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Sipos D, Varga A, Kappéter Á, Halda-Kiss B, Kása P, Pál S, Kocsis B, Péterfi Z. Encapsulation protocol for fecal microbiota transplantation. Front Cell Infect Microbiol 2024; 14:1424376. [PMID: 38988813 PMCID: PMC11233434 DOI: 10.3389/fcimb.2024.1424376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 06/10/2024] [Indexed: 07/12/2024] Open
Abstract
Introduction Clostridioides difficile infections (CDI) continue to pose a challenge for clinicians. Fecal microbiota transplantation (FMT) is an effective treatment option in CDI. Furthermore, recent and ongoing studies suggest potential benefits of FMT in other diseases as well. Methods We would like to present a novel protocol for encapsulation of lyophilized fecal material. Our method provides with better compliance as well as improved flexibility, storage and safety. Results FMT was conducted in 28 patients with an overall success rate of 82,14% using apsules containing lyophilized stool. 16 of patients were given capsules with lessened bacteria counts. The success rate in this group was 93,75%. Discussion The results highlight the still unanswered questions about the mechanism of action and contribute to a wider use of FMT in the clinical praxis and in research.
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Affiliation(s)
- Dávid Sipos
- 1st Department of Internal Medicine - Department of Infectology, University of Pécs Clinical Centre, Pécs, Hungary
| | - Adorján Varga
- Department of Medical Microbiology and Immunology, University of Pécs Medical School, Clinical Centre, Pécs, Hungary
| | - Ágnes Kappéter
- 1st Department of Internal Medicine - Department of Infectology, University of Pécs Clinical Centre, Pécs, Hungary
| | - Bernadett Halda-Kiss
- 1st Department of Internal Medicine - Department of Infectology, University of Pécs Clinical Centre, Pécs, Hungary
| | - Péter Kása
- Institute of Pharmaceutical Technology and Biopharmacy, University of Pécs Faculty of Pharmacy, Pécs, Hungary
| | - Szilárd Pál
- Institute of Pharmaceutical Technology and Biopharmacy, University of Pécs Faculty of Pharmacy, Pécs, Hungary
| | - Béla Kocsis
- Department of Medical Microbiology and Immunology, University of Pécs Medical School, Clinical Centre, Pécs, Hungary
| | - Zoltán Péterfi
- 1st Department of Internal Medicine - Department of Infectology, University of Pécs Clinical Centre, Pécs, Hungary
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Ke S, Villafuerte Gálvez JA, Sun Z, Cao Y, Pollock NR, Chen X, Kelly CP, Liu YY. Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591969. [PMID: 38746249 PMCID: PMC11092666 DOI: 10.1101/2024.04.30.591969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Clostridioides difficile infection (CDI) is one of the leading causes of healthcare- and antibiotic-associated diarrhea. While fecal microbiota transplantation (FMT) has emerged as a promising therapy for recurrent CDI, its exact mechanisms of action and long-term safety are not fully understood. Defined consortia of clonal bacterial isolates, known as live biotherapeutic products (LBPs), have been proposed as an alternative therapeutic option. However, the rational design of LBPs remains challenging. Here, we employ a computational pipeline and three independent metagenomic datasets to systematically identify microbial strains that have the potential to inhibit CDI. We first constructed the CDI-related microbial genome catalog, comprising 3,741 non-redundant metagenome-assembled genomes (nrMAGs) at the strain level. We then identified multiple potential protective nrMAGs that can be candidates for the design of microbial consortia targeting CDI, including strains from Dorea formicigenerans, Oscillibacter welbionis, and Faecalibacterium prausnitzii. Importantly, some of these potential protective nrMAGs were found to play an important role in the success of FMT, and the majority of the top protective nrMAGs can be validated by various previously reported findings. Our results demonstrate a computational framework for the rational selection of microbial strains targeting CDI, paving the way for the computational design of microbial consortia against other enteric infections.
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Affiliation(s)
- Shanlin Ke
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Javier A Villafuerte Gálvez
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Zheng Sun
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yangchun Cao
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People’s Republic of China
| | - Nira R Pollock
- Division of Infectious Disease, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Ciarán P Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
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3
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Tikunov AY, Fedorets VA, Shrainer EV, Morozov VV, Bystrova VI, Tikunova NV. Intestinal Microbiome Changes and Clinical Outcomes of Patients with Ulcerative Colitis after Fecal Microbiota Transplantation. J Clin Med 2023; 12:7702. [PMID: 38137770 PMCID: PMC10743744 DOI: 10.3390/jcm12247702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND AND AIMS Ulcerative colitis (UC) is a chronic inflammatory disease that affects many people. One of the possible ways to treat UC is fecal microbiota transplantation (FMT). In this study, changes in the intestinal microbiome and clinical outcomes of 20 patients with UC after FMT were estimated. METHODS FMT enemas were administrated ten times, once a day, and fecal microbiota from three donors was used for each enema. The clinical outcomes were assessed after eight weeks and then via a patient survey. The 16S rRNA profiles of the gut microbiota were compared between three samplings: samples from 20 patients with UC before and after FMT and samples from 18 healthy volunteers. RESULTS Clinical remission was achieved in 19 (95%) patients at week 8. Adverse events occurred in five patients, including one non-responder. A significant increase in average biodiversity was shown in samples after FMT compared to samples before FMT, as well as a decrease in the proportion of some potentially pathogenic bacteria. CONCLUSION The efficacy of FMT for UC treatment was confirmed; however, the duration of remission varied substantially, possibly due to different characteristics of the initial microbiota of patients. Targeted analysis of a patient's microbiome before FMT could increase the treatment efficacy.
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Affiliation(s)
- Artem Y. Tikunov
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Valeria A. Fedorets
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Evgenia V. Shrainer
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
- Department of Obstetrics and Gynecology, V. Zelman Institute for Medicine and Psychology, Novosibirsk National Research State University, 630090 Novosibirsk, Russia
| | - Vitaliy V. Morozov
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
| | - Valeria I. Bystrova
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
- Department of Obstetrics and Gynecology, V. Zelman Institute for Medicine and Psychology, Novosibirsk National Research State University, 630090 Novosibirsk, Russia
| | - Nina V. Tikunova
- Federal State Public Scientific Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (V.A.F.); (E.V.S.); (V.V.M.); (V.I.B.)
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Li P, Roos S, Luo H, Ji B, Nielsen J. Metabolic engineering of human gut microbiome: Recent developments and future perspectives. Metab Eng 2023; 79:1-13. [PMID: 37364774 DOI: 10.1016/j.ymben.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/10/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
Abstract
Many studies have demonstrated that the gut microbiota is associated with human health and disease. Manipulation of the gut microbiota, e.g. supplementation of probiotics, has been suggested to be feasible, but subject to limited therapeutic efficacy. To develop efficient microbiota-targeted diagnostic and therapeutic strategies, metabolic engineering has been applied to construct genetically modified probiotics and synthetic microbial consortia. This review mainly discusses commonly adopted strategies for metabolic engineering in the human gut microbiome, including the use of in silico, in vitro, or in vivo approaches for iterative design and construction of engineered probiotics or microbial consortia. Especially, we highlight how genome-scale metabolic models can be applied to advance our understanding of the gut microbiota. Also, we review the recent applications of metabolic engineering in gut microbiome studies as well as discuss important challenges and opportunities.
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Affiliation(s)
- Peishun Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Stefan Roos
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE75007, Uppsala, Sweden
| | - Hao Luo
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Boyang Ji
- BioInnovation Institute, Ole Maaløes Vej 3, DK2200, Copenhagen, Denmark
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200, Copenhagen, Denmark.
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5
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Kappéter Á, Sipos D, Varga A, Vigvári S, Halda-Kiss B, Péterfi Z. Migraine as a Disease Associated with Dysbiosis and Possible Therapy with Fecal Microbiota Transplantation. Microorganisms 2023; 11:2083. [PMID: 37630643 PMCID: PMC10458656 DOI: 10.3390/microorganisms11082083] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/04/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Migraine is a painful neurological condition characterized by severe pain on one or both sides of the head. It may be linked to changes in the gut microbiota, which are influenced by antibiotic use and other factors. Dysbiosis, which develops and persists as a result of earlier antibiotic therapy, changes the composition of the intestinal flora, and can lead to the development of various diseases such as metabolic disorders, obesity, hematological malignancies, neurological or behavioral disorders, and migraine. Metabolites produced by the gut microbiome have been shown to influence the gut-brain axis. The use of probiotics as a dietary supplement may reduce the number and severity of migraine episodes. Dietary strategies can affect the course of migraines and are a valuable tool for improving migraine management. With fecal microbiota transplantation, gut microbial restoration is more effective and more durable. Changes after fecal microbiota transplantation were studied in detail, and many data help us to interpret the successful interventions. The microbiological alteration of the gut microflora can lead to normalization of the inflammatory mediators, the serotonin pathway, and influence the frequency and intensity of migraine pain.
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Affiliation(s)
- Ágnes Kappéter
- 1st Department of Internal Medicine, Department of Infectology, University of Pecs Clinical Centre, H7623 Pécs, Hungary; (Á.K.); (D.S.); (S.V.); (B.H.-K.)
| | - Dávid Sipos
- 1st Department of Internal Medicine, Department of Infectology, University of Pecs Clinical Centre, H7623 Pécs, Hungary; (Á.K.); (D.S.); (S.V.); (B.H.-K.)
| | - Adorján Varga
- Department of Medical Microbiology and Immunology, University of Pecs Clinical Centre, H7624 Pécs, Hungary;
| | - Szabolcs Vigvári
- 1st Department of Internal Medicine, Department of Infectology, University of Pecs Clinical Centre, H7623 Pécs, Hungary; (Á.K.); (D.S.); (S.V.); (B.H.-K.)
| | - Bernadett Halda-Kiss
- 1st Department of Internal Medicine, Department of Infectology, University of Pecs Clinical Centre, H7623 Pécs, Hungary; (Á.K.); (D.S.); (S.V.); (B.H.-K.)
| | - Zoltán Péterfi
- 1st Department of Internal Medicine, Department of Infectology, University of Pecs Clinical Centre, H7623 Pécs, Hungary; (Á.K.); (D.S.); (S.V.); (B.H.-K.)
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6
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Queen J, Shaikh F, Sears CL. Understanding the mechanisms and translational implications of the microbiome for cancer therapy innovation. NATURE CANCER 2023; 4:1083-1094. [PMID: 37525016 DOI: 10.1038/s43018-023-00602-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 06/21/2023] [Indexed: 08/02/2023]
Abstract
The intersection of the microbiota and cancer and the mechanisms that define these interactions are a fascinating, rapidly evolving area of cancer biology and therapeutics. Here we present recent insights into the mechanisms by which specific bacteria or their communities contribute to carcinogenesis and discuss the bidirectional interplay between microbiota and host gene or epigenome signaling. We conclude with comments on manipulation of the microbiota for the therapeutic benefit of patients with cancer.
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Affiliation(s)
- Jessica Queen
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fyza Shaikh
- Cancer Immunology Program, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cynthia L Sears
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Cancer Immunology Program, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Microbiology and Molecular Immunology, Bloomberg School of Public Health, Baltimore, MD, USA.
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7
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Salia S, Martin Y, Burke FF, Myles LA, Jackman L, Halievski K, Bambico FR, Swift-Gallant A. Antibiotic-induced socio-sexual behavioral deficits are reversed via cecal microbiota transplantation but not androgen treatment. Brain Behav Immun Health 2023; 30:100637. [PMID: 37256194 PMCID: PMC10225889 DOI: 10.1016/j.bbih.2023.100637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/03/2023] [Accepted: 05/07/2023] [Indexed: 06/01/2023] Open
Abstract
Recent evidence has demonstrated a sex-specific role of the gut microbiome on social behavior such as anxiety, possibly driven by a reciprocal relationship between the gut microbiome and gonadal hormones. For instance, gonadal hormones drive sex differences in gut microbiota composition, and certain gut bacteria can produce androgens from glucocorticoids. We thus asked whether the gut microbiome can influence androgen-dependent socio-sexual behaviors. We first treated C57BL/6 mice with broad-spectrum antibiotics (ABX) in drinking water to deplete the gut microbiota either transiently during early development (embryonic day 16-postnatal day [PND] 21) or in adulthood (PND 60-85). We hypothesized that if ABX interferes with androgens, then early ABX would interfere with critical periods for sexual differentiation of brain and thus lead to long-term decreases in males' socio-sexual behavior, while adult ABX would interfere with androgens' activational effects on behavior. We found that in males but not females, early and adult ABX treatment decreased territorial aggression, and adult ABX also decreased sexual odor preference. We then assessed whether testosterone and/or cecal microbiota transplantation (CMT) via oral gavage could prevent ABX-induced socio-sexual behavioral deficits in adult ABX-treated males. Mice were treated with same- or other-sex control cecum contents or with testosterone for two weeks. While testosterone was not effective in rescuing any behavior, we found that male CMT restored both olfactory preference and aggression in adult ABX male mice, while female CMT restored olfactory preference but not aggression. These results suggest sex-specific effects of the gut microbiome on socio-sexual behaviors, independent of androgens.
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8
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Raeisi H, Noori M, Azimirad M, Mohebbi SR, Asadzadeh Aghdaei H, Yadegar A, Zali MR. Emerging applications of phage therapy and fecal virome transplantation for treatment of Clostridioides difficile infection: challenges and perspectives. Gut Pathog 2023; 15:21. [PMID: 37161478 PMCID: PMC10169144 DOI: 10.1186/s13099-023-00550-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/02/2023] [Indexed: 05/11/2023] Open
Abstract
Clostridioides difficile, which causes life-threatening diarrheal disease, is considered an urgent threat to healthcare setting worldwide. The current standards of care solely rely on conventional antibiotic treatment, however, there is a risk of promoting recurrent C. difficile infection (rCDI) because of the emergence of antibiotic-resistant strains. Globally, the alarming spread of antibiotic-resistant strains of C. difficile has resulted in a quest for alternative therapeutics. The use of fecal microbiota transplantation (FMT), which involves direct infusion of fecal suspension from a healthy donor into a diseased recipient, has been approved as a highly efficient therapeutic option for patients with rCDI. Bacteriophages or phages are a group of viruses that can infect and destroy bacterial hosts, and are recognized as the dominant viral component of the human gut microbiome. Accumulating data has demonstrated that phages play a vital role in microbial balance of the human gut microbiome. Recently, phage therapy and fecal virome transplantation (FVT) have been introduced as promising alternatives for the treatment of C. difficile -related infections, in particular drug-resistant CDI. Herein, we review the latest updates on C. difficile- specific phages, and phage-mediated treatments, and highlight the current and future prospects of phage therapy in the management of CDI.
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Affiliation(s)
- Hamideh Raeisi
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Noori
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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9
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Garbuzenko DV. Therapeutic possibilities of gut microbiota modulation in acute decompensation of liver cirrhosis. World J Hepatol 2023; 15:525-537. [PMID: 37206649 PMCID: PMC10190690 DOI: 10.4254/wjh.v15.i4.525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/01/2023] [Accepted: 03/30/2023] [Indexed: 04/20/2023] Open
Abstract
The formation of liver cirrhosis (LC) is an unfavorable event in the natural history of chronic liver diseases and with the development of portal hypertension and/or impaired liver function can cause a fatal outcome. Decompensation of LC is considered the most important stratification variable for the risk of death. It is currently postulated that decompensation of LC occurs through an acute (including acute-on-chronic liver failure) and non-acute pathway. Acute decompensation of LC is accompanied by the development of life-threatening complications, characterized by an unfavorable prognosis and high mortality. Progress in understanding the underlying molecular mechanisms has led to the search for new interventions, drugs, and biological substances that can affect key links in the pathogenesis of acute decompensation in LC, for example the impaired gut-liver axis and associated systemic inflammation. Given that particular alterations in the composition and function of gut microbiota play a crucial role here, the study of the therapeutic possibilities of its modulation has emerged as one of the top concerns in modern hepatology. This review summarized the investigations that describe the theoretical foundations and therapeutic potential of gut microbiota modulation in acute decompensation of LC. Despite the encouraging preliminary data, the majority of the suggested strategies have only been tested in animal models or in preliminary clinical trials; additional multicenter randomized controlled trials must demonstrate their efficacy in larger patient populations.
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10
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Dahiya M, Jovel J, Monaghan T, Wong K, Elhenawy W, Chui L, McAlister F, Kao D. In Silico Analysis of Changes in Predicted Metabolic Capabilities of Intestinal Microbiota after Fecal Microbial Transplantation for Treatment of Recurrent Clostridioides difficile Infection. Microorganisms 2023; 11:microorganisms11041078. [PMID: 37110500 PMCID: PMC10143790 DOI: 10.3390/microorganisms11041078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
IMPORTANCE Although highly effective in treating recurrent Clostridioides difficile infection (RCDI), the mechanisms of action of fecal microbial transplantation (FMT) are not fully understood. AIM The aim of this study was to explore microbially derived products or pathways that could contribute to the therapeutic efficacy of FMT. METHODS Stool shotgun metagenomic sequencing data from 18 FMT-treated RCDI patients at 4 points in time were used for the taxonomic and functional profiling of their gut microbiome. The abundance of the KEGG orthology (KO) groups was subjected to univariate linear mixed models to assess the significance of the observed differences between 0 (pre-FMT), 1, 4, and 12 weeks after FMT. RESULTS Of the 59,987 KO groups identified by shotgun metagenomic sequencing, 27 demonstrated a statistically significant change after FMT. These KO groups are involved in many cellular processes, including iron homeostasis, glycerol metabolism, and arginine regulation, all of which have been implicated to play important roles in bacterial growth and virulence in addition to modulating the intestinal microbial composition. CONCLUSION Our findings suggest potential changes in key KO groups post-FMT, which may contribute to FMT efficacy beyond the restored microbial composition/diversity and metabolism of bile acids and short-chain fatty acids. Future larger studies that include a fecal metabolomics analysis combined with animal model validation work are required to further elucidate the molecular mechanisms.
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Affiliation(s)
- Monica Dahiya
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Juan Jovel
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Tanya Monaghan
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
| | - Karen Wong
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Wael Elhenawy
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Linda Chui
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB T6G 2R3, Canada
| | - Finlay McAlister
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Dina Kao
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
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11
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Chopra T, Hecht G, Tillotson G. Gut microbiota and microbiota-based therapies for Clostridioides difficile infection. Front Med (Lausanne) 2023; 9:1093329. [PMID: 36698844 PMCID: PMC9868170 DOI: 10.3389/fmed.2022.1093329] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
Clostridioides difficile infection poses significant clinical challenges due to its recurrent nature. Current antibiotic management does not address the underlying issue, that of a disturbed gastrointestinal microbiome, called dysbiosis. This provides a supportive environment for the germination of C. difficile spores which lead to infection and toxin production as well as an array of other health conditions. The use of microbiome restoration therapies such as live biotherapeutics can reverse dysbiosis and lead to good clinical outcomes. Several such therapies are under clinical investigation.
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Affiliation(s)
- Teena Chopra
- Division of Infectious Diseases, Wayne State University, Detroit, MI, United States,*Correspondence: Teena Chopra,
| | - Gail Hecht
- Department of Medicine, Loyola University Chicago Stritch School of Medicine, Maywood, IL, United States
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12
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Matzaras R, Nikopoulou A, Protonotariou E, Christaki E. Gut Microbiota Modulation and Prevention of Dysbiosis as an Alternative Approach to Antimicrobial Resistance: A Narrative Review. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2022; 95:479-494. [PMID: 36568836 PMCID: PMC9765331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background: The importance of gut microbiota in human health is being increasingly studied. Imbalances in gut microbiota have been associated with infection, inflammation, and obesity. Antibiotic use is the most common and significant cause of major alterations in the composition and function of the gut microbiota and can result in colonization with multidrug-resistant bacteria. Methods: The purpose of this review is to present existing evidence on how microbiota modulation and prevention of gut dysbiosis can serve as tools to combat antimicrobial resistance. Results: While the spread of antibiotic-resistant pathogens requires antibiotics with novel mechanisms of action, the number of newly discovered antimicrobial classes remains very low. For this reason, the application of alternative modalities to combat antimicrobial resistance is necessary. Diet, probiotics/prebiotics, selective oropharyngeal or digestive decontamination, and especially fecal microbiota transplantation (FMT) are under investigation with FMT being the most studied. But, as prevention is better than cure, the implementation of antimicrobial stewardship programs and strict infection control measures along with newly developed chelating agents could also play a crucial role in decreasing colonization with multidrug resistant organisms. Conclusion: New alternative tools to fight antimicrobial resistance via gut microbiota modulation, seem to be effective and should remain the focus of further research and development.
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Affiliation(s)
- Rafail Matzaras
- Infectious Diseases Unit, Department of Medicine,
University General Hospital of Ioannina, University of Ioannina, Ioannina,
Greece
| | - Anna Nikopoulou
- Department of Internal Medicine, G. Papanikolaou
General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Efthimia Protonotariou
- Department of Microbiology, AHEPA University Hospital,
Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eirini Christaki
- Infectious Diseases Unit, Department of Medicine,
University General Hospital of Ioannina, University of Ioannina, Ioannina,
Greece,To whom all correspondence should be addressed:
Eirini Christaki, University General Hospital of Ioannina, St. Niarchou,
Ioannina, Greece; ; ORCID:
https://www.orcid.org/0000-0002-8152-6367
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13
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Mullish BH, McDonald JAK, Marchesi JR. Intestinal microbiota transplantation: do not forget the metabolites. Lancet Gastroenterol Hepatol 2022; 7:594. [PMID: 35709819 DOI: 10.1016/s2468-1253(22)00101-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022]
Affiliation(s)
- Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion, and Reproduction, St Mary's Hospital Campus, Imperial College London, London W2 1NY, UK.
| | - Julie A K McDonald
- MRC Centre for Molecular Bacteriology and Infection, Flowers Building, Imperial College London, London, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion, and Reproduction, St Mary's Hospital Campus, Imperial College London, London W2 1NY, UK
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14
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Long-Term Safety Following Faecal Microbiota Transplantation as a Treatment for Recurrent Clostridioides difficile Infection Compared with Patients Treated with a Fixed Bacterial Mixture: Results from a Retrospective Cohort Study. Cells 2022; 11:cells11030435. [PMID: 35159245 PMCID: PMC8834574 DOI: 10.3390/cells11030435] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 02/08/2023] Open
Abstract
Faecal microbiota transplantation (FMT) is the recommended treatment for recurrent C. difficile infection (rCDI) following a second recurrence. FMT is considered safe in the short term when procedures for the screening of donors and transferred material are followed. However, the long-term safety profile of FMT treatment is largely unknown. In a retrospective cohort study, we assessed the long-term safety of patients treated for rCDI with FMT or a fixed bacterial mixture, rectal bacteriotherapy (RBT). The overall survival, risk of hospital admission, onset of certain pre-specified diseases (cancer, diabetes mellitus, hypertension and inflammatory bowel disease) and risk of being diagnosed with a multidrug-resistant organism were assessed by undertaking a review of the treated patients’ medical records for up to five years following treatment. A total of 280 patients were treated for rCDI with FMT (n = 145) or RBT (n = 135) between 2016 and 2020. In the five years following treatment, there were no differences in survival (adjusted hazard ratio (aHR) 1.03; 95% CI 0.68–1.56), p = 0.89), risk of hospital admission ((aHR 0.92; 95% CI 0.72–1.18), p = 0.5) or onset of any of the analysed diseases. In conclusion, FMT was not associated with increased mortality, risk of hospital admission or onset of disease following treatment when compared with RBT.
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15
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Ghani R, Mullish BH, Roberts LA, Davies FJ, Marchesi JR. The potential utility of fecal (or intestinal) microbiota transplantation in controlling infectious diseases. Gut Microbes 2022; 14:2038856. [PMID: 35230889 PMCID: PMC8890388 DOI: 10.1080/19490976.2022.2038856] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/25/2022] [Indexed: 02/04/2023] Open
Abstract
The intestinal microbiota is recognized to play a role in the defense against infection, but conversely also acts as a reservoir for potentially pathogenic organisms. Disruption to the microbiome can increase the risk of invasive infection from these organisms; therefore, strategies to restore the composition of the gut microbiota are a potential strategy of key interest to mitigate this risk. Fecal (or Intestinal) Microbiota Transplantation (FMT/IMT), is the administration of minimally manipulated screened healthy donor stool to an affected recipient, and remains the major 'whole microbiome' therapeutic approach at present. Driven by the marked success of using FMT in the treatment of recurrent Clostridioides difficile infection, the potential use of FMT in treating other infectious diseases is an area of active research. In this review, we discuss key examples of this treatment based on recent findings relating to the interplay between microbiota and infection, and potential further exploitations of FMT/IMT.
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Affiliation(s)
- Rohma Ghani
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Benjamin H. Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Lauren A. Roberts
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Frances J. Davies
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Julian R. Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
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16
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Phanchana M, Harnvoravongchai P, Wongkuna S, Phetruen T, Phothichaisri W, Panturat S, Pipatthana M, Charoensutthivarakul S, Chankhamhaengdecha S, Janvilisri T. Frontiers in antibiotic alternatives for Clostridioides difficile infection. World J Gastroenterol 2021; 27:7210-7232. [PMID: 34876784 PMCID: PMC8611198 DOI: 10.3748/wjg.v27.i42.7210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/12/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile (C. difficile) is a gram-positive, anaerobic spore-forming bacterium and a major cause of antibiotic-associated diarrhea. Humans are naturally resistant to C. difficile infection (CDI) owing to the protection provided by healthy gut microbiota. When the gut microbiota is disturbed, C. difficile can colonize, produce toxins, and manifest clinical symptoms, ranging from asymptomatic diarrhea and colitis to death. Despite the steady-if not rising-prevalence of CDI, it will certainly become more problematic in a world of antibiotic overuse and the post-antibiotic era. C. difficile is naturally resistant to most of the currently used antibiotics as it uses multiple resistance mechanisms. Therefore, current CDI treatment regimens are extremely limited to only a few antibiotics, which include vancomycin, fidaxomicin, and metronidazole. Therefore, one of the main challenges experienced by the scientific community is the development of alternative approaches to control and treat CDI. In this Frontier article, we collectively summarize recent advances in alternative treatment approaches for CDI. Over the past few years, several studies have reported on natural product-derived compounds, drug repurposing, high-throughput library screening, phage therapy, and fecal microbiota transplantation. We also include an update on vaccine development, pre- and pro-biotics for CDI, and toxin antidote approaches. These measures tackle CDI at every stage of disease pathology via multiple mechanisms. We also discuss the gaps and concerns in these developments. The next epidemic of CDI is not a matter of if but a matter of when. Therefore, being well-equipped with a collection of alternative therapeutics is necessary and should be prioritized.
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Affiliation(s)
- Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | | | - Supapit Wongkuna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Tanaporn Phetruen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Wichuda Phothichaisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Supakan Panturat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Methinee Pipatthana
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sitthivut Charoensutthivarakul
- School of Bioinnovation and Bio-based Product Intelligence, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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17
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Monaghan TM, Seekatz AM, Mullish BH, Moore-Gillon CCER, Dawson LF, Ahmed A, Kao D, Chan WC. Clostridioides difficile: innovations in target discovery and potential for therapeutic success. Expert Opin Ther Targets 2021; 25:949-963. [PMID: 34793686 DOI: 10.1080/14728222.2021.2008907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Clostridioides difficile infection (CDI) remains a worldwide clinical problem. Increased incidence of primary infection, occurrence of hypertoxigenic ribotypes, and more frequent occurrence of drug resistant, recurrent, and non-hospital CDI, emphasizes the urgent unmet need of discovering new therapeutic targets. AREAS COVERED We searched PubMed and Web of Science databases for articles identifying novel therapeutic targets or treatments for C. difficile from 2001 to 2021. We present an updated review on current preclinical efforts on designing inhibitory compounds against these drug targets and indicate how these could become the focus of future therapeutic approaches. We also evaluate the increasing exploitability of gut microbial-derived metabolites and host-derived therapeutics targeting VEGF-A, immune targets and pathways, ion transporters, and microRNAs as anti-C. difficile therapeutics, which have yet to reach clinical trials. Our review also highlights the therapeutic potential of re-purposing currently available agents . We conclude by considering translational hurdles and possible strategies to mitigate these problems. EXPERT OPINION Considerable progress has been made in the development of new anti-CDI drug candidates. Nevertheless, a greater comprehension of CDI pathogenesis and host-microbe interactions is beginning to uncover potential novel therapeutic targets, which can be exploited to plug gaps in the CDI drug discovery pipeline.
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Affiliation(s)
- 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
| | - Anna M Seekatz
- Biological Sciences, Clemson University, Clemson, SC, USA
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Claudia C E R Moore-Gillon
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Lisa F Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ammar Ahmed
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Dina Kao
- Department of Gastroenterology, Zeidler Ledcor Centre, University of Alberta, Edmonton, Alberta, Canada
| | - Weng C Chan
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, UK
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18
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Innes AJ, Mullish BH, Ghani R, Szydlo RM, Apperley JF, Olavarria E, Palanicawandar R, Kanfer EJ, Milojkovic D, McDonald JAK, Brannigan ET, Thursz MR, Williams HRT, Davies FJ, Marchesi JR, Pavlů J. Fecal Microbiota Transplant Mitigates Adverse Outcomes Seen in Patients Colonized With Multidrug-Resistant Organisms Undergoing Allogeneic Hematopoietic Cell Transplantation. Front Cell Infect Microbiol 2021; 11:684659. [PMID: 34513724 PMCID: PMC8430254 DOI: 10.3389/fcimb.2021.684659] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
The gut microbiome can be adversely affected by chemotherapy and antibiotics prior to hematopoietic cell transplantation (HCT). This affects graft success and increases susceptibility to multidrug-resistant organism (MDRO) colonization and infection. We performed an initial retrospective analysis of our use of fecal microbiota transplantation (FMT) from healthy donors as therapy for MDRO-colonized patients with hematological malignancy. FMT was performed on eight MDRO-colonized patients pre-HCT (FMT-MDRO group), and outcomes compared with 11 MDRO colonized HCT patients from the same period. At 12 months, survival was significantly higher in the FMT-MDRO group (70% versus 36% p = 0.044). Post-HCT, fewer FMT-MDRO patients required intensive care (0% versus 46%, P = 0.045) or experienced fever (0.29 versus 0.11 days, P = 0.027). Intestinal MDRO decolonization occurred in 25% of FMT-MDRO patients versus 11% non-FMT MDRO patients. Despite the significant differences and statistically comparable patient/transplant characteristics, as the sample size was small, a matched-pair analysis between both groups to non-MDRO colonized control cohorts (2:1 matching) was performed. At 12 months, the MDRO group who did not have an FMT had significantly lower survival (36.4% versus 61.9% respectively, p=0.012), and higher non relapse mortality (NRM; 60.2% versus 16.7% respectively, p=0.009) than their paired non-MDRO-colonized cohort. Conversely, there was no difference in survival (70% versus 43.4%, p=0.14) or NRM (12.5% versus 31.2% respectively, p=0.24) between the FMT-MDRO group and their paired non-MDRO cohort. Collectively, these data suggest that negative clinical outcomes, including mortality associated with MDRO colonization, may be ameliorated by pre-HCT FMT, even in the absence of intestinal MDRO decolonization. Further work is needed to explore this observed benefit.
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Affiliation(s)
- Andrew J Innes
- Centre for Haematology, Imperial College London at Hammersmith Hospital, London, United Kingdom
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Rohma Ghani
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Richard M Szydlo
- Centre for Haematology, Imperial College London at Hammersmith Hospital, London, United Kingdom
| | - Jane F Apperley
- Centre for Haematology, Imperial College London at Hammersmith Hospital, London, United Kingdom
| | - Eduardo Olavarria
- Centre for Haematology, Imperial College London at Hammersmith Hospital, London, United Kingdom
| | - Renuka Palanicawandar
- Centre for Haematology, Imperial College London at Hammersmith Hospital, London, United Kingdom
| | - Edward J Kanfer
- Centre for Haematology, Imperial College London at Hammersmith Hospital, London, United Kingdom
| | - Dragana Milojkovic
- Centre for Haematology, Imperial College London at Hammersmith Hospital, London, United Kingdom
| | - Julie A K McDonald
- Medical Research Council (MRC) Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Eimear T Brannigan
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, United Kingdom
| | - Mark R Thursz
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Horace R T Williams
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Frances J Davies
- Medical Research Council (MRC) Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Jiří Pavlů
- Centre for Haematology, Imperial College London at Hammersmith Hospital, London, United Kingdom
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19
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The role of the microbiome in gastrointestinal inflammation. Biosci Rep 2021; 41:228872. [PMID: 34076695 PMCID: PMC8201460 DOI: 10.1042/bsr20203850] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
The microbiome plays an important role in maintaining human health. Despite multiple factors being attributed to the shaping of the human microbiome, extrinsic factors such diet and use of medications including antibiotics appear to dominate. Mucosal surfaces, particularly in the gut, are highly adapted to be able to tolerate a large population of microorganisms whilst still being able to produce a rapid and effective immune response against infection. The intestinal microbiome is not functionally independent from the host mucosa and can, through presentation of microbe-associated molecular patterns (MAMPs) and generation of microbe-derived metabolites, fundamentally influence mucosal barrier integrity and modulate host immunity. In a healthy gut there is an abundance of beneficial bacteria that help to preserve intestinal homoeostasis, promote protective immune responses, and limit excessive inflammation. The importance of the microbiome is further highlighted during dysbiosis where a loss of this finely balanced microbial population can lead to mucosal barrier dysfunction, aberrant immune responses, and chronic inflammation that increases the risk of disease development. Improvements in our understanding of the microbiome are providing opportunities to harness members of a healthy microbiota to help reverse dysbiosis, reduce inflammation, and ultimately prevent disease progression.
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20
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Varga A, Kocsis B, Sipos D, Kása P, Vigvári S, Pál S, Dembrovszky F, Farkas K, Péterfi Z. How to Apply FMT More Effectively, Conveniently and Flexible - A Comparison of FMT Methods. Front Cell Infect Microbiol 2021; 11:657320. [PMID: 34150673 PMCID: PMC8213398 DOI: 10.3389/fcimb.2021.657320] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/18/2021] [Indexed: 01/02/2023] Open
Abstract
Purpose Metronidazol and vancomycin were long the two best options against Clostridioides (formerly Clostridium) difficile infections (CDI). Now, the cost of new drugs such as fidaxomicin directs us towards alternative treatment options, such as faecal microbiota transplant (FMT). Its effectiveness is similar to fidaxomicin. There are questions regarding its safety, but the biggest challenges are prejudice and inconvenience. Most protocols refer to FMT applied in the form of a solution. We investigated different modalities of FMT. Methods Instead of using nasoenteric tubes or colonoscopy, we place frozen or lyophilised stool in non-coated, size “00”, hard gelatine capsules or enterosolvent, size “0” capsules. Results We found that non-coated, size “00”, hard gelatine capsules are appropriate for conducting FMT. Capsules containing lyophilised supernatant with a low number of bacteria have been proven to be non-inferior to other FMT modalities. The primary cure rate in the supernatant group was 93.75%, and 66.67% in the sediment group. The overall cure rate was 82.14%. Depending on the protocol, 4–7 capsules are sufficient per patient. Capsules can be stored for up to one year at -20°C. Conclusions FMT is a feasible alternative to antibiotic treatments in CDI. Our method makes the process flexible and less inconvenient to patients. Long storage time allows a consistent supply of capsules, while small volume and formulation make the procedure tolerable.
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Affiliation(s)
- Adorján Varga
- Department of Medical Microbiology and Immunology, University of Pécs Clinical Centre, Pécs, Hungary
| | - Béla Kocsis
- Department of Medical Microbiology and Immunology, University of Pécs Clinical Centre, Pécs, Hungary
| | - Dávid Sipos
- 1stDepartment of Internal Medicine - Department of Infectology, University of Pécs Clinical Centre, Pécs, Hungary
| | - Péter Kása
- Institute of Pharmaceutical Technology and Biopharmacy, University of Pécs Faculty of Pharmacy, Pécs, Hungary
| | - Szabolcs Vigvári
- 1stDepartment of Internal Medicine - Department of Infectology, University of Pécs Clinical Centre, Pécs, Hungary
| | - Szilárd Pál
- Institute of Pharmaceutical Technology and Biopharmacy, University of Pécs Faculty of Pharmacy, Pécs, Hungary
| | - Fanni Dembrovszky
- Institute for Translational Medicine, University of Pécs Medical School, Pécs, Hungary
| | - Kornélia Farkas
- Institute of Bioanalysis, University of Pécs Medical School, Pécs, Hungary
| | - Zoltán Péterfi
- 1stDepartment of Internal Medicine - Department of Infectology, University of Pécs Clinical Centre, Pécs, Hungary
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21
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Mullish BH, Allegretti JR. The contribution of bile acid metabolism to the pathogenesis of Clostridioides difficile infection. Therap Adv Gastroenterol 2021; 14:17562848211017725. [PMID: 34104212 PMCID: PMC8165815 DOI: 10.1177/17562848211017725] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 04/26/2021] [Indexed: 02/04/2023] Open
Abstract
Clostridioides difficile infection (CDI) remains a major global cause of gastrointestinal infection, with significant associated morbidity, mortality and impact upon healthcare system resources. Recent antibiotic use is a key risk factor for the condition, with the marked antibiotic-mediated perturbations in gut microbiome diversity and composition that underpin the pathogenesis of CDI being well-recognised. However, only relatively recently has further insight been gained into the specific mechanistic links between these gut microbiome changes and CDI, with alteration of gut microbial metabolites - in particular, bile acid metabolism - being a particular area of focus. A variety of in vitro, ex vivo, animal model and human studies have now demonstrated that loss of gut microbiome members with bile-metabolising capacity (including bile salt hydrolases, and 7-α-dehydroxylase) - with a resulting alteration of the gut bile acid milieu - contributes significantly to the disease process in CDI. More specifically, this microbiome disruption results in the enrichment of primary conjugated bile acids (including taurocholic acid, which promotes the germination of C. difficile spores) and loss of secondary bile acids (which inhibit the growth of C. difficile, and may bind to and limit activity of toxins produced by C. difficile). These bile acid changes are also associated with reduced activity of the farnesoid X receptor pathway, which may exacerbate C. difficile colitis throughout its impact upon gut barrier function and host immune/inflammatory response. Furthermore, a key mechanism of efficacy of faecal microbiota transplant (FMT) in treating recurrent CDI has been shown to be restoration of gut microbiome bile metabolising functionality; ensuring the presence of this functionality among defined microbial communities (and other 'next generation' FMT products) designed to treat CDI may be critical to their success.
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Affiliation(s)
- Benjamin H. Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
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22
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Joly A, Leulier F, De Vadder F. Microbial Modulation of the Development and Physiology of the Enteric Nervous System. Trends Microbiol 2020; 29:686-699. [PMID: 33309188 DOI: 10.1016/j.tim.2020.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/15/2022]
Abstract
The gastrointestinal tract harbors an intrinsic neuronal network, the enteric nervous system (ENS). The ENS controls motility, fluid homeostasis, and blood flow, but also interacts with other components of the intestine such as epithelial and immune cells. Recent studies indicate that gut microbiota diversification, which occurs alongside postnatal ENS maturation, could be critical for the development and function of the ENS. Here we discuss the possibility that this functional relationship starts in utero, whereby the maternal microbiota would prime the developing ENS and shape its physiology. We review ENS/microbiota interactions and their modulation in physiological and pathophysiological contexts. While microbial modulation of the ENS physiology is now well established, further studies are required to understand the contribution of the gut microbiota to the development and pathology of the ENS and to reveal the precise mechanisms underlying microbiota-to-ENS communications.
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Affiliation(s)
- Amélie Joly
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
| | - François Leulier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France
| | - Filipe De Vadder
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, Lyon, France.
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