1
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Zhao F, Wang J. Another piece of puzzle for the human microbiome: the gut virome under dietary modulation. J Genet Genomics 2024:S1673-8527(24)00098-5. [PMID: 38710286 DOI: 10.1016/j.jgg.2024.04.013] [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: 03/02/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024]
Abstract
The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community and preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.
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Affiliation(s)
- Fengxiang Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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2
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Wortelboer K, Herrema H. Opportunities and challenges in phage therapy for cardiometabolic diseases. Trends Endocrinol Metab 2024:S1043-2760(24)00083-3. [PMID: 38637223 DOI: 10.1016/j.tem.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024]
Abstract
The worldwide prevalence of cardiometabolic diseases (CMD) is increasing, and emerging evidence implicates the gut microbiota in this multifactorial disease development. Bacteriophages (phages) are viruses that selectively target a bacterial host; thus, phage therapy offers a precise means of modulating the gut microbiota, limiting collateral damage on the ecosystem. Several studies demonstrate the potential of phages in human disease, including alcoholic and steatotic liver disease. In this opinion article we discuss the potential of phage therapy as a predefined medicinal product for CMD and discuss its current challenges, including the generation of effective phage combinations, product formulation, and strict manufacturing requirements.
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Affiliation(s)
- Koen Wortelboer
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands; Amsterdam Gastroenterology, Endocrinology, and Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam UMC, Amsterdam, The Netherlands; Amsterdam Cardiovascular Sciences, Diabetes, and Metabolism, Amsterdam UMC, Amsterdam, The Netherlands
| | - Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands; Amsterdam Gastroenterology, Endocrinology, and Metabolism, Endocrinology, Metabolism and Nutrition, Amsterdam UMC, Amsterdam, The Netherlands; Amsterdam Cardiovascular Sciences, Diabetes, and Metabolism, Amsterdam UMC, Amsterdam, The Netherlands.
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3
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Ritz NL, Draper LA, Bastiaanssen TFS, Turkington CJR, Peterson VL, van de Wouw M, Vlckova K, Fülling C, Guzzetta KE, Burokas A, Harris H, Dalmasso M, Crispie F, Cotter PD, Shkoporov AN, Moloney GM, Dinan TG, Hill C, Cryan JF. The gut virome is associated with stress-induced changes in behaviour and immune responses in mice. Nat Microbiol 2024; 9:359-376. [PMID: 38316929 PMCID: PMC10847049 DOI: 10.1038/s41564-023-01564-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/17/2023] [Indexed: 02/07/2024]
Abstract
The microbiota-gut-brain axis has been shown to play an important role in the stress response, but previous work has focused primarily on the role of the bacteriome. The gut virome constitutes a major portion of the microbiome, with bacteriophages having the potential to remodel bacteriome structure and activity. Here we use a mouse model of chronic social stress, and employ 16S rRNA and whole metagenomic sequencing on faecal pellets to determine how the virome is modulated by and contributes to the effects of stress. We found that chronic stress led to behavioural, immune and bacteriome alterations in mice that were associated with changes in the bacteriophage class Caudoviricetes and unassigned viral taxa. To determine whether these changes were causally related to stress-associated behavioural or physiological outcomes, we conducted a faecal virome transplant from mice before stress and autochthonously transferred it to mice undergoing chronic social stress. The transfer of the faecal virome protected against stress-associated behaviour sequelae and restored stress-induced changes in select circulating immune cell populations, cytokine release, bacteriome alterations and gene expression in the amygdala. These data provide evidence that the virome plays a role in the modulation of the microbiota-gut-brain axis during stress, indicating that these viral populations should be considered when designing future microbiome-directed therapies.
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Affiliation(s)
- Nathaniel L Ritz
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Christopher J R Turkington
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Veronica L Peterson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Marcel van de Wouw
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- Department of Pediatrics, University of Calgary, Calgary, Canada
| | - Klara Vlckova
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Katherine E Guzzetta
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Aurelijus Burokas
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Biological Models, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Hugh Harris
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Marion Dalmasso
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Normandie Univ, UNICAEN, UNIROUEN, ABTE, 14000, Caen, France
| | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Andrey N Shkoporov
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Gerard M Moloney
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Corke, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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4
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Yu Y, Wang W, Zhang F. The Next Generation Fecal Microbiota Transplantation: To Transplant Bacteria or Virome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301097. [PMID: 37914662 PMCID: PMC10724401 DOI: 10.1002/advs.202301097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 09/02/2023] [Indexed: 11/03/2023]
Abstract
Fecal microbiota transplantation (FMT) has emerged as a promising therapeutic approach for dysbiosis-related diseases. However, the clinical practice of crude fecal transplants presents limitations in terms of acceptability and reproductivity. Consequently, two alternative solutions to FMT are developed: transplanting bacteria communities or virome. Advanced methods for transplanting bacteria mainly include washed microbiota transplantation and bacteria spores treatment. Transplanting the virome is also explored, with the development of fecal virome transplantation, which involves filtering the virome from feces. These approaches provide more palatable options for patients and healthcare providers while minimizing research heterogeneity. In general, the evolution of the next generation of FMT in global trends is fecal microbiota components transplantation which mainly focuses on transplanting bacteria or virome.
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Affiliation(s)
- You Yu
- Department of Microbiota Medicine & Medical Center for Digestive DiseasesThe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
| | - Weihong Wang
- Department of Microbiota Medicine & Medical Center for Digestive DiseasesThe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
| | - Faming Zhang
- Department of Microbiota Medicine & Medical Center for Digestive DiseasesThe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
- Department of Microbiota MedicineSir Run Run HospitalNanjing Medical UniversityNanjing211166China
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5
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Wang H, Xu S, Li S, Su B, Sherrill-Mix S, Liang G. Virome in immunodeficiency: what we know currently. Chin Med J (Engl) 2023; 136:2647-2657. [PMID: 37914672 PMCID: PMC10684123 DOI: 10.1097/cm9.0000000000002899] [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: 07/30/2023] [Indexed: 11/03/2023] Open
Abstract
ABSTRACT Over the past few years, the human virome and its complex interactions with microbial communities and the immune system have gained recognition as a crucial factor in human health. Individuals with compromised immune function encounter distinctive challenges due to their heightened vulnerability to a diverse range of infectious diseases. This review aims to comprehensively explore and analyze the growing evidence regarding the role of the virome in immunocompromised disease status. By surveying the latest literature, we present a detailed overview of virome alterations observed in various immunodeficiency conditions. We then delve into the influence and mechanisms of these virome changes on the pathogenesis of specific diseases in immunocompromised individuals. Furthermore, this review explores the clinical relevance of virome studies in the context of immunodeficiency, highlighting the potential diagnostic and therapeutic gains from a better understanding of virome contributions to disease manifestations.
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Affiliation(s)
- Hu Wang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Siqi Xu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Scott Sherrill-Mix
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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6
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Wu D, Zhang C, Liu Y, Yao J, Yang X, Wu S, Du J, Yang X. Beyond faecal microbiota transplantation, the non-negligible role of faecal virome or bacteriophage transplantation. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023; 56:893-908. [PMID: 36890066 DOI: 10.1016/j.jmii.2023.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/09/2023] [Accepted: 02/18/2023] [Indexed: 02/27/2023]
Abstract
Intestinal microbiota, which contains bacteria, archaea, fungi, protists, and viruses including bacteriophages, is symbiotic and evolves together with humans. The balanced intestinal microbiota plays indispensable roles in maintaining and regulating host metabolism and health. Dysbiosis has been associated with not only intestinal diseases but other diseases such as neurology disorders and cancers. Faecal microbiota transplantation (FMT) or faecal virome or bacteriophage transplantation (FVT or FBT), transfers faecal bacteria or viruses, with a focus on bacteriophage, from one healthy individual to another individual (normally unhealthy condition), and aims to restore the balanced gut microbiota and assist in subduing diseases. In this review, we summarized the applications of FMT and FVT in clinical settings, discussed the advantages and challenges of FMT and FVT currently and proposed several considerations prospectively. We further provided our understanding of why FMT and FVT have their limitations and raised the possible future development strategy of FMT and FVT.
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Affiliation(s)
- Dengyu Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Chenguang Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Yanli Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Juan Du
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Xin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.
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7
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Wortelboer K, de Jonge PA, Scheithauer TPM, Attaye I, Kemper EM, Nieuwdorp M, Herrema H. Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety. Nat Commun 2023; 14:5600. [PMID: 37699894 PMCID: PMC10497675 DOI: 10.1038/s41467-023-41329-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
Bacteriophages (phages) are bacterial viruses that have been shown to shape microbial communities. Previous studies have shown that faecal virome transplantation can decrease weight gain and normalize blood glucose tolerance in diet-induced obese mice. Therefore, we performed a double-blind, randomised, placebo-controlled pilot study in which 24 individuals with metabolic syndrome were randomised to a faecal filtrate transplantation (FFT) from a lean healthy donor (n = 12) or placebo (n = 12). The primary outcome, change in glucose metabolism, and secondary outcomes, safety and longitudinal changes within the intestinal bacteriome and phageome, were assessed from baseline up to 28 days. All 24 included subjects completed the study and are included in the analyses. While the overall changes in glucose metabolism are not significantly different between both groups, the FFT is well-tolerated and without any serious adverse events. The phage virion composition is significantly altered two days after FFT as compared to placebo, which coincides with more virulent phage-microbe interactions. In conclusion, we provide evidence that gut phages can be safely administered to transiently alter the gut microbiota of recipients.
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Affiliation(s)
- Koen Wortelboer
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands
| | - Patrick A de Jonge
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands
| | - Torsten P M Scheithauer
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands
| | - Ilias Attaye
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Vascular Medicine, Amsterdam, The Netherlands
| | - E Marleen Kemper
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Department of Pharmacy and Clinical Pharmacology, Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Vascular Medicine, Amsterdam, The Netherlands
- Amsterdam UMC location Vrije University Medical Center, Department of Internal Medicine, Diabetes Center, Amsterdam, The Netherlands
| | - Hilde Herrema
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, Amsterdam, The Netherlands.
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands.
- Amsterdam Gastroenterology Endocrinology Metabolism, Endocrinology, metabolism and nutrition, Amsterdam, The Netherlands.
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8
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Chen L, Hou X, Chu H. The Novel Role of Phage Particles in Chronic Liver Diseases. Microorganisms 2023; 11:1181. [PMID: 37317156 DOI: 10.3390/microorganisms11051181] [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: 03/20/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 06/16/2023] Open
Abstract
The gut microbiome is made up of bacteria, fungi, viruses and archaea, all of which are closely related with human health. As the main component of enterovirus, the role of bacteriophages (phages) in chronic liver disease has been gradually recognized. Chronic liver diseases, including alcohol-related liver disease and nonalcoholic fatty liver disease, exhibit alterations of the enteric phages. Phages shape intestinal bacterial colonization and regulate bacterial metabolism. Phages adjoining to intestinal epithelial cells prevent bacteria from invading the intestinal barrier, and mediate intestinal inflammatory response. Phages are also observed increasing intestinal permeability and migrating to peripheral blood and organs, likely contributing to inflammatory injury in chronic liver diseases. By preying on harmful bacteria, phages can improve the gut microbiome of patients with chronic liver disease and thus act as an effective treatment method.
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Affiliation(s)
- Liuying Chen
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
| | - Huikuan Chu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China
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9
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Ezzatpour S, Mondragon Portocarrero ADC, Cardelle-Cobas A, Lamas A, López-Santamarina A, Miranda JM, Aguilar HC. The Human Gut Virome and Its Relationship with Nontransmissible Chronic Diseases. Nutrients 2023; 15:977. [PMID: 36839335 PMCID: PMC9960951 DOI: 10.3390/nu15040977] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
The human gastrointestinal tract contains large communities of microorganisms that are in constant interaction with the host, playing an essential role in the regulation of several metabolic processes. Among the gut microbial communities, the gut bacteriome has been most widely studied in recent decades. However, in recent years, there has been increasing interest in studying the influences that other microbial groups can exert on the host. Among them, the gut virome is attracting great interest because viruses can interact with the host immune system and metabolic functions; this is also the case for phages, which interact with the bacterial microbiota. The antecedents of virome-rectification-based therapies among various diseases were also investigated. In the near future, stool metagenomic investigation should include the identification of bacteria and phages, as well as their correlation networks, to better understand gut microbiota activity in metabolic disease progression.
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Affiliation(s)
- Shahrzad Ezzatpour
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Alicia del Carmen Mondragon Portocarrero
- Laboratorio de Higiene, Inspección y Control de Alimentos (LHICA), Departamento de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Alejandra Cardelle-Cobas
- Laboratorio de Higiene, Inspección y Control de Alimentos (LHICA), Departamento de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Alexandre Lamas
- Laboratorio de Higiene, Inspección y Control de Alimentos (LHICA), Departamento de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Aroa López-Santamarina
- Laboratorio de Higiene, Inspección y Control de Alimentos (LHICA), Departamento de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - José Manuel Miranda
- Laboratorio de Higiene, Inspección y Control de Alimentos (LHICA), Departamento de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Hector C. Aguilar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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10
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Liu Q, Xu Z, Dai M, Su Q, Leung Chan FK, Ng SC. Faecal microbiota transplantations and the role of bacteriophages. Clin Microbiol Infect 2022:S1198-743X(22)00579-1. [PMID: 36414201 DOI: 10.1016/j.cmi.2022.11.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/06/2022] [Accepted: 11/13/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND Bacteriophages are a major component of the human gut microbiota. Emerging evidence suggests that gut bacteriophages play an important role in the intricate dynamics with bacteria, and their transfer may be associated with the efficacy of faecal microbiota transplantation (FMT). OBJECTIVES To summarize our current knowledge of the changes in gut bacteriophage communities during FMT and their association with FMT outcome. SOURCES PubMed, Web of Science, and Google Scholar were searched for articles on FMT and bacteriophages published between May 2013 and January 2022. CONTENT Preclinical and clinical studies have reported associations between gut bacteriophage profiles and FMT. FMT was associated with donor-specific engraftment of bacteriophages, characterized by increased viral diversity and richness, and the bacteriophage composition resembled the donor's profile after FMT. Limited studies showed that cure after FMT was more likely when an increased fraction of the recipient enteric virome was occupied by donor-derived taxa, including Caudovirales in Clostridioides difficile infection. Faecal virome transplant involving the transfer of the gut virome communities alone may also induce phenotypical and microbiome improvement in various diseases. IMPLICATIONS The accumulating evidence that bacteriophages play roles in FMT efficacy has attracted considerable interest. Better characterization of bacteriophages and an understanding of their underlying mechanisms in FMT are warranted.
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Affiliation(s)
- Qin Liu
- Microbiota I-Center, Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhilu Xu
- Microbiota I-Center, Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Min Dai
- Microbiota I-Center, Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qi Su
- Microbiota I-Center, Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis Ka Leung Chan
- Microbiota I-Center, Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Microbiota I-Center, Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China; Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
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11
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Sinha A, Li Y, Mirzaei MK, Shamash M, Samadfam R, King IL, Maurice CF. Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis. MICROBIOME 2022; 10:105. [PMID: 35799219 PMCID: PMC9264660 DOI: 10.1186/s40168-022-01275-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs) including Crohn's disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages), is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown. RESULTS Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs. CONCLUSIONS Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease. Video Abstract.
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Affiliation(s)
- Anshul Sinha
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Yue Li
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, Guangdong, China
| | - Mohammadali Khan Mirzaei
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- Institute of Virology, Helmholtz Center Munich and Technical University of Munich, 85764, Neuherberg, Bavaria, Germany
| | - Michael Shamash
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Rana Samadfam
- Charles River Laboratories, 22022 Transcanadienne, Senneville, QC, H9X 3R3, Canada
| | - Irah L King
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada.
| | - Corinne F Maurice
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada.
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12
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Roles of the gut virome and mycobiome in faecal microbiota transplantation. Lancet Gastroenterol Hepatol 2022; 7:472-484. [DOI: 10.1016/s2468-1253(21)00303-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022]
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13
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Schwarz C, Mathieu J, Laverde Gomez JA, Yu P, Alvarez PJJ. Renaissance for Phage-Based Bacterial Control. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4691-4701. [PMID: 34793127 DOI: 10.1021/acs.est.1c06232] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jenny A Laverde Gomez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
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14
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Waller KMJ, Leong RW, Paramsothy S. An update on fecal microbiota transplantation for the treatment of gastrointestinal diseases. J Gastroenterol Hepatol 2022; 37:246-255. [PMID: 34735024 DOI: 10.1111/jgh.15731] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022]
Abstract
Our understanding of the microbiome and its implications for human health and disease continues to develop. Fecal microbiota transplantation (FMT) is now an established treatment for recurrent Clostridioides difficile infection. There is also increasing evidence for the efficacy of FMT in inducing remission for mild-moderate ulcerative colitis. However, for other indications, data for FMT are limited, with randomized controlled trials rare, typically small and often conflicting. Studies are continuing to explore the role of FMT for many other conditions, including Crohn's disease, functional gut disorders, metabolic syndrome, modulating responses to chemotherapy, eradication of multidrug resistant organisms, and the gut-brain axis. In light of safety, logistical, and regulatory challenges, there is a move to standardized products including narrow spectrum consortia. However, the mechanisms underpinning FMT remain incompletely understood, including the role of non-bacterial components, which may limit success of novel microbial approaches.
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Affiliation(s)
- Karen M J Waller
- Gastroenterology and Liver Services, Concord Repatriation General Hospital, Sydney, New South Wales, Australia.,Concord Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Rupert W Leong
- Gastroenterology and Liver Services, Concord Repatriation General Hospital, Sydney, New South Wales, Australia.,Concord Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Sudarshan Paramsothy
- Gastroenterology and Liver Services, Concord Repatriation General Hospital, Sydney, New South Wales, Australia.,Concord Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales, Australia
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15
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El Haddad L, Mendoza JF, Jobin C. Bacteriophage-mediated manipulations of microbiota in gastrointestinal diseases. Front Microbiol 2022; 13:1055427. [PMID: 36466675 PMCID: PMC9714271 DOI: 10.3389/fmicb.2022.1055427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
Although some gastrointestinal diseases could be managed using various antibiotics regimen, this therapeutic approach lacks precision and damages the microbiota. Emerging literature suggests that phages may play a key role in restoring the gut microbiome balance and controlling disease progression either with exogenous phage intervention or filtered fecal transplantation or even engineered phages. In this review, we will discuss the current phage applications aiming at controlling the bacterial population and preventing infection, inflammation, and cancer progression in the context of gastrointestinal diseases.
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Affiliation(s)
- Lynn El Haddad
- Department of Medicine, University of Florida, Gainesville, FL, United States.,Department of Molecular Genetics and Microbiology, Gainesville, FL, United States
| | - Jesus F Mendoza
- Department of Medicine, University of Florida, Gainesville, FL, United States
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL, United States.,Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL, United States.,Department of Infectious Diseases and Immunology, University of Florida, Gainesville, FL, United States
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16
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Hallowell HA, Higgins KV, Roberts M, Johnson RM, Bayne J, Maxwell HS, Brandebourg T, Hiltbold Schwartz E. Longitudinal Analysis of the Intestinal Microbiota in the Obese Mangalica Pig Reveals Alterations in Bacteria and Bacteriophage Populations Associated With Changes in Body Composition and Diet. Front Cell Infect Microbiol 2021; 11:698657. [PMID: 34737972 PMCID: PMC8560744 DOI: 10.3389/fcimb.2021.698657] [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: 04/21/2021] [Accepted: 09/13/2021] [Indexed: 11/29/2022] Open
Abstract
Due to its immunomodulatory potential, the intestinal microbiota has been implicated as a contributing factor in the development of the meta-inflammatory state that drives obesity-associated insulin resistance and type 2 diabetes. A better understanding of this link would facilitate the development of targeted treatments and therapies to treat the metabolic complications of obesity. To this end, we validated and utilized a novel swine model of obesity, the Mangalica pig, to characterize changes in the gut microbiota during the development of an obese phenotype, and in response to dietary differences. In the first study, we characterized the metabolic phenotype and gut microbiota in lean and obese adult Mangalica pigs. Obese or lean groups were created by allowing either ad libitum (obese) or restricted (lean) access to a standard diet for 54 weeks. Mature obese pigs were significantly heavier and exhibited 170% greater subcutaneous adipose tissue mass, with no differences in muscle mass compared to their lean counterparts. Obese pigs displayed impaired glucose tolerance and hyperinsulinemia following oral glucose challenge, indicating that a metabolic phenotype also manifested with changes in body composition. Consistent with observations in human obesity, the gut microbiota of obese pigs displayed altered bacterial composition. In the second study, we characterized the longitudinal changes in the gut microbiota in response to diet and aging in growing Mangalica pigs that were either limit fed a standard diet, allowed ad libitum access to a standard diet, or allowed ad libitum access to a high fat-supplemented diet over an 18-week period. As expected, weight gain was highest in pigs fed the high fat diet compared to ad libitum and limit fed groups. Furthermore, the ad libitum and high fat groups displayed significantly greater adiposity consistent with the development of obesity relative to the limit fed pigs. The intestinal microbiota was generally resilient to differences in dietary intake (limit fed vs ad libitum), though changes in the microbiota of pigs fed the high fat diet mirrored changes observed in mature obese pigs during the first study. This is consistent with the link observed between the microbiota and adiposity. In contrast to intestinal bacterial populations, bacteriophage populations within the gut microbiota responded rapidly to differences in diet, with significant compositional changes in bacteriophage genera observed between the dietary treatment groups as pigs aged. These studies are the first to describe the development of the intestinal microbiota in the Mangalica pig, and are the first to provide evidence that changes in body composition and dietary conditions are associated with changes in the microbiome of this novel porcine model of obesity.
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Affiliation(s)
- Haley A Hallowell
- Department of Biological Sciences, Auburn University, College of Science and Mathematics, Auburn, AL, United States
| | - Keah V Higgins
- Department of Biological Sciences, Auburn University, College of Science and Mathematics, Auburn, AL, United States
| | - Morgan Roberts
- Department of Animal Sciences, College of Agriculture, Auburn University, Auburn, AL, United States
| | - Robert M Johnson
- Department of Biological Sciences, Auburn University, College of Science and Mathematics, Auburn, AL, United States
| | - Jenna Bayne
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Herris Stevens Maxwell
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Terry Brandebourg
- Department of Animal Sciences, College of Agriculture, Auburn University, Auburn, AL, United States
| | - Elizabeth Hiltbold Schwartz
- Department of Biological Sciences, Auburn University, College of Science and Mathematics, Auburn, AL, United States
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17
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Chaffringeon L, Lamy-Besnier Q, Debarbieux L, De Sordi L. The intestinal virome: lessons from animal models. Curr Opin Virol 2021; 51:141-148. [PMID: 34700287 DOI: 10.1016/j.coviro.2021.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 12/28/2022]
Abstract
Mucosal surfaces in contact with the environment host specific microbiota. The intestinal tract harbours the most abundant and diverse bacterial and viral populations interacting with each other as well as with the host. Viruses of the microbiota are important components of this ecosystem, as shown by viral alterations associated with various pathologies. However, practical and ethical constraints limit functional studies of the virome in humans, making animal models invaluable experimental tools to understand its impact on intestinal physiology. In this review, we present the recent advances in the study of virome in animal models. We focus on the strategies used to characterise viral changes in disease models and approaches to modulate the microbiota using viruses. In reviewing the interplay between viruses, bacteria, and the animal host, we highlight the potential and limitations of these models in elucidating the role of the virome in determining human health and disease.
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Affiliation(s)
- Lorenzo Chaffringeon
- Sorbonne Université, INSERM, Centre de Recherche St Antoine, UMRS_938, Paris, France; Department of Microbiology, Institut Pasteur, Paris, F-75015, France; Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, Paris, France
| | - Quentin Lamy-Besnier
- Department of Microbiology, Institut Pasteur, Paris, F-75015, France; Université de Paris, Paris, France
| | | | - Luisa De Sordi
- Sorbonne Université, INSERM, Centre de Recherche St Antoine, UMRS_938, Paris, France; Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, Paris, France.
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18
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Cullin N, Azevedo Antunes C, Straussman R, Stein-Thoeringer CK, Elinav E. Microbiome and cancer. Cancer Cell 2021; 39:1317-1341. [PMID: 34506740 DOI: 10.1016/j.ccell.2021.08.006] [Citation(s) in RCA: 207] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/05/2021] [Accepted: 08/13/2021] [Indexed: 12/14/2022]
Abstract
The human microbiome constitutes a complex multikingdom community that symbiotically interacts with the host across multiple body sites. Host-microbiome interactions impact multiple physiological processes and a variety of multifactorial disease conditions. In the past decade, microbiome communities have been suggested to influence the development, progression, metastasis formation, and treatment response of multiple cancer types. While causal evidence of microbial impacts on cancer biology is only beginning to be unraveled, enhanced molecular understanding of such cancer-modulating interactions and impacts on cancer treatment are considered of major scientific importance and clinical relevance. In this review, we describe the molecular pathogenic mechanisms shared throughout microbial niches that contribute to the initiation and progression of cancer. We highlight advances, limitations, challenges, and prospects in understanding how the microbiome may causally impact cancer and its treatment responsiveness, and how microorganisms or their secreted bioactive metabolites may be potentially harnessed and targeted as precision cancer therapeutics.
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Affiliation(s)
- Nyssa Cullin
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Camila Azevedo Antunes
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, 234 Herzl Street, 7610001 Rehovot, Israel
| | - Christoph K Stein-Thoeringer
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Eran Elinav
- Microbiome and Cancer Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Immunology, Weizmann Institute of Science, 234 Herzl Street, 7610001 Rehovot, Israel.
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19
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Bokoliya SC, Dorsett Y, Panier H, Zhou Y. Procedures for Fecal Microbiota Transplantation in Murine Microbiome Studies. Front Cell Infect Microbiol 2021; 11:711055. [PMID: 34621688 PMCID: PMC8490673 DOI: 10.3389/fcimb.2021.711055] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Fecal microbiota transplantation (FMT) has been widely recognized as an approach to determine the microbiome’s causal role in gut dysbiosis-related disease models and as a novel disease-modifying therapy. Despite potential beneficial FMT results in various disease models, there is a variation and complexity in procedural agreement among research groups for performing FMT. The viability of the microbiome in feces and its successful transfer depends on various aspects of donors, recipients, and lab settings. This review focuses on the technical practices of FMT in animal studies. We first document crucial factors required for collecting, handling, and processing donor fecal microbiota for FMT. Then, we detail the description of gut microbiota depletion methods, FMT dosages, and routes of FMT administrations in recipients. In the end, we describe assessments of success rates of FMT with sustainability. It is critical to work under the anaerobic condition to preserve as much of the viability of bacteria. Utilization of germ- free mice or depletion of recipient gut microbiota by antibiotics or polyethylene glycol are two common recipient preparation approaches to achieve better engraftment. Oral-gastric gavage preferred by most researchers for fast and effective administration of FMT in mice. Overall, this review highlights various methods that may lead to developing the standard and reproducible protocol for FMT.
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Affiliation(s)
- Suresh C Bokoliya
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
| | - Yair Dorsett
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
| | - Hunter Panier
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
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20
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Carroll-Portillo A, Lin HC. Exploring Mucin as Adjunct to Phage Therapy. Microorganisms 2021; 9:microorganisms9030509. [PMID: 33670927 PMCID: PMC7997181 DOI: 10.3390/microorganisms9030509] [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: 01/28/2021] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
Conventional phage therapy using bacteriophages (phages) for specific targeting of pathogenic bacteria is not always useful as a therapeutic for gastrointestinal (GI) dysfunction. Complex dysbiotic GI disorders such as small intestinal bowel overgrowth (SIBO), ulcerative colitis (UC), or Crohn’s disease (CD) are even more difficult to treat as these conditions have shifts in multiple populations of bacteria within the microbiome. Such community-level structural changes in the gut microbiota may require an alternative to conventional phage therapy such as fecal virome transfer or a phage cocktail capable of targeting multiple bacterial species. Additionally, manipulation of the GI microenvironment may enhance beneficial bacteria–phage interactions during treatment. Mucin, produced along the entire length of the GI tract to protect the underlying mucosa, is a prominent contributor to the GI microenvironment and may facilitate bacteria–phage interactions in multiple ways, potentially serving as an adjunct during phage therapy. In this review, we will describe what is known about the role of mucin within the GI tract and how its facilitation of bacteria–phage interactions should be considered in any effort directed at optimizing effectiveness of a phage therapy for gastrointestinal dysbiosis.
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Affiliation(s)
- Amanda Carroll-Portillo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Henry C. Lin
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA;
- Medicine Service, New Mexico VA Health Care System, Albuquerque, NM 87108, USA
- Correspondence: ; Tel.: +1-505-265-1711 (ext. 4552)
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21
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García-Cabrerizo R, Carbia C, O Riordan KJ, Schellekens H, Cryan JF. Microbiota-gut-brain axis as a regulator of reward processes. J Neurochem 2021; 157:1495-1524. [PMID: 33368280 DOI: 10.1111/jnc.15284] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/08/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022]
Abstract
Our gut harbours trillions of microorganisms essential for the maintenance of homeostasis and host physiology in health and disease. In the last decade, there has been a growing interest in understanding the bidirectional pathway of communication between our microbiota and the central nervous system. With regard to reward processes there is accumulating evidence from both animal and human studies that this axis may be a key factor in gating reward valence. Focusing on the mesocorticolimbic pathway, we will discuss how the intestinal microbiota is involved in regulating brain reward functions, both in natural (i.e. eating, social or sexual behaviours) and non-natural reinforcers (drug addiction behaviours including those relevant to alcohol, psychostimulants, opioids and cannabinoids). We will integrate preclinical and clinical evidence suggesting that the microbiota-gut-brain axis could be implicated in the development of disorders associated with alterations in the reward system and how it may be targeted as a promising therapeutic strategy. Cover Image for this issue: https://doi.org/10.1111/jnc.15065.
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Affiliation(s)
| | - Carina Carbia
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Harriet Schellekens
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
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22
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Gheorghe CE, Ritz NL, Martin JA, Wardill HR, Cryan JF, Clarke G. Investigating causality with fecal microbiota transplantation in rodents: applications, recommendations and pitfalls. Gut Microbes 2021; 13:1941711. [PMID: 34328058 PMCID: PMC8331043 DOI: 10.1080/19490976.2021.1941711] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/04/2023] Open
Abstract
In recent years, studies investigating the role of the gut microbiota in health and diseases have increased enormously - making it essential to deepen and question the research methodology employed. Fecal microbiota transplantation (FMT) in rodent studies (either from human or animal donors) allows us to better understand the causal role of the intestinal microbiota across multiple fields. However, this technique lacks standardization and requires careful experimental design in order to obtain optimal results. By comparing several studies in which rodents are the final recipients of FMT, we summarize the common practices employed. In this review, we document the limitations of this method and highlight different parameters to be considered while designing FMT Studies. Standardizing this method is challenging, as it differs according to the research topic, but avoiding common pitfalls is feasible. Several methodological questions remain unanswered to this day and we offer a discussion on issues to be explored in future studies.
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Affiliation(s)
- Cassandra E. Gheorghe
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Nathaniel L. Ritz
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jason A. Martin
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Hannah R. Wardill
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia
- Adelaide Medical School, the University of Adelaide, Adelaide, Australia
| | - John F. Cryan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- INFANT Research Centre, University College Cork, Cork, Ireland
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23
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Rasmussen TS, Mentzel CMJ, Kot W, Castro-Mejía JL, Zuffa S, Swann JR, Hansen LH, Vogensen FK, Hansen AK, Nielsen DS. Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model. Gut 2020; 69:2122-2130. [PMID: 32165408 DOI: 10.1136/gutjnl-2019-320005] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/11/2020] [Accepted: 02/21/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Development of obesity and type 2 diabetes (T2D) are associated with gut microbiota (GM) changes. The gut viral community is predominated by bacteriophages (phages), which are viruses that attack bacteria in a host-specific manner. The antagonistic behaviour of phages has the potential to alter the GM. As a proof-of-concept, we demonstrate the efficacy of faecal virome transplantation (FVT) from lean donors for shifting the phenotype of obese mice into closer resemblance of lean mice. DESIGN The FVT consisted of viromes with distinct profiles extracted from the caecal content of mice from different vendors that were fed a low-fat (LF) diet for 14 weeks. Male C57BL/6NTac mice were divided into five groups: LF (as diet control), high-fat (HF) diet, HF+ampicillin (Amp), HF+Amp+FVT and HF+FVT. At weeks 6 and 7 of the study, the HF+FVT and HF+Amp+FVT mice were treated with FVT by oral gavage. The Amp groups were treated with Amp 24 hours prior to first FVT treatment. RESULTS Six weeks after first FVT, the HF+FVT mice showed a significant decrease in weight gain compared with the HF group. Further, glucose tolerance was comparable between the LF and HF+FVT mice, while the other HF groups all had impaired glucose tolerance. These observations were supported by significant shifts in GM composition, blood plasma metabolome and expression levels of genes associated with obesity and T2D development. CONCLUSIONS Transfer of caecal viral communities from mice with a lean phenotype into mice with an obese phenotype led to reduced weight gain and normalised blood glucose parameters relative to lean mice. We hypothesise that this effect is mediated via FVT-induced GM changes.
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Affiliation(s)
| | | | - Witold Kot
- Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Simone Zuffa
- Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | | | | | | | - Axel Kornerup Hansen
- Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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Huang R, Ju Z, Zhou PK. A gut dysbiotic microbiota-based hypothesis of human-to-human transmission of non-communicable diseases. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:141030. [PMID: 32726703 DOI: 10.1016/j.scitotenv.2020.141030] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Non-communicable diseases (NCDs) have replaced communicable diseases as the leading cause of premature death worldwide over the past century. Increasing numbers of studies have reported a link between NCDs and dysbiotic gut microbiota. Some gut microbiota, such as Helicobacter pylori, have been implicated in person-to-person transmission. Based on these reports, we develop a hypothesis regarding dysbiotic microbiota-associated NCDs, and explore how the presence of communicable NCDs could be confirmedexperimentally. We have also reviewed reports on environmental factors, including a high-fat diet, alcohol, smoking, exercise, radiation and air pollution, which have been associated with dysbiotic microbiota, and determined whether any of these parameters were also associated with NCDs. This review discusses the potential mechanism by which dysbiotic microbiota induced by environmental factors are directly or indirectly involved in person-to-person transmission. The hypothetical interplay between the environment, gut microbiota and host can be tested through high-throughput sequencing, animal models, and cell studies, although each of these modalities presents specific challenges. Confirmation of a causative association of dysbiotic microbiota with NCDs would represent a paradigm shift in efforts to prevent and control these diseases, and should stimulate additional studies on the associations among environmental factors, gut microbiota, and NCDs.
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Affiliation(s)
- Ruixue Huang
- Department of Occupational and Environmental Health, Central South University, Changsha, 410078, China.
| | - Zhao Ju
- Department of Occupational and Environmental Health, Central South University, Changsha, 410078, China
| | - Ping-Kun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing 100850, PR China; Institute for Chemical Carcinogenesis, State Key Laboratory of Respiratory, Guangzhou Medical University, Guangzhou 511436, PR China.
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25
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Yan A, Butcher J, Mack D, Stintzi A. Virome Sequencing of the Human Intestinal Mucosal-Luminal Interface. Front Cell Infect Microbiol 2020; 10:582187. [PMID: 33194818 PMCID: PMC7642909 DOI: 10.3389/fcimb.2020.582187] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/14/2020] [Indexed: 01/12/2023] Open
Abstract
While the human gut virome has been increasingly explored in recent years, nearly all studies have been limited to fecal sampling. The mucosal-luminal interface has been established as a viable sample type for profiling the microbial biogeography of the gastrointestinal tract. We have developed a protocol to extract nucleic acids from viruses at the mucosal-luminal interface of the proximal and distal colon. Colonic viromes from pediatric patients with Crohn's disease demonstrated high interpatient diversity and low but significant intrapatient variation between sites. Whole metagenomics was also performed to explore virome-bacteriome interactions and to compare the viral communities observed in virome and whole metagenomic sequencing. A site-specific study of the human gut virome is a necessary step to advance our understanding of virome-bacteriome-host interactions in human diseases.
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Affiliation(s)
- Austin Yan
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - James Butcher
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - David Mack
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Inflammatory Bowel Disease Centre and CHEO Research Institute, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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26
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Federici S, Nobs SP, Elinav E. Phages and their potential to modulate the microbiome and immunity. Cell Mol Immunol 2020; 18:889-904. [PMID: 32901128 DOI: 10.1038/s41423-020-00532-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages (hence termed phages) are viruses that target bacteria and have long been considered as potential future treatments against antibiotic-resistant bacterial infection. However, the molecular nature of phage interactions with bacteria and the human host has remained elusive for decades, limiting their therapeutic application. While many phages and their functional repertoires remain unknown, the advent of next-generation sequencing has increasingly enabled researchers to decode new lytic and lysogenic mechanisms by which they attack and destroy bacteria. Furthermore, the last decade has witnessed a renewed interest in the utilization of phages as therapeutic vectors and as a means of targeting pathogenic or commensal bacteria or inducing immunomodulation. Importantly, the narrow host range, immense antibacterial repertoire, and ease of manipulating phages may potentially allow for their use as targeted modulators of pathogenic, commensal and pathobiont members of the microbiome, thereby impacting mammalian physiology and immunity along mucosal surfaces in health and in microbiome-associated diseases. In this review, we aim to highlight recent advances in phage biology and how a mechanistic understanding of phage-bacteria-host interactions may facilitate the development of novel phage-based therapeutics. We provide an overview of the challenges of the therapeutic use of phages and how these could be addressed for future use of phages as specific modulators of the human microbiome in a variety of infectious and noncommunicable human diseases.
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Affiliation(s)
- Sara Federici
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Samuel P Nobs
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel. .,Cancer-Microbiome Division Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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27
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Fecal transplants as a microbiome-based therapeutic. Curr Opin Microbiol 2020; 56:16-23. [PMID: 32615390 DOI: 10.1016/j.mib.2020.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 02/06/2023]
Abstract
Impaired microbiome diversity and composition can develop into a potent etiological agent of disease and increase susceptibility to infection. Given this, interventions targeting the microbiome have developed rapidly, with healthy donor feces being a de facto source of beneficial communities employed to rebalance patients' microbiomes. Recent evidence has demonstrated that bacterial and viral richness, short chain fatty acid production, bile acid conversion as well as presence of bacterial and fungal pathobionts are associated with therapy efficacy; however, little is known of the influence of host factors such as genetics, medications, and diet. Here, current knowledge on factors associated with fecal transplant efficacy, as well as efforts to transition to other forms of therapy are reviewed.
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28
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Rasmussen TS, Koefoed AK, Jakobsen RR, Deng L, Castro-Mejía JL, Brunse A, Neve H, Vogensen FK, Nielsen DS. Bacteriophage-mediated manipulation of the gut microbiome – promises and presents limitations. FEMS Microbiol Rev 2020; 44:507-521. [DOI: 10.1093/femsre/fuaa020] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/02/2020] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT
Gut microbiome (GM) composition and function are linked to human health and disease, and routes for manipulating the GM have become an area of intense research. Due to its high treatment efficacy, the use of fecal microbiota transplantation (FMT) is generally accepted as a promising experimental treatment for patients suffering from GM imbalances (dysbiosis), e.g. caused by recurrent Clostridioides difficile infections (rCDI). Mounting evidence suggests that bacteriophages (phages) play a key role in successful FMT treatment by restoring the dysbiotic bacterial GM. As a refinement to FMT, removing the bacterial component of donor feces by sterile filtration, also referred to as fecal virome transplantation (FVT), decreases the risk of invasive infections caused by bacteria. However, eukaryotic viruses and prophage-encoded virulence factors remain a safety issue. Recent in vivo studies show how cascading effects are initiated when phage communities are transferred to the gut by e.g. FVT, which leads to changes in the GM composition, host metabolome, and improve host health such as alleviating symptoms of obesity and type-2-diabetes (T2D). In this review, we discuss the promises and limitations of FVT along with the perspectives of using FVT to treat various diseases associated with GM dysbiosis.
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Anna Kirstine Koefoed
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Rasmus Riemer Jakobsen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Ling Deng
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Josué L Castro-Mejía
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Anders Brunse
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9, 2nd floor - 1870, Frederiksberg, Denmark
| | - Horst Neve
- Institute of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1 - 24103, Kiel, Germany
| | - Finn Kvist Vogensen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Dennis Sandris Nielsen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
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Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths. Microorganisms 2020; 8:microorganisms8040483. [PMID: 32231141 PMCID: PMC7232386 DOI: 10.3390/microorganisms8040483] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/20/2022] Open
Abstract
Gut microbiota refers to a complex network of microbes, which exerts a marked influence on the host’s health. It is composed of bacteria, fungi, viruses, and helminths. Bacteria, or collectively, the bacteriome, comprises a significant proportion of the well-characterized microbiome. However, the other communities referred to as ‘dark matter’ of microbiomes such as viruses (virome), fungi (mycobiome), archaea (archaeome), and helminths have not been completely elucidated. Development of new and improved metagenomics methods has allowed the identification of complete genomes from the genetic material in the human gut, opening new perspectives on the understanding of the gut microbiome composition, their importance, and potential clinical applications. Here, we review the recent evidence on the viruses, fungi, archaea, and helminths found in the mammalian gut, detailing their interactions with the resident bacterial microbiota and the host, to explore the potential impact of the microbiome on host’s health. The role of fecal virome transplantations, pre-, pro-, and syn-biotic interventions in modulating the microbiome and their related concerns are also discussed.
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