101
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Matisz C, Gruber A. Neuroinflammatory remodeling of the anterior cingulate cortex as a key driver of mood disorders in gastrointestinal disease and disorders. Neurosci Biobehav Rev 2022; 133:104497. [DOI: 10.1016/j.neubiorev.2021.12.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 11/10/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023]
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Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults. Nat Commun 2022; 13:586. [PMID: 35102136 PMCID: PMC8803835 DOI: 10.1038/s41467-022-28048-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022] Open
Abstract
Bacterial bloodstream infections are a major cause of morbidity and mortality among patients undergoing hematopoietic cell transplantation (HCT). Although previous research has demonstrated that pathogens may translocate from the gut microbiome into the bloodstream to cause infections, the mechanisms by which HCT patients acquire pathogens in their microbiome have not yet been described. Here, we use linked-read and short-read metagenomic sequencing to analyze 401 stool samples collected from 149 adults undergoing HCT and hospitalized in the same unit over three years, many of whom were roommates. We use metagenomic assembly and strain-specific comparison methods to search for high-identity bacterial strains, which may indicate transmission between the gut microbiomes of patients. Overall, the microbiomes of patients who share time and space in the hospital do not converge in taxonomic composition. However, we do observe six pairs of patients who harbor identical or nearly identical strains of the pathogen Enterococcus faecium, or the gut commensals Akkermansia muciniphila and Hungatella hathewayi. These shared strains may result from direct transmission between patients who shared a room and bathroom, acquisition from a common hospital source, or transmission from an unsampled intermediate. We also identify multiple patients with identical strains of species commonly found in commercial probiotics, including Lactobacillus rhamnosus and Streptococcus thermophilus. In summary, our findings indicate that sharing of identical pathogens between the gut microbiomes of multiple patients is a rare phenomenon. Furthermore, the observed potential transmission of commensal, immunomodulatory microbes suggests that exposure to other humans may contribute to microbiome reassembly post-HCT. Here, Siranosian et al. provide evidence for rare transmission of commensal and pathogenic bacteria between the microbiomes of hospitalized adults, with important factors being roommate overlap and exposure to broad-spectrum antibiotics.
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103
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Sawayama H, Miyamoto Y, Yoshida N, Baba H. Essential updates 2020/2021: Colorectal diseases (benign)—Current topics in the surgical and medical treatment of benign colorectal diseases. Ann Gastroenterol Surg 2022; 6:321-335. [PMID: 35634190 PMCID: PMC9130914 DOI: 10.1002/ags3.12548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/27/2021] [Indexed: 11/23/2022] Open
Abstract
The development of new drugs for inflammatory bowel disease (IBD) is remarkable, and treatment strategies using multiple agents and various techniques are required; however, the treatment strategy is likely to be complex. Therefore, appropriate evaluation of traditional surgical treatment strategies and accurate knowledge of the efficacy and limitations of novel treatments are required. Total infectious complications were found to be associated with the use of corticosteroids and anti‐tumor necrosis factor‐α agents, but not with immunomodulators, anti‐integrin agents, and 5‐aminosalicylic acid. Regarding surgical procedures for IBD, conceived anastomosis methods, including Kono‐S for Crohn's disease stenosis, are associated with better outcomes than conventional techniques. Autologous cell transplantation for Crohn's fistulae has been shown to have a favorable outcome. Diverticulitis is increasing and will be treated more frequently in the future. Risk factors for the incidence of diverticulitis and differences in pathogenesis according to right or left side diverticulitis have been reported. Antibiotic therapy may be omitted for uncomplicated diverticulitis. Moreover, regarding surgical procedures, both bowel resection and anastomosis are associated with favorable short‐term outcomes, higher stoma closure rate, and superior medical economy compared to Hartmann's procedure. Risk factors for recurrence after diverticulitis surgery may provide better postoperative follow‐up. In this review, we explore the current topics of colorectal benign diseases, focusing on IBD and diverticulitis, based on clinical trials and meta‐analyses from 2020‐2021. This review consolidates the available knowledge and improves the quality of surgical procedures and perioperative management for IBD and diverticulitis.
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Affiliation(s)
- Hiroshi Sawayama
- Department of Gastroenterological Surgery Graduate School of Medical Sciences Kumamoto University Kumamoto Japan
| | - Yuji Miyamoto
- Department of Gastroenterological Surgery Graduate School of Medical Sciences Kumamoto University Kumamoto Japan
| | - Naoya Yoshida
- Department of Gastroenterological Surgery Graduate School of Medical Sciences Kumamoto University Kumamoto Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery Graduate School of Medical Sciences Kumamoto University Kumamoto Japan
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104
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Junca H, Pieper DH, Medina E. The emerging potential of microbiome transplantation on human health interventions. Comput Struct Biotechnol J 2022; 20:615-627. [PMID: 35140882 PMCID: PMC8801967 DOI: 10.1016/j.csbj.2022.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 02/08/2023] Open
Abstract
The human microbiome has been the subject of intense research over the past few decades, in particular as a promising area for new clinical interventions. The microbiota colonizing the different body surfaces are of benefit for multiple physiological and metabolic processes of the human host and increasing evidence suggests an association between disturbances in the composition and functionality of the microbiota and several pathological conditions. This has provided a rationale for beneficial modulation of the microbiome. One approach being explored for modulating the microbiota in diseased individuals is transferring microbiota or microbiota constituents from healthy donors via microbiome transplantation. The great success of fecal microbiome transplantation for the treatment of Clostridioides difficile infections has encouraged the application of this procedure for the treatment of other diseases such as vaginal disorders via transplantation of vaginal microbiota, or of skin pathologies via the transplantation of skin microbiota. Microbiome modulation could even become a novel strategy for improving the efficacy of cancer therapies. This review discusses the principle, advantages and limitations of microbiome transplantation as well as different clinical contexts where microbiome transplantation has been applied.
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Affiliation(s)
- Howard Junca
- Microbial Interactions and Processes Research Group, Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Eva Medina
- Infection Immunology Research Group, Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany
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105
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Huus KE, Frankowski M, Pučić-Baković M, Vučković F, Lauc G, Mullish BH, Marchesi JR, Monaghan TM, Kao D, Finlay BB. Changes in IgA-targeted microbiota following fecal transplantation for recurrent Clostridioides difficile infection. Gut Microbes 2022; 13:1-12. [PMID: 33382360 PMCID: PMC7781654 DOI: 10.1080/19490976.2020.1862027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Secretory immunoglobulin A (IgA) interacts with intestinal microbiota and promotes mucosal homeostasis. IgA-bacteria interactions are altered during inflammatory diseases, but how these interactions are shaped by bacterial, host, and environmental factors remains unclear. In this study, we utilized IgA-SEQ to profile IgA-bound fecal bacteria in 48 recurrent Clostridioides difficile patients before and after successful fecal microbiota transplantation (FMT) to gain further insight. Prior to FMT, Escherichia coli was the most highly IgA-targeted taxon; following restoration of the microbiota by FMT, highly IgA-targeted taxa included multiple Firmicutes species. Post-FMT IgA-targeting was unaffected by the route of FMT delivery (colonoscopy versus capsule), suggesting that both methods lead to the establishment of healthy immune-bacterial interactions in the gut. Interestingly, IgA-targeting in FMT recipients closely resembled the IgA-targeting patterns of the donors, and fecal donor identity was significantly associated with IgA-targeting of the recipient microbiota. These data support the concept that intrinsic bacterial properties drive IgA recognition across genetically distinct human hosts. Together, this study suggests that IgA-bacterial interactions are reestablished in human FMT recipients to resemble that of the healthy fecal donor.
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Affiliation(s)
- Kelsey E Huus
- Michael Smith Laboratories and the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Frano Vučković
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Gordan Lauc
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia,Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK,School of Biosciences, Cardiff University, Cardiff, UK
| | - Tanya M Monaghan
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,CONTACT Tanya M Monaghan NIHR Nottingham Biomedical Research Centre, University of Nottingham, 2185 East Mall Vancouver, BC, V6T 1Z4, Nottingham, UK
| | - Dina Kao
- Division of Gastroenterology,Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - B. Brett Finlay
- Michael Smith Laboratories and the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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106
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Manrique P, Zhu Y, van der Oost J, Herrema H, Nieuwdorp M, de Vos WM, Young M. Gut bacteriophage dynamics during fecal microbial transplantation in subjects with metabolic syndrome. Gut Microbes 2022; 13:1-15. [PMID: 33794724 PMCID: PMC8023239 DOI: 10.1080/19490976.2021.1897217] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Metabolic Syndrome (MetS) is a growing public health concern worldwide. Individuals with MetS have an increased risk for cardiovascular (CV) disease and type 2 diabetes (T2D). These diseases - in part preventable with the treatment of MetS - increase the chances of premature death and pose a great economic burden to health systems. A healthy gut microbiota is associated with a reduction in MetS, T2D, and CV disease. Treatment of MetS with fecal microbiota transplantation (FMT) can be effective, however, its success rate is intermediate and difficult to predict. Because bacteriophages significantly affect the microbiota membership and function, the aim of this pilot study was to explore the dynamics of the gut bacteriophage community after FMT in MetS subjects. We performed a longitudinal study of stool bacteriophages from healthy donors and MetS subjects before and after FMT treatment. Subjects were assigned to either a control group (self-stool transplant, n = 3) or a treatment group (healthy-donor-stool transplant; n-recipients = 6, n-donors = 5). Stool samples were collected over an 18-week period and bacteriophage-like particles were purified and sequenced. We found that FMT from healthy donors significantly alters the gut bacteriophage community. Subjects with better clinical outcome clustered closer to the heathy donor group, suggesting that throughout the treatment, their bacteriophage community was more similar to healthy donors. Finally, we identified bacteriophage groups that could explain these differences and we examined their prevalence in individuals from a larger cohort of MetS FMT trial.Trial information- http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=2705; NTR 2705.
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Affiliation(s)
- Pilar Manrique
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
| | - Yifan Zhu
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hilde Herrema
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, AZ Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, AZ Amsterdam, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands,RPU Human Microbiology, University of Helsinki, Faculty of Medicine, Helsinki, Finland
| | - Mark Young
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, USA,CONTACT Mark Young Department of Plant Sciences & Plant Pathology, Montana State University, P.O. Box 173150, Bozeman, MT59717-3150, USA
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107
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He R, Li P, Wang J, Cui B, Zhang F, Zhao F. The interplay of gut microbiota between donors and recipients determines the efficacy of fecal microbiota transplantation. Gut Microbes 2022; 14:2100197. [PMID: 35854629 PMCID: PMC9302524 DOI: 10.1080/19490976.2022.2100197] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is a promising treatment for microbiota dysbiosis associated diseases, such as Clostridioides difficile infection (CDI) and inflammatory bowel disease (IBD). The engraftment of donor bacteria is essential for the effectiveness of FMT, which to some extent depends on the matching of donors and recipients. However, how different types of donor-derived bacteria affect FMT efficacy has not been fully dissected. We recruited two longitudinal IBD cohorts of 103 FMT recipients and further analyzed 1,280 microbiota datasets from 14 public CDI and IBD studies to uncover the effect of donor-derived microbiota in recipients. We found that two enterotypes, RCPT/E and RCPT/B (dominated by Enterobacteriaceae and Bacteroides, respectively), consistently exist in both CDI and IBD patients. Based on a time-course-based multi-cohort analysis of FMT fecal samples, we observed the interplay between recipient and donor-derived microbiota during FMT, in which the FMT outcome was significantly associated with the enterotype and microbiota distance between donor and recipient after FMT. We proposed a new measurement, the ratio of colonizers to residents after FMT (C2R), to quantify the engraftment of donor-derived bacteria in the recipients, and then constructed an enterotype-based statistical model for donor-recipient matching, which was validated by both cross-validation and an additional IBD FMT cohort (n = 42). We believe that with the accumulation of FMT multi-omics datasets, machine learning-based methods will be helpful for rational donor selection for improving efficacy and precision FMT practices.
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Affiliation(s)
- Ruiqiao He
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pan Li
- Medical Center for Digestive Diseases, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Holistic Integrative Enterology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jinfeng Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Bota Cui
- Medical Center for Digestive Diseases, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Holistic Integrative Enterology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Faming Zhang
- Medical Center for Digestive Diseases, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Holistic Integrative Enterology, Nanjing Medical University, Nanjing, Jiangsu, China
- CONTACT Faming Zhang Key Laboratory of Holistic Integrative Enterology, Nanjing Medical University, Nanjing, Jiangsu210011, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Fangqing Zhao Beijing Institutes of Life Science, Beijing Institutes of Life Science, Beijing, China
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108
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Zou Y, Song X, Liu N, Sun W, Liu B. Intestinal Flora: A Potential New Regulator of Cardiovascular Disease. Aging Dis 2022; 13:753-772. [PMID: 35656118 PMCID: PMC9116925 DOI: 10.14336/ad.2021.1022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Although substantial progress has been made in reducing the burden of the disease by preventing the risk factors of cardiovascular disease (CVD), potential risk factors still exist and lead to its progression. In recent years, numerous studies have revealed that intestinal flora can interfere with the physiological processes of the host through changes in composition and function or related metabolites. Intestinal flora thus affects the occurrence and development of a variety of CVDs, including atherosclerosis, ischemic heart disease, and heart failure. Moreover, studies have found that interventions for intestinal flora and its metabolites provide new opportunities for CVD treatment. This article mainly discusses the interaction between the human intestinal flora and its metabolites, the occurrence and development of CVD, and the potential of intestinal flora as a new target for the diagnosis and treatment of CVD.
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Affiliation(s)
| | | | | | - Wei Sun
- Correspondence should be addressed to: Dr. Sun Wei () and Bin Liu (), Department of Cardiology, The Second Hospital of Jilin University, Changchun, China
| | - Bin Liu
- Correspondence should be addressed to: Dr. Sun Wei () and Bin Liu (), Department of Cardiology, The Second Hospital of Jilin University, Changchun, China
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109
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Wu Z, Zhang B, Chen F, Xia R, Zhu D, Chen B, Lin A, Zheng C, Hou D, Li X, Zhang S, Chen Y, Hou K. Fecal microbiota transplantation reverses insulin resistance in type 2 diabetes: A randomized, controlled, prospective study. Front Cell Infect Microbiol 2022; 12:1089991. [PMID: 36704100 PMCID: PMC9872724 DOI: 10.3389/fcimb.2022.1089991] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES Recent studies have shown that fecal microbiota transplantation (FMT) improved the metabolic profiles of patients with type 2 diabetes mellitus (T2DM), yet the effectiveness in reversing insulin resistance and increasing metformin sensitivity in T2DM patients have not been reported. In this study, we evaluated the improvements of T2DM patients and their gut microbiota by FMT alone and FMT plus metformin. METHODS A total of 31 patients with newly diagnosed T2DM were randomized to intervention by metformin, FMT, or FMT plus metformin in the study. Patients were followed up at baseline and week 4 after treatment. Blood and stool samples were collected and subject to analyze clinical parameters and microbial communities by metagenomic sequencing, respectively. RESULTS FMT alone and FMT plus metformin significantly improved the clinical indicators HOMA-IR and BMI in T2DM, besides fasting blood glucose, postprandial blood glucose, and hemoglobin A1c that were also controlled by metformin. Donor microbiota effectively colonized in T2DM with slightly higher colonization ration in FMT than FMT plus metformin within 4 weeks, resulting in increased microbial diversity and community changes from baseline after treatment. A total of 227 species and 441 species were significantly alerted after FMT and FMT plus metformin, respectively. FMT were significantly associated with the clinical parameters. Among them, Chlorobium phaeovibrioides, Bifidibacterium adolescentis and Synechococcus sp.WH8103 were potential due to their significantly negative correlations with HOMA-IR. CONCLUSIONS FMT with or without metformin significantly improve insulin resistance and body mass index and gut microbial communities of T2DM patients by colonization of donor-derived microbiota.
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Affiliation(s)
- Zezhen Wu
- Department of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, Shantou, China
- Graduate School of Shantou University Medical College, Shantou, Guangdong, China
| | - Bangzhou Zhang
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, Shantou, China
- School of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Fengwu Chen
- Department of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, Shantou, China
| | - Rongmu Xia
- Clinical Research Center, The Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Dan Zhu
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, Shantou, China
| | - Baolong Chen
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, Shantou, China
| | - Aiqiang Lin
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, Shantou, China
| | - Chuyan Zheng
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, Shantou, China
| | - Ducheng Hou
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, Shantou, China
| | - Xiaoyu Li
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, Shantou, China
| | - Shuo Zhang
- Department of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, Shantou, China
- Graduate School of Shantou University Medical College, Shantou, Guangdong, China
| | - Yongsong Chen
- Department of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- *Correspondence: Kaijian Hou, ; Yongsong Chen,
| | - Kaijian Hou
- Department of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, Shantou, China
- School of Public Health, Shantou University, Shantou, China
- *Correspondence: Kaijian Hou, ; Yongsong Chen,
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110
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6515943. [DOI: 10.1093/femsec/fiac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/17/2022] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
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111
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Wu L, Lu XJ, Lin DJ, Chen WJ, Xue XY, Liu T, Xu JT, Xie YT, Li MQ, Lin WY, Zhang Q, Wu QP, He XX. Washed microbiota transplantation improves patients with metabolic syndrome in South China. Front Cell Infect Microbiol 2022; 12:1044957. [PMID: 36457852 PMCID: PMC9705737 DOI: 10.3389/fcimb.2022.1044957] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Metabolic syndrome (MS) is a growing public health problem worldwide. The clinical impact of fecal microbiota transplantation (FMT) from healthy donors in MS patients is unclear, especially in southern Chinese populations. This study aimed to investigate the effect of washed microbiota transplantation (WMT) in MS patients in southern China. METHODS The clinical data of patients with different indications receiving 1-3 courses of WMT were retrospectively collected. The changes of BMI, blood glucose, blood lipids, blood pressure and other indicators before and after WMT were compared, such as fasting blood glucose (FBG), glycated hemoglobin (HbA1c), total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-c)), high-density lipoprotein cholesterol (HDL-c), non-high-density lipoprotein (non-HDL-c), systolic blood pressure (SBP), diastolic blood pressure (DBP), etc. At the same time, comprehensive efficacy evaluation and atherosclerotic cardiovascular disease (ASCVD) grade assessment were performed on MS patients. Finally, 16S rRNA gene amplicon sequencing was performed on fecal samples of MS patients before and after transplantation. RESULTS A total of 237 patients were included, including 42 in the MS group and 195 in the non-MS group. For MS patients, WMT significantly improved the comprehensive efficacy of MS in short term 40.48% (p<0.001), medium term 36.00% (p=0.003), and long term 46.15% (p=0.020). Short-term significantly reduced FBG (p=0.023), TG (p=0.030), SBP (p=0.026) and BMI (p=0.031), and increased HDL-c (p=0.036). The medium term had a significant reduction in FBG (p=0.048), TC (p=0.022), LDL-c (p=0.043), non-HDL-c (p=0.024) and BMI (p=0.048). WMT had a significant short term (p=0.029) and medium term (p=0.011) ASCVD downgrading effect in the high-risk group of MS patients. WMT improved gut microbiota in MS patients. CONCLUSION WMT had a significant improvement effect on MS patients and a significant downgrade effect on ASCVD risk in the high-risk group of patients with MS. WMT could restore gut microbiota homeostasis in MS patients. Therefore, the regulation of gut microbiota by WMT may provide a new clinical approach for the treatment of MS.
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Affiliation(s)
- Lei Wu
- Department of Gastroenterology, Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xin-Jian Lu
- Department of Gastroenterology, Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - De-Jiang Lin
- Department of Gastroenterology, Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Wen-Jia Chen
- Department of Gastroenterology, Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Xing-Ying Xue
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Tao Liu
- Department of Gastroenterology, Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Jia-Ting Xu
- Department of Gastroenterology, Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Ya-Ting Xie
- Department of Gastroenterology, Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Man-Qing Li
- Department of Gastroenterology, Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Wen-Ying Lin
- Department of Gastroenterology, Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Qing Zhang
- Department of Gastroenterology, Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Qing-Ping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Xing-Xiang He, ; Qing-Ping Wu,
| | - Xing-Xiang He
- Department of Gastroenterology, Research Center for Engineering Techniques of Microbiota-Targeted Therapies of Guangdong Province, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- *Correspondence: Xing-Xiang He, ; Qing-Ping Wu,
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112
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Nzabarushimana E, Tang H. Functional profile of host microbiome indicates Clostridioides difficile infection. Gut Microbes 2022; 14:2135963. [PMID: 36289064 PMCID: PMC9621045 DOI: 10.1080/19490976.2022.2135963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 02/04/2023] Open
Abstract
Clostridioides difficile infection (CDI) is a gastro-intestinal (GI) infection that illustrates how perturbations in symbiotic host-microbiome interactions render the GI tract vulnerable to the opportunistic pathogens. CDI also serves as an example of how such perturbations could be reversed via gut microbiota modulation mechanisms, especially fecal microbiota transplantation (FMT). However, microbiome-mediated diagnosis of CDI remains understudied. Here, we evaluated the diagnostic capabilities of the fecal microbiome on the prediction of CDI. We used the metagenomic sequencing data from ten previous studies, encompassing those acquired from CDI patients treated by FMT, CDI-negative patients presenting other intestinal health conditions, and healthy volunteers taking antibiotics. We designed a hybrid species/function profiling approach that determines the abundances of microbial species in the community contributing to its functional profile. These functionally informed taxonomic profiles were then used for classification of the microbial samples. We used logistic regression (LR) models using these features, which showed high prediction accuracy (with an average A U C ≥ 0.91 ), substantiating that the species/function composition of the gut microbiome has a robust diagnostic prediction of CDI. We further assessed the confounding impact of antibiotic therapy on CDI prediction and found that it is distinguishable from the CDI impact. Finally, we devised a log-odds score computed from the output of the LR models to quantify the likelihood of CDI in a gut microbiome sample and applied it to evaluating the effectiveness of FMT based on post-FMT microbiome samples. The results showed that the gut microbiome of patients exhibited a gradual but steady improvement after receiving successful FMT, indicating the restoration of the normal microbiome functions.
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Affiliation(s)
- Etienne Nzabarushimana
- Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Haixu Tang
- Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana, USA
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Li Y, Wang Y, Zhang T. Fecal Microbiota Transplantation in Autism Spectrum Disorder. Neuropsychiatr Dis Treat 2022; 18:2905-2915. [PMID: 36544550 PMCID: PMC9762410 DOI: 10.2147/ndt.s382571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders that begin in infancy. In recent years, the incidence of ASD in the world is increasing year by year. At present, the etiology and pathogenesis of ASD are not clear, and effective treatments are still lacking. In addition to neurobehavioral symptoms, children with ASD often have obvious gastrointestinal symptoms. Gut microbiota is a large microbial community in the human gut, which is closely related to the nervous system and can affect brain development and behavior through the neuroendocrine, neuroimmune and autonomic nervous systems, forming a microbiota-gut-brain axis connection. Recent studies have shown that children with ASD have significant gut microbiota and metabolic disorders, and fecal microbiota transplantation (FMT) is expected to improve ASD-related symptoms by regulating gut microbiota and metabolism. This review paper will therefore focus on FMT in the treatment of ASD, and FMT is effective in improving gastrointestinal and neurobehavioral symptoms in children with ASD.
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Affiliation(s)
- Youran Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yizhong Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ting Zhang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Zou B, Liu SX, Li XS, He JY, Dong C, Ruan ML, Xu L, Bai T, Huang ZH, Shu SN. Long-term safety and efficacy of fecal microbiota transplantation in 74 children: A single-center retrospective study. Front Pediatr 2022; 10:964154. [PMID: 36304525 PMCID: PMC9595213 DOI: 10.3389/fped.2022.964154] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) is an effective treatment for intestinal and extra-intestinal disorders. Nonetheless, long-term safety and efficacy remain major challenges for FMT applications. To date, few long-term follow-up studies have been published on FMT in children. METHODS Retrospective reviewed the medical charts of 74 patients who underwent 508 FMT courses between August 2014 and July 2019 at our medical center. All the FMT procedures followed uniform standards. Baseline characteristics pre-FMT and follow-up data were collected at 1, 3, 6, 12, 36, 60, and 84 months after FMT. All potential influencing factors for adverse events (AEs) were analyzed and assessed using regression analyses. RESULTS A total of 70 (13.7%) short-term AEs occurred in twenty-six patients (35.1%). Most AEs (88.5%) occurred within 2 days post-FMT. A total of 91.4% of the AEs were self-limiting. Ulcerative colitis (UC) and within four times of FMT were associated with a higher rate of AEs (p = 0.028 and p = 0.021, respectively). The primary clinical remission rate after FMT was as high as 72.9%. Twenty-five children were followed for more than 5 years after FMT. The clinical remission rates gradually decreased over time after FMT. During follow-up, none of the patients developed autoimmune, metabolic, or rheumatologic disorders or tumor-related diseases. However, nine children developed rhinitis, five developed rhinitis, were underweight, and six developed constipation. CONCLUSIONS FMT is a safe and effective treatment for dysbiosis in children. The long-term efficacy of FMT for each disease decreased over time. Moreover, multiple FMTs are recommended 3 months post-FMT for recurrent diseases.
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Affiliation(s)
- Biao Zou
- Pediatric Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng-Xuan Liu
- Pediatric Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xue-Song Li
- Pediatric Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia-Yi He
- Pediatric Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chen Dong
- Pediatric Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng-Ling Ruan
- Pediatric Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Xu
- Pediatric Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Bai
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhi-Hua Huang
- Pediatric Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sai-Nan Shu
- Pediatric Department, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Sung JJY, Wong SH. What is unknown in using microbiota as a therapeutic? J Gastroenterol Hepatol 2022; 37:39-44. [PMID: 34668228 DOI: 10.1111/jgh.15716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/17/2022]
Abstract
Fecal microbiota transplantation (FMT) has been used extensively in the treatment of various gastrointestinal and extraintestinal conditions, despite that there are still a lot of missing gaps in our knowledge in the gut microbiota and its behavior. This article describes the unknowns in microbiota biology (undetected microbes, uncertain colonization, unclear mechanisms of action, uncertain indications, unsure long-term efficacy, or side effects). We discuss how these unknowns may affect the therapeutic uses of FMT, and the potentials and caveats of other related microbiota-based therapies. When used as an experimental therapy or last resort in difficult conditions, caution should be taken against inadvertent complications. Clear documentations of post-treatment events should be made mandatory, classified, and graded as in clinical trials. Further robust scientific experiments and properly designed clinical studies are needed.
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Affiliation(s)
- Joseph J Y Sung
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Sunny H Wong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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Understanding the Role of the Gut Microbiome and Microbial Metabolites in Non-Alcoholic Fatty Liver Disease: Current Evidence and Perspectives. Biomolecules 2021; 12:biom12010056. [PMID: 35053205 PMCID: PMC8774162 DOI: 10.3390/biom12010056] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide. NAFLD begins as a relatively benign hepatic steatosis which can evolve to non-alcoholic steatohepatitis (NASH); the risk of cirrhosis and hepatocellular carcinoma (HCC) increases when fibrosis is present. NAFLD represents a complex process implicating numerous factors—genetic, metabolic, and dietary—intertwined in a multi-hit etiopathogenetic model. Recent data have highlighted the role of gut dysbiosis, which may render the bowel more permeable, leading to increased free fatty acid absorption, bacterial migration, and a parallel release of toxic bacterial products, lipopolysaccharide (LPS), and proinflammatory cytokines that initiate and sustain inflammation. Although gut dysbiosis is present in each disease stage, there is currently no single microbial signature to distinguish or predict which patients will evolve from NAFLD to NASH and HCC. Using 16S rRNA sequencing, the majority of patients with NAFLD/NASH exhibit increased numbers of Bacteroidetes and differences in the presence of Firmicutes, resulting in a decreased F/B ratio in most studies. They also present an increased proportion of species belonging to Clostridium, Anaerobacter, Streptococcus, Escherichia, and Lactobacillus, whereas Oscillibacter, Flavonifaractor, Odoribacter, and Alistipes spp. are less prominent. In comparison to healthy controls, patients with NASH show a higher abundance of Proteobacteria, Enterobacteriaceae, and Escherichia spp., while Faecalibacterium prausnitzii and Akkermansia muciniphila are diminished. Children with NAFLD/NASH have a decreased proportion of Oscillospira spp. accompanied by an elevated proportion of Dorea, Blautia, Prevotella copri, and Ruminococcus spp. Gut microbiota composition may vary between population groups and different stages of NAFLD, making any conclusive or causative claims about gut microbiota profiles in NAFLD patients challenging. Moreover, various metabolites may be involved in the pathogenesis of NAFLD, such as short-chain fatty acids, lipopolysaccharide, bile acids, choline and trimethylamine-N-oxide, and ammonia. In this review, we summarize the role of the gut microbiome and metabolites in NAFLD pathogenesis, and we discuss potential preventive and therapeutic interventions related to the gut microbiome, such as the administration of probiotics, prebiotics, synbiotics, antibiotics, and bacteriophages, as well as the contribution of bariatric surgery and fecal microbiota transplantation in the therapeutic armamentarium against NAFLD. Larger and longer-term prospective studies, including well-defined cohorts as well as a multi-omics approach, are required to better identify the associations between the gut microbiome, microbial metabolites, and NAFLD occurrence and progression.
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Santos-Laso A, Gutiérrez-Larrañaga M, Alonso-Peña M, Medina JM, Iruzubieta P, Arias-Loste MT, López-Hoyos M, Crespo J. Pathophysiological Mechanisms in Non-Alcoholic Fatty Liver Disease: From Drivers to Targets. Biomedicines 2021; 10:biomedicines10010046. [PMID: 35052726 PMCID: PMC8773141 DOI: 10.3390/biomedicines10010046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 02/07/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is characterized by the excessive and detrimental accumulation of liver fat as a result of high-caloric intake and/or cellular and molecular abnormalities. The prevalence of this pathological event is increasing worldwide, and is intimately associated with obesity and type 2 diabetes mellitus, among other comorbidities. To date, only therapeutic strategies based on lifestyle changes have exhibited a beneficial impact on patients with NAFLD, but unfortunately this approach is often difficult to implement, and shows poor long-term adherence. For this reason, great efforts are being made to elucidate and integrate the underlying pathological molecular mechanism, and to identify novel and promising druggable targets for therapy. In this regard, a large number of clinical trials testing different potential compounds have been performed, albeit with no conclusive results yet. Importantly, many other clinical trials are currently underway with results expected in the near future. Here, we summarize the key aspects of NAFLD pathogenesis and therapeutic targets in this frequent disorder, highlighting the most recent advances in the field and future research directions.
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Affiliation(s)
- Alvaro Santos-Laso
- Department of Gastroenterology and Hepatology, Marqués de Valdecilla University Hospital, Valdecilla Biomedical Research Institute (IDIVAL), 39008 Santander, Spain; (M.A.-P.); (J.M.M.); (P.I.); (M.T.A.-L.)
- Correspondence: (A.S.-L.); (J.C.)
| | - María Gutiérrez-Larrañaga
- Department of Immunology, Marqués de Valdecilla University Hospital, Valdecilla Biomedical Research Institute (IDIVAL), 39008 Santander, Spain; (M.G.-L.); (M.L.-H.)
| | - Marta Alonso-Peña
- Department of Gastroenterology and Hepatology, Marqués de Valdecilla University Hospital, Valdecilla Biomedical Research Institute (IDIVAL), 39008 Santander, Spain; (M.A.-P.); (J.M.M.); (P.I.); (M.T.A.-L.)
| | - Juan M. Medina
- Department of Gastroenterology and Hepatology, Marqués de Valdecilla University Hospital, Valdecilla Biomedical Research Institute (IDIVAL), 39008 Santander, Spain; (M.A.-P.); (J.M.M.); (P.I.); (M.T.A.-L.)
| | - Paula Iruzubieta
- Department of Gastroenterology and Hepatology, Marqués de Valdecilla University Hospital, Valdecilla Biomedical Research Institute (IDIVAL), 39008 Santander, Spain; (M.A.-P.); (J.M.M.); (P.I.); (M.T.A.-L.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), 28029 Madrid, Spain
| | - María Teresa Arias-Loste
- Department of Gastroenterology and Hepatology, Marqués de Valdecilla University Hospital, Valdecilla Biomedical Research Institute (IDIVAL), 39008 Santander, Spain; (M.A.-P.); (J.M.M.); (P.I.); (M.T.A.-L.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), 28029 Madrid, Spain
| | - Marcos López-Hoyos
- Department of Immunology, Marqués de Valdecilla University Hospital, Valdecilla Biomedical Research Institute (IDIVAL), 39008 Santander, Spain; (M.G.-L.); (M.L.-H.)
| | - Javier Crespo
- Department of Gastroenterology and Hepatology, Marqués de Valdecilla University Hospital, Valdecilla Biomedical Research Institute (IDIVAL), 39008 Santander, Spain; (M.A.-P.); (J.M.M.); (P.I.); (M.T.A.-L.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), 28029 Madrid, Spain
- Correspondence: (A.S.-L.); (J.C.)
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Casado-Bedmar M, Viennois E. MicroRNA and Gut Microbiota: Tiny but Mighty-Novel Insights into Their Cross-talk in Inflammatory Bowel Disease Pathogenesis and Therapeutics. J Crohns Colitis 2021; 16:992-1005. [PMID: 34918052 PMCID: PMC9282881 DOI: 10.1093/ecco-jcc/jjab223] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022]
Abstract
MicroRNAs [miRNAs], small non-coding RNAs, have recently been described as crucial contributors to intestinal homeostasis. They can interact with the gut microbiota in a reciprocal manner and deeply affect host health status, leading to several disorders when unbalanced. Inflammatory bowel disease [IBD] is a chronic inflammation of the gastrointestinal tract that co-occurs with alterations of the gut microbiota, and whose aetiology remains largely unclear. On one hand, host miRNA could be playing a relevant role in IBD pathophysiology by shaping the gut microbiota. The gut microbiome, on the other hand, may regulate the expression of host miRNAs, resulting in intestinal epithelial dysfunction, altered autophagy, and immune hyperactivation. Interestingly, it has been hypothesised that their reciprocal impact may be used for therapeutic goals. This review describes the latest research and suggests mechanisms through which miRNA and intestinal microbiota, as joint actors, may participate specifically in IBD pathophysiology. Furthermore, we discuss the diagnostic power and therapeutic potential resulting from their bidirectional communication after faecal transplantation, probiotics intake, or anti-miRNAs or miRNA mimics administration. The current literature is summarised in the present work in a comprehensive manner, hoping to provide a better understanding of the miRNA-microbiota cross-talk and to facilitate their application in IBD.
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Affiliation(s)
- Maite Casado-Bedmar
- INSERM, U1149, Center for Research on Inflammation, Université de Paris, Paris, France
| | - Emilie Viennois
- Corresponding author: Emilie Viennois, INSERM, U1149, Center for Research on Inflammation, Université de Paris, 75018 Paris, France.
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He J, He X, Ma Y, Yang L, Fang H, Shang S, Xia H, Lian G, Tang H, Wang Q, Wang J, Lin Z, Wen J, Liu Y, Zhai C, Wang W, Jiang X, Xuan J, Liu M, Lu S, Li X, Wang H, Ouyang C, Cao M, Lin A, Zhang B, Wu D, Chen Y, Xiao C. A comprehensive approach to stool donor screening for faecal microbiota transplantation in China. Microb Cell Fact 2021; 20:216. [PMID: 34838016 PMCID: PMC8626716 DOI: 10.1186/s12934-021-01705-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 11/09/2021] [Indexed: 12/31/2022] Open
Abstract
Background Faecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridium difficile infections and chronic gastrointestional infections. However, the risks of FMT and the selection process of suitable donors remain insufficiently characterized. The eligibility rate for screening, underlying microbial basis, and core ethical issues of stool donors for FMT are yet to be elucidated in China. Results The potential stool donors were screened from December 2017 to December 2019 with the help of an online survey, clinical assessments, and stool and blood testing. Bioinformatics analyses were performed, and the composition and stability of gut microbiota in stool obtained from eligible donors were dynamically observed using metagenomics. Meanwhile, we build a donor microbial evaluation index (DoMEI) for stool donor screening. In the screening process, we also focused on ethical principles and requirements. Of the 2071 participants, 66 donors were selected via the screening process (3.19% success rate). Although there were significant differences in gut microbiota among donors, we found that the changes in the gut microbiota of the same donor were typically more stable than those between donors over time. Conclusions DoMEI provides a potential reference index for regular stool donor re-evaluation. In this retrospective study, we summarised the donor recruitment and screening procedure ensuring the safety and tolerability for FMT in China. Based on the latest advances in this field, we carried out rigorous recommendation and method which can assist stool bank and clinicians to screen eligible stool donor for FMT. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01705-0.
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Affiliation(s)
- Jianquan He
- School of Medicine, Xiamen University, Xiamen, China
| | - Xingxiang He
- Department of Gastroenterology, The First Affiliated Hospital of Clinical Medicine of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yonghui Ma
- School of Medicine, Xiamen University, Xiamen, China
| | - Luxi Yang
- School of Medicine, Xiamen University, Xiamen, China
| | - Haiming Fang
- Department of Gastroenterology and Hepatology, The Second Hospital of Anhui Medical Univerisity, Hefei, China
| | - Shu Shang
- Department of Gastroenterology, The Fifth People's Hospital of Shenyang, Shenyang, China
| | - Huping Xia
- Anorectal Diagnosis and Treatment Center, The General Hospital of Xinjiang Military Region, Wulumuqi, China
| | - Guanghui Lian
- Department of Gastroenterology, Xiangya Hospital, Changsha, China
| | - Hailing Tang
- Department of Gastroenterology, Xi'an Central Hospital, Xi'an, China
| | - Qizhi Wang
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Junping Wang
- Department of Gastroenterology, The Affiliated People's Hospital of Shanxi Medical University, Taiyuan, China
| | - Zhihui Lin
- Department of Gastroenterology, Fujian Provincial Hospital, Fuzhou, China
| | - Jianbo Wen
- Department of Gastroenterology, Pingxiang People's Hospital, Pingxiang, China
| | - Yuedong Liu
- Department of Gastroenterology, The Third Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Chunbao Zhai
- Department of Proctology, The Affiliated People's Hospital of Shanxi Medical University, Taiyuan, China
| | - Wen Wang
- Department of Gastroenterology, 900th Hospital of PLA, Fuzhou, China
| | - Xueliang Jiang
- Department of Gastroenterology, The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ji Xuan
- Department of Gastroenterology, Jinling Hospital, Nanjing, China
| | - Morong Liu
- Department of Gastroenterology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shiyun Lu
- Department of Gastroenterology, Fujian Provincial Hospital, Fuzhou, China
| | - Xuejun Li
- Department of Gastroenterology, The Second Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, China
| | - Han Wang
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Cong Ouyang
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Man Cao
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | - Aiqiang Lin
- Xiamen Treatgut Biotechnology Co., Ltd., Xiamen, China
| | | | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ye Chen
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Charalambous EG, Mériaux SB, Guebels P, Muller CP, Leenen FAD, Elwenspoek MMC, Thiele I, Hertel J, Turner JD. Early-Life Adversity Leaves Its Imprint on the Oral Microbiome for More Than 20 Years and Is Associated with Long-Term Immune Changes. Int J Mol Sci 2021; 22:ijms222312682. [PMID: 34884490 PMCID: PMC8657988 DOI: 10.3390/ijms222312682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
The early-life microbiome (ELM) interacts with the psychosocial environment, in particular during early-life adversity (ELA), defining life-long health trajectories. The ELM also plays a significant role in the maturation of the immune system. We hypothesised that, in this context, the resilience of the oral microbiomes, despite being composed of diverse and distinct communities, allows them to retain an imprint of the early environment. Using 16S amplicon sequencing on the EpiPath cohort, we demonstrate that ELA leaves an imprint on both the salivary and buccal oral microbiome 24 years after exposure to adversity. Furthermore, the changes in both communities were associated with increased activation, maturation, and senescence of both innate and adaptive immune cells, although the interaction was partly dependent on prior herpesviridae exposure and current smoking. Our data suggest the presence of multiple links between ELA, Immunosenescence, and cytotoxicity that occur through long-term changes in the microbiome.
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Affiliation(s)
- Eleftheria G. Charalambous
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.G.C.); (S.B.M.); (P.G.); (C.P.M.); (F.A.D.L.); (M.M.C.E.)
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de Université, L-4365 Esch-sur-Alzette, Luxembourg
| | - Sophie B. Mériaux
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.G.C.); (S.B.M.); (P.G.); (C.P.M.); (F.A.D.L.); (M.M.C.E.)
| | - Pauline Guebels
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.G.C.); (S.B.M.); (P.G.); (C.P.M.); (F.A.D.L.); (M.M.C.E.)
| | - Claude P. Muller
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.G.C.); (S.B.M.); (P.G.); (C.P.M.); (F.A.D.L.); (M.M.C.E.)
| | - Fleur A. D. Leenen
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.G.C.); (S.B.M.); (P.G.); (C.P.M.); (F.A.D.L.); (M.M.C.E.)
| | - Martha M. C. Elwenspoek
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.G.C.); (S.B.M.); (P.G.); (C.P.M.); (F.A.D.L.); (M.M.C.E.)
| | - Ines Thiele
- School of Medicine, National University of Ireland, H91 YR71 Galway, Ireland; (I.T.); (J.H.)
- Ryan Institute, National University of Galway, H91 TK33 Galway, Ireland
- Division of Microbiology, National University of Galway, H91 TK33 Galway, Ireland
- APC Microbiome Ireland, T12 HW58 Cork, Ireland
| | - Johannes Hertel
- School of Medicine, National University of Ireland, H91 YR71 Galway, Ireland; (I.T.); (J.H.)
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Jonathan D. Turner
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (E.G.C.); (S.B.M.); (P.G.); (C.P.M.); (F.A.D.L.); (M.M.C.E.)
- Correspondence: ; Tel.: +352-26970-629
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Rinott E, Youngster I, Meir AY, Tsaban G, Kaplan A, Zelicha H, Rubin E, Koren O, Shai I. Autologous fecal microbiota transplantation can retain the metabolic achievements of dietary interventions. Eur J Intern Med 2021; 92:17-23. [PMID: 33883079 DOI: 10.1016/j.ejim.2021.03.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND We recently reported that autologous fecal microbiota transplantation (aFMT), derived from the time of maximal weight-loss and administrated in the regain-phase, might preserve weight loss and glycemic control in moderately obese subjects, and is associated with specific microbiome signatures. Here, we sought to explore the global effect of aFMT on adipokines, inflammatory markers and blood cholesterol and on the overall gut microbiome preservation. METHODS In the DIRECT-PLUS weight-loss trial, abdominally obese participants were randomized to three distinct weight-loss diets. Following the expected weight loss phase (0-6 m), 90 participants were randomized to receive their personal frozen fecal microbiota or placebo oral capsules (ten 1 g-capsules over ten sessions-total=100 g) during the expected weight regain phase (8-14 m). RESULTS Of the 90 participants (age=52 yr; 0-6 m weight loss=-8.3 kg), 95.6% ingested at least 80/100 oral aFMT/placebo capsules over 6 months. Overall, the gut microbiome community structure was associated with plasma levels of leptin, cholesterol and interleukin-6 at baseline and after 6 m, whereas 6 m (weight loss phase) changes in specific microbiome species associated with the dynamic of leptin and inflammatory biomarkers. Following the 8-14 m aFMT administration phase, aFMT maintained decreased levels of leptin (ΔaFMT=-3.54 ng/mL vs. Δplacebo=-0.82 ng/mL;P = 0.04), C-reactive-protein (ΔaFMT=-1.45 mg/L vs. Δplacebo=-0.66 mg/L;P = 0.009), Interleukin-6 (ΔaFMT=-0.03pg/mL vs. Δplacebo=1.11pg/mL;P = 0.03) and total cholesterol (ΔaFMT=2.2 mg/dl vs. Δplacebo=13.1 mg/dl;P = 0.04) achieved in the weight loss phase. Overall, aFMT induced a significant preservatory effect on personal gut microbiome global composition (P = 0.03;Jensen-Shannon distance), as compared to placebo. CONCLUSIONS aFMT treatment in the regain phase might retain weight-loss induced metabolic benefits. These findings may suggest a novel aFMT treatment approach for personal metabolic attainment preservation.
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Affiliation(s)
- Ehud Rinott
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ilan Youngster
- Pediatric Division and Center for Microbiome Research, Shamir Medical Center, Be'er Ya'akov, Israel; Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Anat Yaskolka Meir
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gal Tsaban
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Alon Kaplan
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Hila Zelicha
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Elad Rubin
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Iris Shai
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Aggarwala V, Mogno I, Li Z, Yang C, Britton GJ, Chen-Liaw A, Mitcham J, Bongers G, Gevers D, Clemente JC, Colombel JF, Grinspan A, Faith J. Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes. Nat Microbiol 2021; 6:1309-1318. [PMID: 34580445 PMCID: PMC8993687 DOI: 10.1038/s41564-021-00966-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023]
Abstract
Fecal microbiota transplantation (FMT) has been successfully applied to treat recurrent Clostridium difficile infection in humans, but a precise method to measure which bacterial strains stably engraft in recipients and evaluate their association with clinical outcomes is lacking. We assembled a collection of >1,000 different bacterial strains that were cultured from the fecal samples of 22 FMT donors and recipients. Using our strain collection combined with metagenomic sequencing data from the same samples, we developed a statistical approach named Strainer for the detection and tracking of bacterial strains from metagenomic sequencing data. We applied Strainer to evaluate a cohort of 13 FMT longitudinal clinical interventions and detected stable engraftment of 71% of donor microbiota strains in recipients up to 5 years post-FMT. We found that 80% of recipient gut bacterial strains pre-FMT were eliminated by FMT and that post-FMT the strains present persisted up to 5 years later, together with environmentally acquired strains. Quantification of donor bacterial strain engraftment in recipients independently explained (precision 100%, recall 95%) the clinical outcomes (relapse or success) after initial and repeat FMT. We report a compendium of bacterial species and strains that consistently engraft in recipients over time that could be used in defined live biotherapeutic products as an alternative to FMT. Our analytical framework and Strainer can be applied to systematically evaluate either FMT or defined live bacterial therapeutic studies by quantification of strain engraftment in recipients.
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Affiliation(s)
- Varun Aggarwala
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ilaria Mogno
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhihua Li
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chao Yang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Josephine Mitcham
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerold Bongers
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dirk Gevers
- Janssen Human Microbiome Institute, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Jose C Clemente
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ari Grinspan
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Georgiou K, Marinov B, Farooqi AA, Gazouli M. Gut Microbiota in Lung Cancer: Where Do We Stand? Int J Mol Sci 2021; 22:10429. [PMID: 34638770 PMCID: PMC8508914 DOI: 10.3390/ijms221910429] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/19/2021] [Accepted: 09/26/2021] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota (GM) is considered to constitute a powerful "organ" capable of influencing the majority of the metabolic, nutritional, physiological, and immunological processes of the human body. To date, five microbial-mediated mechanisms have been revealed that either endorse or inhibit tumorigenesis. Although the gastrointestinal and respiratory tracts are distant physically, they have common embryonic origin and similarity in structure. The lung microbiota is far less understood, and it is suggested that the crosslink between the human microbiome and lung cancer is a complex, multifactorial relationship. Several pathways linking their respective microbiota have reinforced the existence of a gut-lung axis (GLA). Regarding implications of specific GM in lung cancer therapy, a few studies showed that the GM considerably affects immune checkpoint inhibitor (ICI) therapy by altering the differentiation of regulatory T cells and thus resulting in changes in immunomodulation mechanisms, as discovered by assessing drug metabolism directly and by assessing the host immune modulation response. Additionally, the GM may increase the efficacy of chemotherapeutic treatment in lung cancer. The mechanism underlying the role of the GLA in the pathogenesis and progression of lung cancer and its capability for diagnosis, manipulation, and treatment need to be further explored.
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Affiliation(s)
- Konstantinos Georgiou
- 1st Department of Propaedeutic Surgery, Hippokration General Hospital of Athens, Athens Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Blagoi Marinov
- Medical Simulation Training Center at Research Institute of Medical University of Plovdiv, Tsentar, 4002 Plovdiv, Bulgaria;
| | - Ammad Ahmad Farooqi
- Institute of Biomedical and Genetic Engineering (IBGE), 24 Mauve Area, Sector G-9/1, Islamabad 54000, Pakistan;
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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Free Faecal Water: Analysis of Horse Faecal Microbiota and the Impact of Faecal Microbial Transplantation on Symptom Severity. Animals (Basel) 2021; 11:ani11102776. [PMID: 34679798 PMCID: PMC8533009 DOI: 10.3390/ani11102776] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Free faecal water (FFW) in equines causes soiling of the hindquarters and tail and may also include additional symptoms. The cause of FFW is unknown. In this study it was investigated whether the microbes present in the last part of the gut (i.e., the hindgut microbiota) may be involved. From the analysis of faecal samples, it was found that horses suffering from FFW had no differences in their hindgut microbiota compared to healthy horses stabled at the same location. However, subsequent treatment of the FFW horses with a faecal microbiota transplantation (FMT) from a healthy donor animal resulted in a decrease in FFW symptom severity. Nevertheless, animals did not respond uniformly to this treatment, with some only having temporary decreases in FFW symptom severity. No lasting changes in the hindgut microbiota of the FFW horses occurred as a result of the faecal transplant. The practical implication of these findings is that FMT can potentially be used to temporarily alleviate FFW symptom severity in horses, although future studies using controls are needed to confirm the effectiveness of FMT to treat FFW. Abstract Free faecal water (FFW) in equines results in pollution of the hindquarters and tail and can also involve clinical signs. Though the cause of FFW is unknown, it was hypothesized that it may involve the gut microbiota. This hypothesis was addressed as follows. First, the faecal prokaryotic community composition of horses suffering from FFW relative to healthy controls (n = 10) was compared. Second, FFW horses were treated with a standardised faecal microbiota transplantation (FMT) protocol (n = 10), followed by assessment of FFW symptom severity and faecal prokaryotic community composition over a follow-up period of 168 days. No significant differences were found in the faecal microbiota composition of FFW horses compared to healthy controls (p > 0.05). Relative to before FMT, FFW symptom severity decreased in affected horses 14 days after FMT (p = 0.02) and remained decreased for the remainder of the study (p < 0.02). However, individual animal responses to FMT varied. FMT had no effect on FFW horse faecal prokaryotic community composition in terms of alpha or beta diversity. Alpha diversity of the donor inocula used in the FMT was always lower than that of the faecal microbiota of the FFW treated horses (p < 0.001). In conclusion, whilst findings indicate FFW horses do not have an altered hindgut microbiota, some horses that received FMT had a temporary alleviation of FFW symptom severity without causing changes in the faecal microbiota. Future studies using controls are now needed to confirm the effectiveness of FMT to treat FFW.
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Koo H, Morrow CD. Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy. BMC Microbiol 2021; 21:251. [PMID: 34544375 PMCID: PMC8454007 DOI: 10.1186/s12866-021-02312-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/06/2021] [Indexed: 02/08/2023] Open
Abstract
Background To understand inter-individual variability of fecal microbe transplantation (FMT) to enhance anti-PD-1 immunotherapy (IT) for melanoma, we analyzed the data sets from two recent publications with a microbial strain-tracking tool to determine if donor strains were dominant in the recipient feces following FMT. Results Analysis of the Baruch et al. data set found that the presence of commensal donor microbes in recipient feces post-FMT did not correlate with the patient response to IT. From the Davar et al., data set, we found 4 patients that responded to IT had donor’s related strain post-FMT, while 2 patients that did not respond to the IT also had donor’s strain post-FMT. Importantly, we identified no donor microbes in the feces in one recipient post-FMT that responded to IT. Furthermore, in depth analysis from two patients who responded to IT revealed both donor and recipient strains at different times post-FMT. Colonization of the gastrointestinal tract niches is important for the interaction with the host immune system. Using a separate data set, we show that mucosa from the cecum, transverse colon, and sigmoid colon share strains, providing a large reservoir of niches containing recipient microbes. Conclusions We demonstrated using strain-tracking analysis individual variation with the respect to the presence of fecal dominant donor microbes in the recipient following FMT that did not correlate with the response to anti-PD-1 immunotherapy. The inter-individual differences of FMT to enhance IT might be explained by the variability of the donor microbes to occupy and outcompete recipient microbes for the gastrointestinal niches. The result from our study supports the use of new approaches to clear the niches in the gastrointestinal tract to promote donor colonization to reduce inter-individual variability of IT for melanoma and potentially other cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02312-0.
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Affiliation(s)
- Hyunmin Koo
- Department of Genetics Hugh Kaul Personalized Medicine Institute, University of Alabama at Birmingham, Alabama, Birmingham, USA.
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology Hugh Kaul Personalized Medicine Institute, University of Alabama at Birmingham, Alabama, Birmingham, USA.
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The Role of Fecal Microbiota Transplantation in the Treatment of Inflammatory Bowel Disease. J Clin Med 2021; 10:jcm10184055. [PMID: 34575166 PMCID: PMC8465860 DOI: 10.3390/jcm10184055] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/12/2022] Open
Abstract
The exact pathogenesis of inflammatory bowel disease (IBD) is still not completely understood. It is hypothesized that a genetic predisposition leads to an exaggerated immune response to an environmental trigger, leading to uncontrolled inflammation. As there is no known causative treatment, current management strategies for inflammatory bowel disease focus on correcting the excessive immune response to environmental (including microbial) triggers. In recent years, there has been growing interest in new avenues of treatment, including targeting the microbial environment itself. Fecal microbiota transplantation (FMT) is a novel treatment modality showing promising results in early studies. The article discusses the rationale for the use of FMT in inflammatory bowel disease and the yet-unresolved questions surrounding its optimal use in practice.
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Chu ND, Crothers JW, Nguyen LTT, Kearney SM, Smith MB, Kassam Z, Collins C, Xavier R, Moses PL, Alm EJ. Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease. mBio 2021; 12:e0097521. [PMID: 34281401 PMCID: PMC8406238 DOI: 10.1128/mbio.00975-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/09/2021] [Indexed: 12/26/2022] Open
Abstract
For fecal microbiota transplantation (FMT) to be successful in immune diseases like inflammatory bowel disease, it is assumed that therapeutic microbes and their beneficial functions and immune interactions must colonize a recipient patient and persist in sufficient quantity and for a sufficient period of time to produce a clinical benefit. Few studies, however, have comprehensively profiled the colonization and persistence of transferred microbes along with the transfer of their microbial functions and interactions with the host immune system. Using 16S, metagenomic, and immunoglobulin A (IgA) sequencing, we analyzed hundreds of longitudinal microbiome samples from a randomized controlled trial of 12 patients with ulcerative colitis who received fecal transplant or placebo for 12 weeks. We uncovered diverse competitive dynamics among donor and patient strains, showing that persistence of transferred microbes is far from static. Indeed, one patient experienced a dramatic loss of donor bacteria 10 weeks into the trial, coinciding with a bloom of pathogenic bacteria and worsening symptoms. We evaluated the transfer of microbial functions, including desired ones, such as butyrate production, and unintended ones, such as antibiotic resistance. By profiling bacteria coated with IgA, we identified bacteria associated with inflammation and found that microbial interactions with the host immune system can be transferred across people, which could play a role in gut microbiome therapeutics for immune-related diseases. Our findings shed light on the colonization dynamics of gut microbes and their functions in the context of FMT to treat a complex disease-information that may provide a foundation for developing more-targeted therapeutics. IMPORTANCE Fecal microbiota transplantation (FMT)-transferring fecal microbes from a healthy donor to a sick patient-has shown promise for gut diseases such as inflammatory bowel disease. Unlike pharmaceuticals, however, fecal transplants are complex mixtures of living organisms, which must then interact with the microbes and immune system of the recipient. We sought to understand these interactions by tracking the microbes of 12 inflammatory bowel disease patients who received fecal transplants for 12 weeks. We uncovered a range of dynamics. For example, one patient experienced successful transfer of donor bacteria, only to lose them after 10 weeks. We similarly evaluated transfer of microbial functions, including how they interacted with the recipient's immune system. Our findings shed light on the colonization dynamics of gut microbes, as well as their functions in the context of FMT-information that may provide a critical foundation for the development of more-targeted therapeutics.
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Affiliation(s)
- Nathaniel D. Chu
- Center for Microbiome Informatics and Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Le T. T. Nguyen
- Center for Microbiome Informatics and Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sean M. Kearney
- Center for Microbiome Informatics and Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Zain Kassam
- Finch Therapeutics, Somerville, Massachusetts, USA
| | - Cheryl Collins
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Ramnik Xavier
- Center for Microbiome Informatics and Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Peter L. Moses
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Eric J. Alm
- Center for Microbiome Informatics and Therapeutics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Graduate Program in Microbiology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
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Separation of Donor and Recipient Microbial Diversity Allows Determination of Taxonomic and Functional Features of Gut Microbiota Restructuring following Fecal Transplantation. mSystems 2021; 6:e0081121. [PMID: 34402648 PMCID: PMC8407411 DOI: 10.1128/msystems.00811-21] [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] [Indexed: 12/11/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is currently used in medicine to treat recurrent clostridial colitis and other intestinal diseases. However, neither the therapeutic mechanism of FMT nor the mechanism that allows the donor bacteria to colonize the intestine of the recipient has yet been clearly described. From a biological point of view, FMT can be considered a useful model for studying the ecology of host-associated microbial communities. FMT experiments can shed light on the relationship features between the host and its gut microbiota. This creates the need for experimentation with approaches to metagenomic data analysis which may be useful for the interpretation of observed biological phenomena. Here, the recipient intestine colonization analysis tool (RECAST) novel computational approach is presented, which is based on the metagenomic read sorting process per their origin in the recipient’s post-FMT stool metagenome. Using the RECAST algorithm, taxonomic/functional annotation, and machine learning approaches, the metagenomes from three FMT studies, including healthy volunteers, patients with clostridial colitis, and patients with metabolic syndrome, were analyzed. Using our computational pipeline, the donor-derived and recipient-derived microbes which formed the recipient post-FMT stool metagenomes (successful microbes) were identified. Their presence is well explained by a higher relative abundance in donor/pre-FMT recipient metagenomes or other metagenomes from the human population. In addition, successful microbes are enriched with gene groups potentially related to antibiotic resistance, including antimicrobial peptides. Interestingly, the observed reorganization features are universal and independent of the disease. IMPORTANCE We assumed that the enrichment of successful gut microbes by lantibiotic/antibiotic resistance genes can be related to gut microbiota colonization resistance by third-party microbe phenomena and resistance to bacterium-derived or host-derived antimicrobial substances. According to this assumption, competition between the donor-derived and recipient-derived microbes as well as host immunity may play a key role in the FMT-related colonization and redistribution of recipient gut microbiota structure. Author Video: An author video summary of this article is available.
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Abstract
Despite identification of numerous associations between microbiomes and diseases, the complexity of the human microbiome has hindered identification of individual species and strains that are causative in host phenotype or disease. Uncovering causative microbes is vital to fully understand disease processes and to harness the potential therapeutic benefits of microbiota manipulation. Developments in sequencing technology, animal models, and bacterial culturing have facilitated the discovery of specific microbes that impact the host and are beginning to advance the characterization of host-microbiome interaction mechanisms. We summarize the historical and contemporary experimental approaches taken to uncover microbes from the microbiota that affect host biology and describe examples of commensals that have specific effects on the immune system, inflammation, and metabolism. There is still much to learn, and we lay out challenges faced by the field and suggest potential remedies for common pitfalls encountered in the hunt for causative commensal microbes. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Cui J, Lin Z, Tian H, Yang B, Zhao D, Ye C, Li N, Qin H, Chen Q. Long-Term Follow-Up Results of Fecal Microbiota Transplantation for Irritable Bowel Syndrome: A Single-Center, Retrospective Study. Front Med (Lausanne) 2021; 8:710452. [PMID: 34395484 PMCID: PMC8362996 DOI: 10.3389/fmed.2021.710452] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
Objective: This study aimed to investigate the long-term efficacy of fecal microbiota transplantation (FMT) in patients with irritable bowel syndrome (IBS). Study Methods: In this single-center long-term follow-up study, FMT treatment was administered to patients with moderate to severe IBS (IBS severity scoring system (IBS-SSS) > 175). After 1 year of treatment, it was decided whether to repeat FMT based on IBS-SSS score (IBS-SSS > 175). Baseline characteristics before and after FMT and questionnaires were completed at 1, 3, 6, 12, 24, 36, 48, and 60 months after FMT. The study outcomes included treatment efficacy rates, change of IBS-SSS, IBS-specific quality of life and fatigue, effect on stool frequency, Bristol Stool Scale for IBS-C and IBS-D, and side effects. Results: A total of 227 patients (47.58% IBS-C, 39.21% IBS-D, and 13.22% IBS-M) were recruited (142 females and 85 males with a mean age of 41.89 ± 13.57 years). The efficacy rates were 108 (51.92%), 147 (74.62%), 125 (74.41 %), 88 (71.54%), 78 (75.00%), 65 (73.03%), 45 (61.64%), and 37 (62.71%) at different follow-up time points. The total IBS-SSS score was 321.37 ± 73.89 before FMT, which significantly decreased after 1 month. The IBS-specific quality of life (IBS-QoL) score was 40.24 ± 11.34 before FMT, increased gradually, and was significantly higher at 3 months compared to before FMT. The total Fatigue Assessment Scale (FAS) score was 47 ± 8.64 before FMT and was significantly lower at 3 months. During follow-up, 89 (39.21%) side effects occurred that were alleviated by symptomatic treatment, and no serious adverse events were detected. Conclusion: Based on 60 months of long-term follow-up, the safety and efficacy of FMT for IBS was established. However, as the treatment effect declines over time, periodic and repetitive FMT is required for a sustained effect.
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Affiliation(s)
- Jiaqu Cui
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Zhiliang Lin
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Hongliang Tian
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Bo Yang
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Di Zhao
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Chen Ye
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Ning Li
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Huanlong Qin
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University, Shanghai, China
| | - Qiyi Chen
- Intestinal Microenvironment Treatment Center of General Surgery, Shanghai Tenth People's Hospital, Tenth People's Hospital of Tongji University, Shanghai, China
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Marrs T, Walter J. Pros and cons: Is faecal microbiota transplantation a safe and efficient treatment option for gut dysbiosis? Allergy 2021; 76:2312-2317. [PMID: 33483999 DOI: 10.1111/all.14750] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/03/2021] [Accepted: 01/13/2021] [Indexed: 12/24/2022]
Abstract
Faecal Microbiota Transplantation (FMT) is well established as an effective treatment for Clostridioides difficile infection (CDI), restoring gut microbiome diversity and function. The utility of FMT is currently being explored in relation to other immune-mediated pathologies, such as allergic disease, inflammatory bowel diseases and autoimmune diseases. Clinical trials in these areas are ongoing, and the altered gut microbiota (dysbiosis) that is often observed in these pathologies provides a rationale for the application of FMT to restore the microbiome. However, there is controversy on the risk-benefit ratio as it relates to the use of FMTs in pathologies other than CDI. In this Pro and Con article, we present the arguments for and against the use of FMT in immune-mediated pathologies, such as allergic disease. We further identify research gaps and recommend how these may be addressed in future studies.
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Affiliation(s)
- Tom Marrs
- Children's Allergies, Evelina London, Guy's and St Thomas' NHS Foundation Trust, London, UK
- Department of Paediatric Allergy, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Jens Walter
- APC Microbiome, Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland
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Danne C, Rolhion N, Sokol H. Recipient factors in faecal microbiota transplantation: one stool does not fit all. Nat Rev Gastroenterol Hepatol 2021; 18:503-513. [PMID: 33907321 DOI: 10.1038/s41575-021-00441-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/15/2021] [Indexed: 02/08/2023]
Abstract
Faecal microbiota transplantation (FMT) is a promising therapy for chronic diseases associated with gut microbiota alterations. FMT cures 90% of recurrent Clostridioides difficile infections. However, in complex diseases, such as inflammatory bowel disease, irritable bowel syndrome and metabolic syndrome, its efficacy remains variable. It is accepted that donor selection and sample administration are key determinants of FMT success, yet little is known about the recipient factors that affect it. In this Perspective, we discuss the effects of recipient parameters, such as genetics, immunity, microbiota and lifestyle, on donor microbiota engraftment and clinical efficacy. Emerging evidence supports the possibility that controlling inflammation in the recipient intestine might facilitate engraftment by reducing host immune system pressure on the newly transferred microbiota. Deciphering FMT engraftment rules and developing novel therapeutic strategies are priorities to alleviate the burden of chronic diseases associated with an altered gut microbiota such as inflammatory bowel disease.
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Affiliation(s)
- Camille Danne
- INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France.,Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France.,Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France
| | - Nathalie Rolhion
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France.,Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France.,French Group of Fecal Microbiota Transplantation (GFTF), Paris, France
| | - Harry Sokol
- INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France. .,Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France. .,Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France. .,French Group of Fecal Microbiota Transplantation (GFTF), Paris, France. .,AP-HP Fecal Microbiota transplantation Center, Saint Antoine Hospital, Paris, France.
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Gopalakrishnan V, Dozier EA, Glover MS, Novick S, Ford M, Morehouse C, Warrener P, Caceres C, Hess S, Sellman BR, Cohen TS. Engraftment of Bacteria after Fecal Microbiota Transplantation Is Dependent on Both Frequency of Dosing and Duration of Preparative Antibiotic Regimen. Microorganisms 2021; 9:1399. [PMID: 34209573 PMCID: PMC8306289 DOI: 10.3390/microorganisms9071399] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 01/04/2023] Open
Abstract
The gut microbiota has emerged as a key mediator of human physiology, and germ-free mice have been essential in demonstrating a role for the microbiome in disease. Preclinical models using conventional mice offer the advantage of working with a mature immune system. However, optimal protocols for fecal microbiota transplant (FMT) engraftment in conventional mice are yet to be established. Conventional BALB/c mice were randomized to receive 3-day (3d) or 3-week (3w) antibiotic (ABX) regimen in their drinking water followed by 1 or 5-daily FMTs from a human donor. Fecal samples were collected longitudinally and characterized using 16S ribosomal RNA (rRNA) sequencing. Semi-targeted metabolomic profiling of fecal samples was also done with liquid chromatography-mass spectrometry (LC-MS). Lastly, we sought to confirm our findings in BKS mice. Recovery of baseline diversity scores were greatest in the 3d groups, driven by re-emergence of mouse commensal microbiota, whereas the most resemblance to donor microbiota was seen in the 3w + 5-FMT group. Amplicon sequence variants (ASVs) that were linked to the input material (human ASVs) engrafted to a significantly greater extent when compared to mouse ASVs in the 3-week groups but not the 3-day groups. Lastly, comparison of metabolomic profiles revealed distinct functional profiles by ABX regimen. These results indicate successful model optimization and emphasize the importance of ABX duration and frequency of FMT dosing; the most stable and reliable colonization by donor ASVs was seen in the 3wk + 5-FMT group.
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Affiliation(s)
- Vancheswaran Gopalakrishnan
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Elizabeth Ashley Dozier
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Matthew S. Glover
- Dynamic Omics, Antibody Discovery & Protein Engineering, R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (M.S.G.); (S.H.)
| | - Steven Novick
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA;
| | - Michael Ford
- Animal Sciences and Technologies, R & D, AstraZeneca, Gaithersburg, MD 20878, USA;
| | - Christopher Morehouse
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Paul Warrener
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Carolina Caceres
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Sonja Hess
- Dynamic Omics, Antibody Discovery & Protein Engineering, R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (M.S.G.); (S.H.)
| | - Bret R. Sellman
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
| | - Taylor S. Cohen
- Microbiome Discovery, Microbial Sciences, BioPharmaceuticals R & D, AstraZeneca, Gaithersburg, MD 20878, USA; (V.G.); (E.A.D.); (C.M.); (P.W.); (C.C.); (B.R.S.)
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van Lier YF, Davids M, Haverkate NJE, de Groot PF, Donker ML, Meijer E, Heubel-Moenen FCJI, Nur E, Zeerleder SS, Nieuwdorp M, Blom B, Hazenberg MD. Donor fecal microbiota transplantation ameliorates intestinal graft-versus-host disease in allogeneic hematopoietic cell transplant recipients. Sci Transl Med 2021; 12:12/556/eaaz8926. [PMID: 32801142 DOI: 10.1126/scitranslmed.aaz8926] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/28/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022]
Abstract
Disruption of the intestinal microbiota occurs frequently in allogeneic hematopoietic cell transplantation (allo-HCT) recipients and predisposes them to development of graft-versus-host disease (GvHD). In a prospective, single-center, single-arm study, we investigated the effect of donor fecal microbiota transplantation (FMT) on symptoms of steroid-refractory or steroid-dependent, acute or late-onset acute intestinal GvHD in 15 individuals who had undergone allo-HCT. Study participants received a fecal suspension from an unrelated healthy donor via nasoduodenal infusion. Donor FMT was well tolerated, and infection-related adverse events did not seem to be related to the FMT procedure. In 10 of 15 study participants, a complete clinical response was observed within 1 month after FMT, without additional interventions to alleviate GvHD symptoms. This response was accompanied by an increase in gut microbial α-diversity, a partial engraftment of donor bacterial species, and increased abundance of butyrate-producing bacteria, including Clostridiales and Blautia species. In 6 of the 10 responding donor FMT recipients, immunosuppressant drug therapy was successfully tapered. Durable remission of steroid-refractory or steroid-dependent GvHD after donor FMT was associated with improved survival at 24 weeks after donor FMT. This study highlights the potential of donor FMT as a treatment for steroid-refractory or steroid-dependent GvHD, but larger clinical trials are needed to confirm the safety and efficacy of this procedure.
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Affiliation(s)
- Yannouck F van Lier
- Department of Hematology, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands.,Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity (AII), Cancer Center Amsterdam, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Mark Davids
- Department of Vascular Medicine, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Nienke J E Haverkate
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity (AII), Cancer Center Amsterdam, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Pieter F de Groot
- Department of Vascular Medicine, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Marjolein L Donker
- Department of Hematology, Amsterdam UMC, location VUMC, 1081 HV Amsterdam, Netherlands
| | - Ellen Meijer
- Department of Hematology, Amsterdam UMC, location VUMC, 1081 HV Amsterdam, Netherlands
| | | | - Erfan Nur
- Department of Hematology, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Sacha S Zeerleder
- Department of Hematology, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands.,Department of Immunopathology, Sanquin Research, 1066 CX Amsterdam, Netherlands.,Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland.,Department for BioMedical Research, University of Bern, 3010 Bern, Switzerland
| | - Max Nieuwdorp
- Department of Vascular Medicine, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands.,Diabetes Center, Department of Internal Medicine, Amsterdam UMC, location VUMC, 1081 HV Amsterdam, Netherlands.,Institute for Cardiovascular Research (ICaR), Amsterdam UMC, location VUMC, 1081 HV Amsterdam, Netherlands.,Wallenberg Laboratory, University of Gothenburg, SE-413 45 Goteborg, Sweden
| | - Bianca Blom
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity (AII), Cancer Center Amsterdam, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands
| | - Mette D Hazenberg
- Department of Hematology, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands. .,Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity (AII), Cancer Center Amsterdam, Amsterdam UMC, location AMC, 1105 AZ Amsterdam, Netherlands.,Department of Hematopoiesis, Sanquin Research, 1066 CX Amsterdam, Netherlands
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135
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Suzuki K, Nakaoka S, Fukuda S, Masuya H. Energy landscape analysis elucidates the multistability of ecological communities across environmental gradients. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1469] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kenta Suzuki
- Integrated Bioresource Information Division BioResource Research Center RIKEN 3‐1‐1 Koyadai Tsukuba Ibaraki 305‐0074 Japan
| | - Shinji Nakaoka
- Laboratory of Mathematical Biology Faculty of Advanced Life Science Hokkaido University Kita‐10 Nishi‐8Kita‐ku Sapporo Hokkaido 060‐0819 Japan
- PRESTO Japan Science and Technology Agency 4‐1‐8 Honcho Kawaguchi Saitama 332‐0012 Japan
| | - Shinji Fukuda
- PRESTO Japan Science and Technology Agency 4‐1‐8 Honcho Kawaguchi Saitama 332‐0012 Japan
- Institute for Advanced Biosciences Keio University 246‐2 MizukamiKakuganji Tsuruoka Yamagata 997‐0052 Japan
- Intestinal Microbiota Project Kanagawa Institute of Industrial Science and Technology 3‐25‐13 TonomachiKawasaki‐ku Kawasaki Kanagawa 210‐0821 Japan
- Transborder Medical Research Center University of Tsukuba 1‐1‐1 Tennodai Tsukuba Ibaraki 305‐8575 Japan
| | - Hiroshi Masuya
- Integrated Bioresource Information Division BioResource Research Center RIKEN 3‐1‐1 Koyadai Tsukuba Ibaraki 305‐0074 Japan
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Koopen AM, Almeida EL, Attaye I, Witjes JJ, Rampanelli E, Majait S, Kemper M, Levels JHM, Schimmel AWM, Herrema H, Scheithauer TPM, Frei W, Dragsted L, Hartmann B, Holst JJ, O'Toole PW, Groen AK, Nieuwdorp M. Effect of Fecal Microbiota Transplantation Combined With Mediterranean Diet on Insulin Sensitivity in Subjects With Metabolic Syndrome. Front Microbiol 2021; 12:662159. [PMID: 34177842 PMCID: PMC8222733 DOI: 10.3389/fmicb.2021.662159] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Background Recent studies demonstrate that a Mediterranean diet has beneficial metabolic effects in metabolic syndrome subjects. Since we have shown that fecal microbiota transplantation (FMT) from lean donors exerts beneficial effects on insulin sensitivity, in the present trial, we investigated the potential synergistic effects on insulin sensitivity of combining a Mediterranean diet with donor FMT in subjects with metabolic syndrome. Design Twenty-four male subjects with metabolic syndrome were put on a Mediterranean diet and after a 2-week run-in phase, the subjects were randomized to either lean donor (n = 12) or autologous (n = 12) FMT. Changes in the gut microbiota composition and bacterial strain engraftment after the 2-week dietary regimens and 6 weeks post-FMT were the primary endpoints. The secondary objectives were changes in glucose fluxes (both hepatic and peripheral insulin sensitivity), postprandial plasma incretin (GLP-1) levels, subcutaneous adipose tissue inflammation, and plasma metabolites. Results Consumption of the Mediterranean diet resulted in a reduction in body weight, HOMA-IR, and lipid levels. However, no large synergistic effects of combining the diet with lean donor FMT were seen on the gut microbiota diversity after 6 weeks. Although we did observe changes in specific bacterial species and plasma metabolites, no significant beneficial effects on glucose fluxes, postprandial incretins, or subcutaneous adipose tissue inflammation were detected. Conclusions In this small pilot randomized controlled trial, no synergistic beneficial metabolic effects of combining a Mediterranean diet with lean donor FMT on glucose metabolism were achieved. However, we observed engraftment of specific bacterial species. Future trials are warranted to test the combination of other microbial interventions and diets in metabolic syndrome.
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Affiliation(s)
- Annefleur M Koopen
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands
| | - Eduardo L Almeida
- APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, Ireland
| | - Ilias Attaye
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands
| | - Julia J Witjes
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands
| | - Elena Rampanelli
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands
| | - Soumia Majait
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands
| | - Marleen Kemper
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands
| | - Johannes H M Levels
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands
| | - Alinda W M Schimmel
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands
| | - Hilde Herrema
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands
| | - Torsten P M Scheithauer
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands
| | - Werner Frei
- APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, Ireland
| | - Lars Dragsted
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Bolette Hartmann
- Novo Nordisk Foundation Center for Basic Metabolic Research, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens J Holst
- Novo Nordisk Foundation Center for Basic Metabolic Research, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Paul W O'Toole
- APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, Ireland
| | - Albert K Groen
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands
| | - Max Nieuwdorp
- Department of Internal Medicine and (Experimental) Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, Netherlands.,Department of Internal Medicine, Diabetes Center, Amsterdam University Medical Center, Location VU University Medical Center, Amsterdam, Netherlands
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Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, Kuhn M, Bahram M, Nielsen HB, Bork P. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host Microbe 2021; 29:1167-1176.e9. [PMID: 34111423 PMCID: PMC8288446 DOI: 10.1016/j.chom.2021.05.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/19/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023]
Abstract
Human gut bacterial strains can co-exist with their hosts for decades, but little is known about how these microbes persist and disperse, and evolve thereby. Here, we examined these processes in 5,278 adult and infant fecal metagenomes, longitudinally sampled in individuals and families. Our analyses revealed that a subset of gut species is extremely persistent in individuals, families, and geographic regions, represented often by locally successful strains of the phylum Bacteroidota. These “tenacious” bacteria show high levels of genetic adaptation to the human host but a high probability of loss upon antibiotic interventions. By contrast, heredipersistent bacteria, notably Firmicutes, often rely on dispersal strategies with weak phylogeographic patterns but strong family transmissions, likely related to sporulation. These analyses describe how different dispersal strategies can lead to the long-term persistence of human gut microbes with implications for gut flora modulations. Bacterial strains may persist within family members through transfer Bacteria adapt dispersal strategies: heredipersistent, spatiopersistent, and tenacious Dispersal strategies correlate with genetic bottlenecks and effective population size
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Affiliation(s)
- Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, NR4 7UQ Norwich, UK; Digital Biology, Earlham Institute, NR4 7UZ Norwich, UK; European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.
| | - Toni I Gossmann
- Department of Animal Behaviour, Bielefeld University, Bielefeld DE-33501, Germany
| | - Clémence Frioux
- Gut Microbes and Health, Quadram Institute Bioscience, NR4 7UQ Norwich, UK; Inria, INRAE, CNRS, Univ. Bordeaux, 33405 Talence, France
| | - Ezgi Özkurt
- Gut Microbes and Health, Quadram Institute Bioscience, NR4 7UQ Norwich, UK; Digital Biology, Earlham Institute, NR4 7UZ Norwich, UK
| | - Pernille Neve Myers
- Clinical Microbiomics A/S, Copenhagen, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Pamela Ferretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Michael Kuhn
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 750 07 Uppsala, Sweden; Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia
| | | | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Max Delbrück Center for Molecular Medicine, Berlin, Germany; Yonsei Frontier Lab (YFL), Yonsei University, Seoul 03722, South Korea; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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Fecal microbiota transplantation in human metabolic diseases: From a murky past to a bright future? Cell Metab 2021; 33:1098-1110. [PMID: 34077717 DOI: 10.1016/j.cmet.2021.05.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/26/2021] [Accepted: 05/05/2021] [Indexed: 12/15/2022]
Abstract
Fecal microbiota transplantation (FMT) is gaining considerable traction as a therapeutic approach to influence the course of a plethora of chronic conditions, ranging from metabolic syndrome and malignancies to auto-immune and neurological diseases, and helped to establish the contribution of the gut microbiome to these conditions. Although FMT procedures have yielded important mechanistic insights, their use in clinical practice may be limited due to practical objections in the setting of metabolic diseases. While its applicability is established to treat recurrent Clostridiodes difficile, FMT is emerging in ulcerative colitis and various other diseases. A particularly new insight is that FMTs may not only alter insulin sensitivity but may also alter the course of type 1 diabetes by attenuating underlying auto-immunity. In this review, we will outline the major principles and pitfalls of FMT and where optimization of study design and the procedure itself will further advance the field of cardiometabolic medicine.
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139
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Kubasova T, Seidlerova Z, Rychlik I. Ecological Adaptations of Gut Microbiota Members and Their Consequences for Use as a New Generation of Probiotics. Int J Mol Sci 2021; 22:5471. [PMID: 34067354 PMCID: PMC8196900 DOI: 10.3390/ijms22115471] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 12/16/2022] Open
Abstract
In this review, we link ecological adaptations of different gut microbiota members with their potential for use as a new generation of probiotics. Gut microbiota members differ in their adaptations to survival in aerobic environments. Interestingly, there is an inverse relationship between aerobic survival and abundance or potential for prolonged colonization of the intestinal tract. Facultative anaerobes, aerotolerant Lactobacilli and endospore-forming Firmicutes exhibit high fluctuation, and if such bacteria are to be used as probiotics, they must be continuously administered to mimic their permanent supply from the environment. On the other hand, species not expressing any form of aerobic resistance, such as those from phylum Bacteroidetes, commonly represent host-adapted microbiota members characterized by vertical transmission from mothers to offspring, capable of long-term colonization following a single dose administration. To achieve maximal probiotic efficacy, the mode of their administration should thus reflect their natural ecology.
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Affiliation(s)
| | | | - Ivan Rychlik
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (T.K.); (Z.S.)
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140
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Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators. Nat Commun 2021; 12:2907. [PMID: 34006865 PMCID: PMC8131609 DOI: 10.1038/s41467-021-23029-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
We propose microbiome disease “architectures”: linking >1 million microbial features (species, pathways, and genes) to 7 host phenotypes from 13 cohorts using a pipeline designed to identify associations that are robust to analytical model choice. Here, we quantify conservation and heterogeneity in microbiome-disease associations, using gene-level analysis to identify strain-specific, cross-disease, positive and negative associations. We find coronary artery disease, inflammatory bowel diseases, and liver cirrhosis to share gene-level signatures ascribed to the Streptococcus genus. Type 2 diabetes, by comparison, has a distinct metagenomic signature not linked to any one specific species or genus. We additionally find that at the species-level, the prior-reported connection between Solobacterium moorei and colorectal cancer is not consistently identified across models—however, our gene-level analysis unveils a group of robust, strain-specific gene associations. Finally, we validate our findings regarding colorectal cancer and inflammatory bowel diseases in independent cohorts and identify that features inversely associated with disease tend to be less reproducible than features enriched in disease. Overall, our work is not only a step towards gene-based, cross-disease microbiome diagnostic indicators, but it also illuminates the nuances of the genetic architecture of the human microbiome, including tension between gene- and species-level associations. Here, combing the massive gene-universe of the gut microbiome to identify strain-specific, cross-disease, associations across seven human diseases, the authors introduce the concept of microbiome architecture, defined as the complete set of positive and negative associations between microbial genes and human host disease, highlighting microbiome architectures as potential diagnostic indicators.
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Wilson BC, Vatanen T, Jayasinghe TN, Leong KSW, Derraik JGB, Albert BB, Chiavaroli V, Svirskis DM, Beck KL, Conlon CA, Jiang Y, Schierding W, Holland DJ, Cutfield WS, O’Sullivan JM. Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity. MICROBIOME 2021; 9:107. [PMID: 33985595 PMCID: PMC8120839 DOI: 10.1186/s40168-021-01060-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/24/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND Donor selection is an important factor influencing the engraftment and efficacy of fecal microbiota transplantation (FMT) for complex conditions associated with microbial dysbiosis. However, the degree, variation, and stability of strain engraftment have not yet been assessed in the context of multiple donors. METHODS We conducted a double-blinded randomized control trial of FMT in 87 adolescents with obesity. Participants were randomized to receive multi-donor FMT (capsules containing the fecal microbiota of four sex-matched lean donors) or placebo (saline capsules). Following a bowel cleanse, participants ingested a total of 28 capsules over two consecutive days. Capsules from individual donors and participant stool samples collected at baseline, 6, 12, and 26 weeks post-treatment were analyzed by shotgun metagenomic sequencing allowing us to track bacterial strain engraftment and its functional implications on recipients' gut microbiomes. RESULTS Multi-donor FMT sustainably altered the structure and the function of the gut microbiome. In what was effectively a microbiome competition experiment, we discovered that two donor microbiomes (one female, one male) dominated strain engraftment and were characterized by high microbial diversity and a high Prevotella to Bacteroides (P/B) ratio. Engrafted strains led to enterotype-level shifts in community composition and provided genes that altered the metabolic potential of the community. Despite our attempts to standardize FMT dose and origin, FMT recipients varied widely in their engraftment of donor strains. CONCLUSION Our study provides evidence for the existence of FMT super-donors whose microbiomes are highly effective at engrafting in the recipient gut. Dominant engrafting male and female donor microbiomes harbored diverse microbial species and genes and were characterized by a high P/B ratio. Yet, the high variability of strain engraftment among FMT recipients suggests the host environment also plays a critical role in mediating FMT receptivity. TRIAL REGISTRATION The Gut Bugs trial was registered with the Australian New Zealand Clinical Trials Registry ( ACTRN12615001351505 ). TRIAL PROTOCOL The trial protocol is available at https://bmjopen.bmj.com/content/9/4/e026174 . Video Abstract.
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Affiliation(s)
- Brooke C. Wilson
- The Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Tommi Vatanen
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- The Broad Institute of MIT and Harvard, Cambridge, MA USA
| | | | - Karen S. W. Leong
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- A Better Start–National Science Challenge, Auckland, New Zealand
| | - José G. B. Derraik
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- A Better Start–National Science Challenge, Auckland, New Zealand
| | - Benjamin B. Albert
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- A Better Start–National Science Challenge, Auckland, New Zealand
| | | | - Darren M. Svirskis
- School of Pharmacy, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Kathryn L. Beck
- School of Sport, Exercise and Nutrition, College of Health, Massey University, Auckland, New Zealand
| | - Cathryn A. Conlon
- School of Sport, Exercise and Nutrition, College of Health, Massey University, Auckland, New Zealand
| | - Yannan Jiang
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | | | - David J. Holland
- Department of Infectious Diseases, Counties Manukau District Health Board, Auckland, New Zealand
| | - Wayne S. Cutfield
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- A Better Start–National Science Challenge, Auckland, New Zealand
| | - Justin M. O’Sullivan
- The Liggins Institute, University of Auckland, Auckland, New Zealand
- A Better Start–National Science Challenge, Auckland, New Zealand
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Xu B, Qin W, Yan Y, Tang Y, Zhou S, Huang J, Xie C, Ma L, Yan X. Gut microbiota contributes to the development of endometrial glands in gilts during the ovary-dependent period. J Anim Sci Biotechnol 2021; 12:57. [PMID: 33947457 PMCID: PMC8097987 DOI: 10.1186/s40104-021-00578-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/01/2021] [Indexed: 12/26/2022] Open
Abstract
Background The hyper-prolificacy Meishan gilts achieved a superior endometrial gland development (EGD) than white crossbred gilts during the ovary-independent period (before 60 d of age). Then, the EGD continues under the management of ovary-derived steroid hormones that regulated by gut microbiota (after 60 d of age). However, whether Meishan gilts’ superiority in EGD lasting to the ovary-dependent period (after 60 d of age) and the role of gut microbiota in this period both remain unclear. Methods Meishan gilts and Landrace x Yorkshire (LxY) gilts were raised under the same housing and feeding conditions until sexual maturity and then we compared their EGD and gut microbiota. Meanwhile, we transplanted fecal microbiota from Meishan gilts to L×Y gilts to explore the role of gut microbiota in EGD. We sampled plasma every 3 weeks and collected the uterus, ovary, liver, and rectal feces after the sacrifice. We then determined the hormone concentrations and expressions of the EGD-related genes. We also profiled the gut microbiota using 16S rDNA sequencing and metabolites of plasma and liver tissue using untargeted metabolomics. Finally, the correlation analysis and significant test was conducted between FMT-shifted gut microbes and EGD-related indices. Results Meishan gilts have larger endometrial gland area (P < 0.001), longer uterine horn length (P < 0.01) but lighter uterine horn weight (P < 0.05), a distinctive gut microbiota compared with L×Y gilts. Fecal microbiota transplantation (FMT) increased endometrial gland area (P < 0.01). FMT markedly shifted the metabolite profiles of both liver and plasma, and these differential metabolites enriched in steroid hormone biosynthesis pathway. FMT increased estradiol and insulin-like growth factor 1 but decreased progesterone dynamically. FMT also increased the expression of the EGD-related genes estrogen receptor 1 gene, epithelial cadherin, and forkhead box protein A2. There is a significant correlation between FMT-shifted gut microbes and EGD-related indices. Conclusion Sexually matured Meishan gilts achieved a superior EGD than LxY gilts. Meanwhile, gut microbiota contribute to the EGD potentially via regulating of steroid hormones during the ovary-dependent period. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00578-y.
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Affiliation(s)
- Baoyang Xu
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.,Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Wenxia Qin
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.,Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Yiqin Yan
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.,Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Yimei Tang
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.,Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Shuyi Zhou
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.,Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Juncheng Huang
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.,Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Chunlin Xie
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.,Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Libao Ma
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. .,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China. .,Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China.
| | - Xianghua Yan
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. .,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China. .,Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China.
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Fujimoto K, Kimura Y, Allegretti JR, Yamamoto M, Zhang YZ, Katayama K, Tremmel G, Kawaguchi Y, Shimohigoshi M, Hayashi T, Uematsu M, Yamaguchi K, Furukawa Y, Akiyama Y, Yamaguchi R, Crowe SE, Ernst PB, Miyano S, Kiyono H, Imoto S, Uematsu S. Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation. Gastroenterology 2021; 160:2089-2102.e12. [PMID: 33577875 PMCID: PMC8684800 DOI: 10.1053/j.gastro.2021.02.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/27/2021] [Accepted: 02/03/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI). However, the overall mechanisms underlying FMT success await comprehensive elucidation, and the safety of FMT has recently become a serious concern because of the occurrence of drug-resistant bacteremia transmitted by FMT. We investigated whether functional restoration of the bacteriomes and viromes by FMT could be an indicator of successful FMT. METHODS The human intestinal bacteriomes and viromes from 9 patients with rCDI who had undergone successful FMT and their donors were analyzed. Prophage-based and CRISPR spacer-based host bacteria-phage associations in samples from recipients before and after FMT and in donor samples were examined. The gene functions of intestinal microorganisms affected by FMT were evaluated. RESULTS Metagenomic sequencing of both the viromes and bacteriomes revealed that FMT does change the characteristics of intestinal bacteriomes and viromes in recipients after FMT compared with those before FMT. In particular, many Proteobacteria, the fecal abundance of which was high before FMT, were eliminated, and the proportion of Microviridae increased in recipients. Most temperate phages also behaved in parallel with the host bacteria that were altered by FMT. Furthermore, the identification of bacterial and viral gene functions before and after FMT revealed that some distinctive pathways, including fluorobenzoate degradation and secondary bile acid biosynthesis, were significantly represented. CONCLUSIONS The coordinated action of phages and their host bacteria restored the recipients' intestinal flora. These findings show that the restoration of intestinal microflora functions reflects the success of FMT.
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Affiliation(s)
- Kosuke Fujimoto
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan,Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan,Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yasumasa Kimura
- Division of Systems Immunology, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Jessica R. Allegretti
- Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Mako Yamamoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yao-zhong Zhang
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Kotoe Katayama
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Georg Tremmel
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yunosuke Kawaguchi
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Masaki Shimohigoshi
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Tetsuya Hayashi
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Miho Uematsu
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yutaka Akiyama
- Department of Computer Science, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Rui Yamaguchi
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Sheila E. Crowe
- Department of Medicine, University of California, San Diego, La Jolla, California
| | - Peter B. Ernst
- Division of Gastroenterology, Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, University of California San Diego, San Diego, La Jolla, California,Division of Comparative Pathology and Medicine, Department of Pathology, University of California San Diego, San Diego, La Jolla, California,Center for Veterinary Sciences and Comparative Medicine, University of California, San Diego, La Jolla, California
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Hiroshi Kiyono
- Division of Gastroenterology, Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, University of California San Diego, San Diego, La Jolla, California,Division of Comparative Pathology and Medicine, Department of Pathology, University of California San Diego, San Diego, La Jolla, California,Department of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan,International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Satoshi Uematsu
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan; Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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Genetically determined hypertensive phenotype affects gut microbiota composition, but not vice versa. J Hypertens 2021; 39:1790-1799. [PMID: 34397627 DOI: 10.1097/hjh.0000000000002864] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Research suggests reciprocal crosstalk between the host and gut bacteria. This study evaluated the interaction between gut microbiota and arterial blood pressure (BP) in rats. METHODS Continuous telemetry recordings of BP were started in 7-week-old normotensive Wistar--Kyoto rats (WKY) and spontaneously hypertensive rats (SHR). Two weeks later, half of the WKY and SHR were subjected to cross-transplantation of fecal matter, with stools harvested from either WKY or SHR and BP measurements until the age of 14 weeks. The composition of gut bacteria was assessed through analysis of the bacterial 16S ribosomal RNA gene sequence. The concentration of microbiota-derived metabolites was evaluated using HPLC-MS. RESULTS There was a significant difference between WKY and SHR in the composition of gut bacteria at the start and end of the study. This was accompanied by significant histological differences in the colon. SHR, but not WKY, showed a gradual increase in BP throughout the experiment. For both WKY and SHR, there was no significant difference in BP or metabolic parameters between animals receiving fecal transplantation from either SHR or WKY. CONCLUSION Genetically induced hypertension in SHR is associated with alterations in the composition of gut bacteria and histological morphology of the colon. An inter-strain fecal transplant does not affect BP and does not produce long-term changes in gut bacteria composition. We propose that the impact of the host genotype and/or phenotype on the gut bacteria may be greater than the impact of the gut bacteria on the host BP.
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Pan C, Li J, Hou W, Lin S, Wang L, Pang Y, Wang Y, Liu J. Polymerization-Mediated Multifunctionalization of Living Cells for Enhanced Cell-Based Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007379. [PMID: 33629757 DOI: 10.1002/adma.202007379] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/20/2020] [Indexed: 06/12/2023]
Abstract
Surface decoration of living cells by exogenous substances offers a unique tool for understanding and tuning cell behaviors, which plays a critical role in cell-based therapy. Here, a facile yet versatile approach for decorating individual living cells with multimodal coatings is reported. By simply co-depositing with dopamine under a cytocompatible condition, various functional small molecules and polymers can be encoded to form a multifunctional coating on a cell's surface. The accessibility and versatility of this method to decorate diverse cells, including bacteria, fungi, and mammalian cells is demonstrated. With the ability to tune surface functions, ligand co-deposited gut microbiota is prepared as oral therapeutics for targeted treatment of colitis. Given the dual cytoprotective and targeting effects of the coating, decorated cells show more than 30-times higher bioavailability in the gut and fourfold higher accumulation in the inflamed tissue in comparison with those of uncoated bacteria. Multimodal therapeutic cells further validate strikingly increased treatment efficacy over clinical aminosalicylic acid in colitis mice. Decorating with multifunctional coatings proposes a robust platform for developing multimodal cells for enhanced cell-based therapy.
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Affiliation(s)
- Chao Pan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Juanjuan Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Weiliang Hou
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Sisi Lin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Lu Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yan Pang
- Department of Ophthalmology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200011, China
| | - Yufeng Wang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jinyao Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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146
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Hamilton-Williams EE, Lorca GL, Norris JM, Dunne JL. A Triple Threat? The Role of Diet, Nutrition, and the Microbiota in T1D Pathogenesis. Front Nutr 2021; 8:600756. [PMID: 33869260 PMCID: PMC8046917 DOI: 10.3389/fnut.2021.600756] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
In recent years the role of the intestinal microbiota in health and disease has come to the forefront of medical research. Alterations in the intestinal microbiota and several of its features have been linked to numerous diseases, including type 1 diabetes (T1D). To date, studies in animal models of T1D, as well as studies in human subjects, have linked several intestinal microbiota alterations with T1D pathogenesis. Features that are most often linked with T1D pathogenesis include decreased microbial diversity, the relative abundance of specific strains of individual microbes, and altered metabolite production. Alterations in these features as well as others have provided insight into T1D pathogenesis and shed light on the potential mechanism by which the microbiota plays a role in T1D pathogenesis, yet the underlying factors leading to these alterations remains unknown. One potential mechanism for alteration of the microbiota is through diet and nutrition. Previous studies have shown associations of diet with islet autoimmunity, but a direct contributing factor has yet to be identified. Diet, through introduction of antigens and alteration of the composition and function of the microbiota, may elicit the immune system to produce autoreactive responses that result in the destruction of the beta cells. Here, we review the evidence associating diet induced changes in the intestinal microbiota and their contribution to T1D pathogenesis. We further provide a roadmap for determining the effect of diet and other modifiable factors on the entire microbiota ecosystem, including its impact on both immune and beta cell function, as it relates to T1D. A greater understanding of the complex interactions between the intestinal microbiota and several interacting systems in the body (immune, intestinal integrity and function, metabolism, beta cell function, etc.) may provide scientifically rational approaches to prevent development of T1D and other childhood immune and allergic diseases and biomarkers to evaluate the efficacy of interventions.
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Affiliation(s)
- Emma E. Hamilton-Williams
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Graciela L. Lorca
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, United States
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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Nakatsuji T, Hata TR, Tong Y, Cheng JY, Shafiq F, Butcher AM, Salem SS, Brinton SL, Rudman Spergel AK, Johnson K, Jepson B, Calatroni A, David G, Ramirez-Gama M, Taylor P, Leung DYM, Gallo RL. Development of a human skin commensal microbe for bacteriotherapy of atopic dermatitis and use in a phase 1 randomized clinical trial. Nat Med 2021; 27:700-709. [PMID: 33619370 PMCID: PMC8052297 DOI: 10.1038/s41591-021-01256-2] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 01/15/2021] [Indexed: 01/31/2023]
Abstract
Staphylococcus aureus colonizes patients with atopic dermatitis (AD) and exacerbates disease by promoting inflammation. The present study investigated the safety and mechanisms of action of Staphylococcus hominis A9 (ShA9), a bacterium isolated from healthy human skin, as a topical therapy for AD. ShA9 killed S. aureus on the skin of mice and inhibited expression of a toxin from S. aureus (psmα) that promotes inflammation. A first-in-human, phase 1, double-blinded, randomized 1-week trial of topical ShA9 or vehicle on the forearm skin of 54 adults with S. aureus-positive AD (NCT03151148) met its primary endpoint of safety, and participants receiving ShA9 had fewer adverse events associated with AD. Eczema severity was not significantly different when evaluated in all participants treated with ShA9 but a significant decrease in S. aureus and increased ShA9 DNA were seen and met secondary endpoints. Some S. aureus strains on participants were not directly killed by ShA9, but expression of mRNA for psmα was inhibited in all strains. Improvement in local eczema severity was suggested by post-hoc analysis of participants with S. aureus directly killed by ShA9. These observations demonstrate the safety and potential benefits of bacteriotherapy for AD.
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Affiliation(s)
- Teruaki Nakatsuji
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Tissa R Hata
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Yun Tong
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Joyce Y Cheng
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Faiza Shafiq
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Anna M Butcher
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Secilia S Salem
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Samantha L Brinton
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA
| | - Amanda K Rudman Spergel
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Keli Johnson
- Rho Federal Systems Division, Inc., Durham, NC, USA
| | - Brett Jepson
- Rho Federal Systems Division, Inc., Durham, NC, USA
| | | | - Gloria David
- Rho Federal Systems Division, Inc., Durham, NC, USA
| | - Marco Ramirez-Gama
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Patricia Taylor
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Donald Y M Leung
- Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Richard L Gallo
- Department of Dermatology, University of California, San Diego, La Jolla, CA, USA.
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Groussin M, Poyet M, Sistiaga A, Kearney SM, Moniz K, Noel M, Hooker J, Gibbons SM, Segurel L, Froment A, Mohamed RS, Fezeu A, Juimo VA, Lafosse S, Tabe FE, Girard C, Iqaluk D, Nguyen LTT, Shapiro BJ, Lehtimäki J, Ruokolainen L, Kettunen PP, Vatanen T, Sigwazi S, Mabulla A, Domínguez-Rodrigo M, Nartey YA, Agyei-Nkansah A, Duah A, Awuku YA, Valles KA, Asibey SO, Afihene MY, Roberts LR, Plymoth A, Onyekwere CA, Summons RE, Xavier RJ, Alm EJ. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell 2021; 184:2053-2067.e18. [PMID: 33794144 DOI: 10.1016/j.cell.2021.02.052] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/27/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022]
Abstract
Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.
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Affiliation(s)
- Mathieu Groussin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Mathilde Poyet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ainara Sistiaga
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA; GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Sean M Kearney
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katya Moniz
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mary Noel
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Chief Dull Knife College, Lame Deer, MT, USA
| | - Jeff Hooker
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Chief Dull Knife College, Lame Deer, MT, USA
| | - Sean M Gibbons
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institute for Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Laure Segurel
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; UMR7206 Eco-anthropologie, CNRS-MNHN-Univ Paris Diderot-Sorbonne, Paris, France
| | - Alain Froment
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut de Recherche pour le Développement UMR 208, Muséum National d'Histoire Naturelle, Paris, France
| | - Rihlat Said Mohamed
- SA MRC / Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Alain Fezeu
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut de Recherche pour le Développement, Yaounde, Cameroon
| | - Vanessa A Juimo
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut de Recherche pour le Développement, Yaounde, Cameroon
| | - Sophie Lafosse
- UMR7206 Eco-anthropologie, CNRS-MNHN-Univ Paris Diderot-Sorbonne, Paris, France
| | - Francis E Tabe
- Faculté de Médecine et des Sciences Biomédicales, Université Yaoundé 1, Yaoundé, Cameroun
| | - Catherine Girard
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Université de Montréal, Département de sciences biologiques, C.P. 6128, succursale Centre-ville, Montréal, QC, Canada; Centre d'études nordiques, Département de biochimie, de microbiologie et de bio-informatique, Université Laval, 1030 rue de la Médecine, Québec, QC, Canada
| | - Deborah Iqaluk
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Resolute Bay, Nunavut, Canada
| | - Le Thanh Tu Nguyen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - B Jesse Shapiro
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Université de Montréal, Département de sciences biologiques, C.P. 6128, succursale Centre-ville, Montréal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Jenni Lehtimäki
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental sciences, University of Helsinki, Helsinki, Finland; Environmental Policy Centre, Finnish Environment Institute SYKE, Helsinki, Finland
| | - Lasse Ruokolainen
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental sciences, University of Helsinki, Helsinki, Finland
| | - Pinja P Kettunen
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental sciences, University of Helsinki, Helsinki, Finland
| | - Tommi Vatanen
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; The Liggins Institute, University of Auckland, Auckland 1023, New Zealand
| | - Shani Sigwazi
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Tumaini University Makumira, Arusha, Tanzania
| | - Audax Mabulla
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Archaeology and Heritage Studies, University of Dar es Salaam, Tanzania
| | - Manuel Domínguez-Rodrigo
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Prehistory Unit, Department of History and Philosophy, University of Alcalá, Alcalá de Henares, Madrid, Spain; Institute of Evolution in Africa, University of Alcalá de Henares, Madrid, Spain
| | - Yvonne A Nartey
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Adwoa Agyei-Nkansah
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine and Therapeutics, University of Ghana Medical School and Korle Bu Teaching Hospital, Accra, Ghana
| | - Amoako Duah
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, St. Dominic Hospital, Akwatia, Ghana
| | - Yaw A Awuku
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Internal Medicine and Therapeutics, School of Medical Sciences University of Cape Coast, Cape Coast, Ghana
| | - Kenneth A Valles
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Medical Scientist Training Program, Mayo Clinic, Rochester, 55905, USA
| | - Shadrack O Asibey
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Catholic University College, Sunyani, Ghana
| | - Mary Y Afihene
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lewis R Roberts
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA
| | - Amelie Plymoth
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Charles A Onyekwere
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Lagos State University College of Medicine, Lagos, Nigeria
| | - Roger E Summons
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA.
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149
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Gweon TG, Na SY. Next Generation Fecal Microbiota Transplantation. Clin Endosc 2021; 54:152-156. [PMID: 33761228 PMCID: PMC8039740 DOI: 10.5946/ce.2021.053] [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: 01/16/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is considered as an effective treatment for Clostridioides difficile infection. However, the precise mechanism of FMT is yet to be determined. Human stool consists of the gut microbiota, bacterial debris, and metabolic products. Of these, the intestinal microbiota is the most important factor that exerts therapeutic efficacy in FMT. Fresh donor stool, blended with normal saline, has been employed for traditional FMT. Nevertheless, stool processing is a major impediment in FMT. Frozen stool and capsule formulations have similar efficacy to that of fresh stool. In addition, several novel stool products have been identified. A stool bank that provides stool products with pre-screened donor stool has been established to help physicians and thereby facilitate FMT. Recent next-generation sequencing techniques have been key in facilitating the detailed analysis of the microbiota and gut environment of individual donors and recipients.
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Affiliation(s)
- Tae-Geun Gweon
- Division of Gastroenterology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Division of Gastroenterology, Department of Internal Medicine, Bucheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Bucheon, Korea
| | - Soo-Young Na
- Division of Gastroenterology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Division of Gastroenterology, Department of Internal Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Korea
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150
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Modulating the Gut Microbiota of Humans by Dietary Intervention with Plant Glycans. Appl Environ Microbiol 2021; 87:AEM.02757-20. [PMID: 33355114 DOI: 10.1128/aem.02757-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The human colon contains a community of microbial species, mostly bacteria, which is often referred to as the gut microbiota. The community is considered essential to human well-being by conferring additional energy-harvesting capacity, niche exclusion of pathogens, and molecular signaling activities that are integrated into human physiological processes. Plant polysaccharides (glycans, dietary fiber) are an important source of carbon and energy that supports the maintenance and functioning of the gut microbiota. Therefore, the daily quantity and quality of plant glycans consumed by the human host have the potential to influence health. Members of the gut microbiota differ in ability to utilize different types of plant glycans. Dietary interventions with specific glycans could modulate the microbiota, counteracting ecological perturbations that disrupt the intricate relationships between microbiota and host (dysbiosis). This review considers prospects and research options for modulation of the gut microbiota by the formulation of diets that, when consumed habitually, would correct dysbiosis by building diverse consortia that boost functional resilience. Traditional "prebiotics" favor bifidobacteria and lactobacilli, whereas dietary mixtures of plant glycans that are varied in chemical complexity would promote high-diversity microbiotas. It is concluded that research should aim at improving knowledge of bacterial consortia that, through shared nourishment, degrade and ferment plant glycans. The consortia may vary in composition from person to person, but functional outputs will be consistent in a given context because of metabolic redundancy among bacteria. Thus, the individuality of gut microbiotas could be encompassed, functional resilience encouraged, and correction of dysbiosis achieved.
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