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Govender P, Ghai M. Population-specific differences in the human microbiome: Factors defining the diversity. Gene 2024; 933:148923. [PMID: 39244168 DOI: 10.1016/j.gene.2024.148923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/15/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Differences in microbial communities at different body habitats define the microbiome composition of the human body. The gut, oral, skin vaginal fluid and tissue microbiome, are pivotal for human development and immune response and cross talk between these microbiomes is evident. Population studies reveal that various factors, such as host genetics, diet, lifestyle, aging, and geographical location are strongly associated with population-specific microbiome differences. The present review discusses the factors that shape microbiome diversity in humans, and microbiome differences in African, Asian and Caucasian populations. Gut microbiome studies show that microbial species Bacteroides is commonly found in individuals living in Western countries (Caucasian populations), while Prevotella is prevalent in non-Western countries (African and Asian populations). This association is mainly due to the high carbohydrate, high fat diet in western countries in contrast to high fibre, low fat diets in African/ Asian regions. Majority of the microbiome studies focus on the bacteriome component; however, interesting findings reveal that increased bacteriophage richness, which makes up the virome component, correlates with decreased bacterial diversity, and causes microbiome dysbiosis. An increase of Caudovirales (bacteriophages) is associated with a decrease in enteric bacteria in inflammatory bowel diseases. Future microbiome studies should evaluate the interrelation between bacteriome and virome to fully understand their significance in the pathogenesis and progression of human diseases. With ethnic health disparities becoming increasingly apparent, studies need to emphasize on the association of population-specific microbiome differences and human diseases, to develop microbiome-based therapeutics. Additionally, targeted phage therapy is emerging as an attractive alternative to antibiotics for bacterial infections. With rapid rise in microbiome research, focus should be on standardizing protocols, advanced bioinformatics tools, and reducing sequencing platform related biases. Ultimately, integration of multi-omics data (genomics, transcriptomics, proteomics and metabolomics) will lead to precision models for personalized microbiome therapeutics advancement.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
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2
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Zakerska-Banaszak O, Zuraszek-Szymanska J, Eder P, Ladziak K, Slomski R, Skrzypczak-Zielinska M. The Role of Host Genetics and Intestinal Microbiota and Metabolome as a New Insight into IBD Pathogenesis. Int J Mol Sci 2024; 25:9589. [PMID: 39273536 DOI: 10.3390/ijms25179589] [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: 07/12/2024] [Revised: 08/30/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
Inflammatory bowel disease (IBD) is an incurable, chronic disorder of the gastrointestinal tract whose incidence increases every year. Scientific research constantly delivers new information about the disease and its multivariate, complex etiology. Nevertheless, full discovery and understanding of the complete mechanism of IBD pathogenesis still pose a significant challenge to today's science. Recent studies have unanimously confirmed the association of gut microbial dysbiosis with IBD and its contribution to the regulation of the inflammatory process. It transpires that the altered composition of pathogenic and commensal bacteria is not only characteristic of disturbed intestinal homeostasis in IBD, but also of viruses, parasites, and fungi, which are active in the intestine. The crucial function of the microbial metabolome in the human body is altered, which causes a wide range of effects on the host, thus providing a basis for the disease. On the other hand, human genomic and functional research has revealed more loci that play an essential role in gut homeostasis regulation, the immune response, and intestinal epithelial function. This review aims to organize and summarize the currently available knowledge concerning the role and interaction of crucial factors associated with IBD pathogenesis, notably, host genetic composition, intestinal microbiota and metabolome, and immune regulation.
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Affiliation(s)
| | | | - Piotr Eder
- Department of Gastroenterology, Dietetics and Internal Medicine, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Karolina Ladziak
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Ryszard Slomski
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
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3
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Tian X, Li S, Wang C, Zhang Y, Feng X, Yan Q, Guo R, Wu F, Wu C, Wang Y, Huo X, Ma X. Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease. MICROBIOME 2024; 12:130. [PMID: 39026313 PMCID: PMC11256409 DOI: 10.1186/s40168-024-01832-x] [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: 10/31/2023] [Accepted: 05/08/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.
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Affiliation(s)
- Xiangge Tian
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Chao Wang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Yanyan Zhang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Chunxue Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Yan Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
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4
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Sabbaghian M, Gheitasi H, Shekarchi AA, Tavakoli A, Poortahmasebi V. The mysterious anelloviruses: investigating its role in human diseases. BMC Microbiol 2024; 24:40. [PMID: 38281930 PMCID: PMC10823751 DOI: 10.1186/s12866-024-03187-7] [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: 11/14/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024] Open
Abstract
Anelloviruses (AVs) that infect the human population are members of the Anelloviridae family. They are widely distributed in human populations worldwide. Torque teno virus (TTV) was the first virus of this family to be identified and is estimated to be found in the serum of 80-90% of the human population. Sometime after the identification of TTV, Torque teno mini virus (TTMV) and Torque teno midi virus (TTMDV) were also identified and classified in this family. Since identifying these viruses, have been detected in various types of biological fluids of the human body, including blood and urine, as well as vital organs such as the liver and kidney. They can be transmitted from person to person through blood transfusions, fecal-oral contact, and possibly sexual intercourse. Recent studies on these newly introduced viruses show that although they are not directly related to human disease, they may be indirectly involved in initiating or exacerbating some human population-related diseases and viral infections. Among these diseases, we can mention various types of cancers, immune system diseases, viral infections, hepatitis, and AIDS. Also, they likely use the microRNAs (miRNAs) they encode to fulfill this cooperative role. Also, in recent years, the role of proliferation and their viral load, especially TTV, has been highlighted to indicate the immune system status of immunocompromised people or people who undergo organ transplants. Here, we review the possible role of these viruses in diseases that target humans and highlight them as important viruses that require further study. This review can provide new insights to researchers.
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Affiliation(s)
- Mohammad Sabbaghian
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamidreza Gheitasi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Akbar Shekarchi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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Ligeti B, Szepesi-Nagy I, Bodnár B, Ligeti-Nagy N, Juhász J. ProkBERT family: genomic language models for microbiome applications. Front Microbiol 2024; 14:1331233. [PMID: 38282738 PMCID: PMC10810988 DOI: 10.3389/fmicb.2023.1331233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/11/2023] [Indexed: 01/30/2024] Open
Abstract
Background In the evolving landscape of microbiology and microbiome analysis, the integration of machine learning is crucial for understanding complex microbial interactions, and predicting and recognizing novel functionalities within extensive datasets. However, the effectiveness of these methods in microbiology faces challenges due to the complex and heterogeneous nature of microbial data, further complicated by low signal-to-noise ratios, context-dependency, and a significant shortage of appropriately labeled datasets. This study introduces the ProkBERT model family, a collection of large language models, designed for genomic tasks. It provides a generalizable sequence representation for nucleotide sequences, learned from unlabeled genome data. This approach helps overcome the above-mentioned limitations in the field, thereby improving our understanding of microbial ecosystems and their impact on health and disease. Methods ProkBERT models are based on transfer learning and self-supervised methodologies, enabling them to use the abundant yet complex microbial data effectively. The introduction of the novel Local Context-Aware (LCA) tokenization technique marks a significant advancement, allowing ProkBERT to overcome the contextual limitations of traditional transformer models. This methodology not only retains rich local context but also demonstrates remarkable adaptability across various bioinformatics tasks. Results In practical applications such as promoter prediction and phage identification, the ProkBERT models show superior performance. For promoter prediction tasks, the top-performing model achieved a Matthews Correlation Coefficient (MCC) of 0.74 for E. coli and 0.62 in mixed-species contexts. In phage identification, ProkBERT models consistently outperformed established tools like VirSorter2 and DeepVirFinder, achieving an MCC of 0.85. These results underscore the models' exceptional accuracy and generalizability in both supervised and unsupervised tasks. Conclusions The ProkBERT model family is a compact yet powerful tool in the field of microbiology and bioinformatics. Its capacity for rapid, accurate analyses and its adaptability across a spectrum of tasks marks a significant advancement in machine learning applications in microbiology. The models are available on GitHub (https://github.com/nbrg-ppcu/prokbert) and HuggingFace (https://huggingface.co/nerualbioinfo) providing an accessible tool for the community.
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Affiliation(s)
- Balázs Ligeti
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - István Szepesi-Nagy
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Babett Bodnár
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Noémi Ligeti-Nagy
- Language Technology Research Group, HUN-REN Hungarian Research Centre for Linguistics, Budapest, Hungary
| | - János Juhász
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
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6
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Pandey H, Jain D, Tang DWT, Wong SH, Lal D. Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease. Intest Res 2024; 22:15-43. [PMID: 37935653 PMCID: PMC10850697 DOI: 10.5217/ir.2023.00080] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 11/09/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a multifactorial disease, which is thought to be an interplay between genetic, environment, microbiota, and immune-mediated factors. Dysbiosis in the gut microbial composition, caused by antibiotics and diet, is closely related to the initiation and progression of IBD. Differences in gut microbiota composition between IBD patients and healthy individuals have been found, with reduced biodiversity of commensal microbes and colonization of opportunistic microbes in IBD patients. Gut microbiota can, therefore, potentially be used for diagnosing and prognosticating IBD, and predicting its treatment response. Currently, there are no curative therapies for IBD. Microbiota-based interventions, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, have been recognized as promising therapeutic strategies. Clinical studies and studies done in animal models have provided sufficient evidence that microbiota-based interventions may improve inflammation, the remission rate, and microscopic aspects of IBD. Further studies are required to better understand the mechanisms of action of such interventions. This will help in enhancing their effectiveness and developing personalized therapies. The present review summarizes the relationship between gut microbiota and IBD immunopathogenesis. It also discusses the use of gut microbiota as a noninvasive biomarker and potential therapeutic option.
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Affiliation(s)
| | | | - Daryl W. T. Tang
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Sunny H. Wong
- Centre for Microbiome Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Devi Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
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7
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Jansen D, Falony G, Vieira-Silva S, Simsek C, Marcelis T, Caenepeel C, Machiels K, Raes J, Vermeire S, Matthijnssens J. Community Types of the Human Gut Virome are Associated with Endoscopic Outcome in Ulcerative Colitis. J Crohns Colitis 2023; 17:1504-1513. [PMID: 37052201 PMCID: PMC10588789 DOI: 10.1093/ecco-jcc/jjad061] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 04/14/2023]
Abstract
BACKGROUND Inflammatory bowel disease [IBD] is a major debilitating disease. Recently, the gut microbiota has gained attention as an important factor involved in the pathophysiology of IBD. As a complement to the established bacterial 'enterotypes' associated with IBD, we focused here on viruses. We investigated the intestinal virome of IBD patients undergoing biological therapy for the presence of virome configurations associated with IBD, and to uncover how those configurations are associated with therapeutic success. METHODS Viral-like particle enrichment followed by deep sequencing was performed on 432 faecal samples from 181 IBD patients starting biological therapy. Redundancy analysis and Dirichlet Multinomial Mixtures were applied to determine covariates of the virome composition and to condense the gut virota into 'viral community types', respectively. RESULTS Patients were stratified based on unsupervised clustering into two viral community types. Community type CA showed a low α-diversity and a high relative abundance of Caudoviricetes [non-CrAss] phages and was associated with the dysbiotic Bact2-enterotype. Community type CrM showed a high α-diversity and a high relative abundance of Crassvirales and Malgrandaviricetes phages. During post-interventional analysis, endoscopic outcome was associated with gut virome composition. Remitting UC patients had a high percentage of community type CrM, a high Shannon diversity and a low lysogenic potential. Pre-interventional analyses also identified five novel phages associated with treatment success. CONCLUSIONS This study proposed two gut virome configurations that may be involved in the pathophysiology of IBD. Interestingly, those viral configurations are further associated with therapeutic success, suggesting a potential clinical relevance.
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Affiliation(s)
- Daan Jansen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Gwen Falony
- KU Leuven, Department of Microbiology Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, Leuven, Belgium
- Center for Microbiology, VIB, B-3000 Leuven, Belgium
| | - Sara Vieira-Silva
- KU Leuven, Department of Microbiology Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Ceren Simsek
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Tine Marcelis
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Clara Caenepeel
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Kathleen Machiels
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, Leuven, Belgium
- Center for Microbiology, VIB, B-3000 Leuven, Belgium
| | - Séverine Vermeire
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
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Massimino L, Palmieri O, Facoetti A, Fuggetta D, Spanò S, Lamparelli LA, D'Alessio S, Cagliani S, Furfaro F, D'Amico F, Zilli A, Fiorino G, Parigi TL, Noviello D, Latiano A, Bossa F, Latiano T, Pirola A, Mologni L, Piazza RG, Abbati D, Perri F, Bonini C, Peyrin-Biroulet L, Malesci A, Jairath V, Danese S, Ungaro F. Gut virome-colonising Orthohepadnavirus genus is associated with ulcerative colitis pathogenesis and induces intestinal inflammation in vivo. Gut 2023; 72:1838-1847. [PMID: 36788014 PMCID: PMC10511988 DOI: 10.1136/gutjnl-2022-328375] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/06/2023] [Indexed: 02/16/2023]
Abstract
OBJECTIVES Ulcerative colitis (UC) is a chronic inflammatory disorder of unknown aetiology. Gut virome dysbiosis is fundamental in UC progression, although its role in the early phases of the disease is far from fully understood. Therefore, we sought to investigate the role of a virome-associated protein encoded by the Orthohepadnavirus genus, the hepatitis B virus X protein (HBx), in UC aetiopathogenesis. DESIGN HBx positivity of UC patient-derived blood and gut mucosa was assessed by RT-PCR and Sanger sequencing and correlated with clinical characteristics by multivariate analysis. Transcriptomics was performed on HBx-overexpressing endoscopic biopsies from healthy donors.C57BL/6 mice underwent intramucosal injections of liposome-conjugated HBx-encoding plasmids or the control, with or without antibiotic treatment. Multidimensional flow cytometry analysis was performed on colonic samples from HBx-treated and control animals. Transepithelial electrical resistance measurement, proliferation assay, chromatin immunoprecipitation assay with sequencing and RNA-sequencing were performed on in vitro models of the gut barrier. HBx-silencing experiments were performed in vitro and in vivo. RESULTS HBx was detected in about 45% of patients with UC and found to induce colonic inflammation in mice, while its silencing reverted the colitis phenotype in vivo. HBx acted as a transcriptional regulator in epithelial cells, provoking barrier leakage and altering both innate and adaptive mucosal immunity ex vivo and in vivo. CONCLUSION This study described HBx as a contributor to the UC pathogenesis and provides a new perspective on the virome as a target for tailored treatments.
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Affiliation(s)
- Luca Massimino
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Orazio Palmieri
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Foggia, Italy
| | - Amanda Facoetti
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milano, Italy
- Faculty of Medicine, Università Vita Salute San Raffaele, Milano, Italy
| | - Davide Fuggetta
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milano, Italy
- Faculty of Medicine, Università Vita Salute San Raffaele, Milano, Italy
| | - Salvatore Spanò
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Luigi Antonio Lamparelli
- IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | | | - Stefania Cagliani
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milano, Italy
- Faculty of Medicine, Università Vita Salute San Raffaele, Milano, Italy
| | - Federica Furfaro
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Ferdinando D'Amico
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Alessandra Zilli
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Gionata Fiorino
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
- Faculty of Medicine, Università Vita Salute San Raffaele, Milano, Italy
| | - Tommaso Lorenzo Parigi
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
- Faculty of Medicine, Università Vita Salute San Raffaele, Milano, Italy
| | - Daniele Noviello
- Department of Pathophysiology and Transplantation, University of Milan, Milano, Italy
| | - Anna Latiano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Foggia, Italy
| | - Fabrizio Bossa
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Foggia, Italy
| | - Tiziana Latiano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Foggia, Italy
| | | | - Luca Mologni
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
| | - Rocco Giovanni Piazza
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza, Italy
- Hematology and Clinical Research Unit, San Gerardo Hospital, Monza, Italy
| | - Danilo Abbati
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Francesco Perri
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Foggia, Italy
| | - Chiara Bonini
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milano, Italy
- Faculty of Medicine, Università Vita Salute San Raffaele, Milano, Italy
| | - Laurent Peyrin-Biroulet
- Inserm NGERE, University of Lorraine, Nancy, France
- Department of Hepato-Gastroenterology, University Hospital Centre Nancy, Nancy, France
| | - Alberto Malesci
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
- Faculty of Medicine, Università Vita Salute San Raffaele, Milano, Italy
| | - Vipul Jairath
- Department of Medicine, Division of Gastroenterology, Western University, London, Ontario, Canada
| | - Silvio Danese
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milano, Italy
- Faculty of Medicine, Università Vita Salute San Raffaele, Milano, Italy
| | - Federica Ungaro
- Department of Gastroenterology and Digestive Endoscopy, IRCCS Ospedale San Raffaele, Milano, Italy
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milano, Italy
- Faculty of Medicine, Università Vita Salute San Raffaele, Milano, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
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Zhang Y, Sharma S, Tom L, Liao YT, Wu VCH. Gut Phageome-An Insight into the Role and Impact of Gut Microbiome and Their Correlation with Mammal Health and Diseases. Microorganisms 2023; 11:2454. [PMID: 37894111 PMCID: PMC10609124 DOI: 10.3390/microorganisms11102454] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
The gut microbiota, including bacteria, archaea, fungi, and viruses, compose a diverse mammalian gut environment and are highly associated with host health. Bacteriophages, the viruses that infect bacteria, are the primary members of the gastrointestinal virome, known as the phageome. However, our knowledge regarding the gut phageome remains poorly understood. In this review, the critical role of the gut phageome and its correlation with mammalian health were summarized. First, an overall profile of phages across the gastrointestinal tract and their dynamic roles in shaping the surrounding microorganisms was elucidated. Further, the impacts of the gut phageome on gastrointestinal fitness and the bacterial community were highlighted, together with the influence of diets on the gut phageome composition. Additionally, new reports on the role of the gut phageome in the association of mammalian health and diseases were reviewed. Finally, a comprehensive update regarding the advanced phage benchwork and contributions of phage-based therapy to prevent/treat mammalian diseases was provided. This study provides insights into the role and impact of the gut phagenome in gut environments closely related to mammal health and diseases. The findings provoke the potential applications of phage-based diagnosis and therapy in clinical and agricultural fields. Future research is needed to uncover the underlying mechanism of phage-bacterial interactions in gut environments and explore the maintenance of mammalian health via phage-regulated gut microbiota.
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Affiliation(s)
| | | | | | | | - Vivian C. H. Wu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA 94710, USA
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10
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Abstract
The gut microbiome is a dense and metabolically active consortium of microorganisms and viruses located in the lower gastrointestinal tract of the human body. Bacteria and their viruses (phages) are the most abundant members of the gut microbiome. Investigating their biology and the interplay between the two is important if we are to understand their roles in human health and disease. In this review, we summarize recent advances in resolving the taxonomic structure and ecological functions of the complex community of phages in the human gut-the gut phageome. We discuss how age, diet, and geography can all have a significant impact on phageome composition. We note that alterations to the gut phageome have been observed in several diseases such as inflammatory bowel disease, irritable bowel syndrome, and colorectal cancer, and we evaluate whether these phageome changes can directly or indirectly contribute to disease etiology and pathogenesis. We also highlight how lack of standardization in studying the gut phageome has contributed to variation in reported results.
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Affiliation(s)
- Ciara A Tobin
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
| | - Andrey N Shkoporov
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
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11
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Pargin E, Roach MJ, Skye A, Papudeshi B, Inglis LK, Mallawaarachchi V, Grigson SR, Harker C, Edwards RA, Giles SK. The human gut virome: composition, colonization, interactions, and impacts on human health. Front Microbiol 2023; 14:963173. [PMID: 37293229 PMCID: PMC10244655 DOI: 10.3389/fmicb.2023.963173] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease states, but it is unknown to what extent the gut virome impacts everyday human health. New experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome colonization begins at birth and is considered unique and stable in adulthood. The stable virome is highly specific to each individual and is modulated by varying factors such as age, diet, disease state, and use of antibiotics. The gut virome primarily comprises bacteriophages, predominantly order Crassvirales, also referred to as crAss-like phages, in industrialized populations and other Caudoviricetes (formerly Caudovirales). The stability of the virome's regular constituents is disrupted by disease. Transferring the fecal microbiome, including its viruses, from a healthy individual can restore the functionality of the gut. It can alleviate symptoms of chronic illnesses such as colitis caused by Clostridiodes difficile. Investigation of the virome is a relatively novel field, with new genetic sequences being published at an increasing rate. A large percentage of unknown sequences, termed 'viral dark matter', is one of the significant challenges facing virologists and bioinformaticians. To address this challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, and utilizing cutting-edge bioinformatic tools to quantify and classify viral species. Here, we review the literature surrounding the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the viral dark matter veiling our understanding of the gut virome.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sarah K. Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
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12
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Chen X, Mendes BG, Alves BS, Duan Y. Phage therapy in gut microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:93-118. [PMID: 37770177 DOI: 10.1016/bs.pmbts.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Phage therapy, the use of bacteriophage viruses for bacterial infection treatment, has been around for almost a century, but with the increase in antibiotic use, its importance has declined rapidly. There has been renewed interest in revisiting this practice due to the general decline in the effectiveness of antibiotics, combined with improved understanding of human microbiota and advances in sequencing technologies. Phage therapy has been proposed as a clinical alternative to restore the gut microbiota in the absence of an effective treatment. That is due to its immunomodulatory and bactericidal effects against its target bacteria. In the gastrointestinal diseases field, phage therapy has been studied mainly as a promising tool in infectious diseases treatment, such as cholera and diarrhea. However, many studies have been conducted in non-communicable diseases, such as the targeting of adherent invasive Escherichia coli in Crohn's disease, the treatment of Clostridioides difficile in ulcerative colitis, the eradication of Fusobacterium nucleatum in colorectal cancer, the targeting of alcohol-producing Klebsiella pneumoniae in non-alcoholic fatty liver disease, or Enterococcus faecalis in alcohol-associated hepatitis. This review will summarize the changes in the gut microbiota and the phageome in association with some gastrointestinal and liver diseases and highlight the recent scientific advances in phage therapy as a therapeutic tool for their treatment.
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Affiliation(s)
- Xingyao Chen
- Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Beatriz G Mendes
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Campus Universitário Trindade, Florianópolis, Santa Catarina, Brazil
| | - Bruno Secchi Alves
- Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Campus Universitário Trindade, Florianópolis, Santa Catarina, Brazil
| | - Yi Duan
- Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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13
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Dehghani T, Gholizadeh O, Daneshvar M, Nemati MM, Akbarzadeh S, Amini P, Afkhami H, Kohansal M, Javanmard Z, Poortahmasebi V. Association Between Inflammatory Bowel Disease and Viral Infections. Curr Microbiol 2023; 80:195. [PMID: 37106245 PMCID: PMC10139670 DOI: 10.1007/s00284-023-03305-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/17/2023] [Indexed: 04/29/2023]
Abstract
Chronic inflammatory gastrointestinal diseases such as Crohn's disease (CD) and ulcerative colitis (UC) are known as inflammatory bowel disorders (IBD). Patients with inflammatory bowel illnesses are more susceptible to viral infections. In people with IBD, viral infections have emerged as a significant issue. Viral infections are often difficult to identify and have a high morbidity and fatality rate. We reviewed studies on viral infections and IBD, concentrating on Cytomegalovirus (CMV), SARS-CoV-2, Epstein-Barr virus (EBV), enteric viruses, and hepatitis B virus (HBV). Also, the effect of IBD on these viral infections is discussed. These data suggest that patients with IBD are more likely to get viral infections. As a result, practitioners should be aware of the increased risk of viral infections in inflammatory bowel disease patients.
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Affiliation(s)
- Tannaz Dehghani
- Internal Medicine, Lorestan University of Medical Sciences, Lorestan, Iran
| | - Omid Gholizadeh
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mohammad Mahdi Nemati
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Sama Akbarzadeh
- Department of Animal Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Parya Amini
- Faculty of Medicine, Yasouj University of Medical Sciences, Yasouj, Iran
| | - Hamed Afkhami
- Department of Medical Microbiology, Faculty of Medicine, Shahed University of Medical Science, Tehran, Iran
| | - Maryam Kohansal
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Zahra Javanmard
- Department of Medical Microbiology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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14
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Tamayo-Trujillo R, Guevara-Ramírez P, Cadena-Ullauri S, Paz-Cruz E, Ruiz-Pozo VA, Zambrano AK. Human virome: Implications in cancer. Heliyon 2023; 9:e14086. [PMID: 36873548 PMCID: PMC9957661 DOI: 10.1016/j.heliyon.2023.e14086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023] Open
Abstract
In recent years, the human virome has gained importance, especially after the SARS-CoV-2 pandemic, due to its possible involvement in autoimmune, inflammatory diseases, and cancer. Characterization of the human virome can be carried out by shotgun next-generation sequencing (metagenomics), which allows the identification of all viral communities in an environmental sample and the discovery of new viral families not previously described. Variations in viral quantity and diversity have been associated with disease development, mainly due to their effect on gut bacterial microbiota. Phages can regulate bacterial flora through lysogeny; this is associated with increased susceptibility to infections, chronic inflammation, or cancer. The virome characterization in different human body ecological niches could help elucidate these particles' role in disease. Hence, it is important to understand the virome's influence on human health and disease. The present review highlights the significance of the human virome and how it is associated with disease, focusing on virome composition, characterization, and its association with cancer.
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15
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Stockdale SR, Shkoporov AN, Khokhlova EV, Daly KM, McDonnell SA, O' Regan O, Nolan JA, Sutton TDS, Clooney AG, Ryan FJ, Sheehan D, Lavelle A, Draper LA, Shanahan F, Ross RP, Hill C. Interpersonal variability of the human gut virome confounds disease signal detection in IBD. Commun Biol 2023; 6:221. [PMID: 36841913 PMCID: PMC9968284 DOI: 10.1038/s42003-023-04592-w] [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: 05/04/2022] [Accepted: 02/14/2023] [Indexed: 02/27/2023] Open
Abstract
Viruses are increasingly recognised as important components of the human microbiome, fulfilling numerous ecological roles including bacterial predation, immune stimulation, genetic diversification, horizontal gene transfer, microbial interactions, and augmentation of metabolic functions. However, our current view of the human gut virome is tainted by previous sequencing requirements that necessitated the amplification of starting nucleic acids. In this study, we performed an original longitudinal analysis of 40 healthy control, 19 Crohn's disease, and 20 ulcerative colitis viromes over three time points without an amplification bias, which revealed and highlighted the interpersonal individuality of the human gut virome. In contrast to a 16 S rRNA gene analysis of matched samples, we show that α- and β-diversity metrics of unamplified viromes are not as efficient at discerning controls from patients with inflammatory bowel disease. Additionally, we explored the intrinsic properties of unamplified gut viromes and show there is considerable interpersonal variability in viral taxa, infrequent longitudinal persistence of intrapersonal viruses, and vast fluctuations in the abundance of temporal viruses. Together, these properties of unamplified faecal viromes confound the ability to discern disease associations but significantly advance toward an unbiased and accurate representation of the human gut virome.
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Affiliation(s)
| | | | | | - Karen M Daly
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | | | - Orla O' Regan
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - James A Nolan
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | | | - Adam G Clooney
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - Feargal J Ryan
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - Donal Sheehan
- Department of Medicine, University College Cork, Co, Cork, Ireland
| | - Aonghus Lavelle
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
- Department of Medicine, University College Cork, Co, Cork, Ireland
| | | | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
- Department of Medicine, University College Cork, Co, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Co, Cork, Ireland.
- School of Microbiology, University College Cork, Co, Cork, Ireland.
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16
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Gut Microbiome and Neurodevelopmental Disorders: A Link Yet to Be Disclosed. Microorganisms 2023; 11:microorganisms11020487. [PMID: 36838452 PMCID: PMC9964594 DOI: 10.3390/microorganisms11020487] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Τhe importance of the gut microbiome and its functions has only recently been recognized and researched in greater depth. The establishment of the human gut microbiome begins in utero, forming its adult-like phenotype in the first 2-3 years of life. Several factors affect and alter the gut microbiome composition and its metabolic functions, such as early onset of breastfeeding, mode of delivery, antibiotic administration, or exposure to chemical substances, among others. Existing data support the important connection between health status and gut microbiome homeostasis. In cases when this balance is disturbed, several disorders may arise, such as inflammatory reactions that lead to atopy, eczema, or allergic asthma. The so-called gut-brain axis refers to the complex biochemical pathways between the central nervous system and the gastrointestinal system. One of the most fascinating areas of ongoing research is the broad spectrum of neurodevelopmental disorders (NDDs) and how gut health may be associated with such disorders. The prevalence of NDDs, such as autism spectrum disorder or attention deficit hyperactivity disorder, has increased over recent years. Whether gut microbiota homeostasis plays a role in these disorders is not yet fully understood. The aim of this narrative review is to provide an account of current knowledge on how gut health is linked with these disorders. We performed a literature review in order to identify and synthesize available data that highlights the potential association between NDDs and a balanced gut microbiome in terms of composition and proper function. The connection between the gut microbiome and NDDs offers promising new opportunities for future research.
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17
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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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18
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Khadka S, Omura S, Sato F, Tsunoda I. Adjuvant Injections Altered the Ileal and Fecal Microbiota Differently with Changes in Immunoglobulin Isotypes and Antimycobacterial Antibody Responses. Int J Mol Sci 2023; 24:ijms24032818. [PMID: 36769136 PMCID: PMC9917480 DOI: 10.3390/ijms24032818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Alterations in the gut microbiota, "dysbiosis," have been reported in autoimmune diseases, including multiple sclerosis (MS), and their animal models. Although the animal models were induced by injections of autoantigens with adjuvants, including complete Freund's adjuvant (CFA) and pertussis toxin (PT), the effects of adjuvant injections on the microbiota are largely unknown. We aimed to clarify whether adjuvant injections could affect the microbiota in the ileum and feces. Using 16S rRNA sequencing, we found decreased alpha diversities of the gut microbiota in mice injected with CFA and PT, compared with naïve mice. Overall, microbial profiles visualized by principal component analysis demonstrated dysbiosis in feces, but not in the ileum, of adjuvant-injected mice, where the genera Lachnospiraceae NK4A136 group and Alistipes contributed to dysbiosis. When we compared the relative abundances of individual bacteria, we found changes in 16 bacterial genera in feces and seven genera in the ileum of adjuvant-injected mice, in which increased serum levels of antibody against mycobacteria (a component of CFA) and total IgG2c were correlated with the genus Facklamia. On the other hand, increased IgG1 and IgA concentrations were correlated with the genus Atopostipes. Therefore, adjuvant injections alone could alter the overall microbial profiles (i.e., microbiota) and individual bacterial abundances with altered antibody responses; dysbiosis in animal models could be partly due to adjuvant injections.
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19
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Schackart KE, Graham JB, Ponsero AJ, Hurwitz BL. Evaluation of computational phage detection tools for metagenomic datasets. Front Microbiol 2023; 14:1078760. [PMID: 36760501 PMCID: PMC9902911 DOI: 10.3389/fmicb.2023.1078760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023] Open
Abstract
Introduction As new computational tools for detecting phage in metagenomes are being rapidly developed, a critical need has emerged to develop systematic benchmarks. Methods In this study, we surveyed 19 metagenomic phage detection tools, 9 of which could be installed and run at scale. Those 9 tools were assessed on several benchmark challenges. Fragmented reference genomes are used to assess the effects of fragment length, low viral content, phage taxonomy, robustness to eukaryotic contamination, and computational resource usage. Simulated metagenomes are used to assess the effects of sequencing and assembly quality on the tool performances. Finally, real human gut metagenomes and viromes are used to assess the differences and similarities in the phage communities predicted by the tools. Results We find that the various tools yield strikingly different results. Generally, tools that use a homology approach (VirSorter, MARVEL, viralVerify, VIBRANT, and VirSorter2) demonstrate low false positive rates and robustness to eukaryotic contamination. Conversely, tools that use a sequence composition approach (VirFinder, DeepVirFinder, Seeker), and MetaPhinder, have higher sensitivity, including to phages with less representation in reference databases. These differences led to widely differing predicted phage communities in human gut metagenomes, with nearly 80% of contigs being marked as phage by at least one tool and a maximum overlap of 38.8% between any two tools. While the results were more consistent among the tools on viromes, the differences in results were still significant, with a maximum overlap of 60.65%. Discussion: Importantly, the benchmark datasets developed in this study are publicly available and reusable to enable the future comparability of new tools developed.
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Affiliation(s)
- Kenneth E. Schackart
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
| | - Jessica B. Graham
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
| | - Alise J. Ponsero
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Bonnie L. Hurwitz
- Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, United States
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
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20
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Characterization of the Urinary Metagenome and Virome in Healthy Children. Biomedicines 2022; 10:biomedicines10102412. [PMID: 36289674 PMCID: PMC9599034 DOI: 10.3390/biomedicines10102412] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
Recent advances in next-generation sequencing and metagenomic studies have provided insights into the microbial profile of different body sites. However, research on the microbial composition of urine is limited, particularly in children. The goal of this study was to optimize and develop reproducible metagenome and virome protocols using a small volume of urine samples collected from healthy children. We collected midstream urine specimens from 40 healthy children. Using the metagenomics shotgun approach, we tested various protocols. Different microbial roots such as Archaea, Bacteria, Eukaryota, and Viruses were successfully identified using our optimized urine protocol. Our data reflected much variation in the microbial fingerprints of children. Girls had significantly higher levels of Firmicutes, whereas boys had significantly higher levels of Actinobacteria. The genus Anaerococcus dominated the urinary bacteriome of healthy girls, with a significant increase in Anaerococcus prevotii, Anaerococcus vaginalis, and Veillonella parvula (p-value < 0.001) when compared with that of boys. An increased relative abundance of Xylanimonas and Arthrobacter, with a significantly high abundance of Arthrobacter sp. FB24 (p-value 0.0028) and Arthrobacter aurescences (p-value 0.015), was observed in boys. The urinary mycobiome showed a significant rise in the genus Malassezia and Malassezia globose fungus (p-value 0.009) in girls, whereas genus Saccharomyces (p-value 0.009) was significantly high in boys. The beta diversity of the urinary mycobiome was found to differ between different age groups. Boys had significantly more Mastadenovirus and Human mastadenovirus-A in their urinary virome than girls. With increasing age, we noticed an increase in the relative abundance of the order Caudovirales. Our optimized protocols allowed us to identify the unique microbes for each sex by using an adequate volume of urine (3−10 mL) to screen for the bacteriome, mycobiome, and virome profiles in the urine of healthy children. To the best of our knowledge, this is the first study to characterize the metagenomics profiles of urine in a healthy pediatric population.
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21
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Clinton NA, Hameed SA, Agyei EK, Jacob JC, Oyebanji VO, Jabea CE. Crosstalk between the Intestinal Virome and Other Components of the Microbiota, and Its Effect on Intestinal Mucosal Response and Diseases. J Immunol Res 2022; 2022:7883945. [PMID: 36203793 PMCID: PMC9532165 DOI: 10.1155/2022/7883945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
In recent years, there has been ample evidence illustrating the effect of microbiota on gut immunity, homeostasis, and disease. Most of these studies have engaged more efforts in understanding the role of the bacteriome in gut mucosal immunity and disease. However, studies on the virome and its influence on gut mucosal immunity and pathology are still at infancy owing to limited metagenomic tools. Nonetheless, the existing studies on the virome have largely been focused on the bacteriophages as these represent the main component of the virome with little information on endogenous retroviruses (ERVs) and eukaryotic viruses. In this review, we describe the gut virome, and its role in gut mucosal response and disease progression. We also explore the crosstalk between the virome and other microorganisms in the gut mucosa and elaborate on how these interactions shape the gut mucosal immunity going from bacteriophages through ERVs to eukaryotic viruses. Finally, we elucidate the potential contribution of this crosstalk in the pathogenesis of inflammatory bowel diseases and colon cancer.
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Affiliation(s)
- Njinju Asaba Clinton
- Health and Empowerment Foundation, Cameroon
- Mbonge District Hospital, Cameroon
- University of Buea, Cameroon
| | | | - Eugene Kusi Agyei
- Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology, Ghana
| | | | | | - Cyril Ekabe Jabea
- Health and Empowerment Foundation, Cameroon
- Mbonge District Hospital, Cameroon
- University of Buea, Cameroon
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22
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Fernandes D, Andreyev J. The Role of the Human Gut Microbiome in Inflammatory Bowel Disease and Radiation Enteropathy. Microorganisms 2022; 10:1613. [PMID: 36014031 PMCID: PMC9415405 DOI: 10.3390/microorganisms10081613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
The human gut microbiome plays a key role in regulating host physiology. In a stable state, both the microbiota and the gut work synergistically. The overall homeostasis of the intestinal flora can be affected by multiple factors, including disease states and the treatments given for those diseases. In this review, we examine the relatively well-characterised abnormalities that develop in the microbiome in idiopathic inflammatory bowel disease, and compare and contrast them to those that are found in radiation enteropathy. We discuss how these changes may exert their effects at a molecular level, and the possible role of manipulating the microbiome through the use of a variety of therapies to reduce the severity of the underlying condition.
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Affiliation(s)
- Darren Fernandes
- The Department of Gastroenterology, United Lincolnshire NHS Trust, Lincoln County Hospital, Lincoln LN2 5QY, UK
| | - Jervoise Andreyev
- The Department of Gastroenterology, United Lincolnshire NHS Trust, Lincoln County Hospital, Lincoln LN2 5QY, UK
- The Biomedical Research Centre, Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham NG7 2RD, UK
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23
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Taylo LJ, Keeler EL, Bushman FD, Collman RG. The enigmatic roles of Anelloviridae and Redondoviridae in humans. Curr Opin Virol 2022; 55:101248. [PMID: 35870315 DOI: 10.1016/j.coviro.2022.101248] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 12/26/2022]
Abstract
Anelloviridae and Redondoviridae are virus families with small, circular, single-stranded DNA genomes that are common components of the human virome. Despite their small genome size of less than 5000 bases, they are remarkably successful - anelloviruses colonize over 90% of adult humans, while the recently discovered redondoviruses have been found at up to 80% prevalence in some populations. Anelloviruses are present in blood and many organs, while redondoviruses are found mainly in the ororespiratory tract. Despite their high prevalence, little is known about their biology or pathogenic potential. In this review, we discuss anelloviruses and redondoviruses and explore their enigmatic roles in human health and disease.
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Affiliation(s)
- Louis J Taylo
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emma L Keeler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ronald G Collman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Pulmonary, Allergy and Critical Care Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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24
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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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25
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Li Q, Zhou S, Wang Y, Cong J. Changes of intestinal microbiota and microbiota-based treatments in IBD. Arch Microbiol 2022; 204:442. [PMID: 35776212 DOI: 10.1007/s00203-022-03069-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/13/2022] [Indexed: 12/15/2022]
Abstract
Inflammatory bowel disease (IBD) has gained increasing attention from researchers in terms of its pathophysiology as a global disease with a growing incidence. Although the exact etiology of IBD is still unknown currently, various studies have made us realize that it is related to the dysbiosis of intestinal microbiota and the link between the two may not just be a simple causal relationship, but also a dynamic and complicated one. The intestinal microbiota has been confirmed to be closely related to the occurrence, development, and treatment of IBD. Therefore, this review focuses on the changes in the structure, function, and metabolites of intestinal bacteria, fungi, and viruses in influencing IBD, as well as various approaches to IBD treatment by changing disordered intestinal microbiota. Ultimately, more clinical studies will be needed to focus on the efficacy of intestinal microbiota-based treatments in IBD, because of the existence of both advantages and disadvantages.
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Affiliation(s)
- Qianyu Li
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Siyu Zhou
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Yanna Wang
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Jing Cong
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China.
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26
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Liang G, Gao H, Bushman FD. The pediatric virome in health and disease. Cell Host Microbe 2022; 30:639-649. [PMID: 35550667 DOI: 10.1016/j.chom.2022.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/22/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022]
Abstract
Associations between the global microbiome and diseases of children have been studied extensively; however, research on the viral component of the microbiome, the "virome," is less advanced. The analysis of disease associations with the virome is often technically challenging, requiring a close examination of the "virome dark matter." The gut is a particularly rich source of viral particles, and now multiple studies have reported intriguing associations of the virome with childhood diseases. For example, virome studies have elucidated new lineages of gut viruses that appear to be tightly associated with childhood diarrhea, and consistent patterns are starting to emerge from virome studies in pediatric IBD. In this review, we summarize the methods for studying the virome and recent research on the nature of the virome during childhood, focusing on specific studies of the intestinal virome in pediatric diseases.
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Affiliation(s)
- Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Hongyan Gao
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA.
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27
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Chen L, Wang J. Gut microbiota and inflammatory bowel disease. WIREs Mech Dis 2022; 14:e1540. [PMID: 35266651 DOI: 10.1002/wsbm.1540] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/14/2022]
Abstract
Gut microbiota refers to the complex aggregation of microbes in gut, including bacteria, archaea, fungi, and viruses, and they exert marked influence on the host's health. Perturbations in the gut microbiota have been closely linked to initiation and progression of IBD, which has become a disease with accelerating incidence worldwide, but it remains to be thoroughly investigated how microbial involvement might contribute to IBD. In this review, we discuss the current research findings concerning alterations in the gut microbiota, trans-kingdom interaction between the members of the gut microbiota, their interactions with the immune system of host, their potential role in the IBD pathogenesis, and the relationship between gut microbiota and IBD. We hope to provide a better understanding of the causes of IBD and shed light on the development of microbiome-based therapeutic approaches, which might be a promising strategy to alleviate, manage, and eventually cure IBD. This article is categorized under: Infectious Diseases > Genetics/Genomics/Epigenetics Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Liang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, China
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28
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Bai GH, Lin SC, Hsu YH, Chen SY. The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications. Viruses 2022; 14:278. [PMID: 35215871 PMCID: PMC8876576 DOI: 10.3390/v14020278] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 02/07/2023] Open
Abstract
The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases, viral metagenomic approaches have been used to explore known components of the virome and discover new viruses from various types of samples. The virome has attracted substantial interest since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Increasing numbers of studies and review articles have documented the diverse virome in various sites in the human body, as well as interactions between the human host and the virome with regard to health and disease. However, there have been few studies of direct causal relationships. Viral metagenomic analyses often lack standard references and are potentially subject to bias. Moreover, most virome-related review articles have focused on the gut virome and did not investigate the roles of the virome in other sites of the body in human disease. This review presents an overview of viral metagenomics, with updates regarding the relations between alterations in the human virome and the pathogenesis of human diseases, recent findings related to COVID-19, and therapeutic applications related to the human virome.
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Affiliation(s)
- Geng-Hao Bai
- School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan;
- Department of Education, Taipei Medical University Hospital, Taipei City 11031, Taiwan
| | - Sheng-Chieh Lin
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan;
- Department of Pediatrics, Division of Allergy, Asthma and Immunology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
| | - Yi-Hsiang Hsu
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA;
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shih-Yen Chen
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 11031, Taiwan;
- Department of Pediatrics, Division of Pediatric Gastroenterology and Hepatology, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
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29
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Qv L, Mao S, Li Y, Zhang J, Li L. Roles of Gut Bacteriophages in the Pathogenesis and Treatment of Inflammatory Bowel Disease. Front Cell Infect Microbiol 2021; 11:755650. [PMID: 34900751 PMCID: PMC8656360 DOI: 10.3389/fcimb.2021.755650] [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: 08/09/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, are chronic, relapsing intestinal inflammatory disorders. Although the molecular mechanisms governing the pathogenesis of IBD are not completely clear, the main factors are presumed to be a complex interaction between genetic predisposition, host immune response and environmental exposure, especially the intestinal microbiome. Currently, most studies have focused on the role of gut bacteria in the onset and development of IBD, whereas little attention has been paid to the enteroviruses. Among of them, viruses that infect prokaryotes, called bacteriophages (phages) occupy the majority (90%) in population. Moreover, several recent studies have reported the capability of regulating the bacterial population in the gut, and the direct and indirect influence on host immune response. The present review highlights the roles of gut phages in IBD pathogenesis and explores the potentiality of phages as a therapeutic target for IBD treatment.
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Affiliation(s)
- Lingling Qv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Sunbing Mao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yongjun Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jia Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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30
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Liang G, Cobián-Güemes AG, Albenberg L, Bushman F. The gut virome in inflammatory bowel diseases. Curr Opin Virol 2021; 51:190-198. [PMID: 34763180 DOI: 10.1016/j.coviro.2021.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 02/06/2023]
Abstract
Dysbiosis of the microbiome has been extensively studied in inflammatory bowel diseases (IBD). The roles of bacteria and fungi have been studied in detail, but viral communities, an important component of the microbiome, have been less thoroughly investigated. Metagenomics provided a way to fill this gap by using DNA sequencing to enumerate all viruses in a sample, termed the 'virome'. Such methods have now been employed in several studies to assess associations between viral communities and IBD, yielding several commonly seen properties, including an increase in tailed bacteriophage (Caudovirales) and a decrease in the spherical Microviridae. Numerous studies of single human viruses have been carried out, but no one virus has emerged as tightly associated, focusing attention on whole virome communities and further factors. This review provides an overview of research on the human virome in IBD, with emphasis on (1) dynamics of the gut virome, (2) candidate mechanisms of virome alterations with disease, (3) methods for studying the virome, and (4) potentially actionable implications of virome data.
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Affiliation(s)
- Guanxiang Liang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6076, USA.
| | - Ana Georgina Cobián-Güemes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6076, USA
| | - Lindsey Albenberg
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104-4399, USA
| | - Frederic Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6076, USA.
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31
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Fitzgerald RS, Sanderson IR, Claesson MJ. Paediatric Inflammatory Bowel Disease and its Relationship with the Microbiome. MICROBIAL ECOLOGY 2021; 82:833-844. [PMID: 33666710 PMCID: PMC8551107 DOI: 10.1007/s00248-021-01697-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/19/2021] [Indexed: 05/07/2023]
Abstract
Paediatric inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the digestive tract, comprising of Crohn's disease (CD), ulcerative colitis (UC), and, where classification is undetermined, inflammatory bowel disease unclassified (IBDU). Paediatric IBD incidence is increasing globally, with prevalence highest in the developed world. Though no specific causative agent has been identified for paediatric IBD, it is believed that a number of factors may contribute to the development of the disease, including genetics and the environment. Another potential component in the development of IBD is the microbiota in the digestive tract, particularly the gut. While the exact role that the microbiome plays in IBD is unclear, many studies acknowledge the complex relationship between the gut bacteria and pathogenesis of IBD. In this review, we look at the increasing number of studies investigating the role the microbiome and other biomes play in paediatric patients with IBD, particularly changes associated with IBD, varying disease states, and therapeutics. The paediatric IBD microbiome is significantly different to that of healthy children, with decreased diversity and differences in bacterial composition (such as a decrease in Firmicutes). Changes in the microbiome relating to various treatments of IBD and disease severity have also been observed in multiple studies. Changes in diversity and composition may also extend to other biomes in paediatric IBD, such as the virome and the mycobiome. Research into biome differences in IBD paediatric patients may help progress our understanding of the aetiology of the disease.
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Affiliation(s)
- Rachel S Fitzgerald
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ian R Sanderson
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Marcus J Claesson
- School of Microbiology, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
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32
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Van Espen L, Bak EG, Beller L, Close L, Deboutte W, Juel HB, Nielsen T, Sinar D, De Coninck L, Frithioff-Bøjsøe C, Fonvig CE, Jacobsen S, Kjærgaard M, Thiele M, Fullam A, Kuhn M, Holm JC, Bork P, Krag A, Hansen T, Arumugam M, Matthijnssens J. A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog. mSystems 2021; 6:e0038221. [PMID: 34665009 PMCID: PMC8525569 DOI: 10.1128/msystems.00382-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/02/2021] [Indexed: 01/06/2023] Open
Abstract
Gut viruses are important, yet often neglected, players in the complex human gut microbial ecosystem. Recently, the number of human gut virome studies has been increasing; however, we are still only scratching the surface of the immense viral diversity. In this study, 254 virus-enriched fecal metagenomes from 204 Danish subjects were used to generate the Danish Enteric Virome Catalog (DEVoC) containing 12,986 nonredundant viral scaffolds, of which the majority was previously undescribed, encoding 190,029 viral genes. The DEVoC was used to compare 91 healthy DEVoC gut viromes from children, adolescents, and adults that were used to create the DEVoC. Gut viromes of healthy Danish subjects were dominated by phages. While most phage genomes (PGs) only occurred in a single subject, indicating large virome individuality, 39 PGs were present in more than 10 healthy subjects. Among these 39 PGs, the prevalences of three PGs were associated with age. To further study the prevalence of these 39 prevalent PGs, 1,880 gut virome data sets of 27 studies from across the world were screened, revealing several age-, geography-, and disease-related prevalence patterns. Two PGs also showed a remarkably high prevalence worldwide-a crAss-like phage (20.6% prevalence), belonging to the tentative AlphacrAssvirinae subfamily, and a previously undescribed circular temperate phage infecting Bacteroides dorei (14.4% prevalence), called LoVEphage because it encodes lots of viral elements. Due to the LoVEphage's high prevalence and novelty, public data sets in which the LoVEphage was detected were de novo assembled, resulting in an additional 18 circular LoVEphage-like genomes (67.9 to 72.4 kb). IMPORTANCE Through generation of the DEVoC, we added numerous previously uncharacterized viral genomes and genes to the ever-increasing worldwide pool of human gut viromes. The DEVoC, the largest human gut virome catalog generated from consistently processed fecal samples, facilitated the analysis of the 91 healthy Danish gut viromes. Characterizing the biggest cohort of healthy gut viromes from children, adolescents, and adults to date confirmed the previously established high interindividual variation in human gut viromes and demonstrated that the effect of age on the gut virome composition was limited to the prevalence of specific phage (groups). The identification of a previously undescribed prevalent phage illustrates the usefulness of developing virome catalogs, and we foresee that the DEVoC will benefit future analysis of the roles of gut viruses in human health and disease.
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Affiliation(s)
- Lore Van Espen
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Emilie Glad Bak
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leen Beller
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Lila Close
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Ward Deboutte
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Helene Bæk Juel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Trine Nielsen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Deniz Sinar
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Lander De Coninck
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Christine Frithioff-Bøjsøe
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
| | - Cilius Esmann Fonvig
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
| | - Suganya Jacobsen
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Maria Kjærgaard
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Maja Thiele
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens-Christian Holm
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Children’s Obesity Clinic, accredited European Centre for Obesity Management, Department of Paediatrics, Copenhagen University Hospital Holbaek, Holbaek, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Aleksander Krag
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manimozhiyan Arumugam
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jelle Matthijnssens
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Division of Clinical & Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
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33
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Hsieh SY, Tariq MA, Telatin A, Ansorge R, Adriaenssens EM, Savva GM, Booth C, Wileman T, Hoyles L, Carding SR. Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome. Viruses 2021; 13:2093. [PMID: 34696523 PMCID: PMC8537689 DOI: 10.3390/v13102093] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 01/04/2023] Open
Abstract
The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as "viral dark matter". However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating "rare" members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.
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Affiliation(s)
- Shen-Yuan Hsieh
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Mohammad A. Tariq
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Andrea Telatin
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Rebecca Ansorge
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Evelien M. Adriaenssens
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - George M. Savva
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Catherine Booth
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
| | - Tom Wileman
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science & Technology, Nottingham Trent University, Nottingham NG11 8NS, UK;
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (S.-Y.H.); (A.T.); (R.A.); (E.M.A.); (G.M.S.); (C.B.); (T.W.); (S.R.C.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
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34
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Sultan S, El-Mowafy M, Elgaml A, Ahmed TAE, Hassan H, Mottawea W. Metabolic Influences of Gut Microbiota Dysbiosis on Inflammatory Bowel Disease. Front Physiol 2021; 12:715506. [PMID: 34646151 PMCID: PMC8502967 DOI: 10.3389/fphys.2021.715506] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic medical disorders characterized by recurrent gastrointestinal inflammation. While the etiology of IBD is still unknown, the pathogenesis of the disease results from perturbations in both gut microbiota and the host immune system. Gut microbiota dysbiosis in IBD is characterized by depleted diversity, reduced abundance of short chain fatty acids (SCFAs) producers and enriched proinflammatory microbes such as adherent/invasive E. coli and H2S producers. This dysbiosis may contribute to the inflammation through affecting either the immune system or a metabolic pathway. The immune responses to gut microbiota in IBD are extensively discussed. In this review, we highlight the main metabolic pathways that regulate the host-microbiota interaction. We also discuss the reported findings indicating that the microbial dysbiosis during IBD has a potential metabolic impact on colonocytes and this may underlie the disease progression. Moreover, we present the host metabolic defectiveness that adds to the impact of symbiont dysbiosis on the disease progression. This will raise the possibility that gut microbiota dysbiosis associated with IBD results in functional perturbations of host-microbiota interactions, and consequently modulates the disease development. Finally, we shed light on the possible therapeutic approaches of IBD through targeting gut microbiome.
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Affiliation(s)
- Salma Sultan
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Mohammed El-Mowafy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Abdelaziz Elgaml
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Horus University, New Damietta, Egypt
| | - Tamer A E Ahmed
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hebatoallah Hassan
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Walid Mottawea
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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35
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Massimino L, Lamparelli LA, Houshyar Y, D'Alessio S, Peyrin-Biroulet L, Vetrano S, Danese S, Ungaro F. The Inflammatory Bowel Disease Transcriptome and Metatranscriptome Meta-Analysis (IBD TaMMA) framework. NATURE COMPUTATIONAL SCIENCE 2021; 1:511-515. [PMID: 38217242 PMCID: PMC10766544 DOI: 10.1038/s43588-021-00114-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/16/2021] [Indexed: 01/15/2024]
Abstract
Inflammatory bowel disease (IBD) is a class of chronic disorders whose etiogenesis is still unknown. Despite the high number of IBD-related omics studies, the RNA-sequencing data produced results that are hard to compare because of the experimental variability and different data analysis approaches. We here introduce the IBD Transcriptome and Metatranscriptome Meta-Analysis (TaMMA) framework, a comprehensive survey of publicly available IBD RNA-sequencing datasets. IBD TaMMA is an open-source platform where scientists can explore simultaneously the freely available IBD-associated transcriptomics and microbial profiles thanks to its interactive interface, resulting in a useful tool to the IBD community.
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Affiliation(s)
- Luca Massimino
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.
- IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy.
| | | | - Yashar Houshyar
- IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Laurent Peyrin-Biroulet
- Inserm NGERE, University of Lorraine, Vandoeuvre-les-Nancy, France
- Nancy University Hospital, Vandoeuvre-les-Nancy, France
| | - Stefania Vetrano
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Silvio Danese
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Federica Ungaro
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.
- IBD Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy.
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36
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Karpinska-Leydier K, Amirthalingam J, Alshowaikh K, Iroshani Jayarathna A, Salibindla DBAMR, Paidi G, Ergin HE. Correlation Between the Gut Microbiome and Immunotherapy Response in Inflammatory Bowel Disease: A Systematic Review of the Literature. Cureus 2021; 13:e16808. [PMID: 34350086 PMCID: PMC8325948 DOI: 10.7759/cureus.16808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/01/2021] [Indexed: 11/09/2022] Open
Abstract
Inflammatory bowel disease (IBD) is an autoimmune disease associated with dysbiosis within the gastrointestinal tract. Characteristic taxonomic shifts of microbial populations are observed in disease progression and remission; however, despite similarities, there are many differences among individuals presenting with IBD including IBD subset, clinical course, and response to therapy. Much is still unknown about how these taxonomic shifts interact with immunotherapy and how genetic variants contribute. In this systematic review, we aimed to compile information on the interactions of the gut microbiome with immunotherapy in the course of disease and treatment of IBD patients. This systematic review was conducted as per the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and the PubMed database was methodically screened for literature search including keywords and Medical Subject Headings (MeSH) terms for relevant articles. The quality appraisal was completed using the Cochrane Tool, Newcastle-Ottawa checklist, and the Scale for the Assessment of Narrative Review Articles (SANRA) checklist, as appropriate, and 11 relevant articles were included in this systematic review. Our review concludes that although there are characteristic taxonomic shifts between diseased and healthy patients, genetic variants are an important consideration in the predictive quality of disease and treatment decisions. The comparison between interactions of microbial populations and treatment in addition to the role of genetic variants may provide insight into treatment non-responders. Due to our limitations in current knowledge including the complexity of the microcosm, ethnic genetic variations among human populations, and our focus on relevant articles published in English over the past six years, we may have missed relevant studies. Future studies should focus on the comparison between Western and other cultural populations as well as further implementation of Genome-Wide Association Studies (GWAS) in clinical predictability.
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Affiliation(s)
| | - Jashvini Amirthalingam
- Neurology, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Khadija Alshowaikh
- Obstetrics and Gynecology, California Institute of Behavioral Neurosciences & Psychology, Fairfield , USA
| | | | | | - Gokul Paidi
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Huseyin Ekin Ergin
- General Practice, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
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37
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王 展, 徐 开, 周 宏. [Characteristics of gut virome and microbiome in patients with stroke]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:862-869. [PMID: 34238738 PMCID: PMC8267978 DOI: 10.12122/j.issn.1673-4254.2021.06.08] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To explore the differences in gut virome and microbiome between patients with stroke and healthy volunteers. OBJECTIVE Fifteen patients with acute ischemic stroke treated in the Department of Neurology of Nanfang Hospital between February, 2014 and February, 2016 and 15 healthy volunteers matched for age and sex were enrolled in this study. Virome sequencing and 16S rRNA sequencing were performed on stool samples of all the participants, and the composition and structures of the virome and microbiome were compared between the two groups. OBJECTIVE No significant difference was found in the overall diversity of virome between the stroke patients and the healthy volunteers (alpha diversity: P=0.320; beta diversity: P=0.169, R2=0.037), but virome composition differed significantly between the two groups. The relative abundance of Bacteroides phage B40_8 and Cronobacter phage CS01 increased significantly in patients with stroke. The structures and composition of the microbiome in patients with stroke also differed significantly from those of the healthy volunteers (alpha diversity: P=0.950; beta diversity: P=0.005, R2=0.117). The relative abundance of Megasphaera increased while that of Bifidobacterium decreased in patients with stroke. Correlation analysis showed that in the virome of stroke patients, the relative abundance of the phage preying Streptococcus was positively correlated with that of their hosts (r=0.550, P=0.036), while in the virome of healthy volunteers, the relative abundance of the phage preying Faecalibacterium (r=0.520, P=0.049), Bilophila (r=0.541, P=0.040) and Roseburia (r=0.526, P=0.046) were positively correlated with that of their respective hosts. OBJECTIVE Stroke patients have similar overall diversity of the virome to healthy volunteers but different virome composition and interaction patterns between the virome and microbiome. The gut microbiome also differs between stroke patients and healthy volunteers. The relative abundance of opportunistic pathogens increases but that of symbiotic bacteria decreases in stroke patients.
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Affiliation(s)
- 展强 王
- />南方医科大学珠江医院检验医学部,广东 广州 510280Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - 开宇 徐
- />南方医科大学珠江医院检验医学部,广东 广州 510280Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - 宏伟 周
- />南方医科大学珠江医院检验医学部,广东 广州 510280Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
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38
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Pratama AA, Bolduc B, Zayed AA, Zhong ZP, Guo J, Vik DR, Gazitúa MC, Wainaina JM, Roux S, Sullivan MB. Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation. PeerJ 2021; 9:e11447. [PMID: 34178438 PMCID: PMC8210812 DOI: 10.7717/peerj.11447] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/22/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs). RESULTS The in silico benchmarking of five commonly used virus identification tools show that gene-content-based tools consistently performed well for long (≥3 kbp) contigs, while k-mer- and blast-based tools were uniquely able to detect viruses from short (≤3 kbp) contigs. Notably, however, the performance increase of k-mer- and blast-based tools for short contigs was obtained at the cost of increased false positives (sometimes up to ∼5% for virome and ∼75% bulk samples), particularly when eukaryotic or mobile genetic element sequences were included in the test datasets. For viral classification, variously sized genome fragments were assessed using gene-sharing network analytics to quantify drop-offs in taxonomic assignments, which revealed correct assignations ranging from ∼95% (whole genomes) down to ∼80% (3 kbp sized genome fragments). A similar trend was also observed for other viral classification tools such as VPF-class, ViPTree and VIRIDIC, suggesting that caution is warranted when classifying short genome fragments and not full genomes. Finally, we highlight how fragmented assemblies can lead to erroneous identification of AMGs and outline a best-practices workflow to curate candidate AMGs in viral genomes assembled from metagenomes. CONCLUSION Together, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses 'hidden' in diverse sequence datasets.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Ahmed A. Zayed
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Zhi-Ping Zhong
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States of America
| | - Jiarong Guo
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | - Dean R. Vik
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
| | | | - James M. Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
- Infectious Diseases Institute at The Ohio State University, Ohio State University, Columbus, OH, United States of America
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States of America
- Environmental and Geodetic Engineering, Ohio State University, Department of Civil, Columbus, OH, United States of America
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39
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Tisza MJ, Buck CB. A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. Proc Natl Acad Sci U S A 2021; 118:e2023202118. [PMID: 34083435 PMCID: PMC8201803 DOI: 10.1073/pnas.2023202118] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Despite remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This gap persists, even though many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases, and all of them encompass large amounts of viral sequence data. The lack of a comprehensive database for human-associated viruses has historically stymied efforts to interrogate the impact of the virome on human health. This study probes thousands of datasets to uncover sequences from over 45,000 unique virus taxa, with historically high per-genome completeness. Large publicly available case-control studies are reanalyzed, and over 2,200 strong virus-disease associations are found.
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Affiliation(s)
- Michael J Tisza
- Laboratory of Cellular Oncology, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Christopher B Buck
- Laboratory of Cellular Oncology, National Cancer Institute, NIH, Bethesda, MD 20892
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40
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Townsend EM, Kelly L, Muscatt G, Box JD, Hargraves N, Lilley D, Jameson E. The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome. Front Cell Infect Microbiol 2021; 11:643214. [PMID: 34150671 PMCID: PMC8213399 DOI: 10.3389/fcimb.2021.643214] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.
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Affiliation(s)
- Eleanor M Townsend
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Lucy Kelly
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - George Muscatt
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Joshua D Box
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Nicole Hargraves
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Daniel Lilley
- Warwick Medical School, The University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
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41
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Xiao W, Ma Z(S. Inter-Individual Diversity Scaling Analysis of the Human Virome With Classic Diversity-Area Relationship (DAR) Modeling. Front Genet 2021; 12:627128. [PMID: 33959147 PMCID: PMC8095712 DOI: 10.3389/fgene.2021.627128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/30/2021] [Indexed: 11/13/2022] Open
Abstract
The human virome is a critical component of the human microbiome, and it is believed to hold the richest diversity within human microbiomes. Yet, the inter-individual scaling (changes) of the human virome has not been formally investigated to the best of our knowledge. Here we fill the gap by applying diversity-area relationship (DAR) modeling (a recent extension to the classic species-area law in biodiversity and biogeography research) for analyzing four large datasets of the human virome with three DAR profiles: DAR scaling (z)-measuring the inter-individual heterogeneity in virome diversity, MAD (maximal accrual diversity: D max ) and LGD ratio (ratio of local diversity to global diversity)-measuring the percentage of individual to population level diversity. Our analyses suggest: (i) The diversity scaling parameter (z) is rather resilient against the diseases as indicated by the lack of significant differences between the healthy and diseased treatments. (ii) The potential maximal accrual diversity (D max ) is less resilient and may vary between the healthy and diseased groups or between different body sites. (iii) The LGD ratio of bacterial communities is much smaller than for viral communities, and relates to the comparatively greater heterogeneity between local vs. global diversity levels found for bacterial-biomes.
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Affiliation(s)
- Wanmeng Xiao
- Computational Biology and Medical Ecology Laboratory, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Zhanshan (Sam) Ma
- Computational Biology and Medical Ecology Laboratory, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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42
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Fulci V, Stronati L, Cucchiara S, Laudadio I, Carissimi C. Emerging Roles of Gut Virome in Pediatric Diseases. Int J Mol Sci 2021; 22:4127. [PMID: 33923593 PMCID: PMC8073368 DOI: 10.3390/ijms22084127] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
In the last decade, the widespread application of shotgun metagenomics provided extensive characterization of the bacterial "dark matter" of the gut microbiome, propelling the development of dedicated, standardized bioinformatic pipelines and the systematic collection of metagenomic data into comprehensive databases. The advent of next-generation sequencing also unravels a previously underestimated viral population (virome) present in the human gut. Despite extensive efforts to characterize the human gut virome, to date, little is known about the childhood gut virome. However, alterations of the gut virome in children have been linked to pathological conditions such as inflammatory bowel disease, type 1 diabetes, malnutrition, diarrhea and celiac disease.
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Affiliation(s)
- Valerio Fulci
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Laura Stronati
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Salvatore Cucchiara
- Department of Women’s and Children’s Health, Sapienza University of Rome, 00161 Rome, Italy;
| | - Ilaria Laudadio
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Claudia Carissimi
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
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43
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Fernández L, Duarte AC, Rodríguez A, García P. The relationship between the phageome and human health: are bacteriophages beneficial or harmful microbes? Benef Microbes 2021; 12:107-120. [PMID: 33789552 DOI: 10.3920/bm2020.0132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the context of the global antibiotic resistance crisis, bacteriophages are increasingly becoming promising antimicrobial agents against multi-resistant bacteria. Indeed, a huge effort is being made to bring phage-derived products to the market, a process that will also require revising the current regulations in order to facilitate their approval. However, despite the evidence supporting the safety of phages for humans, the general public would still be reluctant to use 'viruses' for therapeutic purposes. In this scenario, we consider that it is important to discuss the role of these microorganisms in the equilibrium of the microbiota and how this relates to human health. To do that, this review starts by examining the role of phages as key players in bacterial communities (including those that naturally inhabit the human body), modulating the species composition and contributing to maintain a 'healthy' status quo. Additionally, in specific situations, e.g. an infectious disease, bacteriophages can be used as target-specific antimicrobials against pathogenic bacteria (phage therapy), while being harmless to the desirable microbiota. Apart from that, incipient research shows the potential application of these viruses to treat diseases caused by bacterial dysbiosis. This latter application would be comparable to the use of probiotics or prebiotics, since bacteriophages can indirectly improve the growth of beneficial bacteria in the gastrointestinal tract by removing undesirable competitors. On the other hand, possible adverse effects do not appear to be an impediment to promote phage therapy. Nonetheless, it is important to remember their potentially negative impact, mainly concerning their immunogenicity or their potential spread of virulence and antibiotic resistance genes, especially by temperate phages. Overall, we believe that phages should be largely considered beneficial microbes, although it is paramount not to overlook their potential risks.
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Affiliation(s)
- L Fernández
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
| | - A C Duarte
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
| | - A Rodríguez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
| | - P García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
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Xu Y, Xu X, Ocansey DKW, Cao H, Qiu W, Tu Q, Mao F. CircRNAs as promising biomarkers of inflammatory bowel disease and its associated-colorectal cancer. Am J Transl Res 2021; 13:1580-1593. [PMID: 33841681 PMCID: PMC8014397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
In recent years, research on the pathogenesis of inflammatory bowel disease (IBD) and its associated-colorectal cancer has been well documented to involve environmental, genetic, immune, and intestinal microbiota factors. Evidence indicates that, regardless of the current high global incidence of IBD with over 3.5 million cases in Europe and North America only, it continues to emerge in newly industrialized countries across Asia, Middle East, and South America. Individuals with IBD have significant increased risk of gastrointestinal and extra-intestinal malignancies, particularly, colorectal cancer (CRC) and lymphomas. Among the significant areas of exploration in IBD and its associated-CRC is the search for effective and reliable diagnostic and prognostic markers, and treatment targets. To this effect, the role of non-coding RNAs in IBD and its associated-CRC has attracted research attention, among which microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) get more detailed exploration while little is known about circular RNAs (circRNAs). This review focuses on the emerging role of circRNAs in the diagnosis, prognosis, and treatment of IBD and its associated-CRC. It introduces the biogenesis of circRNAs and brings an up-to-date report on those found within IBD and CRC environment, as well as their participation toward the promotion or suppression of the conditions, and their diagnostic potentials.
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Affiliation(s)
- Yuting Xu
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
| | - Xinwei Xu
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
- Directorate of University Health Services, University of Cape CoastGhana
| | - Hua Cao
- Nanjing Jiangning HospitalNanjing 211100, Jiangsu, China
| | - Wei Qiu
- Nanjing Jiangning HospitalNanjing 211100, Jiangsu, China
| | - Qiang Tu
- Nanjing Jiangning HospitalNanjing 211100, Jiangsu, China
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
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The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis. Animals (Basel) 2021; 11:ani11030745. [PMID: 33803123 PMCID: PMC7998804 DOI: 10.3390/ani11030745] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/16/2021] [Accepted: 02/26/2021] [Indexed: 01/17/2023] Open
Abstract
The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.
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Iliev ID, Cadwell K. Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases. Gastroenterology 2021; 160:1050-1066. [PMID: 33347881 PMCID: PMC7956156 DOI: 10.1053/j.gastro.2020.06.100] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
The intestinal microbiota comprises diverse fungal and viral components, in addition to bacteria. These microbes interact with the immune system and affect human physiology. Advances in metagenomics have associated inflammatory and autoimmune diseases with alterations in fungal and viral species in the gut. Studies of animal models have found that commensal fungi and viruses can activate host-protective immune pathways related to epithelial barrier integrity, but can also induce reactions that contribute to events associated with inflammatory bowel disease. Changes in our environment associated with modernization and the COVID-19 pandemic have exposed humans to new fungi and viruses, with unknown consequences. We review the lessons learned from studies of animal viruses and fungi commonly detected in the human gut and how these might affect health and intestinal disease.
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Affiliation(s)
- Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, New York; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, New York.
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine, Skirball Institute, New York University Grossman School of Medicine, New York, New York; Department of Microbiology, New York University Grossman School of Medicine, New York, New York; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Langone Health, New York, New York.
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Tarris G, de Rougemont A, Charkaoui M, Michiels C, Martin L, Belliot G. Enteric Viruses and Inflammatory Bowel Disease. Viruses 2021; 13:v13010104. [PMID: 33451106 PMCID: PMC7828589 DOI: 10.3390/v13010104] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 12/16/2022] Open
Abstract
Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), is a multifactorial disease in which dietary, genetic, immunological, and microbial factors are at play. The role of enteric viruses in IBD remains only partially explored. To date, epidemiological studies have not fully described the role of enteric viruses in inflammatory flare-ups, especially that of human noroviruses and rotaviruses, which are the main causative agents of viral gastroenteritis. Genome-wide association studies have demonstrated the association between IBD, polymorphisms of the FUT2 and FUT3 genes (which drive the synthesis of histo-blood group antigens), and ligands for norovirus and rotavirus in the intestine. The role of autophagy in defensin-deficient Paneth cells and the perturbations of cytokine secretion in T-helper 1 and T-helper 17 inflammatory pathways following enteric virus infections have been demonstrated as well. Enteric virus interactions with commensal bacteria could play a significant role in the modulation of enteric virus infections in IBD. Based on the currently incomplete knowledge of the complex phenomena underlying IBD pathogenesis, future studies using multi-sampling and data integration combined with new techniques such as human intestinal enteroids could help to decipher the role of enteric viruses in IBD.
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Affiliation(s)
- Georges Tarris
- Department of Pathology, University Hospital of Dijon, F 21000 Dijon, France; (G.T.); (L.M.)
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology, University Hospital of Dijon, F 21000 Dijon, France;
| | - Alexis de Rougemont
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology, University Hospital of Dijon, F 21000 Dijon, France;
| | - Maëva Charkaoui
- Department of Hepatogastroenterology, University Hospital of Dijon, F 21000 Dijon, France; (M.C.); (C.M.)
| | - Christophe Michiels
- Department of Hepatogastroenterology, University Hospital of Dijon, F 21000 Dijon, France; (M.C.); (C.M.)
| | - Laurent Martin
- Department of Pathology, University Hospital of Dijon, F 21000 Dijon, France; (G.T.); (L.M.)
| | - Gaël Belliot
- National Reference Centre for Gastroenteritis Viruses, Laboratory of Virology, University Hospital of Dijon, F 21000 Dijon, France;
- Correspondence: ; Tel.: +33-380-293-171; Fax: +33-380-293-280
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Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat Microbiol 2021; 6:960-970. [PMID: 34168315 PMCID: PMC8241571 DOI: 10.1038/s41564-021-00928-6] [Citation(s) in RCA: 211] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023]
Abstract
Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.
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Iljazovic A, Roy U, Gálvez EJC, Lesker TR, Zhao B, Gronow A, Amend L, Will SE, Hofmann JD, Pils MC, Schmidt-Hohagen K, Neumann-Schaal M, Strowig T. Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation. Mucosal Immunol 2021; 14:113-124. [PMID: 32433514 PMCID: PMC7790746 DOI: 10.1038/s41385-020-0296-4] [Citation(s) in RCA: 212] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
Diverse microbial signatures within the intestinal microbiota have been associated with intestinal and systemic inflammatory diseases, but whether these candidate microbes actively modulate host phenotypes or passively expand within the altered microbial ecosystem is frequently not known. Here we demonstrate that colonization of mice with a member of the genus Prevotella, which has been previously associated to colitis in mice, exacerbates intestinal inflammation. Our analysis revealed that Prevotella intestinalis alters composition and function of the ecosystem resulting in a reduction of short-chain fatty acids, specifically acetate, and consequently a decrease in intestinal IL-18 levels during steady state. Supplementation of IL-18 to Prevotella-colonized mice was sufficient to reduce intestinal inflammation. Hence, we conclude that intestinal Prevotella colonization results in metabolic changes in the microbiota, which reduce IL-18 production and consequently exacerbate intestinal inflammation, and potential systemic autoimmunity.
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Affiliation(s)
- Aida Iljazovic
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Urmi Roy
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- Hannover Medical School, Hannover, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Bei Zhao
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Achim Gronow
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Sabine E Will
- Bacterial Metabolomics, Leibniz institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Julia D Hofmann
- Department of Bioinformatics and Biochemistry, BRICS, Technische Universität Braunschweig, Braunschweig, Germany
| | - Marina C Pils
- Mouse Pathology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Kerstin Schmidt-Hohagen
- Department of Bioinformatics and Biochemistry, BRICS, Technische Universität Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany.
- Hannover Medical School, Hannover, Germany.
- Centre for Individualised Infection Medicine, Hannover, Germany.
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Zhuang X, Liu C, Zhan S, Tian Z, Li N, Mao R, Zeng Z, Chen M. Gut Microbiota Profile in Pediatric Patients With Inflammatory Bowel Disease: A Systematic Review. Front Pediatr 2021; 9:626232. [PMID: 33604319 PMCID: PMC7884334 DOI: 10.3389/fped.2021.626232] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022] Open
Abstract
Background and Aim: Accumulating evidence have implicated gut microbiota alterations in pediatric and adult patients with inflammatory bowel disease (IBD); however, the results of different studies are often inconsistent and even contradictory. It is believed that early changes in new-onset and treatment-naïve pediatric patients are more informative. We performed a systematic review to investigate the gut microbiota profiles in pediatric IBD and identify specific microbiota biomarkers associated with this disorder. Methods: Electronic databases were searched from inception to 31 July 2020 for studies that observed gut microbiota alterations in pediatric patients with IBD. Study quality was assessed using the Newcastle-Ottawa scale. Results: A total of 41 original studies investigating gut microbiota profiles in pediatric patients with IBD were included in this review. Several studies have reported a decrease in α-diversity and an overall difference in β-diversity. Although no specific gut microbiota alterations were consistently reported, a gain in Enterococcus and a significant decrease in Anaerostipes, Blautia, Coprococcus, Faecalibacterium, Roseburia, Ruminococcus, and Lachnospira were found in the majority of the included articles. Moreover, there is insufficient data to show specific microbiota bacteria associated with disease activity, location, and behavior in pediatric IBD. Conclusions: This systematic review identified evidence for differences in the abundance of some bacteria in pediatric patients with IBD when compared to patients without IBD; however, no clear overall conclusion could be drawn from the included studies due to inconsistent results and heterogeneous methodologies. Further studies with large samples that follow more rigorous and standardized methodologies are needed.
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Affiliation(s)
- Xiaojun Zhuang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Caiguang Liu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shukai Zhan
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhenyi Tian
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Na Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ren Mao
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhirong Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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