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Zuo T, Sun Y, Wan Y, Yeoh YK, Zhang F, Cheung CP, Chen N, Luo J, Wang W, Sung JJY, Chan PKS, Wang K, Chan FKL, Miao Y, Ng SC. Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization. Cell Host Microbe 2020; 28:741-751.e4. [PMID: 32910902 DOI: 10.1016/j.chom.2020.08.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/06/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022]
Abstract
The human-gut-DNA virome is highly diverse and individual specific, but little is known of its variation at a population level. Here, we report the fecal DNA virome of 930 healthy adult subjects from two regions in China (Hong Kong and Yunnan) spanning six ethnicities (Han, Zang, Miao, Bai, Dai, and Hani), and including urban and rural residents for each ethnicity. Twenty host factors were found to significantly correlate with the human-gut virome variation, with geography carrying the strongest impact and ethnicity-distinct diets associating with certain viral species. Urbanization enhances interindividual dissimilarities between gut viromes, with the duration of urban residence associating with multiple bacteriophages, including Lactobacillus phage and Lactococcus phage. Overall, the gut virome presents more heterogeneity relative to the bacterial microbiome across the examined Chinese populations. This study highlights population-based variations and the importance of host and environmental factors in shaping the DNA virome in the human gut.
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Affiliation(s)
- Tao Zuo
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Yang Sun
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Yating Wan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun Kit Yeoh
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Fen Zhang
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun Pan Cheung
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Nan Chen
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Juan Luo
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Wen Wang
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Joseph J Y Sung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kunhua Wang
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China
| | - Francis K L Chan
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Yinglei Miao
- The First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Yunnan Institute of Digestive Diseases, Kunming, China.
| | - Siew C Ng
- Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China; Li Ka Shing Institute of Health Science, State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, China.
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202
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Federici S, Nobs SP, Elinav E. Phages and their potential to modulate the microbiome and immunity. Cell Mol Immunol 2020; 18:889-904. [PMID: 32901128 DOI: 10.1038/s41423-020-00532-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages (hence termed phages) are viruses that target bacteria and have long been considered as potential future treatments against antibiotic-resistant bacterial infection. However, the molecular nature of phage interactions with bacteria and the human host has remained elusive for decades, limiting their therapeutic application. While many phages and their functional repertoires remain unknown, the advent of next-generation sequencing has increasingly enabled researchers to decode new lytic and lysogenic mechanisms by which they attack and destroy bacteria. Furthermore, the last decade has witnessed a renewed interest in the utilization of phages as therapeutic vectors and as a means of targeting pathogenic or commensal bacteria or inducing immunomodulation. Importantly, the narrow host range, immense antibacterial repertoire, and ease of manipulating phages may potentially allow for their use as targeted modulators of pathogenic, commensal and pathobiont members of the microbiome, thereby impacting mammalian physiology and immunity along mucosal surfaces in health and in microbiome-associated diseases. In this review, we aim to highlight recent advances in phage biology and how a mechanistic understanding of phage-bacteria-host interactions may facilitate the development of novel phage-based therapeutics. We provide an overview of the challenges of the therapeutic use of phages and how these could be addressed for future use of phages as specific modulators of the human microbiome in a variety of infectious and noncommunicable human diseases.
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Affiliation(s)
- Sara Federici
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Samuel P Nobs
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel. .,Cancer-Microbiome Division Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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203
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204
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Porter NT, Hryckowian AJ, Merrill BD, Fuentes JJ, Gardner JO, Glowacki RWP, Singh S, Crawford RD, Snitkin ES, Sonnenburg JL, Martens EC. Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron. Nat Microbiol 2020; 5:1170-1181. [PMID: 32601452 PMCID: PMC7482406 DOI: 10.1038/s41564-020-0746-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/27/2020] [Indexed: 12/22/2022]
Abstract
A variety of cell surface structures dictate interactions between bacteria and their environment, including their viruses (bacteriophages). Members of the human gut Bacteroidetes characteristically produce several phase-variable capsular polysaccharides (CPSs), but their contributions to bacteriophage interactions are unknown. To begin to understand how CPSs have an impact on Bacteroides-phage interactions, we isolated 71 Bacteroides thetaiotaomicron-infecting bacteriophages from two locations in the United States. Using B. thetaiotaomicron strains that express defined subsets of CPSs, we show that CPSs dictate host tropism for these phages and that expression of non-permissive CPS variants is selected under phage predation, enabling survival. In the absence of CPSs, B. thetaiotaomicron escapes bacteriophage predation by altering expression of eight distinct phase-variable lipoproteins. When constitutively expressed, one of these lipoproteins promotes resistance to multiple bacteriophages. Our results reveal important roles for Bacteroides CPSs and other cell surface structures that allow these bacteria to persist under bacteriophage predation, and hold important implications for using bacteriophages therapeutically to target gut symbionts.
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Affiliation(s)
- Nathan T Porter
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jaime J Fuentes
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Jackson O Gardner
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert W P Glowacki
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Shaleni Singh
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Ryan D Crawford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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205
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The Role of Rhizosphere Bacteriophages in Plant Health. Trends Microbiol 2020; 28:709-718. [DOI: 10.1016/j.tim.2020.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/11/2020] [Accepted: 04/02/2020] [Indexed: 12/12/2022]
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206
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Nallanchakravarthula S, Amruta N, Ramamurthy C. Cancer Microbiome; Opportunities and Challenges. Endocr Metab Immune Disord Drug Targets 2020; 21:215-229. [PMID: 32819239 DOI: 10.2174/1871530320999200818134942] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/03/2020] [Accepted: 06/11/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Microbe-host association has emerged as a modulator in modern medicine. Cancer and its associated host microbes are collectively referred to as the cancer microbiome. The cancer microbiome is complex, and many aspects remain unclear including metabolic plasticity, microenvironment remodeling, cellular communications, and unique signatures within the host, all of which have a vital role in homeostasis and pathogenesis of host physiology. However, the role of the microbiome in cancer initiation, progression, and therapy is still poorly understood and remains to be explored. OBJECTIVE The objective of this review is to elucidate the role of the microbiome in cancer metabolism and the tumor microenvironment. It also focuses on the importance of therapeutic opportunities and challenges in the manipulation of the cancer microbiome. METHODS A literature search was conducted on the role of the microbiome in cancer initiation, progression, and therapy. CONCLUSION The tumor microenvironment and cancer metabolism are significant in host-microbiome interactions. The microbiome can modulate standard cancer therapies like chemotherapy and immunotherapy. Microbiome transplantation has also been demonstrated as an effective therapy against cancer. Furthermore, the modulation of the microbiome also has potential clinical outcomes in modern medicine.
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Affiliation(s)
| | - Narayanappa Amruta
- Department of Neurosurgery, Tulane University, New Orleans, Louisiana, United States
| | - Chitteti Ramamurthy
- C.G. Bhakta Institute of Biotechnology, UkaTarsadia University, Maliba campus, Bardoli Surat (Dist), Gujarat, India
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207
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Paving the Way to Unveil the Diversity and Evolution of Phage Genomes. Viruses 2020; 12:v12090905. [PMID: 32824934 PMCID: PMC7551783 DOI: 10.3390/v12090905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 01/17/2023] Open
Abstract
Phage biology has been developing for the last hundred years, and the potential of phages as tools and treatments has been known since their early discovery. However, the lack of knowledge of the molecular mechanisms coded in phage genomes hindered the development of the field. With current molecular methods, the last decade has been a resurgence of the field. The Special Issue on “Diversity and Evolution of Phage Genomes” is a great example with its 17 manuscripts published. It covers some of the latest methods to sample and characterize environmental and host associated viromes, considering experimental biases and computational developments. Furthermore, the use of molecular tools coupled with traditional methods has allowed to isolate and characterize viruses from different hosts and environments with such diversity that even a new viral class is being proposed. The viruses described cover all different phage families and lifestyles. However, is not only about diversity; the molecular evolution is studied in a set of manuscripts looking at phage-host interactions and their capacity to uncover the frequency and type of mutations behind the bacterial resistance mechanisms and viral pathogenesis, and such methods are opening new ways into identifying potential receptors and characterizing the bacterial host range.
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208
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Enteric Viral Co-Infections: Pathogenesis and Perspective. Viruses 2020; 12:v12080904. [PMID: 32824880 PMCID: PMC7472086 DOI: 10.3390/v12080904] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023] Open
Abstract
Enteric viral co-infections, infections involving more than one virus, have been reported for a diverse group of etiological agents, including rotavirus, norovirus, astrovirus, adenovirus, and enteroviruses. These pathogens are causative agents for acute gastroenteritis and diarrheal disease in immunocompetent and immunocompromised individuals of all ages globally. Despite virus–virus co-infection events in the intestine being increasingly detected, little is known about their impact on disease outcomes or human health. Here, we review what is currently known about the clinical prevalence of virus–virus co-infections and how co-infections may influence vaccine responses. While experimental investigations into enteric virus co-infections have been limited, we highlight in vivo and in vitro models with exciting potential to investigate viral co-infections. Many features of virus–virus co-infection mechanisms in the intestine remain unclear, and further research will be critical.
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209
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Health Impact and Therapeutic Manipulation of the Gut Microbiome. High Throughput 2020; 9:ht9030017. [PMID: 32751130 PMCID: PMC7564083 DOI: 10.3390/ht9030017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 12/12/2022] Open
Abstract
Recent advances in microbiome studies have revealed much information about how the gut virome, mycobiome, and gut bacteria influence health and disease. Over the years, many studies have reported associations between the gut microflora under different pathological conditions. However, information about the role of gut metabolites and the mechanisms by which the gut microbiota affect health and disease does not provide enough evidence. Recent advances in next-generation sequencing and metabolomics coupled with large, randomized clinical trials are helping scientists to understand whether gut dysbiosis precedes pathology or gut dysbiosis is secondary to pathology. In this review, we discuss our current knowledge on the impact of gut bacteria, virome, and mycobiome interactions with the host and how they could be manipulated to promote health.
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210
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Legoff J, Michonneau D, Socie G. The virome in hematology-Stem cell transplantation and beyond. Semin Hematol 2020; 57:19-25. [PMID: 32690140 DOI: 10.1053/j.seminhematol.2020.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 05/06/2020] [Indexed: 12/23/2022]
Abstract
The virome has been recently studied in hematology and mostly in the setting of allogeneic hematopoietic stem cell transplantation. However, in hematology (as in the setting of nonhematological disorders) the study of the microbiome (that indeed includes the virome) is a growing field. The overall field is moving beyond species catalogue to the understanding of the complex ecological relationship that microbes have with each other and with their host. Here we review the existing literature on the virome in transplant recipients and in other settings, and discuss potential applications of the virome study in hematology.
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Affiliation(s)
- Jérôme Legoff
- Université de Paris, INSERM U976, Paris, France; Microbiology department, Virology laboratory, Saint Louis Hospital, Paris, France
| | - David Michonneau
- Université de Paris, INSERM U976, Paris, France; Hematology-Transplantation, Saint Louis Hospital, Paris, France
| | - Gérard Socie
- Université de Paris, INSERM U976, Paris, France; Hematology-Transplantation, Saint Louis Hospital, Paris, France.
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211
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Fujimoto K, Kimura Y, Shimohigoshi M, Satoh T, Sato S, Tremmel G, Uematsu M, Kawaguchi Y, Usui Y, Nakano Y, Hayashi T, Kashima K, Yuki Y, Yamaguchi K, Furukawa Y, Kakuta M, Akiyama Y, Yamaguchi R, Crowe SE, Ernst PB, Miyano S, Kiyono H, Imoto S, Uematsu S. Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts. Cell Host Microbe 2020; 28:380-389.e9. [PMID: 32652061 DOI: 10.1016/j.chom.2020.06.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/12/2020] [Accepted: 06/10/2020] [Indexed: 02/08/2023]
Abstract
The application of bacteriophages (phages) is proposed as a highly specific therapy for intestinal pathobiont elimination. However, the infectious associations between phages and bacteria in the human intestine, which is essential information for the development of phage therapies, have yet to be fully elucidated. Here, we report the intestinal viral microbiomes (viromes), together with bacterial microbiomes (bacteriomes), in 101 healthy Japanese individuals. Based on the genomic sequences of bacteriomes and viromes from the same fecal samples, the host bacteria-phage associations are illustrated for both temperate and virulent phages. To verify the usefulness of the comprehensive host bacteria-phage information, we screened Clostridioides difficile-specific phages and identified antibacterial enzymes whose activity is confirmed both in vitro and in vivo. These comprehensive metagenome analyses reveal not only host bacteria-phage associations in the human intestine but also provide vital information for the development of phage therapies against intestinal pathobionts.
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Affiliation(s)
- Kosuke Fujimoto
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; Division of Metagenome Medicine, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan; Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Yasumasa Kimura
- Division of Systems Immunology, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Masaki Shimohigoshi
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Takeshi Satoh
- Division of Systems Immunology, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Shintaro Sato
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; Mucosal Vaccine Project, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Georg Tremmel
- Laboratory of DNA Information Analysis, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Miho Uematsu
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Yunosuke Kawaguchi
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Yuki Usui
- Division of Systems Immunology, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshiko Nakano
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Tetsuya Hayashi
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Koji Kashima
- Division of Mucosal Immunology, Department of Microbiology and Immunology, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshikazu Yuki
- Division of Mucosal Immunology, Department of Microbiology and Immunology, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Masanori Kakuta
- Laboratory of DNA Information Analysis, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Yutaka Akiyama
- Department of Computer Science, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Rui Yamaguchi
- Laboratory of DNA Information Analysis, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Sheila E Crowe
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Peter B Ernst
- Division of Gastroenterology, Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, University of California, San Diego, La Jolla, CA 92093, USA; Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Center for Veterinary Sciences and Comparative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Hiroshi Kiyono
- Division of Gastroenterology, Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, University of California, San Diego, La Jolla, CA 92093, USA; Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan; International Research and Development Center for Mucosal Vaccines, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan.
| | - Satoshi Uematsu
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; Division of Metagenome Medicine, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan; Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan.
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212
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Boling L, Cuevas DA, Grasis JA, Kang HS, Knowles B, Levi K, Maughan H, McNair K, Rojas MI, Sanchez SE, Smurthwaite C, Rohwer F. Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome. Gut Microbes 2020; 11:721-734. [PMID: 31931655 PMCID: PMC7524278 DOI: 10.1080/19490976.2019.1701353] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The approximately 1011 viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. The responses of three common gut bacteria species, and one opportunistic pathogen, to 117 commonly consumed foods, chemical additives, and plant extracts were tested. Many compounds, including Stevia rebaudiana and bee propolis extracts, exhibited species-specific growth inhibition by prophage induction. Overall, these results show that various foods may change the abundances of gut bacteria by modulating temperate phage and suggests a novel path for landscaping the human gut microbiome.
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Affiliation(s)
- Lance Boling
- Department of Biology, San Diego State University, San Diego, CA, USA,CONTACT Lance Boling Department of Biology, San Diego State University, LS301, 5500 Campanile Dr, San Diego, CA92182USA
| | - Daniel A. Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Juris A. Grasis
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Han Suh Kang
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Ben Knowles
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Katelyn McNair
- Department of Biology, San Diego State University, San Diego, CA, USA,Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | | | | | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, USA
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213
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Khan Mirzaei M, Xue J, Costa R, Ru J, Schulz S, Taranu ZE, Deng L. Challenges of Studying the Human Virome - Relevant Emerging Technologies. Trends Microbiol 2020; 29:171-181. [PMID: 32622559 DOI: 10.1016/j.tim.2020.05.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 01/17/2023]
Abstract
In this review we provide an overview of current challenges and advances in bacteriophage research within the growing field of viromics. In particular, we discuss, from a human virome study perspective, the current and emerging technologies available, their limitations in terms of de novo discoveries, and possible solutions to overcome present experimental and computational biases associated with low abundance of viral DNA or RNA. We summarize recent breakthroughs in metagenomics assembling tools and single-cell analysis, which have the potential to increase our understanding of phage biology, diversity, and interactions with both the microbial community and the human body. We expect that these recent and future advances in the field of viromics will have a strong impact on how we develop phage-based therapeutic approaches.
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Affiliation(s)
- Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Rita Costa
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Sarah Schulz
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Zofia E Taranu
- Aquatic Contaminants Research Division (ACRD), Environment and Climate Change Canada (ECCC), Montréal, QC H2Y 2E7, Canada
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany.
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214
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Jayasinghe TN, Vatanen T, Chiavaroli V, Jayan S, McKenzie EJ, Adriaenssens E, Derraik JGB, Ekblad C, Schierding W, Battin MR, Thorstensen EB, Cameron-Smith D, Forbes-Blom E, Hofman PL, Roy NC, Tannock GW, Vickers MH, Cutfield WS, O'Sullivan JM. Differences in Compositions of Gut Bacterial Populations and Bacteriophages in 5-11 Year-Olds Born Preterm Compared to Full Term. Front Cell Infect Microbiol 2020; 10:276. [PMID: 32612960 PMCID: PMC7309444 DOI: 10.3389/fcimb.2020.00276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/11/2020] [Indexed: 12/17/2022] Open
Abstract
Preterm infants are exposed to major perinatal, post-natal, and early infancy events that could impact on the gut microbiome. These events include infection, steroid and antibiotic exposure, parenteral nutrition, necrotizing enterocolitis, and stress. Studies have shown that there are differences in the gut microbiome during the early months of life in preterm infants. We hypothesized that differences in the gut microbial composition and metabolites in children born very preterm persist into mid-childhood. Participants were healthy prepubertal children aged 5-11 years who were born very preterm (≤32 weeks of gestation; n = 51) or at term (37-41 weeks; n = 50). We recorded the gestational age, birth weight, mode of feeding, mode of birth, age, sex, and the current height and weight of our cohort. We performed a multi'omics [i.e., 16S rRNA amplicon and shotgun metagenomic sequencing, SPME-GCMS (solid-phase microextraction followed by gas chromatography-mass spectrometry)] analysis to investigate the structure and function of the fecal microbiome (as a proxy of the gut microbiota) in our cross-sectional cohort. Children born very preterm were younger (7.8 vs. 8.3 years; p = 0.034), shorter [height-standard deviation score (SDS) 0.31 vs. 0.92; p = 0.0006) and leaner [BMI (body mass index) SDS -0.20 vs. 0.29; p < 0.0001] than the term group. Children born very preterm had higher fecal calprotectin levels, decreased fecal phage richness, lower plasma arginine, lower fecal branched-chain amino acids and higher fecal volatile (i.e., 3-methyl-butanoic acid, butyrolactone, butanoic acid and pentanoic acid) profiles. The bacterial microbiomes did not differ between preterm and term groups. We speculate that the observed very preterm-specific changes were established in early infancy and may impact on the capacity of the very preterm children to respond to environmental changes.
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Affiliation(s)
| | - Tommi Vatanen
- Liggins Institute, University of Auckland, Auckland, New Zealand
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | | | - Sachin Jayan
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | | | - José G. B. Derraik
- Liggins Institute, University of Auckland, Auckland, New Zealand
- A Better Start—National Science Challenge, University of Auckland, Auckland, New Zealand
| | - Cameron Ekblad
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | | | | | | | | | - Paul L. Hofman
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Nicole C. Roy
- AgResearch, Palmerston North, New Zealand
- The Riddet Institute, Massey University, Palmerston North, New Zealand
- The High-Value Nutrition Challenge, Auckland, New Zealand
| | - Gerald W. Tannock
- The Riddet Institute, Massey University, Palmerston North, New Zealand
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Mark H. Vickers
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Wayne S. Cutfield
- Liggins Institute, University of Auckland, Auckland, New Zealand
- Quadram Institute Bioscience, Norwich, United Kingdom
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215
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Leylabadlo HE, Ghotaslou R, Feizabadi MM, Farajnia S, Moaddab SY, Ganbarov K, Khodadadi E, Tanomand A, Sheykhsaran E, Yousefi B, Kafil HS. The critical role of Faecalibacterium prausnitzii in human health: An overview. Microb Pathog 2020; 149:104344. [PMID: 32534182 DOI: 10.1016/j.micpath.2020.104344] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]
Abstract
Faecalibacterium prausnitzii (F. prausnitzii) is one of the most abundant bacterial species in the colon of healthy human adults and representing more than 5% of the total bacterial population. Recently, it has been known as a major actor in human intestinal health and a biosensor. Changes in this species population richness and quantity have been observed in many illnesses and several investigations have reported that abundance of F. prausnitzii is reduced in different intestinal disorders. In the current review, we aim to consider literature from various library databases and electronic searches (Science Direct, PubMed, and Google Scholar) which were randomly collected and serve as an overview of different features of F. prausnitzii including metabolites, anti-inflammatory action, and correlation of dysbiosis of this bacterium with various complications in human.
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Affiliation(s)
- Hamed Ebrahimzadeh Leylabadlo
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Reza Ghotaslou
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Safar Farajnia
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Seyed Yaghoub Moaddab
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | | | - Ehsaneh Khodadadi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Asghar Tanomand
- Department of Microbiology, Maragheh University of Medical Sciences, Maragheh, Iran.
| | - Elham Sheykhsaran
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Bahman Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Hossein Samadi Kafil
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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216
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Liang X, Wagner RE, Li B, Zhang N, Radosevich M. Quorum Sensing Signals Alter in vitro Soil Virus Abundance and Bacterial Community Composition. Front Microbiol 2020; 11:1287. [PMID: 32587586 PMCID: PMC7298970 DOI: 10.3389/fmicb.2020.01287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Cell-density dependent quorum sensing (QS) is fundamental for many coordinated behaviors among bacteria. Most recently several studies have revealed a role for bacterial QS communication in bacteriophage (phage) reproductive decisions. However, QS based phage-host interactions remain largely unknown, with the mechanistic details revealed for only a few phage-host pairs and a dearth of information available at the microbial community level. Here we report on the specific action of eight different individual QS signals (acyl-homoserine lactones; AHLs varying in acyl-chain length from four to 14 carbon atoms) on prophage induction in soil microbial communities. We show QS autoinducers, triggered prophage induction in soil bacteria and the response was significant enough to alter bacterial community composition in vitro. AHL treatment significantly decreased the bacterial diversity (Shannon Index) but did not significantly impact species richness. Exposure to short chain-length AHLs resulted in a decrease in the abundance of different taxa than exposure to higher molecular weight AHLs. Each AHL targeted a different subset of bacterial taxa. Our observations indicate that individual AHLs may trigger prophage induction in different bacterial taxa leading to changes in microbial community structure. The findings also have implications for the role of phage-host interactions in ecologically significant processes such as biogeochemical cycles, and phage mediated transfer of host genes, e.g., photosynthesis and heavy metal/antibiotic resistance.
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Affiliation(s)
- Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Regan E. Wagner
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Bingxue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Ning Zhang
- College of Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
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217
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Antioxidant, Anti-Inflammatory, and Microbial-Modulating Activities of Essential Oils: Implications in Colonic Pathophysiology. Int J Mol Sci 2020; 21:ijms21114152. [PMID: 32532055 PMCID: PMC7313461 DOI: 10.3390/ijms21114152] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/29/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Essential oils (EOs) are a complex mixture of hydrophobic and volatile compounds synthesized from aromatic plants, most of them commonly used in the human diet. In recent years, many studies have analyzed their antimicrobial, antioxidant, anti-inflammatory, immunomodulatory and anticancer properties in vitro and on experimentally induced animal models of colitis and colorectal cancer. However, there are still few clinical studies aimed to understand their role in the modulation of the intestinal pathophysiology. Many EOs and some of their molecules have demonstrated their efficacy in inhibiting bacterial, fungi and virus replication and in modulating the inflammatory and oxidative processes that take place in experimental colitis. In addition to this, their antitumor activity against colorectal cancer models makes them extremely interesting compounds for the modulation of the pathophysiology of the large bowel. The characterization of these EOs is made difficult by their complexity and by the different compositions present in the same oil having different geographical origins. This review tries to shift the focus from the EOs to their individual compounds, to expand their possible applications in modulating colon pathophysiology.
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218
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Rasmussen TS, Koefoed AK, Jakobsen RR, Deng L, Castro-Mejía JL, Brunse A, Neve H, Vogensen FK, Nielsen DS. Bacteriophage-mediated manipulation of the gut microbiome – promises and presents limitations. FEMS Microbiol Rev 2020; 44:507-521. [DOI: 10.1093/femsre/fuaa020] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/02/2020] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT
Gut microbiome (GM) composition and function are linked to human health and disease, and routes for manipulating the GM have become an area of intense research. Due to its high treatment efficacy, the use of fecal microbiota transplantation (FMT) is generally accepted as a promising experimental treatment for patients suffering from GM imbalances (dysbiosis), e.g. caused by recurrent Clostridioides difficile infections (rCDI). Mounting evidence suggests that bacteriophages (phages) play a key role in successful FMT treatment by restoring the dysbiotic bacterial GM. As a refinement to FMT, removing the bacterial component of donor feces by sterile filtration, also referred to as fecal virome transplantation (FVT), decreases the risk of invasive infections caused by bacteria. However, eukaryotic viruses and prophage-encoded virulence factors remain a safety issue. Recent in vivo studies show how cascading effects are initiated when phage communities are transferred to the gut by e.g. FVT, which leads to changes in the GM composition, host metabolome, and improve host health such as alleviating symptoms of obesity and type-2-diabetes (T2D). In this review, we discuss the promises and limitations of FVT along with the perspectives of using FVT to treat various diseases associated with GM dysbiosis.
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Anna Kirstine Koefoed
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Rasmus Riemer Jakobsen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Ling Deng
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Josué L Castro-Mejía
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Anders Brunse
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9, 2nd floor - 1870, Frederiksberg, Denmark
| | - Horst Neve
- Institute of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Straße 1 - 24103, Kiel, Germany
| | - Finn Kvist Vogensen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
| | - Dennis Sandris Nielsen
- Section of Microbiology and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4th floor - 1958, Frederiksberg, Denmark
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219
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Abstract
The emergence of multidrug resistant bacteria in both community- and hospital-acquired infections is recognized as a major public health threat. Phage therapy is increasingly mediatized and researched as an additional tool for combatting antibiotic resistant infections. However, phages exhibit a number of properties that differ from antibiotics and hamper their development as pharmaceutical products and their application in therapy. This paper advocates a paradigm shift in the development and application of infectious disease therapeutics to cater for personalized phage therapy, which could be realized by the year 2035. More specifically, it presents a sustainable and ethical supply chain of instant synthetic phages, based on a community effort, supported and steered by public health organizations, and managed by a platform combining Artificial Intelligence (AI) and Distributed Ledger (DL) Technology.
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Affiliation(s)
- Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
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220
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Cao J, Zhang Y, Dai M, Xu J, Chen L, Zhang F, Zhao N, Wang J. Profiling of Human Gut Virome with Oxford Nanopore Technology. MEDICINE IN MICROECOLOGY 2020. [DOI: 10.1016/j.medmic.2020.100012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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221
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Chervy M, Barnich N, Denizot J. Adherent-Invasive E. coli: Update on the Lifestyle of a Troublemaker in Crohn's Disease. Int J Mol Sci 2020; 21:E3734. [PMID: 32466328 PMCID: PMC7279240 DOI: 10.3390/ijms21103734] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 12/12/2022] Open
Abstract
Besides genetic polymorphisms and environmental factors, the intestinal microbiota is an important factor in the etiology of Crohn's disease (CD). Among microbiota alterations, a particular pathotype of Escherichia coli involved in the pathogenesis of CD abnormally colonizes the intestinal mucosa of patients: the adherent-invasive Escherichia coli (AIEC) pathobiont bacteria, which have the abilities to adhere to and to invade intestinal epithelial cells (IECs), as well as to survive and replicate within macrophages. AIEC have been the subject of many studies in recent years to unveil some genes linked to AIEC virulence and to understand the impact of AIEC infection on the gut and consequently their involvement in CD. In this review, we describe the lifestyle of AIEC bacteria within the intestine, from the interaction with intestinal epithelial and immune cells with an emphasis on environmental and genetic factors favoring their implantation, to their lifestyle in the intestinal lumen. Finally, we discuss AIEC-targeting strategies such as the use of FimH antagonists, bacteriophages, or antibiotics, which could constitute therapeutic options to prevent and limit AIEC colonization in CD patients.
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Affiliation(s)
- Mélissa Chervy
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), 63001 Clermont-Ferrand, France; (M.C.); (N.B.)
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), 63001 Clermont-Ferrand, France; (M.C.); (N.B.)
- Institut Universitaire de Technologie, Génie Biologique, 63172 Aubière, France
| | - Jérémy Denizot
- Université Clermont Auvergne, Inserm U1071, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), 63001 Clermont-Ferrand, France; (M.C.); (N.B.)
- Institut Universitaire de Technologie, Génie Biologique, 63172 Aubière, France
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222
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The intestinal virome in children with cystic fibrosis differs from healthy controls. PLoS One 2020; 15:e0233557. [PMID: 32442222 PMCID: PMC7244107 DOI: 10.1371/journal.pone.0233557] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/07/2020] [Indexed: 02/06/2023] Open
Abstract
Intestinal bacterial dysbiosis is evident in children with cystic fibrosis (CF) and intestinal viruses may be contributory, given their influence on bacterial species diversity and biochemical cycles. We performed a prospective, case-control study on children with CF and age and gender matched healthy controls (HC), to investigate the composition and function of intestinal viral communities. Stool samples were enriched for viral DNA and RNA by viral extraction, random amplification and purification before sequencing (Illumina MiSeq). Taxonomic assignment of viruses was performed using Vipie. Functional annotation was performed using Virsorter. Inflammation was measured by calprotectin and M2-pyruvate kinase (M2-PK). Eight CF and eight HC subjects were included (50% male, mean age 6.9 ± 3.0 and 6.4 ± 5.3 years, respectively, p = 0.8). All CF subjects were pancreatic insufficient. Regarding the intestinal virome, no difference in Shannon index between CF and HC was identified. Taxonomy-based beta-diversity (presence-absence Bray-Curtis dissimilarity) was significantly different between CF and HC (R2 = 0.12, p = 0.001). Myoviridae, Faecalibacterium phage FP Taranis and unclassified Gokushovirinae were significantly decreased in CF compared with HC (q<0.05). In children with CF (compared to HC), the relative abundance of genes annotated to (i) a peptidoglycan-binding domain of the peptidoglycan hydrolases (COG3409) was significantly increased (q<0.05) and (ii) capsid protein (F protein) (PF02305.16) was significantly decreased (q<0.05). Picornavirales, Picornaviridae, and Enterovirus were found to positively correlate with weight and BMI (r = 0.84, q = 0.01). Single-stranded DNA viruses negatively correlated with M2-PK (r = -0.86, q = 0.048). Children with CF have an altered intestinal virome compared to well-matched HC, with both taxonomic and predicted functional changes. Further exploration of Faecalibacterium phages, Gokushovirinae and phage lysins are warranted. Intestinal viruses and their functions may have important clinical implications for intestinal inflammation and growth in children with CF, potentially providing novel therapeutic targets.
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223
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Salehi B, Dimitrijević M, Aleksić A, Neffe-Skocińska K, Zielińska D, Kołożyn-Krajewska D, Sharifi-Rad J, Stojanović-Radić Z, Prabu SM, Rodrigues CF, Martins N. Human microbiome and homeostasis: insights into the key role of prebiotics, probiotics, and symbiotics. Crit Rev Food Sci Nutr 2020; 61:1415-1428. [PMID: 32400169 DOI: 10.1080/10408398.2020.1760202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The interest in the study of the gut microbiome has grown exponentially. Indeed, its impact on health and disease has been increasingly reported, and the importance of keeping gut microbiome homeostasis clearly highlighted. However, and despite many advances, there are still some gaps, as well as the real discernment on the contribution of some species falls far short of what is needed. Anyway, it is already more than a solid fact of its importance in maintaining health and preventing disease, as well as in the treatment of some pathologies. In this sense, and given the existence of some ambiguous opinions, the present review aims to discuss the importance of gut microbiome in homeostasis maintenance, and even the role of probiotics, prebiotics, and symbiotics in both health promotion and disease prevention.
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Affiliation(s)
- Bahare Salehi
- Student Research Committee, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Marina Dimitrijević
- Department of Biology and Ecology, Faculty of Science and Mathematics, University of Niš, Niš, Serbia
| | - Ana Aleksić
- Department of Biology and Ecology, Faculty of Science and Mathematics, University of Niš, Niš, Serbia
| | - Katarzyna Neffe-Skocińska
- Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences (WULS), Warszawa, Poland
| | - Dorota Zielińska
- Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences (WULS), Warszawa, Poland
| | - Danuta Kołożyn-Krajewska
- Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences (WULS), Warszawa, Poland
| | - Javad Sharifi-Rad
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zorica Stojanović-Radić
- Department of Biology and Ecology, Faculty of Science and Mathematics, University of Niš, Niš, Serbia
| | | | - Célia F Rodrigues
- LEPABE - Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Natália Martins
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
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224
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Wan Y, Tang J, Li J, Li J, Yuan J, Wang F, Li D. Contribution of diet to gut microbiota and related host cardiometabolic health: diet-gut interaction in human health. Gut Microbes 2020; 11:603-609. [PMID: 31964203 PMCID: PMC7524383 DOI: 10.1080/19490976.2019.1697149] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Obesity and cardiometabolic diseases in both developed and developing counties in a state of nutrition transition are often related to diet, which also play a major role in shaping human gut microbiota. The human gut harbors diverse microbes that play an essential role in the well-being of their host. Complex interactions between diet and microorganisms may lead to beneficial or detrimental outcomes to host cardiometabolic health. Despite numerous studies using rodent models indicated that high-fat diet may disrupt protective functions of the intestinal barrier and contribute to inflammatory processes, evidence from population-based study is still limited. In our recent study of a 6-month randomized controlled-feeding trial, we showed that high-fat, low-carbohydrate diet was associated with unfavorable changes in gut microbiota, fecal microbial metabolites, and plasma proinflammatory factors in healthy young adults. Here, we provide an overview and extended discussion of our key findings, and outline important future directions.
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Affiliation(s)
- Yi Wan
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Jun Tang
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China
| | - Jiaomei Li
- Institute of Nutrition and Health, Qingdao University, Qingdao, China
| | - Jie Li
- No. 1 Department of Nutrition, Chinese People’s Liberation Army General Hospital, Beijing, China
| | - Jihong Yuan
- No. 1 Department of Nutrition, Chinese People’s Liberation Army General Hospital, Beijing, China
| | - Fenglei Wang
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, China,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Duo Li
- Institute of Nutrition and Health, Qingdao University, Qingdao, China,CONTACT Duo Li Institute of Nutrition and Health, Qingdao University, 308 Ningxia Road, Qingdao266071, China
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225
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Maronek M, Link R, Ambro L, Gardlik R. Phages and Their Role in Gastrointestinal Disease: Focus on Inflammatory Bowel Disease. Cells 2020; 9:E1013. [PMID: 32325706 PMCID: PMC7226564 DOI: 10.3390/cells9041013] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/09/2020] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are a group of chronic autoinflammatory diseases including Crohn's disease and ulcerative colitis. Although the molecular mechanisms governing the pathogenesis of gastrointestinal inflammation are not completely clear, the main factors are presumed to be genetic predisposition, environmental exposure, and the intestinal microbiome. Hitherto, most of the studies focusing on the role of the microbiome studied the action and effect of bacteria. However, the intestinal microbiome comprises other members of the microbial community as well, namely, fungi, protozoa, and viruses. We believe that bacteriophages are among the main orchestrators of the effect of microbiota on the gut mucosa. Therefore, this review aims to summarize the knowledge of the role of intestinal phageome in IBD and to discuss the concept of phage therapy and its future applications.
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Affiliation(s)
- Martin Maronek
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Rene Link
- Institute of Experimental Medicine, Faculty of Medicine, University of Pavol Jozef Šafárik, 040 11 Košice, Slovakia; (R.L.); (L.A.)
| | - Lubos Ambro
- Institute of Experimental Medicine, Faculty of Medicine, University of Pavol Jozef Šafárik, 040 11 Košice, Slovakia; (R.L.); (L.A.)
| | - Roman Gardlik
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
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226
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Liang G, Zhao C, Zhang H, Mattei L, Sherrill-Mix S, Bittinger K, Kessler LR, Wu GD, Baldassano RN, DeRusso P, Ford E, Elovitz MA, Kelly MS, Patel MZ, Mazhani T, Gerber JS, Kelly A, Zemel BS, Bushman FD. The stepwise assembly of the neonatal virome is modulated by breastfeeding. Nature 2020; 581:470-474. [PMID: 32461640 PMCID: PMC7263352 DOI: 10.1038/s41586-020-2192-1] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 02/14/2020] [Indexed: 01/01/2023]
Abstract
The gut of healthy human neonates is usually devoid of viruses at birth, but quickly becomes colonized, in some cases leading to gastrointestinal disorders1–4. Here we report that viral community assembly in neonates takes place in distinct steps. Fluorescent staining of virus-like particles purified from infant meconium/early stool samples show few or no particles, but by one month of life particle numbers achieve 109 per gram, and these numbers appear to persist through life5–7. We investigated the origin of these viral populations using shotgun metagenomic sequencing of viral-enriched preparations and whole microbial communities, and followed up with targeted microbiological analyses. Results indicate that, early after birth, pioneer bacteria colonize the infant gut, and by one month prophage induced from these bacteria provide the predominant population of virus-like particles. By four months of life, identifiable viruses that replicate in human cells become more prominent. Multiple human viruses were more abundant in stool samples from babies exclusively fed formula versus those fed partially or fully on breast milk, paralleling reports that breast milk can be protective against viral infections8–10. Phage populations also differed associated with breastfeeding. Evidently colonization of the infant gut is stepwise, first mainly by temperate bacteriophages induced from pioneer bacteria, and later by viruses that replicate in human cells, with the second phase modulated by breastfeeding.
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Affiliation(s)
- Guanxiang Liang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Huanjia Zhang
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lyanna R Kessler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gary D Wu
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert N Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Patricia DeRusso
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eileen Ford
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michal A Elovitz
- Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew S Kelly
- Division of Pediatric Infectious Diseases, Duke University, Durham, NC, USA
| | - Mohamed Z Patel
- Department of Paediatric and Adolescent Health, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Tiny Mazhani
- Department of Paediatric and Adolescent Health, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Jeffrey S Gerber
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Andrea Kelly
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Babette S Zemel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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227
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Bonilla-Rosso G, Steiner T, Wichmann F, Bexkens E, Engel P. Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota. Proc Natl Acad Sci U S A 2020; 117:7355-7362. [PMID: 32179689 PMCID: PMC7132132 DOI: 10.1073/pnas.2000228117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The honey bee gut microbiota influences bee health and has become an important model to study the ecology and evolution of microbiota-host interactions. Yet, little is known about the phage community associated with the bee gut, despite its potential to modulate bacterial diversity or to govern important symbiotic functions. Here we analyzed two metagenomes derived from virus-like particles, analyzed the prevalence of the identified phages across 73 bacterial metagenomes from individual bees, and tested the host range of isolated phages. Our results show that the honey bee gut virome is composed of at least 118 distinct clusters corresponding to both temperate and lytic phages and representing novel genera with a large repertoire of unknown gene functions. We find that the phage community is prevalent in honey bees across space and time and targets the core members of the bee gut microbiota. The large number and high genetic diversity of the viral clusters seems to mirror the high extent of strain-level diversity in the bee gut microbiota. We isolated eight lytic phages that target the core microbiota member Bifidobacterium asteroides, but that exhibited different host ranges at the strain level, resulting in a nested interaction network of coexisting phages and bacterial strains. Collectively, our results show that the honey bee gut virome consists of a complex and diverse phage community that likely plays an important role in regulating strain-level diversity in the bee gut and that holds promise as an experimental model to study bacteria-phage dynamics in natural microbial communities.
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Affiliation(s)
- Germán Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Théodora Steiner
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Fabienne Wichmann
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Evan Bexkens
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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228
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Beyond Just Bacteria: Functional Biomes in the Gut Ecosystem Including Virome, Mycobiome, Archaeome and Helminths. Microorganisms 2020; 8:microorganisms8040483. [PMID: 32231141 PMCID: PMC7232386 DOI: 10.3390/microorganisms8040483] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/26/2020] [Accepted: 03/26/2020] [Indexed: 12/20/2022] Open
Abstract
Gut microbiota refers to a complex network of microbes, which exerts a marked influence on the host’s health. It is composed of bacteria, fungi, viruses, and helminths. Bacteria, or collectively, the bacteriome, comprises a significant proportion of the well-characterized microbiome. However, the other communities referred to as ‘dark matter’ of microbiomes such as viruses (virome), fungi (mycobiome), archaea (archaeome), and helminths have not been completely elucidated. Development of new and improved metagenomics methods has allowed the identification of complete genomes from the genetic material in the human gut, opening new perspectives on the understanding of the gut microbiome composition, their importance, and potential clinical applications. Here, we review the recent evidence on the viruses, fungi, archaea, and helminths found in the mammalian gut, detailing their interactions with the resident bacterial microbiota and the host, to explore the potential impact of the microbiome on host’s health. The role of fecal virome transplantations, pre-, pro-, and syn-biotic interventions in modulating the microbiome and their related concerns are also discussed.
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229
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Rouse MD, Stanbro J, Roman JA, Lipinski MA, Jacobs A, Biswas B, Regeimbal J, Henry M, Stockelman MG, Simons MP. Impact of Frequent Administration of Bacteriophage on Therapeutic Efficacy in an A. baumannii Mouse Wound Infection Model. Front Microbiol 2020; 11:414. [PMID: 32256472 PMCID: PMC7090133 DOI: 10.3389/fmicb.2020.00414] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/27/2020] [Indexed: 01/21/2023] Open
Abstract
The spread of multidrug antibiotic resistance (MDR) is a widely recognized crisis in the treatment of bacterial infections, including those occurring in military communities. Recently, the World Health Organization published its first ever list of antibiotic-resistant “priority pathogens” – a catalog of 12 families of bacteria that pose the greatest threat to human health with A. baumannii listed in the “Priority 1: Critical” category of pathogens. With the increasing prevalence of antibiotic resistance and limited development of new classes of antibiotics, alternative antimicrobial therapies are needed, with lytic bacteriophage (phage) specifically targeted against each of the high priority bacterial infections as a potential approach currently in development toward regulatory approval for clinical use. Balb/c mice were prophylactically administered PBS or phage selected against A. baumannii strain AB5075. After 3 weeks, mice were anesthetized, wounded (dorsal), and challenged topically with AB5075. Following infection, mice were subsequently treated with PBS or phage for three consecutive days, and evaluated for 3 weeks to assess the safety and efficacy of the phage treatment relative to the control. We assessed mortality, bacterial burden, time to wound closure, systemic and local cytokine profiles, alterations in host cellular immunity, and finally presence of neutralizing antibodies to the phage mixture. In our study, we found that prophylactic phage administration led to a significant reduction in monocyte-related cytokines in serum compared to mice given PBS. However, we detected no significant changes to circulating blood populations or immune cell populations of secondary lymphoid organs compared to PBS-treated mice. Following prophylactic phage administration, we detected a marked increase in total immunoglobulins in serum, particularly IgG2a and IgG2b. Furthermore, we determined that these antibodies were able to specifically target phage and effectively neutralize their ability to lyse their respective target. In regards to their therapeutic efficacy, administration of phage treatment effectively decreased wound size of mice infected with AB5075 without adverse effects. In conclusion, our data demonstrate that phage can serve as a safe and effective novel therapeutic agent against A. baumannii without adverse reactions to the host and pre-exposure to phage does not seem to adversely affect therapeutic efficacy. This study is an important proof of concept to support the efforts to develop phage as a novel therapeutic product for treatment of complex bacterial wound infections.
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Affiliation(s)
- Michael D Rouse
- Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States.,Naval Medical Research Center, Silver Spring, MD, United States
| | - Joshua Stanbro
- Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States.,Naval Medical Research Center, Silver Spring, MD, United States
| | - Jessica A Roman
- Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States.,Naval Medical Research Center, Silver Spring, MD, United States
| | - Michelle A Lipinski
- Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States.,Naval Medical Research Center, Silver Spring, MD, United States
| | - Anna Jacobs
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Biswaijt Biswas
- Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | | | - Matthew Henry
- Naval Medical Research Center, Silver Spring, MD, United States.,Biological Defense Research Directorate, Naval Medical Research Center, Fort Detrick, MD, United States
| | | | - Mark P Simons
- Naval Medical Research Center, Silver Spring, MD, United States
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230
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Abstract
Spondyloarthritis (SpA) is a group of chronic, inflammatory rheumatic diseases mainly affecting the axial skeleton. Although the pathogenesis of the disease remains elusive, alterations of intestinal microbial composition have been demonstrated in patients with SpA and associated with intestinal and systemic immune alterations. Substantial data have been published in recent years in ethnically different patient populations, demonstrating in a consolidated way the presence of alterations in the composition of the microbial flora in patients with SpA. It is not currently possible to establish whether these alterations are intrinsically inherent in the disease, for example, the effect of particular genes that confer susceptibility to the disease itself, or are a consequence of a more systemic inflammatory process that also involves the intestine. However, data deriving from animal models and studies on relatives of patients with SpA strongly suggest that these alterations might precede the onset of the disease. In this review, we will try to critically analyze studies on dysbiosis in SpA and animal models of SpA, analyzing their functional consequences and the impact of biotechnological therapies on intestinal bacterial composition.
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Affiliation(s)
- Daniele Mauro
- Department of Precision Medicine, Università Degli Studi Della Campania L. Vanvitelli, Naples, Italy
| | - Francesco Ciccia
- Department of Precision Medicine, Università Degli Studi Della Campania L. Vanvitelli, Naples, Italy.
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231
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Kazemian N, Mahmoudi M, Halperin F, Wu JC, Pakpour S. Gut microbiota and cardiovascular disease: opportunities and challenges. MICROBIOME 2020; 8:36. [PMID: 32169105 PMCID: PMC7071638 DOI: 10.1186/s40168-020-00821-0] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 03/02/2020] [Indexed: 05/03/2023]
Abstract
Coronary artery disease (CAD) is the most common health problem worldwide and remains the leading cause of morbidity and mortality. Over the past decade, it has become clear that the inhabitants of our gut, the gut microbiota, play a vital role in human metabolism, immunity, and reactions to diseases, including CAD. Although correlations have been shown between CAD and the gut microbiota, demonstration of potential causal relationships is much more complex and challenging. In this review, we will discuss the potential direct and indirect causal roots between gut microbiota and CAD development via microbial metabolites and interaction with the immune system. Uncovering the causal relationship of gut microbiota and CAD development can lead to novel microbiome-based preventative and therapeutic interventions. However, an interdisciplinary approach is required to shed light on gut bacterial-mediated mechanisms (e.g., using advanced nanomedicine technologies and incorporation of demographic factors such as age, sex, and ethnicity) to enable efficacious and high-precision preventative and therapeutic strategies for CAD.
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Affiliation(s)
- Negin Kazemian
- School of Engineering, University of British Columbia, Kelowna, Kelowna, BC, Canada
| | - Morteza Mahmoudi
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI, USA.
| | | | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sepideh Pakpour
- School of Engineering, University of British Columbia, Kelowna, Kelowna, BC, Canada.
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232
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Keshavarzian A, Engen P, Bonvegna S, Cilia R. The gut microbiome in Parkinson's disease: A culprit or a bystander? PROGRESS IN BRAIN RESEARCH 2020; 252:357-450. [PMID: 32247371 DOI: 10.1016/bs.pbr.2020.01.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In recent years, large-scale metagenomics projects such as the Human Microbiome Project placed the gut microbiota under the spotlight of research on its role in health and in the pathogenesis several diseases, as it can be a target for novel therapeutical approaches. The emerging concept of a microbiota modulation of the gut-brain axis in the pathogenesis of neurodegenerative disorders has been explored in several studies in animal models, as well as in human subjects. Particularly, research on changes in the composition of gut microbiota as a potential trigger for alpha-synuclein (α-syn) pathology in Parkinson's disease (PD) has gained increasing interest. In the present review, we first provide the basis to the understanding of the role of gut microbiota in healthy subjects and the molecular basis of the gut-brain interaction, focusing on metabolic and neuroinflammatory factors that could trigger the alpha-synuclein conformational changes and aggregation. Then, we critically explored preclinical and clinical studies reporting on the changes in gut microbiota in PD, as compared to healthy subjects. Furthermore, we examined the relationship between the gut microbiota and PD clinical features, discussing data consistently reported across studies, as well as the potential sources of inconsistencies. As a further step toward understanding the effects of gut microbiota on PD, we discussed the relationship between dysbiosis and response to dopamine replacement therapy, focusing on Levodopa metabolism. We conclude that further studies are needed to determine whether the gut microbiota changes observed so far in PD patients is the cause or, instead, it is merely a consequence of lifestyle changes associated with the disease. Regardless, studies so far strongly suggest that changes in microbiota appears to be impactful in pathogenesis of neuroinflammation. Thus, dysbiotic microbiota in PD could influence the disease course and response to medication, especially Levodopa. Future research will assess the impact of microbiota-directed therapeutic intervention in PD patients.
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Affiliation(s)
- Ali Keshavarzian
- Department of Internal Medicine, Division of Digestive Disease and Nutrition, Rush University Medical Center, Chicago, IL, United States
| | - Phillip Engen
- Department of Internal Medicine, Division of Digestive Disease and Nutrition, Rush University Medical Center, Chicago, IL, United States
| | | | - Roberto Cilia
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Movement Disorders Unit, Milan, Italy.
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233
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Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths in both the USA and the world. Recent research has demonstrated the involvement of the gut microbiota in CRC development and progression. Microbial biomarkers of disease have focused primarily on the bacterial component of the microbiome; however, the viral portion of the microbiome, consisting of both bacteriophages and eukaryotic viruses, together known as the virome, has been lesser studied. Here we review the recent advancements in high-throughput sequencing (HTS) technologies and bioinformatics, which have enabled scientists to better understand how viruses might influence the development of colorectal cancer. We discuss the contemporary findings revealing modulations in the virome and their correlation with CRC development and progression. While a variety of challenges still face viral HTS detection in clinical specimens, we consider herein numerous next steps for future basic and clinical research. Clinicians need to move away from a single infectious agent model for disease etiology by grasping new, more encompassing etiological paradigms, in which communities of various microbial components interact with each other and the host. The reporting and indexing of patient health information, socioeconomic data, and other relevant metadata will enable identification of predictive variables and covariates of viral presence and CRC development. Altogether, the virome has a more profound role in carcinogenesis and cancer progression than once thought, and viruses, specific for either human cells or bacteria, are clinically relevant in understanding CRC pathology, patient prognosis, and treatment development.
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234
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Sausset R, Petit MA, Gaboriau-Routhiau V, De Paepe M. New insights into intestinal phages. Mucosal Immunol 2020; 13:205-215. [PMID: 31907364 PMCID: PMC7039812 DOI: 10.1038/s41385-019-0250-5] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/13/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
Abstract
The intestinal microbiota plays important roles in human health. This last decade, the viral fraction of the intestinal microbiota, composed essentially of phages that infect bacteria, received increasing attention. Numerous novel phage families have been discovered in parallel with the development of viral metagenomics. However, since the discovery of intestinal phages by d'Hérelle in 1917, our understanding of the impact of phages on gut microbiota structure remains scarce. Changes in viral community composition have been observed in several diseases. However, whether these changes reflect a direct involvement of phages in diseases etiology or simply result from modifications in bacterial composition is currently unknown. Here we present an overview of the current knowledge in intestinal phages, their identity, lifestyles, and their possible effects on the gut microbiota. We also gather the main data on phage interactions with the immune system, with a particular emphasis on recent findings.
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Affiliation(s)
- R Sausset
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- Myriade, 68 boulevard de Port Royal, 75005, Paris, France
| | - M A Petit
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - V Gaboriau-Routhiau
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- Laboratory of Intestinal Immunity, INSERM UMR 1163, Institut Imagine, Paris, France
- Université Paris Descartes-Sorbonne Paris Cité, 75006, Paris, France
| | - M De Paepe
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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235
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Cornuault JK, Moncaut E, Loux V, Mathieu A, Sokol H, Petit MA, De Paepe M. The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition. THE ISME JOURNAL 2020; 14:771-787. [PMID: 31827247 PMCID: PMC7031369 DOI: 10.1038/s41396-019-0566-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 11/28/2019] [Indexed: 12/13/2022]
Abstract
Despite an overall temporal stability in time of the human gut microbiota at the phylum level, strong variations in species abundance have been observed. We are far from a clear understanding of what promotes or disrupts the stability of microbiome communities. Environmental factors, like food or antibiotic use, modify the gut microbiota composition, but their overall impacts remain relatively low. Phages, the viruses that infect bacteria, might constitute important factors explaining temporal variations in species abundance. Gut bacteria harbour numerous prophages, or dormant viruses, which can evolve to become ultravirulent phage mutants, potentially leading to important bacterial death. Whether such phenomenon occurs in the mammal's microbiota has been largely unexplored. Here we studied temperate phage-bacteria coevolution in gnotoxenic mice colonised with Roseburia intestinalis, a dominant symbiont of the human gut microbiota, and Escherichia coli, a sub-dominant member of the same microbiota. We show that R. intestinalis L1-82 harbours two active prophages, Jekyll and Shimadzu. We observed the systematic evolution in mice of ultravirulent Shimadzu phage mutants, which led to a collapse of R. intestinalis population. In a second step, phage infection drove the fast counter-evolution of host phage resistance mainly through phage-derived spacer acquisition in a clustered regularly interspaced short palindromic repeats array. Alternatively, phage resistance was conferred by a prophage originating from an ultravirulent phage with a restored ability to lysogenize. Our results demonstrate that prophages are a potential source of ultravirulent phages that can successfully infect most of the susceptible bacteria. This suggests that prophages can play important roles in the short-term temporal variations observed in the composition of the gut microbiota.
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Affiliation(s)
- Jeffrey K Cornuault
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Elisabeth Moncaut
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Valentin Loux
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | - Aurélie Mathieu
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Harry Sokol
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint Antoine, Service de Gastroenterologie, F-75012, Paris, France
- Department of Gastroenterology, Saint-Antoine Hospital, Assistance Publique - Hôpitaux de Paris, UPMC, Paris, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Marianne De Paepe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
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236
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Schulfer A, Santiago-Rodriguez TM, Ly M, Borin JM, Chopyk J, Blaser MJ, Pride DT. Fecal Viral Community Responses to High-Fat Diet in Mice. mSphere 2020; 5:e00833-19. [PMID: 32102942 PMCID: PMC7045389 DOI: 10.1128/msphere.00833-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
Alterations in diet can have significant impact on the host, with high-fat diet (HFD) leading to obesity, diabetes, and inflammation of the gut. Although membership and abundances in gut bacterial communities are strongly influenced by diet, substantially less is known about how viral communities respond to dietary changes. Examining fecal contents of mice as the mice were transitioned from normal chow to HFD, we found significant changes in the relative abundances and the diversity in the gut of bacteria and their viruses. Alpha diversity of the bacterial community was significantly diminished in response to the diet change but did not change significantly in the viral community. However, the diet shift significantly impacted the beta diversity in both the bacterial and viral communities. There was a significant shift away from the relatively abundant Siphoviridae accompanied by increases in bacteriophages from the Microviridae family. The proportion of identified bacteriophage structural genes significantly decreased after the transition to HFD, with a conserved loss of integrase genes in all four experimental groups. In total, this study provides evidence for substantial changes in the intestinal virome disproportionate to bacterial changes, and with alterations in putative viral lifestyles related to chromosomal integration as a result of shift to HFD.IMPORTANCE Prior studies have shown that high-fat diet (HFD) can have profound effects on the gastrointestinal (GI) tract microbiome and also demonstrate that bacteria in the GI tract can affect metabolism and lean/obese phenotypes. We investigated whether the composition of viral communities that also inhabit the GI tract are affected by shifts from normal to HFD. We found significant and reproducible shifts in the content of GI tract viromes after the transition to HFD. The differences observed in virome community membership and their associated gene content suggest that these altered viral communities are populated by viruses that are more virulent toward their host bacteria. Because HFD also are associated with significant shifts in GI tract bacterial communities, we believe that the shifts in the viral community may serve to drive the changes that occur in associated bacterial communities.
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Affiliation(s)
| | | | - Melissa Ly
- Department of Pathology, University of California, San Diego, California, USA
| | - Joshua M Borin
- Division of Biological Sciences, University of California, San Diego, California, USA
| | - Jessica Chopyk
- Department of Pathology, University of California, San Diego, California, USA
| | - Martin J Blaser
- New York University, New York, New York, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - David T Pride
- Department of Pathology, University of California, San Diego, California, USA
- Department of Medicine, University of California, San Diego, California, USA
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237
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Guo Z, Lin H, Ji X, Yan G, Lei L, Han W, Gu J, Huang J. Therapeutic applications of lytic phages in human medicine. Microb Pathog 2020; 142:104048. [PMID: 32035104 DOI: 10.1016/j.micpath.2020.104048] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/03/2020] [Accepted: 02/05/2020] [Indexed: 12/24/2022]
Abstract
The emergence and spread of antibiotic-resistant bacteria constitute a critical issue for modern medicine. Patients with antibiotic-resistant bacterial infections consume more healthcare resources and have worse clinical outcomes than patients with antibiotic-sensitive bacterial infections. Phages are natural predators of bacteria and may therefore be a source of useful antibacterial drugs. Phage therapy possess availability for oral administration, penetration through the bacteria cell wall, and eradication bacterial biofilms. All of these advantages give phage therapy the possibility to turn into applications for infectious diseases. In this mini-review, we focus on the brief history of lytic phage therapy, the life cycles of lytic phages and the therapeutic effects of lytic phages.
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Affiliation(s)
- Zhimin Guo
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, 130021, China
| | - Hua Lin
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, 130021, China
| | - Xufeng Ji
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, 130021, China
| | - Guangmou Yan
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, 130062, China
| | - Liancheng Lei
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, 130062, China
| | - Wenyu Han
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, 130062, China
| | - Jingmin Gu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333, Changchun, 130062, China.
| | - Jing Huang
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, 130021, China.
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238
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Mullish BH, Quraishi MN, Segal JP, Ianiro G, Iqbal TH. The gut microbiome: what every gastroenterologist needs to know. Frontline Gastroenterol 2020; 12:118-127. [PMID: 33613943 PMCID: PMC7873547 DOI: 10.1136/flgastro-2019-101376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 02/04/2023] Open
Abstract
The mucosal surfaces of the body are characterised by complex, specialised microbial communities, often referred to as the microbiome. However, only much more recently-with the development of technologies allowing exploration of the composition and functionality of these communities-has meaningful research in this area become feasible. Over the past few years, there has been rapid growth in interest in the gut microbiome in particular, and its potential contribution to gastrointestinal and liver disease. This interest has already extended beyond clinicians to pharmaceutical companies, medical regulators and other stakeholders, and is high profile among patients and the lay public in general. Such expansion of knowledge holds the intriguing potential for translation into novel diagnostics and therapeutics; however, being such a nascent field, there remain many uncertainties, unanswered questions and areas of debate.
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Affiliation(s)
- Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College of Science Technology and Medicine, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Mohammed Nabil Quraishi
- University of Birmingham Microbiome Treatment Centre, University of Birmingham, Birmingham, UK
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Jonathan P Segal
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Gianluca Ianiro
- Digestive Disease Centre, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Gemelli, Rome, Italy
| | - Tariq H Iqbal
- University of Birmingham Microbiome Treatment Centre, University of Birmingham, Birmingham, UK
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
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239
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Dion MB, Oechslin F, Moineau S. Phage diversity, genomics and phylogeny. Nat Rev Microbiol 2020; 18:125-138. [PMID: 32015529 DOI: 10.1038/s41579-019-0311-5] [Citation(s) in RCA: 381] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2019] [Indexed: 12/23/2022]
Abstract
Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes.
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Affiliation(s)
- Moïra B Dion
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Frank Oechslin
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada. .,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada. .,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada.
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240
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Abstract
With the increasing frequency of antibiotic resistance, it is critical to explore new therapeutic strategies for treating bacterial infections. Here, we use a temperate phage, i.e., one that integrates itself into the bacterial genome, to neutralize the expression of a virulence factor by modifying bacterial function at the genetic level. We show that Shiga toxin production can be significantly reduced in vitro and in the mammalian gut. Alternative to traditional applications of phage therapy that rely on killing bacteria, our genetics-based antivirulence approach introduces a new framework for treating bacterial infections. Elimination or alteration of select members of the gut microbiota is key to therapeutic efficacy. However, the complexity of these microbial inhabitants makes it challenging to precisely target bacteria. Here, we deliver exogenous genes to specific bacteria by genomic integration of temperate phage for long-lasting modification. As a real-world therapeutic test, we engineered λ phage to transcriptionally repress Shiga toxin by using genetic hybrids between λ and other lambdoid phages to overcome resistance encoded by the virulence-expressing prophage. We show that a single dose of engineered phage propagates throughout the bacterial community and reduces Shiga toxin production in an enteric mouse model of infection without markedly affecting bacterial concentrations. Our work reveals a new framework for transferring functions to bacteria within their native environment. IMPORTANCE With the increasing frequency of antibiotic resistance, it is critical to explore new therapeutic strategies for treating bacterial infections. Here, we use a temperate phage, i.e., one that integrates itself into the bacterial genome, to neutralize the expression of a virulence factor by modifying bacterial function at the genetic level. We show that Shiga toxin production can be significantly reduced in vitro and in the mammalian gut. Alternative to traditional applications of phage therapy that rely on killing bacteria, our genetics-based antivirulence approach introduces a new framework for treating bacterial infections.
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241
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Zolfo M, Pinto F, Asnicar F, Manghi P, Tett A, Bushman FD, Segata N. Detecting contamination in viromes using ViromeQC. Nat Biotechnol 2020; 37:1408-1412. [PMID: 31748692 DOI: 10.1038/s41587-019-0334-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
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242
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Mathieu A, Dion M, Deng L, Tremblay D, Moncaut E, Shah SA, Stokholm J, Krogfelt KA, Schjørring S, Bisgaard H, Nielsen DS, Moineau S, Petit MA. Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages. Nat Commun 2020; 11:378. [PMID: 31953385 PMCID: PMC6969025 DOI: 10.1038/s41467-019-14042-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/10/2019] [Indexed: 01/08/2023] Open
Abstract
Bacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown. Here, we cultivate temperate phages produced by 900 E. coli strains isolated from 648 fecal samples from 1-year-old children and obtain coliphages directly from the viral fraction of the same fecal samples. We find that 63% of strains hosted phages, while 24% of the viromes contain phages targeting E. coli. 150 of these phages, half recovered from strain supernatants, half from virome (73% temperate and 27% virulent) were tested for their host range on 75 E. coli strains isolated from the same cohort. Temperate phages barely infected the gut strains, whereas virulent phages killed up to 68% of them. We conclude that in fecal samples from children, temperate coliphages dominate, while virulent ones have greater infectivity and broader host range, likely playing a role in gut microbiota dynamics. The impact of bacteriophages in the human gut microbiome remains poorly understood. Here, the authors characterize coliphages isolated from a large cohort of 1-year-old infants and show that temperate coliphages dominate, while virulent ones have greater infectivity and broader host range.
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Affiliation(s)
- Aurélie Mathieu
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Moïra Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Denise Tremblay
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Elisabeth Moncaut
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej5, 2300S, Copenhagen, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej5, 2300S, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
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243
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Siranosian BA, Tamburini FB, Sherlock G, Bhatt AS. Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages. Nat Commun 2020; 11:280. [PMID: 31941900 PMCID: PMC6962324 DOI: 10.1038/s41467-019-14103-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/04/2019] [Indexed: 12/28/2022] Open
Abstract
CrAss-like phages are double-stranded DNA viruses that are prevalent in human gut microbiomes. Here, we analyze gut metagenomic data from mother-infant pairs and patients undergoing fecal microbiota transplantation to evaluate the patterns of acquisition, transmission and strain diversity of crAss-like phages. We find that crAss-like phages are rarely detected at birth but are increasingly prevalent in the infant microbiome after one month of life. We observe nearly identical genomes in 50% of cases where the same crAss-like clade is detected in both the mother and the infant, suggesting vertical transmission. In cases of putative transmission of prototypical crAssphage (p-crAssphage), we find that a subset of strains present in the mother are detected in the infant, and that strain diversity in infants increases with time. Putative tail fiber proteins are enriched for nonsynonymous strain variation compared to other genes, suggesting a potential evolutionary benefit to maintaining strain diversity in specific genes. Finally, we show that p-crAssphage can be acquired through fecal microbiota transplantation.
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Affiliation(s)
| | | | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA.
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244
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Honap TP, Sankaranarayanan K, Schnorr SL, Ozga AT, Warinner C, Lewis CM. Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion. PLoS One 2020; 15:e0226930. [PMID: 31940321 PMCID: PMC6961876 DOI: 10.1371/journal.pone.0226930] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as compared to industrialized, urban populations. Statistical comparisons showed no association of crAssphage prevalence with variables such as age, sex, body mass index, and health status of individuals. Phylogenetic analyses show that crAssphage strains reconstructed from the same individual over multiple time-points, cluster together. CrAssphage strains from individuals from the same study population do not always cluster together. Some evidence of clustering is seen at the level of broadly defined geographic regions, however, the relative positions of these clusters within the crAssphage phylogeny are not well-supported. We hypothesize that this lack of strong biogeographic structuring is suggestive of an expansion event within crAssphage. Using a Bayesian dating approach, we estimate that this expansion has occurred fairly recently. Overall, we determine that crAssphage presence is associated with an industrialized lifestyle and the absence of strong biogeographic structuring within global crAssphage strains is likely due to a recent population expansion within this bacteriophage.
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Affiliation(s)
- Tanvi P. Honap
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Stephanie L. Schnorr
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Andrew T. Ozga
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Christina Warinner
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Cecil M. Lewis
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
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245
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Kigerl KA, Zane K, Adams K, Sullivan MB, Popovich PG. The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury. Exp Neurol 2020; 323:113085. [PMID: 31654639 PMCID: PMC6918675 DOI: 10.1016/j.expneurol.2019.113085] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/24/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022]
Abstract
Most spinal cord injury (SCI) research programs focus only on the injured spinal cord with the goal of restoring locomotor function by overcoming mechanisms of cell death or axon regeneration failure. Given the importance of the spinal cord as a locomotor control center and the public perception that paralysis is the defining feature of SCI, this "spinal-centric" focus is logical. Unfortunately, such a focus likely will not yield new discoveries that reverse other devastating consequences of SCI including cardiovascular and metabolic disease, bladder/bowel dysfunction and infection. The current review considers how SCI changes the physiological interplay between the spinal cord, the gut and the immune system. A suspected culprit in causing many of the pathological manifestations of impaired spinal cord-gut-immune axis homeostasis is the gut microbiota. After SCI, the composition of the gut microbiota changes, creating a chronic state of gut "dysbiosis". To date, much of what we know about gut dysbiosis was learned from 16S-based taxonomic profiling studies that reveal changes in the composition and abundance of various bacteria. However, this approach has limitations and creates taxonomic "blindspots". Notably, only bacteria can be analyzed. Thus, in this review we also discuss how the application of emerging sequencing technologies can improve our understanding of how the broader ecosystem in the gut is affected by SCI. Specifically, metagenomics will provide researchers with a more comprehensive look at post-injury changes in the gut virome (and mycome). Metagenomics also allows changes in microbe population dynamics to be linked to specific microbial functions that can affect the development and progression of metabolic disease, immune dysfunction and affective disorders after SCI. As these new tools become more readily available and used across the research community, the development of an "ecogenomic" toolbox will facilitate an Eco-Systems Biology approach to study the complex interplay along the spinal cord-gut-immune axis after SCI.
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Affiliation(s)
- Kristina A Kigerl
- The Belford Center for Spinal Cord Injury, the Center for Brain and Spinal Cord Repair, Department of Neuroscience, Wexner Medical Center at The Ohio State University, USA
| | - Kylie Zane
- The Ohio State University College of Medicine, USA
| | - Kia Adams
- The Belford Center for Spinal Cord Injury, the Center for Brain and Spinal Cord Repair, Department of Neuroscience, Wexner Medical Center at The Ohio State University, USA
| | - Matthew B Sullivan
- Departments of Microbiology, Civil, Environmental and Geodetic Engineering at The Ohio State University, USA
| | - Phillip G Popovich
- The Belford Center for Spinal Cord Injury, the Center for Brain and Spinal Cord Repair, Department of Neuroscience, Wexner Medical Center at The Ohio State University, USA.
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246
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Sabino J, Hirten RP, Colombel JF. Review article: bacteriophages in gastroenterology-from biology to clinical applications. Aliment Pharmacol Ther 2020; 51:53-63. [PMID: 31696976 DOI: 10.1111/apt.15557] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 04/25/2019] [Accepted: 10/03/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND The gut microbiota plays an important role in the pathogenesis of several gastrointestinal diseases. Its composition and function are shaped by host-microbiota and intra-microbiota interactions. Bacteriophages (phages) are viruses that target bacteria and have the potential to modulate bacterial communities. AIMS To summarise phage biology and the clinical applications of phages in gastroenterology METHODS: PubMed was searched to identify relevant studies. RESULTS Phages induce bacterial cell lysis, integration of viral DNA into the bacteria and/or coexistence in a stable equilibrium. Bacteria and phages have co-evolved and their dynamic interactions are yet to be fully understood. The increasing need to modulate microbial communities (e.g., gut microbiota, multidrug-resistant bacteria) has been a strong stimulus for research in phages as an antibacterial therapy. In gastroenterology, phage therapy has been mainly studied in infectious diseases such as cholera. However, it is currently being explored in several other circumstances such as treating Clostridioides difficile colitis, targeting adherent-invasive Escherichia coli in Crohn's disease or eradicating Fusobacterium nucleatum in colorectal cancer. Overall, phage therapy has a favourable and acceptable safety profile. Presently, trials with phage therapy are ongoing in Crohn's disease. CONCLUSIONS Phage therapy is a promising therapeutic tool against pathogenic bacteria in the fields of infectious diseases and gastroenterology. Randomised, placebo-controlled trials with phage therapy for gastroenterological diseases are ongoing.
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Affiliation(s)
- João Sabino
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Gastroenterology, University Hospitals of Leuven, Leuven, Belgium
| | - Robert P Hirten
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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247
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Ahern PP, Maloy KJ. Understanding immune-microbiota interactions in the intestine. Immunology 2020; 159:4-14. [PMID: 31777071 PMCID: PMC6904641 DOI: 10.1111/imm.13150] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
The past two decades have seen an explosion in research that aims to understand how the dynamic interplay with the gut microbiota impacts host health and disease, establishing a role for the gut microbiota in a plethora of pathologies. Understanding how health-promoting microbiota are established and how beneficial host-microbiota interactions are maintained is of immense biomedical importance. Despite the enormous progress that has been made, our knowledge of the specific microbiota members that mediate these effects and the mechanisms underlying these interactions is rudimentary. The dearth of information regarding the nature of advantageous host-microbiota interactions, and the factors that cause these relationships to go awry, has hampered our ability to realize the therapeutic potential of the microbiota. Here we discuss key issues that limit current knowledge and describe a path forwards to improving our understanding of the contributions of the microbiota to host health.
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Affiliation(s)
- Philip P. Ahern
- Department of Cardiovascular and Metabolic SciencesCleveland Clinic Lerner Research InstituteClevelandOHUSA
| | - Kevin J. Maloy
- Institute of Infection, Immunity and InflammationCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
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248
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Yuan L, Hensley C, Mahsoub HM, Ramesh AK, Zhou P. Microbiota in viral infection and disease in humans and farm animals. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:15-60. [PMID: 32475521 PMCID: PMC7181997 DOI: 10.1016/bs.pmbts.2020.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The influence of the microbiota on viral infection susceptibility and disease outcome is undisputable although varies among viruses. The purpose of understanding the interactions between microbiota, virus, and host is to identify practical, effective, and safe approaches that target microbiota for the prevention and treatment of viral diseases in humans and animals, as currently there are few effective and reliable antiviral therapies available. The initial step for achieving this goal is to gather clinical evidences, focusing on the viral pathogens-from human and animal studies-that have already been shown to interact with microbiota. The subsequent step is to identify mechanisms, through experimental evidences, to support the development of translational applications that target microbiota. In this chapter, we review evidences of virus infections altering microbiota and of microbiota enhancing or suppressing infectivity, altering host susceptibility to certain viral diseases, and influencing vaccine immunogenicity in humans and farm animals.
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Affiliation(s)
- Lijuan Yuan
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States; Integrated Life Science Building, Blacksburg, VA, United States.
| | - Casey Hensley
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States; Integrated Life Science Building, Blacksburg, VA, United States
| | - Hassan M Mahsoub
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States; Integrated Life Science Building, Blacksburg, VA, United States
| | - Ashwin K Ramesh
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States; Integrated Life Science Building, Blacksburg, VA, United States
| | - Peng Zhou
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States; Integrated Life Science Building, Blacksburg, VA, United States
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Prophages in Lactobacillus reuteri Are Associated with Fitness Trade-Offs but Can Increase Competitiveness in the Gut Ecosystem. Appl Environ Microbiol 2019; 86:AEM.01922-19. [PMID: 31676478 PMCID: PMC6912086 DOI: 10.1128/aem.01922-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022] Open
Abstract
Bacteriophages derived from lysogens are abundant in gut microbiomes. Currently, mechanistic knowledge is lacking on the ecological ramifications of prophage carriage yet is essential to explain the abundance of lysogens in the gut. An extensive screen of the bacterial gut symbiont Lactobacillus reuteri revealed that biologically active prophages are widely distributed in this species. L. reuteri 6475 produces phages throughout the mouse intestinal tract, but phage production is associated with reduced fitness of the lysogen. However, phage production provides a competitive advantage in direct competition with a nonlysogenic strain of L. reuteri that is sensitive to these phages. This combination of increased competition with a fitness trade-off provides a potential explanation for the domination of lysogens in gut ecosystem and how lysogens can coexist with sensitive hosts. The gut microbiota harbors a diverse phage population that is largely derived from lysogens, which are bacteria that contain dormant phages in their genome. While the diversity of phages in gut ecosystems is getting increasingly well characterized, knowledge is limited on how phages contribute to the evolution and ecology of their host bacteria. Here, we show that biologically active prophages are widely distributed in phylogenetically diverse strains of the gut symbiont Lactobacillus reuteri. Nearly all human- and rodent-derived strains, but less than half of the tested strains of porcine origin, contain active prophages, suggesting different roles of phages in the evolution of host-specific lineages. To gain insight into the ecological role of L. reuteri phages, we developed L. reuteri strain 6475 as a model to study its phages. After administration to mice, L. reuteri 6475 produces active phages throughout the intestinal tract, with the highest number detected in the distal colon. Inactivation of recA abolished in vivo phage production, which suggests that activation of the SOS response drives phage production in the gut. In conventional mice, phage production reduces bacterial fitness as fewer wild-type bacteria survive gut transit compared to the mutant lacking prophages. However, in gnotobiotic mice, phage production provides L. reuteri with a competitive advantage over a sensitive host. Collectively, we uncovered that the presence of prophages, although associated with a fitness trade-off, can be advantageous for a gut symbiont by killing a competitor strain in its intestinal niche. IMPORTANCE Bacteriophages derived from lysogens are abundant in gut microbiomes. Currently, mechanistic knowledge is lacking on the ecological ramifications of prophage carriage yet is essential to explain the abundance of lysogens in the gut. An extensive screen of the bacterial gut symbiont Lactobacillus reuteri revealed that biologically active prophages are widely distributed in this species. L. reuteri 6475 produces phages throughout the mouse intestinal tract, but phage production is associated with reduced fitness of the lysogen. However, phage production provides a competitive advantage in direct competition with a nonlysogenic strain of L. reuteri that is sensitive to these phages. This combination of increased competition with a fitness trade-off provides a potential explanation for the domination of lysogens in gut ecosystem and how lysogens can coexist with sensitive hosts.
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Arnaud AP, Rome V, Richard M, Formal M, David-Le Gall S, Boudry G. Post-natal co-development of the microbiota and gut barrier function follows different paths in the small and large intestine in piglets. FASEB J 2019; 34:1430-1446. [PMID: 31914707 DOI: 10.1096/fj.201902514r] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/04/2019] [Accepted: 11/13/2019] [Indexed: 12/17/2022]
Abstract
Gut microbiota and intestinal barrier co-develop after birth, establishing a homeostatic state whereby mucosal cells cohabit with commensal bacteria. We hypothesized that this post-natal co-development follows different timings depending on the intestinal site considered. Jejunal, ileal, and colonic luminal contents and mucosa were sampled in suckling piglets at post-natal day (PND) 0, 2, 7, 14, and 28. Jejunal, ileal, and colonic luminal microbiota (evaluated by 16S DNA sequencing followed by beta-diversity analysis) clustered at PND2 but colonic microbiota diverge afterwards (P < .05). Mucosal permeability, evaluated in Ussing chambers, increased with age in the jejunum and ileum (P < .05) but not the colon. Expression of pattern recognition receptor (PRR) exhibited different patterns (gradual or sharp increase, decrease, or no change with age, P < .05) depending on PRR and intestinal site considered. Principal component analysis of mucosa data revealed clear clustering of colonic samples, irrespective of the age and clustering of jejunal and ileal samples, with gradual changes with age. Correlation analysis highlighted three families correlating with mucosal parameters: Enterobacteriaceae in the jejunum, Peptostreptococcaceae in the ileum, and Micrococcaceae in the colon. In conclusion, small and large intestine display close microbiota composition early in life but distinct mucosal phenotype and follow very different post-natal development.
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Affiliation(s)
- Alexis Pierre Arnaud
- Institut NuMeCan, INRA, INSERM, Univ Rennes, St-Gilles, France.,Service de chirurgie pédiatrique, CHU rennes, University of Rennes 1, Rennes, France
| | - Véronique Rome
- Institut NuMeCan, INRA, INSERM, Univ Rennes, St-Gilles, France
| | - Marion Richard
- Institut NuMeCan, INRA, INSERM, Univ Rennes, St-Gilles, France
| | - Michèle Formal
- Institut NuMeCan, INRA, INSERM, Univ Rennes, St-Gilles, France
| | | | - Gaëlle Boudry
- Institut NuMeCan, INRA, INSERM, Univ Rennes, St-Gilles, France
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