAL 2019; 131:104989. [PMID: 31302481 DOI: 10.1016/j.envint.2019.104989] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/30/2019] [Accepted: 06/30/2019] [Indexed: 06/10/2023]
Abstract
The human gut microbiome (GM) in healthy people is chronically exposed to tetracycline (TET) via environmental exposure and dietary uptake. However, limited information is available on its effect on the GM metabolome and effect on the host, especially at the dietary exposure level. Here, we investigated how TET at both sub-pharmaceutical and dietary exposure levels affects the metabolome and the secretome-induced host immune response by studying several representative gut bacteria. Interestingly, the metabolome showed a highly species-specific pattern with a distinct dose-response relationship. B. fragilis was highly sensitive to TET and vitamin, nucleotide, and amino acid metabolism pathways were the most vulnerable metabolic pathways at dietary exposure level. For key metabolite short chain fatty acids, TET significantly induced the synthesis of butyrate in B. fragilis, rather than C. sporogenes and E. coli. Furthermore, TET induced the release of lipopolysaccharides (LPS) in E. coli and enhanced the immune response; however, there was no obvious effect on B. fragilis. Interestingly, the overall immune response modulation with TET exposure relied on the ratio between E. coli and B. fragilis, possibly due to the neutralization of active LPS from E. coli by the LPS from B. fragilis. Overall, our results showed that the effect of TET from environmental exposure on the host health would be highly dependent on the GM composition, especially for the gut bacterial metabolome and secretome induced immune response.
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Affiliation(s)
- Tharushi P Keerthisinghe
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore; Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 63714, Singapore
| | - Mengjing Wang
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore
| | - Yingdan Zhang
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore
| | - Wu Dong
- College of Animal Science and Technology, Inner Mongolia University for Nationalities/Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, Tongliao 028000, China
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, 639798, Singapore; Analytical Cluster, Nanyang Environment & Water Research Institute, Nanyang Technological University, 637141, Singapore.
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18
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Ezzeldin S, El-Wazir A, Enany S, Muhammad A, Johar D, Osama A, Ahmed E, Shikshaky H, Magdeldin S. Current Understanding of Human Metaproteome Association and Modulation. J Proteome Res 2019; 18:3539-3554. [PMID: 31262181 DOI: 10.1021/acs.jproteome.9b00301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During the last decade, metaproteomics has provided a better understanding and functional characterization of the microbiome. A large body of evidence now reveals interspecies, species of bacteria-host interactions, via the secreted modulatory microbial protein "metaproteome". Although high-throughput state-of-art mass spectrometry has recently empowered metaproteomics, its profile remains unclear, and, most importantly, the exact consequences and underlying mechanism of these protein molecules on the host are insufficiently understood. Here we address the current progress in the study of the human metaproteome, suggesting possible modulation, a metaproteome dysbiotic signature, challenges, and future perspectives.
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Affiliation(s)
- Shahd Ezzeldin
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt
| | - Aya El-Wazir
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine , Suez Canal University , 41522 Ismailia , Egypt.,Center of Excellence of Molecular and Cellular Medicine , Suez Canal University , 41522 Ismailia , Egypt
| | - Shymaa Enany
- Department of Microbiology and Immunology, Faculty of Pharmacy , Suez Canal University , 41522 Ismailia , Egypt
| | - Abdelrahman Muhammad
- Department of Biomedical Engineering , Higher Technological Institute , 44634 Sharqia , Egypt
| | - Dina Johar
- Biomedical Sciences Program, University of Science and Technology , Zewail City of Science and Technology , 12588 Giza , Egypt
| | - Aya Osama
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt
| | - Eman Ahmed
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt.,Department of Pharmacology, Faculty of Veterinary Medicine , Suez Canal University , 41522 Ismailia , Egypt
| | - Hassan Shikshaky
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt
| | - Sameh Magdeldin
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt.,Department of Physiology, Faculty of Veterinary Medicine , Suez Canal University , 41522 Ismailia , Egypt
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19
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Connection between gut microbiome and the development of obesity. Eur J Clin Microbiol Infect Dis 2019; 38:1987-1998. [PMID: 31367997 DOI: 10.1007/s10096-019-03623-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/26/2019] [Indexed: 02/08/2023]
Abstract
The potential role of the gut microbiota in various human diseases has attracted considerable attention worldwide. Here, we discuss the vital role of the intestinal microbiota in the development of obesity. First, we describe how the gut microbiota promotes fat accumulation. Additionally, a high-fat diet leads to structural instability among in the gut microbiota, further leading to an increase in endotoxins, which aggravates obesity. We then discuss how gut microbiota metabolites, including short-chain fatty acids and lipopolysaccharides, affect the host. Finally, we review several strategies for regulating the intestinal flora.
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20
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Wen Y, Jin R, Chen H. Interactions Between Gut Microbiota and Acute Childhood Leukemia. Front Microbiol 2019; 10:1300. [PMID: 31275258 PMCID: PMC6593047 DOI: 10.3389/fmicb.2019.01300] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/24/2019] [Indexed: 01/26/2023] Open
Abstract
Childhood leukemia, the commonest childhood cancer, mainly consists of acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). Though great progresses have been made in the survival rates of childhood leukemia, the long-term health problems of long-term childhood leukemia survivors remain remarkable. In addition, the deep links between risk factors and childhood leukemia need to be elucidated. What can be done to improve the prevention and the prognosis of childhood leukemia is an essential issue. Gut microbiota, referred to as one of the largest symbiotic microorganisms that is accommodated in the gastrointestinal tract of human or animals, is found to be involved in the progression of various diseases. It is reported that microbiota may keep people in good health by participating in metabolism processes and regulating the immune system. Studies have also explored the potential relationships between gut microbiota and childhood leukemia. This review is meant to illustrate the roles of gut microbiota in the onset of acute childhood leukemia, as well as in the progress and prognosis of leukemia and how the treatments for leukemia affect gut microbiota. Besides, this review is focused on the possibility of building or rebuilding a healthy gut microbiota by adjusting the diet construction so as to help clinicians deal with childhood leukemia.
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Affiliation(s)
- Yuxi Wen
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Runming Jin
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Chen
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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21
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Cheng M, Ning K. Stereotypes About Enterotype: the Old and New Ideas. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:4-12. [PMID: 31026581 PMCID: PMC6521238 DOI: 10.1016/j.gpb.2018.02.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/27/2017] [Accepted: 02/09/2018] [Indexed: 12/21/2022]
Abstract
In 2011, the term “enterotype” first appeared to the general public in Nature, which refers to stratification of human gut microbiota. However, with more studies on enterotypes conducted nowadays, doubts about the existence and robustness of enterotypes have also emerged. Here we reviewed current opinions about enterotypes from both conceptual and analytical points of view. We firstly illustrated the definition of the enterotype and various factors influencing enterotypes, such as diet, administration of antibiotics, and age. Then we summarized lines of evidence that pose the concept against the enterotype, and described the current methods for enterotype analysis. Finally, we showed that the concept of enterotype has been extended to other ecological niches. Based on current studies on enterotypes, it has been clear that more studies with larger sample sizes are needed to characterize the enterotypes. Improved computational methods are also required to build sophisticated models, reflecting the dynamics and resilience of enterotypes.
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Affiliation(s)
- Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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22
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Martín-Núñez GM, Cornejo-Pareja I, Coin-Aragüez L, Roca-Rodríguez MDM, Muñoz-Garach A, Clemente-Postigo M, Cardona F, Moreno-Indias I, Tinahones FJ. H. pylori eradication with antibiotic treatment causes changes in glucose homeostasis related to modifications in the gut microbiota. PLoS One 2019; 14:e0213548. [PMID: 30870471 PMCID: PMC6417676 DOI: 10.1371/journal.pone.0213548] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/22/2019] [Indexed: 12/15/2022] Open
Abstract
Background H. pylori infection and eradication cause perturbations of the gut microbiome. The gut microbiota has been identified as a potential contributor to metabolic diseases. We evaluate whether these alterations in intestinal microbiota composition produced by H. pylori infection and its posterior eradication with antibiotic treatment could be associated with glucose homeostasis in metabolically healthy subjects. Methods Forty adult patients infected with H. pylori and 20 control subjects were recruited. The infected subjects were evaluated before and two months after eradication treatment (omeprazole, clarithromycin, amoxicillin). The microbiota composition in fecal samples was determined by 16S rRNA gene (V3-V4) sequencing using Illumina Miseq. Results Patients (pre- and post-H. pylori eradication) showed a decreased bacterial richness and diversity with respect to controls. There was an improvement in glucose homeostasis in subjects two months after H. pylori eradication treatment. Changes in the amount of Rikenellaceae, Butyricimonas, E. biforme, B. fragilis, and Megamonas were inversely associated with changes in the glucose level or related parameters (Hb1ac) in H. pylori eradication subjects. Conclusions H. pylori infection and eradication with antibiotic treatment causes alteration of the human gut microbiome. The increase in SCFA-producing bacteria and glucose-removing bacteria, specifically members of Megamonas, Rikenellaceae and Butyricimonas, has been related with an improvement in glucose homeostasis after H. pylori eradication with antibiotic treatment.
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Affiliation(s)
- Gracia Mª Martín-Núñez
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Cornejo-Pareja
- Departamento de Endocrinología y Nutrición, Hospital Virgen de la Victoria, Málaga, Spain
| | - Leticia Coin-Aragüez
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Araceli Muñoz-Garach
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Endocrinología y Nutrición, Hospital Virgen de la Victoria, Málaga, Spain
| | - Mercedes Clemente-Postigo
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Fernando Cardona
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Moreno-Indias
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco J Tinahones
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga (IBIMA), Hospital Clínico Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
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23
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Moossavi S, Bishehsari F. Microbes: possible link between modern lifestyle transition and the rise of metabolic syndrome. Obes Rev 2019; 20:407-419. [PMID: 30548384 DOI: 10.1111/obr.12784] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 12/13/2022]
Abstract
The rapid decrease in infectious diseases globally has coincided with an increase in the prevalence of obesity and other components of metabolic syndrome. Insulin resistance is a common feature of metabolic syndrome and can be influenced by genetic and non-genetic/environmental factors. The emergence of metabolic syndrome epidemics over only a few decades suggests a more prominent role of the latter. Changes in our environment and lifestyle have indeed paralleled the rise in metabolic syndrome. Gastrointestinal tract microbiota, the composition of which plays a significant role in host physiology, including metabolism and energy homeostasis, are distinctly different within the context of metabolic syndrome. Among humans, recent lifestyle-related changes could be linked to changes in diversity and composition of 'ancient' microbiota. Given the co-adaptation and co-evolution of microbiota with the immune system over a long period of time, it is plausible that such lifestyle-related microbiota changes could trigger aberrant immune responses, thereby predisposing an individual to a variety of diseases. Here, we review current evidence supporting a role for gut microbiota in the ongoing rise of metabolic syndrome. We conclude that population-level shifts in microbiota can play a mediatory role between lifestyle factors and pathogenesis of insulin resistance and metabolic syndrome.
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Affiliation(s)
- S Moossavi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - F Bishehsari
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL, USA
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24
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Shin A, Preidis GA, Shulman R, Kashyap PC. The Gut Microbiome in Adult and Pediatric Functional Gastrointestinal Disorders. Clin Gastroenterol Hepatol 2019; 17:256-274. [PMID: 30153517 PMCID: PMC6314902 DOI: 10.1016/j.cgh.2018.08.054] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/23/2018] [Accepted: 08/21/2018] [Indexed: 02/07/2023]
Abstract
The importance of gut microbiota in gastrointestinal (GI) physiology was well described, but our ability to study gut microbial ecosystems in their entirety was limited by culture-based methods prior to the sequencing revolution. The advent of high-throughput sequencing opened new avenues, allowing us to study gut microbial communities as an aggregate, independent of our ability to culture individual microbes. Early studies focused on association of changes in gut microbiota with different disease states, which was necessary to identify a potential role for microbes and generate novel hypotheses. Over the past few years the field has moved beyond associations to better understand the mechanistic implications of the microbiome in the pathophysiology of complex diseases. This movement also has resulted in a shift in our focus toward therapeutic strategies, which rely on better understanding the mediators of gut microbiota-host cross-talk. It is not surprising the gut microbiome has been implicated in the pathogenesis of functional gastrointestinal disorders given its role in modulating physiological processes such as immune development, GI motility and secretion, epithelial barrier integrity, and brain-gut communication. In this review, we focus on the current state of knowledge and future directions in microbiome research as it pertains to functional gastrointestinal disorders. We summarize the factors that help shape the gut microbiome in human beings. We discuss data from animal models and human studies to highlight existing paradigms regarding the mechanisms underlying microbiota-mediated alterations in physiological processes and their relevance in human interventions. While translation of microbiome science is still in its infancy, the outlook is optimistic and we are advancing in the right direction toward precise mechanism-based microbiota therapies.
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Affiliation(s)
- Andrea Shin
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Geoffrey A Preidis
- Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Robert Shulman
- Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Purna C Kashyap
- Enteric Neuroscience Program, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
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25
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Nanoparticle microarray for high-throughput microbiome metabolomics using matrix-assisted laser desorption ionization mass spectrometry. Anal Bioanal Chem 2018; 411:147-156. [PMID: 30377739 DOI: 10.1007/s00216-018-1436-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/06/2018] [Accepted: 10/17/2018] [Indexed: 01/30/2023]
Abstract
A high-throughput matrix-assisted laser desorption/ionization mass spectrometry (MALDI)-MS-based metabolomics platform was developed using a pre-fabricated microarray of nanoparticles and organic matrices. Selected organic matrices, inorganic nanoparticle (NP) suspensions, and sputter coated metal NPs, as well as various additives, were tested for metabolomics analysis of the turkey gut microbiome. Four NPs and one organic matrix were selected as the optimal matrix set: α-cyano-4-hydroycinnamic acid, Fe3O4 and Au NPs in positive ion mode with 10 mM sodium acetate, and Cu and Ag NPs in negative ion mode with no additive. Using this set of five matrices, over two thousand unique metabolite features were reproducibly detected across intestinal samples from turkeys fed a diet amended with therapeutic or sub-therapeutic antibiotics (200 g/ton or 50 g/ton bacitracin methylene disalicylate (BMD), respectively), or non-amended feed. Among the thousands of unique features, 56 of them were chemically identified using MALDI-MS/MS, with the help of in-parallel liquid chromatography (LC)-MS/MS analysis. Lastly, as a proof of concept application, this protocol was applied to 52 turkey cecal samples at three different time points from the antibiotic feed trial. Statistical analysis indicated variations in the metabolome of turkeys with different ages or treatments. Graphical abstract ᅟ.
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26
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Cerdó T, Ruiz A, Acuña I, Jáuregui R, Jehmlich N, Haange SB, von Bergen M, Suárez A, Campoy C. Gut microbial functional maturation and succession during human early life. Environ Microbiol 2018; 20:2160-2177. [PMID: 29687552 DOI: 10.1111/1462-2920.14235] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/08/2018] [Indexed: 12/20/2022]
Abstract
The evolutional trajectory of gut microbial colonization from birth has been shown to prime for health later in life. Here, we combined cultivation-independent 16S rRNA gene sequencing and metaproteomics to investigate the functional maturation of gut microbiota in faecal samples from full-term healthy infants collected at 6 and 18 months of age. Phylogenetic analysis of the metaproteomes showed that Bifidobacterium provided the highest number of distinct protein groups. Considerable divergences between taxa abundance and protein phylogeny were observed at all taxonomic ranks. Age had a profound effect on early microbiota where compositional and functional diversity of less dissimilar communities increased with time. Comparisons of the relative abundances of proteins revealed the transition of taxon-associated saccharolytic and fermentation strategies from milk and mucin-derived monosaccharide catabolism feeding acetate/propanoate synthesis to complex food-derived hexoses fuelling butanoate production. Furthermore, co-occurrence network analysis uncovered two anti-correlated modules of functional taxa. A low-connected Bifidobacteriaceae-centred guild of facultative anaerobes was succeeded by a rich club of obligate anaerobes densely interconnected around Lachnospiraceae, underpinning their pivotal roles in microbial ecosystem assemblies. Our findings establish a framework to visualize whole microbial community metabolism and ecosystem succession dynamics, proposing opportunities for microbiota-targeted health-promoting strategies early in life.
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Affiliation(s)
- Tomás Cerdó
- Department of Paediatrics, School of Medicine, University of Granada, Granada, Spain.,EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, Granada, Spain
| | - Alicia Ruiz
- EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, Granada, Spain.,Department of Biochemistry and Molecular Biology 2, Biomedical Research Centre, University of Granada, Spain
| | - Inmaculada Acuña
- Department of Biochemistry and Molecular Biology 2, Biomedical Research Centre, University of Granada, Spain
| | - Ruy Jáuregui
- AgResearch Grasslands, Tennent Drive, Private Bag 11008, Palmerston North, New Zealand
| | - Nico Jehmlich
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research- UFZ, Permoserstraße 15, Leipzig, Germany
| | - Sven-Bastian Haange
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research- UFZ, Permoserstraße 15, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research- UFZ, Permoserstraße 15, Leipzig, Germany
| | - Antonio Suárez
- Department of Biochemistry and Molecular Biology 2, Biomedical Research Centre, University of Granada, Spain
| | - Cristina Campoy
- Department of Paediatrics, School of Medicine, University of Granada, Granada, Spain.,EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, Granada, Spain.,Spanish Network of Biomedical Research in Epidemiology and Public Health (CIBERESP), Carlos III Institute, Granada node, Spain
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27
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Abstract
The human GI tract harbors a diverse and dynamic microbial community comprising bacteria, archaea, viruses and eukaryotic microbes, which varies in composition from individual to individual. A healthy microbiota metabolizes various indigestible dietary components of the host, maintains host immune homeostasis and nutrient intake, but, an imbalanced microbiota has been reported to be associated with many diseases, including obesity. Rodent studies have produced evidence in support of the causal role of the gut microbiota in the development of obesity, however, such causal relationship is lacking in humans. The objective of this review is to critically analyze the vast information available on the composition, function and alterations of the gut microbiota in obesity and explore the future prospects of this research area.
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Affiliation(s)
- Shabana
- Department of Microbiology & Molecular Genetics, University of the Punjab, Lahore 54590, Pakistan
| | - Saleem U Shahid
- Department of Microbiology & Molecular Genetics, University of the Punjab, Lahore 54590, Pakistan
| | - Uzma Irfan
- Women University Multan, Multan 66000, Pakistan
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28
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Pernica J, Harman S, Kam A, Bailey J, Carciumaru R, Khan S, Fulford M, Thabane L, Slinger R, Main C, Smieja M, Loeb M. Short-course antimicrobial therapy for paediatric respiratory infections (SAFER): study protocol for a randomized controlled trial. Trials 2018; 19:83. [PMID: 29391051 PMCID: PMC5796490 DOI: 10.1186/s13063-018-2457-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 01/04/2018] [Indexed: 12/17/2022] Open
Abstract
Background Community-acquired pneumonia (CAP) is commonly diagnosed in children. The Infectious Disease Society of America guidelines recommend 10 days of high-dose amoxicillin for the treatment of non-severe CAP but 5-day “short course” therapy may be just as effective. Randomized trials in adults have already demonstrated non-inferiority of 5-day short-course treatment for adults hospitalized with severe CAP and for adults with mild CAP treated as outpatients. Minimizing exposure to antimicrobials is desirable to avoid harms including diarrhoea, rashes, severe allergic reactions, increased circulating antimicrobial resistance, and microbiome disruption. Methods The objective of this multicentre, randomized, non-inferiority, controlled trial is to investigate whether 5 days of high-dose amoxicillin is associated with lower rates of clinical cure 14–21 days later as compared to 10 days of high-dose amoxicillin, the reference standard. Recruitment and enrolment will occur in the emergency departments of McMaster Children’s Hospital and the Children’s Hospital of Eastern Ontario. All children in the study will receive 5 days of amoxicillin after which point they will receive either 5 days of a different formulation of amoxicillin or a placebo. Assuming a clinical failure rate of 5% in the reference arm, a non-inferiority margin of 7.5%, one-sided alpha set at 0.025 and power of 0.80, 270 participants will be required. Participants from a previous feasibility study (n = 60) will be rolled over into the current study. We will be performing multiplex respiratory virus molecular testing, quantification of nasopharyngeal pneumococcal genomic loads, salivary inflammatory marker testing, and faecal microbiome profiling on participants. Discussion This is a pragmatic study seeking to provide high-quality evidence for front-line physicians evaluating children presenting with mild CAP in North American emergency departments in the post-13-valent pneumococcal, conjugate vaccine era. High-quality evidence supporting the non-inferiority of short-course therapy for non-severe paediatric CAP should be generated prior to making changes to established guidelines. Trial registration ClinicalTrials.gov, NCT02380352. Registered on 2 March 2015. Electronic supplementary material The online version of this article (10.1186/s13063-018-2457-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeffrey Pernica
- Division of Infectious Disease, Department of Pediatrics, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
| | - Stuart Harman
- Division of Emergency Medicine, Department of Pediatrics, University of Ottawa, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
| | - April Kam
- Division of Emergency Medicine, Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| | - Jacob Bailey
- Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | | | - Sarah Khan
- Division of Infectious Disease, Department of Pediatrics, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Martha Fulford
- Division of Infectious Disease, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Lehana Thabane
- Department of Health Research Methods, Evidence, and Impact, Hamilton, ON, Canada
| | - Robert Slinger
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Cheryl Main
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Marek Smieja
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Mark Loeb
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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29
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Complementary Methodologies To Investigate Human Gut Microbiota in Host Health, Working towards Integrative Systems Biology. J Bacteriol 2018; 200:JB.00376-17. [PMID: 28874411 DOI: 10.1128/jb.00376-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In 1680, Antonie van Leeuwenhoek noted compositional differences in his oral and fecal microbiota, pioneering the study of the diversity of the human microbiome. From Leeuwenhoek's time to successful modern attempts at changing the gut microbial landscape to cure disease, there has been an exponential increase in the recognition of our resident microbes as part of ourselves. Thus, the human host and microbiome have evolved in parallel to configure a balanced system in which microbes survive in homeostasis with our innate and acquired immune systems, unless disease occurs. A growing number of studies have demonstrated a correlation between the presence/absence of microbial taxa and some of their functional molecules (i.e., genes, proteins, and metabolites) with health and disease states. Nevertheless, misleading experimental design on human subjects and the cost and lack of standardized animal models pose challenges to answering the question of whether changes in microbiome composition are cause or consequence of a certain biological state. In this review, we evaluate the state of the art of methodologies that enable the study of the gut microbiome, encouraging a change in broadly used analytic strategies by choosing effector molecules (proteins and metabolites) in combination with coding nucleic acids. We further explore microbial and effector microbial product imbalances that relate to disease and health.
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30
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Gong L, Cao W, Chi H, Wang J, Zhang H, Liu J, Sun B. Whole cereal grains and potential health effects: Involvement of the gut microbiota. Food Res Int 2017; 103:84-102. [PMID: 29389647 DOI: 10.1016/j.foodres.2017.10.025] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/13/2022]
Abstract
The intakes of whole cereal grains (WCGs) have long been linked to decreased risks of metabolic syndromes (MetS) and several chronic diseases. Owing to the complex range of components of cereals, which may show synergistic activities to mediate these protective effects, the mechanisms by which the benefits of whole cereals arise are not fully understood. The gut microbiota has recently become a new focus of research at the intersection of diet and metabolic health. Moreover, cereals contain various ingredients known as microbiota-accessible substrates that resist digestion in the upper gastrointestinal tract, including resistant starch and non-starch polysaccharides such as β-glucan and arabinoxylans, making them an important fuel for the microbiota. Thus, WCGs may manipulate the ecophysiology of gut microbiota. In this review, the scientific evidence supporting the hypothesis that WCGs prevent MetS by modulating gut microbiota composition and functions are discussed, with focuses on cereal intake-related mechanisms by which gut microbiota contributes to human health and scientific evidences for the effects of WCGs on modulating gut microbiota. Once strong support for the association among WCGs, gut microbiota and host metabolic health can be demonstrated, particular cereals, their processing technologies, or cereal-based foods might be better utilized to prevent and possibly even treat metabolic disease.
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Affiliation(s)
- Lingxiao Gong
- Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Wenyan Cao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Hailin Chi
- Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Jing Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China.
| | - Huijuan Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Jie Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
| | - Baoguo Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health (BTBU), Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), Beijing 100048, China
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31
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Wipperman MF, Fitzgerald DW, Juste MAJ, Taur Y, Namasivayam S, Sher A, Bean JM, Bucci V, Glickman MS. Antibiotic treatment for Tuberculosis induces a profound dysbiosis of the microbiome that persists long after therapy is completed. Sci Rep 2017; 7:10767. [PMID: 28883399 PMCID: PMC5589918 DOI: 10.1038/s41598-017-10346-6] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/08/2017] [Indexed: 02/08/2023] Open
Abstract
Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world’s population and causes substantial mortality worldwide. In its shortest format, treatment of TB requires six months of multidrug therapy with a mixture of broad spectrum and mycobacterial specific antibiotics, and treatment of multidrug resistant TB is longer. The widespread use of this regimen makes this one of the largest exposures of humans to antimicrobials, yet the effects of TB treatment on intestinal microbiome composition and long-term stability are unknown. We compared the microbiome composition, assessed by both 16S rDNA and metagenomic DNA sequencing, of TB cases during antimycobacterial treatment and following cure by 6 months of antibiotics. TB treatment does not perturb overall diversity, but nonetheless dramatically depletes multiple immunologically significant commensal bacteria. The microbiomic perturbation of TB therapy can persist for at least 1.2 years, indicating that the effects of TB treatment are long lasting. These results demonstrate that TB treatment has dramatic effects on the intestinal microbiome and highlight unexpected durable consequences of treatment for the world’s most common infection on human ecology.
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Affiliation(s)
- Matthew F Wipperman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Clinical and Translational Science Center, Weill Cornell Medical College, New York, New York, USA
| | - Daniel W Fitzgerald
- Weill Cornell Medical College, New York, New York, USA.,GHESKIO Centers, Port-au-Prince, Haiti
| | | | - Ying Taur
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sivaranjani Namasivayam
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - James M Bean
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
| | - Vanni Bucci
- Department of Biology, Program in Biotechnology and Biomedical Engineering, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, USA.
| | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA. .,Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA. .,Weill Cornell Medical College, New York, New York, USA.
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32
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Ruiz A, Cerdó T, Jáuregui R, Pieper DH, Marcos A, Clemente A, García F, Margolles A, Ferrer M, Campoy C, Suárez A. One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents. Environ Microbiol 2017; 19:1536-1551. [PMID: 28251782 DOI: 10.1111/1462-2920.13713] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 02/20/2017] [Accepted: 02/24/2017] [Indexed: 01/01/2023]
Abstract
Recent evidence has disclosed a connection between gut microbial glycosidase activity and adiposity in obese. Here, we measured microbial α-glucosidase and β-galactosidase activities and sorted fluorescently labeled β-galactosidase containing (βGAL) microorganisms in faecal samples of eight lean and thirteen obese adolescents that followed a controlled calorie restriction program during one year. β-galactosidase is a highly distributed functional trait, mainly expressed by members of Blautia, Bacteroides, Alcaligenes, Acinetobacter and Propionibacterium. Only long-term calorie restriction induced clear changes in the microbiota of obese adolescents. Long-term calorie restriction induced significant shifts in total and βGAL gut microbiota, reducing the Firmicutes:Bacteroidetes ratio and enhancing the growth of beneficial microorganisms such as Bacteroides, Roseburia, Faecalibacterium and Clostridium XIVa. Moreover, the structure and composition of βGAL community in obese after long-term calorie restriction was highly similar to that of lean adolescents. However, despite this high compositional similarity, microbial metabolic performance was different, split in two metabolic states at a body mass index value of 25. Our study shows that calorie restriction is a strong environmental force reshaping gut microbiota though its metabolic performance is linked to host's adiposity, suggesting that functional redundancy and metabolic plasticity are fundamental properties of gut microbial ecosystem.
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Affiliation(s)
- Alicia Ruiz
- Department of Biochemistry and Molecular Biology 2, Biomedical Research Centre, University of Granada, Spain
| | - Tomás Cerdó
- Departmet of Pediatrics, School of Medicine, University of Granada, Granada, Spain.,EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, Granada, Spain
| | - Ruy Jáuregui
- Tennent Drive, AgResearch Grasslands, Private Bag 11008, Palmerston North, New Zealand
| | - Dietmar H Pieper
- Helmholtz Centre for Infection Research, Microbial Interactions and Processes Research Group, Braunschweig, Germany
| | - Ascensión Marcos
- Department of Metabolism and Nutrition, Institute of Food Science, Technology and Nutrition (ICTAN), Madrid, Spain
| | - Alfonso Clemente
- Department of Physiology and Biochemistry of Animal Nutrition, Estación Experimental del Zaidín, Granada, Spain
| | - Federico García
- Department of Microbiology, Complejo Hospitalario Universitario de Granada, Instituto de Investigación Biosanitaria (IBS), Granada, Spain
| | - Abelardo Margolles
- IPLA-CSIC, Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute, Villaviciosa, Spain
| | | | - Cristina Campoy
- Departmet of Pediatrics, School of Medicine, University of Granada, Granada, Spain.,EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, Granada, Spain
| | - Antonio Suárez
- Department of Biochemistry and Molecular Biology 2, Biomedical Research Centre, University of Granada, Spain
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33
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Laczny CC, Kiefer C, Galata V, Fehlmann T, Backes C, Keller A. BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation. Nucleic Acids Res 2017; 45:W171-W179. [PMID: 28472498 PMCID: PMC5570254 DOI: 10.1093/nar/gkx348] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/11/2017] [Accepted: 04/21/2017] [Indexed: 12/20/2022] Open
Abstract
Metagenomics-based studies of mixed microbial communities are impacting biotechnology, life sciences and medicine. Computational binning of metagenomic data is a powerful approach for the culture-independent recovery of population-resolved genomic sequences, i.e. from individual or closely related, constituent microorganisms. Existing binning solutions often require a priori characterized reference genomes and/or dedicated compute resources. Extending currently available reference-independent binning tools, we developed the BusyBee Web server for the automated deconvolution of metagenomic data into population-level genomic bins using assembled contigs (Illumina) or long reads (Pacific Biosciences, Oxford Nanopore Technologies). A reversible compression step as well as bootstrapped supervised binning enable quick turnaround times. The binning results are represented in interactive 2D scatterplots. Moreover, bin quality estimates, taxonomic annotations and annotations of antibiotic resistance genes are computed and visualized. Ground truth-based benchmarks of BusyBee Web demonstrate comparably high performance to state-of-the-art binning solutions for assembled contigs and markedly improved performance for long reads (median F1 scores: 70.02-95.21%). Furthermore, the applicability to real-world metagenomic datasets is shown. In conclusion, our reference-independent approach automatically bins assembled contigs or long reads, exhibits high sensitivity and precision, enables intuitive inspection of the results, and only requires FASTA-formatted input. The web-based application is freely accessible at: https://ccb-microbe.cs.uni-saarland.de/busybee.
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Affiliation(s)
- Cedric C. Laczny
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Christina Kiefer
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbrücken, Germany
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34
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Rojo D, Méndez-García C, Raczkowska BA, Bargiela R, Moya A, Ferrer M, Barbas C. Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiol Rev 2017; 41:453-478. [PMID: 28333226 PMCID: PMC5812509 DOI: 10.1093/femsre/fuw046] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023] Open
Abstract
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.
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Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
| | | | - Beata Anna Raczkowska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), 46020 Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Paterna, 46980 Valencia, Spain
- These authors contributed equally to this work
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Corresponding author: Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain. Tel: (+34) 915854872; E-mail:
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
- These authors contributed equally to this work
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35
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Ferrer M, Méndez-García C, Rojo D, Barbas C, Moya A. Antibiotic use and microbiome function. Biochem Pharmacol 2017; 134:114-126. [PMID: 27641814 DOI: 10.1016/j.bcp.2016.09.007] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/12/2016] [Indexed: 02/06/2023]
Abstract
Our microbiome should be understood as one of the most complex components of the human body. The use of β-lactam antibiotics is one of the microbiome covariates that influence its composition. The extent to which our microbiota changes after an antibiotic intervention depends not only on the chemical nature of the antibiotic or cocktail of antibiotics used to treat specific infections, but also on the type of administration, duration and dose, as well as the level of resistance that each microbiota develops. We have begun to appreciate that not all bacteria within our microbiota are vulnerable or reactive to different antibiotic interventions, and that their influence on both microbial composition and metabolism may differ. Antibiotics are being used worldwide on a huge scale and the prescription of antibiotics is continuing to rise; however, their effects on our microbiota have been reported for only a limited number of them. This article presents a critical review of the antibiotics or antibiotic cocktails whose use in humans has been linked to changes in the composition of our microbial communities, with a particular focus on the gut, oral, respiratory, skin and vaginal microbiota, and on their molecular agents (genes, proteins and metabolites). We review the state of the art as of June 2016, and cover a total of circa 68 different antibiotics. The data herein are the first to compile information about the bacteria, fungi, archaea and viruses most influenced by the main antibiotic treatments prescribed nowadays.
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Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| | | | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain.
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Aguirre M, Venema K. Challenges in simulating the human gut for understanding the role of the microbiota in obesity. Benef Microbes 2016; 8:31-53. [PMID: 27903093 DOI: 10.3920/bm2016.0113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There is an elevated incidence of cases of obesity worldwide. Therefore, the development of strategies to tackle this condition is of vital importance. This review focuses on the necessity of optimising in vitro systems to model human colonic fermentation in obese subjects. This may allow to increase the resolution and the physiological relevance of the information obtained from this type of studies when evaluating the potential role that the human gut microbiota plays in obesity. In light of the parameters that are currently used for the in vitro simulation of the human gut (which are mostly based on information derived from healthy subjects) and the possible difference with an obese condition, we propose to revise and improve specific standard operating procedures.
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Affiliation(s)
- M Aguirre
- 1 Top Institute of Food and Nutrition, P.O. Box 557, 6700 AA Wageningen, the Netherlands.,2 Department of Human Biology, Faculty of Health, Medicine and Life Sciences, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands.,3 The Netherlands Organization for Applied Scientific Research (TNO), P.O. Box 360, 3700 AJ Zeist, the Netherlands
| | - K Venema
- 1 Top Institute of Food and Nutrition, P.O. Box 557, 6700 AA Wageningen, the Netherlands.,2 Department of Human Biology, Faculty of Health, Medicine and Life Sciences, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands.,4 Beneficial Microbes Consultancy, Johan Karschstraat 3, 6709 TN Wageningen, the Netherlands
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38
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Muñoz-Garach A, Diaz-Perdigones C, Tinahones FJ. Microbiota y diabetes mellitus tipo 2. ACTA ACUST UNITED AC 2016; 63:560-568. [DOI: 10.1016/j.endonu.2016.07.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/13/2016] [Accepted: 07/17/2016] [Indexed: 02/06/2023]
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Wei X, Jiang S, Chen Y, Zhao X, Li H, Lin W, Li B, Wang X, Yuan J, Sun Y. Cirrhosis related functionality characteristic of the fecal microbiota as revealed by a metaproteomic approach. BMC Gastroenterol 2016; 16:121. [PMID: 27716148 PMCID: PMC5051048 DOI: 10.1186/s12876-016-0534-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 09/20/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Intestinal microbiota operated as a whole and was closely related with human health. Previous studies had suggested close relationship between liver cirrhosis (LC) and gut microbiota. METHODS To determine the functional characteristic of the intestinal microbiota specific for liver cirrhosis, the fecal metaproteome of three LC patients with Child-Turcotte-Pugh (CTP) score of A, B, and C, and their spouse were first compared using high-throughput approach based on denaturing polyacrylamide gel electrophoresis and liquid chromatography-tandem mass spectrometry in our study. RESULTS A total of 5,020 proteins (88 % from bacteria, 12 % form human) were identified and annotated based on the GO and KEGG classification. Our results indicated that the LC patients possessed a core metaproteome including 119 proteins, among which 14 proteins were enhanced expressed and 7 proteins were unique for LC patients compared with the normal, which were dominant at the function of carbohydrate metabolism. In addition, LC patients have unique biosynthesis of branched chain amino acid (BCAA), pantothenate, and CoA, enhanced as CTP scores increased. Those three substances were all important in a wide array of key and essential biological roles of life. CONCLUSIONS We observed a highly comparable cirrhosis-specific metaproteome clustering of fecal microbiota and provided the first supportive evidence for the presence of a LC-related substantial functional core mainly involved in carbohydrate, BCAA, pantothenate, and CoA metabolism, suggesting the compensation of intestinal microbiota for the fragile and innutritious body of cirrhotic patients.
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Affiliation(s)
- Xiao Wei
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071, Beijing, China
| | - Shan Jiang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071, Beijing, China
| | - Yuye Chen
- Hospital of Traditional Chinese Medicine, Liquan, 713200, Shanxi, China
| | - Xiangna Zhao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071, Beijing, China
| | - Huan Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071, Beijing, China
| | - Weishi Lin
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071, Beijing, China
| | - Boxing Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071, Beijing, China
| | - Xuesong Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071, Beijing, China
| | - Jing Yuan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071, Beijing, China.
| | - Yansong Sun
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, No. 20 Dongda Street, Fengtai District, 100071, Beijing, China.
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40
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Rajagopala SV, Yooseph S, Harkins DM, Moncera KJ, Zabokrtsky KB, Torralba MG, Tovchigrechko A, Highlander SK, Pieper R, Sender L, Nelson KE. Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis. BMC Genomics 2016; 17:635. [PMID: 27527070 PMCID: PMC4986186 DOI: 10.1186/s12864-016-2965-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/22/2016] [Indexed: 12/12/2022] Open
Abstract
Background An estimated 15,000 children and adolescents under the age of 19 years are diagnosed with leukemia, lymphoma and other tumors in the USA every year. All children and adolescent acute leukemia patients will undergo chemotherapy as part of their treatment regimen. Fortunately, survival rates for most pediatric cancers have improved at a remarkable pace over the past three decades, and the overall survival rate is greater than 90 % today. However, significant differences in survival rate have been found in different age groups (94 % in 1–9.99 years, 82 % in ≥10 years and 76 % in ≥15 years). ALL accounts for about three out of four cases of childhood leukemia. Intensive chemotherapy treatment coupled with prophylactic or therapeutic antibiotic use could potentially have a long-term effect on the resident gastrointestinal (GI) microbiome. The composition of GI microbiome and its changes upon chemotherapy in pediatric and adolescent leukemia patients is poorly understood. In this study, using 16S rRNA marker gene sequences we profile the GI microbial communities of pediatric and adolescent acute leukemia patients before and after chemotherapy treatment and compare with the microbiota of their healthy siblings. Results Our study cohort consisted of 51 participants, made up of matched pediatric and adolescent patients with ALL and a healthy sibling. We elucidated and compared the GI microbiota profiles of patients and their healthy sibling controls via analysis of 16S rRNA gene sequencing data. We assessed the GI microbiota composition in pediatric and adolescent patients with ALL during the course of chemotherapy by comparing stool samples taken before chemotherapy with stool samples collected at varying time points during the chemotherapeutic treatment. The microbiota profiles of both patients and control sibling groups are dominated by members of Bacteroides, Prevotella, and Faecalibacterium. At the genus level, both groups share many taxa in common, but the microbiota diversity of the patient group is significantly lower than that of the control group. It was possible to distinguish between the patient and control groups based on their microbiota profiles. The top taxa include Anaerostipes, Coprococcus, Roseburia, and Ruminococcus2 with relatively higher abundance in the control group. The observed microbiota changes are likely the result of several factors including a direct influence of therapeutic compounds on the gut flora and an indirect effect of chemotherapy on the immune system, which, in turn, affects the microbiota. Conclusions This study provides significant information on GI microbiota populations in immunocompromised children and opens up the potential for developing novel diagnostics based on stool tests and therapies to improve the dysbiotic condition of the microbiota at the time of diagnosis and in the earliest stages of chemotherapy. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2965-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Derek M Harkins
- J. Craig Venter Institute (JCVI), 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | | | - Keri B Zabokrtsky
- Hyundai Cancer Genomics Center, Children's Hospital Orange County (CHOC Children's), Orange, CA, USA.,Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of California-Irvine, Orange, CA, USA
| | | | - Andrey Tovchigrechko
- J. Craig Venter Institute (JCVI), 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | | | - Rembert Pieper
- J. Craig Venter Institute (JCVI), 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Leonard Sender
- Hyundai Cancer Genomics Center, Children's Hospital Orange County (CHOC Children's), Orange, CA, USA.,Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of California-Irvine, Orange, CA, USA.,Division of Oncology, Hyundai Cancer Institute, CHOC Children's, Orange, CA, USA.,Department of Pediatrics, School of Medicine, University of California-Irvine, Orange, CA, USA
| | - Karen E Nelson
- J. Craig Venter Institute (JCVI), 9714 Medical Center Drive, Rockville, MD, 20850, USA. .,JCVI, La Jolla, 92037, CA, USA.
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41
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Serrano-Villar S, Rojo D, Martínez-Martínez M, Deusch S, Vázquez-Castellanos JF, Bargiela R, Sainz T, Vera M, Moreno S, Estrada V, Gosalbes MJ, Latorre A, Seifert J, Barbas C, Moya A, Ferrer M. Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals. EBioMedicine 2016; 8:203-216. [PMID: 27428431 PMCID: PMC4919658 DOI: 10.1016/j.ebiom.2016.04.033] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/01/2016] [Accepted: 04/25/2016] [Indexed: 02/07/2023] Open
Abstract
While changes in gut microbial populations have been described in human immuno-deficiency virus (HIV)-infected patients undergoing antiretroviral therapy (ART), the mechanisms underlying the contributions of gut bacteria and their molecular agents (metabolites and proteins) to immune recovery remain unexplored. To study this, we examined the active fraction of the gut microbiome, through examining protein synthesis and accumulation of metabolites inside gut bacteria and in the bloodstream, in 8 healthy controls and 29 HIV-infected individuals (6 being longitudinally studied). We found that HIV infection is associated to dramatic changes in the active set of gut bacteria simultaneously altering the metabolic outcomes. Effects were accentuated among immunological ART responders, regardless diet, subject characteristics, clinical variables other than immune recovery, the duration and type of ART and sexual preferences. The effect was found at quantitative levels of several molecular agents and active bacteria which were herein identified and whose abundance correlated with HIV immune pathogenesis markers. Although, we cannot rule out the possibility that some changes are partially a random consequence of the disease status, our data suggest that most likely reduced inflammation and immune recovery is a joint solution orchestrated by both the active fraction of the gut microbiota and the host.
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Affiliation(s)
- Sergio Serrano-Villar
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | | | - Simon Deusch
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Jorge F Vázquez-Castellanos
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Talía Sainz
- Department of Pediatric Infectious Diseases, University Hospital La Paz, and La Paz Research Institute (IdiPAZ), Madrid, Spain
| | - Mar Vera
- Centro Sanitario Sandoval, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Vicente Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
| | - María José Gosalbes
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Amparo Latorre
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
| | - Jana Seifert
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain.
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain.
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
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Serrano-Villar S, Rojo D, Martínez-Martínez M, Deusch S, Vázquez-Castellanos JF, Sainz T, Vera M, Moreno S, Estrada V, Gosalbes MJ, Latorre A, Margolles A, Seifert J, Barbas C, Moya A, Ferrer M. HIV infection results in metabolic alterations in the gut microbiota different from those induced by other diseases. Sci Rep 2016; 6:26192. [PMID: 27189771 PMCID: PMC4870624 DOI: 10.1038/srep26192] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/28/2016] [Indexed: 12/14/2022] Open
Abstract
Imbalances in gut bacteria have been associated with multiple diseases. However, whether there are disease-specific changes in gut microbial metabolism remains unknown. Here, we demonstrate that human immunodeficiency virus (HIV) infection (n = 33) changes, at quantifiable levels, the metabolism of gut bacteria. These changes are different than those observed in patients with the auto-immune disease systemic lupus erythaematosus (n = 18), and Clostridium difficile-associated diarrhoea (n = 6). Using healthy controls as a baseline (n = 16), we demonstrate that a trend in the nature and directionality of the metabolic changes exists according to the type of the disease. The impact on the gut microbial activity, and thus the metabolite composition and metabolic flux of gut microbes, is therefore disease-dependent. Our data further provide experimental evidence that HIV infection drastically changed the microbial community, and the species responsible for the metabolism of 4 amino acids, in contrast to patients with the other two diseases and healthy controls. The identification in this present work of specific metabolic deficits in HIV-infected patients may define nutritional supplements to improve the health of these patients.
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Affiliation(s)
- Sergio Serrano-Villar
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | | | - Simon Deusch
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Jorge F Vázquez-Castellanos
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain.,Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Talía Sainz
- Department of Pediatric Infectious Diseases, University Hospital La Paz, and La Paz Research Institute (IdiPAZ), Madrid, Spain
| | - Mar Vera
- Centro Sanitario Sandoval, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Vicente Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
| | - María José Gosalbes
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain.,Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Amparo Latorre
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain.,Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA), CSIC, Villaviciosa, Asturias, Spain
| | - Jana Seifert
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain.,Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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43
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Moya A, Ferrer M. Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance. Trends Microbiol 2016; 24:402-413. [PMID: 26996765 DOI: 10.1016/j.tim.2016.02.002] [Citation(s) in RCA: 324] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/26/2016] [Accepted: 02/01/2016] [Indexed: 02/07/2023]
Abstract
The microbiota should be considered as just another component of the human epigenetic landscape. Thus, health is also a reflection of the diversity and composition of gut microbiota and its metabolic status. In defining host health, it remains unclear whether diversity is paramount, or whether greater weight is held by gut microbiota composition or mono- or multiple-functional capacity of the different taxa and the mechanisms involved. A network-biology approach may shed light on the key gut players acting to protect against, or promote, disorders or diseases. This could be achieved by integrating data on total and active species, proteins and molecules, and their association with host response. In this review, we discuss the utilization of top-down and bottom-up approaches, following a functional hierarchy perspective.
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Affiliation(s)
- Andrés Moya
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain; Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO), Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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44
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Langdon A, Crook N, Dantas G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med 2016; 8:39. [PMID: 27074706 PMCID: PMC4831151 DOI: 10.1186/s13073-016-0294-z] [Citation(s) in RCA: 528] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The widespread use of antibiotics in the past 80 years has saved millions of human lives, facilitated technological progress and killed incalculable numbers of microbes, both pathogenic and commensal. Human-associated microbes perform an array of important functions, and we are now just beginning to understand the ways in which antibiotics have reshaped their ecology and the functional consequences of these changes. Mounting evidence shows that antibiotics influence the function of the immune system, our ability to resist infection, and our capacity for processing food. Therefore, it is now more important than ever to revisit how we use antibiotics. This review summarizes current research on the short-term and long-term consequences of antibiotic use on the human microbiome, from early life to adulthood, and its effect on diseases such as malnutrition, obesity, diabetes, and Clostridium difficile infection. Motivated by the consequences of inappropriate antibiotic use, we explore recent progress in the development of antivirulence approaches for resisting infection while minimizing resistance to therapy. We close the article by discussing probiotics and fecal microbiota transplants, which promise to restore the microbiota after damage of the microbiome. Together, the results of studies in this field emphasize the importance of developing a mechanistic understanding of gut ecology to enable the development of new therapeutic strategies and to rationally limit the use of antibiotic compounds.
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Affiliation(s)
- Amy Langdon
- Center for Genome Sciences, Washington University School of Medicine, Campus Box 8510, 4515 McKinley Research Building, St. Louis, MO, 63108, USA
- Clinical Research Training Center, Washington University School of Medicine, Campus Box 8051, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA
| | - Nathan Crook
- Center for Genome Sciences, Washington University School of Medicine, Campus Box 8510, 4515 McKinley Research Building, St. Louis, MO, 63108, USA
- Department of Pathology & Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Ave, St. Louis, MO, 63110, USA
| | - Gautam Dantas
- Center for Genome Sciences, Washington University School of Medicine, Campus Box 8510, 4515 McKinley Research Building, St. Louis, MO, 63108, USA.
- Department of Pathology & Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Ave, St. Louis, MO, 63110, USA.
- Department of Biomedical Engineering, Washington University in Saint Louis, Campus Box 1097, 1 Brookings Drive, Saint Louis, MO, 63130, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, Campus Box 8230, 660 S. Euclid Ave, St. Louis, MO, 63110, USA.
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45
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Taguer M, Maurice CF. The complex interplay of diet, xenobiotics, and microbial metabolism in the gut: Implications for clinical outcomes. Clin Pharmacol Ther 2016; 99:588-99. [PMID: 26950037 DOI: 10.1002/cpt.366] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/14/2022]
Abstract
From digestion to pathogen resistance and immune system development, the gut microbiota and its collection of microbial genes are redefining what it means to be human. Despite tremendous advances in this field, there is still a limited understanding of how microbial metabolism in the gut impacts human health, which precludes the development of microbiota-targeted therapies. In this article, we discuss the increasing evidence emphasizing the importance of bacterial metabolism in the gut and discuss its intricate links with diet and pharmaceutical compounds leading to altered therapeutic outcomes. We also detail how applying and testing microbial ecology hypotheses will be crucial to fully understand the therapeutic potential of this host-associated community. Going forward, functional and mechanistic studies combining biomedical research, ecology, bioinformatics, statistical modeling, and engineering will be key in our pursuit of personalized medicine.
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Affiliation(s)
- M Taguer
- Department of Microbiology and Immunology, Microbiome and Disease Tolerance Centre, McGill University, Montreal, Quebec, Canada
| | - C F Maurice
- Department of Microbiology and Immunology, Microbiome and Disease Tolerance Centre, McGill University, Montreal, Quebec, Canada
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46
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Raymond F, Ouameur AA, Déraspe M, Iqbal N, Gingras H, Dridi B, Leprohon P, Plante PL, Giroux R, Bérubé È, Frenette J, Boudreau DK, Simard JL, Chabot I, Domingo MC, Trottier S, Boissinot M, Huletsky A, Roy PH, Ouellette M, Bergeron MG, Corbeil J. The initial state of the human gut microbiome determines its reshaping by antibiotics. THE ISME JOURNAL 2016; 10:707-20. [PMID: 26359913 PMCID: PMC4817689 DOI: 10.1038/ismej.2015.148] [Citation(s) in RCA: 224] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/09/2015] [Accepted: 07/15/2015] [Indexed: 02/07/2023]
Abstract
Microbiome studies have demonstrated the high inter-individual diversity of the gut microbiota. However, how the initial composition of the microbiome affects the impact of antibiotics on microbial communities is relatively unexplored. To specifically address this question, we administered a second-generation cephalosporin, cefprozil, to healthy volunteers. Stool samples gathered before antibiotic exposure, at the end of the treatment and 3 months later were analysed using shotgun metagenomic sequencing. On average, 15 billion nucleotides were sequenced for each sample. We show that standard antibiotic treatment can alter the gut microbiome in a specific, reproducible and predictable manner. The most consistent effect of the antibiotic was the increase of Lachnoclostridium bolteae in 16 out of the 18 cefprozil-exposed participants. Strikingly, we identified a subgroup of participants who were enriched in the opportunistic pathogen Enterobacter cloacae after exposure to the antibiotic, an effect linked to lower initial microbiome diversity and to a Bacteroides enterotype. Although the resistance gene content of participants' microbiomes was altered by the antibiotic, the impact of cefprozil remained specific to individual participants. Resistance genes that were not detectable prior to treatment were observed after a 7-day course of antibiotic administration. Specifically, point mutations in beta-lactamase blaCfxA-6 were enriched after antibiotic treatment in several participants. This suggests that monitoring the initial composition of the microbiome before treatment could assist in the prevention of some of the adverse effects associated with antibiotics or other treatments.
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Affiliation(s)
- Frédéric Raymond
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Amin A Ouameur
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Maxime Déraspe
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Naeem Iqbal
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Hélène Gingras
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Bédis Dridi
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Pier-Luc Plante
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Richard Giroux
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Ève Bérubé
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Johanne Frenette
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Dominique K Boudreau
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Jean-Luc Simard
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Isabelle Chabot
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Marc-Christian Domingo
- Institut National de Santé Publique du Québec, Laboratoire de Santé Publique du Québec, Montréal, Québec, Canada
| | - Sylvie Trottier
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Maurice Boissinot
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Ann Huletsky
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Paul H Roy
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Michel G Bergeron
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie, CHU de Québec–Université Laval, Québec, Canada
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47
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Derrien M, Belzer C, de Vos WM. Akkermansia muciniphila and its role in regulating host functions. Microb Pathog 2016; 106:171-181. [PMID: 26875998 DOI: 10.1016/j.micpath.2016.02.005] [Citation(s) in RCA: 636] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 02/07/2016] [Accepted: 02/09/2016] [Indexed: 02/08/2023]
Abstract
Akkermansia muciniphila is an intestinal bacterium that was isolated a decade ago from a human fecal sample. Its specialization in mucin degradation makes it a key organism at the mucosal interface between the lumen and host cells. Although it was isolated quite recently, it has rapidly raised significant interest as A. muciniphila is the only cultivated intestinal representative of the Verrucomicrobia, one of the few phyla in the human gut that can be easily detected in phylogenetic and metagenome analyses. There has also been a growing interest in A. muciniphila, due to its association with health in animals and humans. Notably, reduced levels of A. muciniphila have been observed in patients with inflammatory bowel diseases (mainly ulcerative colitis) and metabolic disorders, which suggests it may have potential anti-inflammatory properties. The aims of this review are to summarize the existing data on the intestinal distribution of A. muciniphila in health and disease, to provide insight into its ecology and its role in founding microbial networks at the mucosal interface, as well as to discuss recent research on its role in regulating host functions that are disturbed in various diseases, with a specific focus on metabolic disorders in both animals and humans.
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Affiliation(s)
- Muriel Derrien
- Danone Nutricia Research, Avenue de la Vauve, 91767 Palaiseau, France.
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands; Immunobiology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Helsinki, Finland.
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48
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Francino MP. Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Front Microbiol 2016; 6:1543. [PMID: 26793178 PMCID: PMC4709861 DOI: 10.3389/fmicb.2015.01543] [Citation(s) in RCA: 459] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/21/2015] [Indexed: 12/12/2022] Open
Abstract
The human microbiome is overly exposed to antibiotics, due, not only to their medical use, but also to their utilization in farm animals and crops. Microbiome composition can be rapidly altered by exposure to antibiotics, with potential immediate effects on health, for instance through the selection of resistant opportunistic pathogens that can cause acute disease. Microbiome alterations induced by antibiotics can also indirectly affect health in the long-term. The mutualistic microbes in the human body interact with many physiological processes, and participate in the regulation of immune and metabolic homeostasis. Therefore, antibiotic exposure can alter many basic physiological equilibria, promoting long-term disease. In addition, excessive antibiotic use fosters bacterial resistance, and the overly exposed human microbiome has become a significant reservoir of resistance genes, contributing to the increasing difficulty in controlling bacterial infections. Here, the complex relationships between antibiotics and the human microbiome are reviewed, with focus on the intestinal microbiota, addressing (1) the effects of antibiotic use on the composition and function of the gut microbiota, (2) the impact of antibiotic-induced microbiota alterations on immunity, metabolism, and health, and (3) the role of the gut microbiota as a reservoir of antibiotic resistances.
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Affiliation(s)
- M P Francino
- Unitat Mixta d'Investigació en Genòmica i Salut, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública/Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValènciaValència, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
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49
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Rojo D, Gosalbes MJ, Ferrari R, Pérez-Cobas AE, Hernández E, Oltra R, Buesa J, Latorre A, Barbas C, Ferrer M, Moya A. Clostridium difficile heterogeneously impacts intestinal community architecture but drives stable metabolome responses. THE ISME JOURNAL 2015; 9:2206-20. [PMID: 25756679 PMCID: PMC4579473 DOI: 10.1038/ismej.2015.32] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 01/12/2015] [Accepted: 02/06/2015] [Indexed: 02/07/2023]
Abstract
Clostridium difficile-associated diarrhoea (CDAD) is caused by C. difficile toxins A and B and represents a serious emerging health problem. Yet, its progression and functional consequences are unclear. We hypothesised that C. difficile can drive major measurable metabolic changes in the gut microbiota and that a relationship with the production or absence of toxins may be established. We tested this hypothesis by performing metabolic profiling on the gut microbiota of patients with C. difficile that produced (n=6) or did not produce (n=4) toxins and on non-colonised control patients (n=6), all of whom were experiencing diarrhoea. We report a statistically significant separation (P-value <0.05) among the three groups, regardless of patient characteristics, duration of the disease, antibiotic therapy and medical history. This classification is associated with differences in the production of distinct molecules with presumptive global importance in the gut environment, disease progression and inflammation. Moreover, although severe impaired metabolite production and biological deficits were associated with the carriage of C. difficile that did not produce toxins, only previously unrecognised selective features, namely, choline- and acetylputrescine-deficient gut environments, characterised the carriage of toxin-producing C. difficile. Additional results showed that the changes induced by C. difficile become marked at the highest level of the functional hierarchy, namely the metabolic activity exemplified by the gut microbial metabolome regardless of heterogeneities that commonly appear below the functional level (gut bacterial composition). We discuss possible explanations for this effect and suggest that the changes imposed by CDAD are much more defined and predictable than previously thought.
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Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - María J Gosalbes
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universidad de Valencia, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Rafaela Ferrari
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universidad de Valencia, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Ana E Pérez-Cobas
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universidad de Valencia, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | | | - Rosa Oltra
- Unidad Enfermedades Infecciosas, Servicio Medicina Interna, Hospital Clínico Universitario de Valencia-INCLIVA, Valencia, Spain
| | - Javier Buesa
- Departamento de Microbiología, Facultad de Medicina, Universidad de Valencia and Hospital Clínico Universitario de Valencia-INCLIVA, Valencia, Spain
| | - Amparo Latorre
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universidad de Valencia, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Manuel Ferrer
- CSIC, Institute of Catalysis, Madrid, Spain
- CSIC, Institute of Catalysis, Madrid 28049, Spain. E-mail:
| | - Andrés Moya
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Instituto Cavanilles de Biodiversidad y Biología Evolutiva de la Universidad de Valencia, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
- Unidad Mixta de Investigación en Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Valencia 46020, Spain. E-mail:
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50
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Pérez-Cobas AE, Moya A, Gosalbes MJ, Latorre A. Colonization Resistance of the Gut Microbiota against Clostridium difficile. Antibiotics (Basel) 2015; 4:337-57. [PMID: 27025628 PMCID: PMC4790290 DOI: 10.3390/antibiotics4030337] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/03/2015] [Indexed: 02/06/2023] Open
Abstract
Antibiotics strongly disrupt the human gut microbiota, which in consequence loses its colonization resistance capacity, allowing infection by opportunistic pathogens such as Clostridium difficile. This bacterium is the main cause of antibiotic-associated diarrhea and a current problem in developed countries, since its incidence and severity have increased during the last years. Furthermore, the emergence of antibiotic resistance strains has reduced the efficiency of the standard treatment with antibiotics, leading to a higher rate of relapses. Here, we review recent efforts focused on the impact of antibiotics in the gut microbiome and their relationship with C. difficile colonization, as well as, in the identification of bacteria and mechanisms involved in the protection against C. difficile infection. Since a healthy gut microbiota is able to avoid pathogen colonization, restoration of the gut microbiota seems to be the most promising approach to face C. difficile infection, especially for recurrent cases. Therefore, it would be possible to design probiotics for patients undergoing antimicrobial therapies in order to prevent or fight the expansion of the pathogen in the gut ecosystem.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
| | - Andrés Moya
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
| | - María José Gosalbes
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
| | - Amparo Latorre
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
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