101
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Shkoporov AN, Khokhlova EV, Stephens N, Hueston C, Seymour S, Hryckowian AJ, Scholz D, Ross RP, Hill C. Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis. BMC Biol 2021; 19:163. [PMID: 34407825 PMCID: PMC8375218 DOI: 10.1186/s12915-021-01084-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/01/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of lysogeny, these viruses demonstrate long-term persistence in the human gut microbiome, dominating the virome in some individuals. RESULTS Here we show that rapid phase variation of alternate capsular polysaccharides in Bacteroides intestinalis cultures plays an important role in a dynamic equilibrium between phage sensitivity and resistance, allowing phage and bacteria to multiply in parallel. The data also suggests the role of a concomitant phage persistence mechanism associated with delayed lysis of infected cells, similar to carrier state infection. From an ecological and evolutionary standpoint, this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other "benign" forms of phage infection when the host is stably present at high abundance. CONCLUSION Long-term persistence of bacteriophage and host could result from mutually beneficial mechanisms driving bacterial strain-level diversity and phage survival in complex environments.
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Affiliation(s)
- Andrey N Shkoporov
- School of Microbiology, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | | | - Niamh Stephens
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cara Hueston
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Samuel Seymour
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Andrew J Hryckowian
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, USA
| | - Dimitri Scholz
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - R Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
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102
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Benler S, Koonin EV. Fishing for phages in metagenomes: what do we catch, what do we miss? Curr Opin Virol 2021; 49:142-150. [PMID: 34139668 DOI: 10.1016/j.coviro.2021.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Metagenomics and metatranscriptomics have become the principal approaches for discovery of novel bacteriophages and preliminary characterization of their ecology and biology. Metagenomic sequencing dramatically expanded the known diversity of tailed and non-tailed phages with double-stranded DNA genomes and those with single-stranded DNA genomes, whereas metatranscriptomics led to the discovery of thousands of new single-stranded RNA phages. Apart from expanding phage diversity, metagenomics studies discover major novel groups of phages with unique features of genome organization, expression strategy and virus-host interaction, such as the putative order 'crAssvirales', which includes the most abundant human-associated viruses. The continued success of metagenomics hinges on the combination of the most powerful computational methods for phage genome assembly and analysis including harnessing CRISPR spacers for the discovery of novel phages and host assignment. Together, these approaches could make a comprehensive characterization of the earth phageome a realistic goal.
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Affiliation(s)
- Sean Benler
- National Center for Biotechnology Information, National Institutes of Health, Bethesda MD, United States.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Institutes of Health, Bethesda MD, United States.
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103
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Townsend EM, Kelly L, Muscatt G, Box JD, Hargraves N, Lilley D, Jameson E. The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome. Front Cell Infect Microbiol 2021; 11:643214. [PMID: 34150671 PMCID: PMC8213399 DOI: 10.3389/fcimb.2021.643214] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.
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Affiliation(s)
- Eleanor M Townsend
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Lucy Kelly
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - George Muscatt
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Joshua D Box
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Nicole Hargraves
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Daniel Lilley
- Warwick Medical School, The University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
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104
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Vallino M, Rossi M, Ottati S, Martino G, Galetto L, Marzachì C, Abbà S. Bacteriophage-Host Association in the Phytoplasma Insect Vector Euscelidius variegatus. Pathogens 2021; 10:pathogens10050612. [PMID: 34067814 PMCID: PMC8156552 DOI: 10.3390/pathogens10050612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/26/2022] Open
Abstract
Insect vectors transmit viruses and bacteria that can cause severe diseases in plants and economic losses due to a decrease in crop production. Insect vectors, like all other organisms, are colonized by a community of various microorganisms, which can influence their physiology, ecology, evolution, and also their competence as vectors. The important ecological meaning of bacteriophages in various ecosystems and their role in microbial communities has emerged in the past decade. However, only a few phages have been described so far in insect microbiomes. The leafhopper Euscelidius variegatus is a laboratory vector of the phytoplasma causing Flavescence dorée, a severe grapevine disease that threatens viticulture in Europe. Here, the presence of a temperate bacteriophage in E. variegatus (named Euscelidius variegatus phage 1, EVP-1) was revealed through both insect transcriptome analyses and electron microscopic observations. The bacterial host was isolated in axenic culture and identified as the bacterial endosymbiont of E. variegatus (BEV), recently assigned to the genus Candidatus Symbiopectobacterium. BEV harbors multiple prophages that become active in culture, suggesting that different environments can trigger different mechanisms, finely regulating the interactions among phages. Understanding the complex relationships within insect vector microbiomes may help in revealing possible microbe influences on pathogen transmission, and it is a crucial step toward innovative sustainable strategies for disease management in agriculture.
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Affiliation(s)
- Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
- Correspondence:
| | - Marika Rossi
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
| | - Sara Ottati
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Gabriele Martino
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Luciana Galetto
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
| | - Cristina Marzachì
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
| | - Simona Abbà
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce 73, 10135 Torino, Italy; (M.R.); (S.O.); (G.M.); (L.G.); (C.M.); (S.A.)
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105
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Li Y, Handley SA, Baldridge MT. The dark side of the gut: Virome-host interactions in intestinal homeostasis and disease. J Exp Med 2021; 218:e20201044. [PMID: 33760921 PMCID: PMC8006857 DOI: 10.1084/jem.20201044] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
The diverse enteric viral communities that infect microbes and the animal host collectively constitute the gut virome. Although recent advances in sequencing and analysis of metaviromes have revealed the complexity of the virome and facilitated discovery of new viruses, our understanding of the enteric virome is still incomplete. Recent studies have uncovered how virome-host interactions can contribute to beneficial or detrimental outcomes for the host. Understanding the complex interactions between enteric viruses and the intestinal immune system is a prerequisite for elucidating their role in intestinal diseases. In this review, we provide an overview of the enteric virome composition and summarize recent findings about how enteric viruses are sensed by and, in turn, modulate host immune responses during homeostasis and disease.
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Affiliation(s)
- Yuhao Li
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Scott A. Handley
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Megan T. Baldridge
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO
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106
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Fujimoto K, Kimura Y, Allegretti JR, Yamamoto M, Zhang YZ, Katayama K, Tremmel G, Kawaguchi Y, Shimohigoshi M, Hayashi T, Uematsu M, Yamaguchi K, Furukawa Y, Akiyama Y, Yamaguchi R, Crowe SE, Ernst PB, Miyano S, Kiyono H, Imoto S, Uematsu S. Functional Restoration of Bacteriomes and Viromes by Fecal Microbiota Transplantation. Gastroenterology 2021; 160:2089-2102.e12. [PMID: 33577875 PMCID: PMC8684800 DOI: 10.1053/j.gastro.2021.02.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/27/2021] [Accepted: 02/03/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI). However, the overall mechanisms underlying FMT success await comprehensive elucidation, and the safety of FMT has recently become a serious concern because of the occurrence of drug-resistant bacteremia transmitted by FMT. We investigated whether functional restoration of the bacteriomes and viromes by FMT could be an indicator of successful FMT. METHODS The human intestinal bacteriomes and viromes from 9 patients with rCDI who had undergone successful FMT and their donors were analyzed. Prophage-based and CRISPR spacer-based host bacteria-phage associations in samples from recipients before and after FMT and in donor samples were examined. The gene functions of intestinal microorganisms affected by FMT were evaluated. RESULTS Metagenomic sequencing of both the viromes and bacteriomes revealed that FMT does change the characteristics of intestinal bacteriomes and viromes in recipients after FMT compared with those before FMT. In particular, many Proteobacteria, the fecal abundance of which was high before FMT, were eliminated, and the proportion of Microviridae increased in recipients. Most temperate phages also behaved in parallel with the host bacteria that were altered by FMT. Furthermore, the identification of bacterial and viral gene functions before and after FMT revealed that some distinctive pathways, including fluorobenzoate degradation and secondary bile acid biosynthesis, were significantly represented. CONCLUSIONS The coordinated action of phages and their host bacteria restored the recipients' intestinal flora. These findings show that the restoration of intestinal microflora functions reflects the success of FMT.
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Affiliation(s)
- Kosuke Fujimoto
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan,Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan,Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yasumasa Kimura
- Division of Systems Immunology, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Jessica R. Allegretti
- Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Mako Yamamoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yao-zhong Zhang
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Kotoe Katayama
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Georg Tremmel
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yunosuke Kawaguchi
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Masaki Shimohigoshi
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Tetsuya Hayashi
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Miho Uematsu
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yutaka Akiyama
- Department of Computer Science, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Rui Yamaguchi
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Sheila E. Crowe
- Department of Medicine, University of California, San Diego, La Jolla, California
| | - Peter B. Ernst
- Division of Gastroenterology, Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, University of California San Diego, San Diego, La Jolla, California,Division of Comparative Pathology and Medicine, Department of Pathology, University of California San Diego, San Diego, La Jolla, California,Center for Veterinary Sciences and Comparative Medicine, University of California, San Diego, La Jolla, California
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Hiroshi Kiyono
- Division of Gastroenterology, Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, University of California San Diego, San Diego, La Jolla, California,Division of Comparative Pathology and Medicine, Department of Pathology, University of California San Diego, San Diego, La Jolla, California,Department of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan,International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Satoshi Uematsu
- Department of Immunology and Genomics, Osaka City University, Graduate School of Medicine, Abeno-ku, Osaka, Japan; Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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107
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Garmaeva S, Gulyaeva A, Sinha T, Shkoporov AN, Clooney AG, Stockdale SR, Spreckels JE, Sutton TDS, Draper LA, Dutilh BE, Wijmenga C, Kurilshikov A, Fu J, Hill C, Zhernakova A. Stability of the human gut virome and effect of gluten-free diet. Cell Rep 2021; 35:109132. [PMID: 34010651 DOI: 10.1016/j.celrep.2021.109132] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 01/12/2021] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiome consists of bacteria, archaea, eukaryotes, and viruses. The gut viruses are relatively underexplored. Here, we longitudinally analyzed the gut virome composition in 11 healthy adults: its stability, variation, and the effect of a gluten-free diet. Using viral enrichment and a de novo assembly-based approach, we demonstrate the quantitative dynamics of the gut virome, including dsDNA, ssDNA, dsRNA, and ssRNA viruses. We observe highly divergent individual viral communities, carrying on an average 2,143 viral genomes, 13.1% of which were present at all 3 time points. In contrast to previous reports, the Siphoviridae family dominates over Microviridae in studied individual viromes. We also show individual viromes to be stable at the family level but to vary substantially at the genera and species levels. Finally, we demonstrate that lower initial diversity of the human gut virome leads to a more pronounced effect of the dietary intervention on its composition.
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Affiliation(s)
- Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Anastasia Gulyaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Andrey N Shkoporov
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Adam G Clooney
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Stephen R Stockdale
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Johanne E Spreckels
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Thomas D S Sutton
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht 3584 CH, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
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108
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Hedžet S, Rupnik M, Accetto T. Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement. Microorganisms 2021; 9:microorganisms9050892. [PMID: 33919474 PMCID: PMC8143477 DOI: 10.3390/microorganisms9050892] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
Intestinal phages are abundant and important components of gut microbiota, yet the isolated and characterized representatives that infect abundant gut bacteria are sparse. Here we describe the isolation of human intestinal phages infecting Bacteroidesuniformis. Bacteroides is one of the most common bacterial groups in the global human gut microbiota; however, to date not many Bacteroides specific phages are known. Phages isolated in this study belong to a novel viral genus, Bacuni, within the Siphoviridae family. Their genomes encode diversity-generating retroelements (DGR), which were shown in other bacteriophages to promote phage adaptation to rapidly changing environmental conditions and to broaden their host range. Three isolated phages showed 99.83% genome identity but one of them infected a distinct B. uniformis strain. The tropism of Bacuni phages appeared to be dependent on the interplay of DGR mediated sequence variations of gene encoding putative phage fimbrial tip proteins and mutations in host genes coding for outer-membrane proteins. We found prophages with up to 85% amino acid similarity over two-thirds of the Bacuni phage genome in the B. acidifaciens and Prevotella sp. genomes. Despite the abundance of Bacteroides within the human microbiome, we found Bacuni phages only in a limited subset of published gut metagenomes.
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Affiliation(s)
- Stina Hedžet
- Centre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, Slovenia; (S.H.); (M.R.)
| | - Maja Rupnik
- Centre for Medical Microbiology, Department for Microbiological Research, National Laboratory for Health, Environment and Food (NLZOH), 2000 Maribor, Slovenia; (S.H.); (M.R.)
- Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Tomaž Accetto
- Animal Science Department, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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109
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Chen H, Liu C, Li Y, Teng Y. Integrating Metagenomic and Bayesian Analyses to Evaluate the Performance and Confidence of CrAssphage as an Indicator for Tracking Human Sewage Contamination in China. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:4992-5000. [PMID: 33715349 DOI: 10.1021/acs.est.1c00071] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recently, crAssphage has been proposed as a human-specific marker for tracking fecal contamination. However, its performance has always been validated in a limited number of host samples, which may obscure our understanding of its utility. Furthermore, few studies have quantified confidence of fecal contamination when using crAssphage. Here, we evaluate the performance and confidence of crAssphage by analyzing a large panel of metagenomic data sets combined with Bayesian analyses. Results demonstrate that crAssphage exhibits superior performance with high host sensitivity and specificity, indicating its suitability for tracking human fecal sources. With the marker, a high confidence (>90%) can be obtained and particularly, multiple samples with positive results provide a near certainty of confidence. The application of crAssphage in the sediments of three Chinese urban rivers shows a high confidence of >97% of human fecal contamination, suggesting the serious challenge of sewage pollution in these environments. Additionally, significant correlation is observed between crAssphage and antibiotic resistance genes (ARGs), expanding the utilization of crAssphage for pollution management of ARGs. This study highlights the benefit of using metagenomic-based analysis for evaluating the performance and confidence of microbial source tracking markers in the coming era of big data with increasing resources in available metagenomic data.
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Affiliation(s)
- Haiyang Chen
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No. 19, Xinjiekouwai Street, Beijing 100875, P. R. China
| | - Chang Liu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No. 19, Xinjiekouwai Street, Beijing 100875, P. R. China
| | - Yuezhao Li
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No. 19, Xinjiekouwai Street, Beijing 100875, P. R. China
| | - Yanguo Teng
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education; College of Water Sciences, Beijing Normal University, No. 19, Xinjiekouwai Street, Beijing 100875, P. R. China
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110
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Taboada B, Morán P, Serrano-Vázquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximenez C, Arias CF. The gut virome of healthy children during the first year of life is diverse and dynamic. PLoS One 2021; 16:e0240958. [PMID: 33852569 PMCID: PMC8046192 DOI: 10.1371/journal.pone.0240958] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/30/2021] [Indexed: 01/21/2023] Open
Abstract
In this work, we determined the diversity and dynamics of the gut virome of infants during the first year of life. Fecal samples were collected monthly, from birth to one year of age, from three healthy children living in a semi-rural village in Mexico. Most of the viral reads were classified into six families of bacteriophages including five dsDNA virus families of the order Caudovirales, with Siphoviridae and Podoviridae being the most abundant. Eukaryotic viruses were detected as early as two weeks after birth and remained present all along the first year of life. Thirty-four different eukaryotic virus families were found, where eight of these families accounted for 98% of all eukaryotic viral reads: Anelloviridae, Astroviridae, Caliciviridae, Genomoviridae, Parvoviridae, Picornaviridae, Reoviridae and the plant-infecting viruses of the Virgaviridae family. Some viruses in these families are known human pathogens, and it is surprising that they were found during the first year of life in infants without gastrointestinal symptoms. The eukaryotic virus species richness found in this work was higher than that observed in previous studies; on average between 7 and 24 virus species were identified per sample. The richness and abundance of the eukaryotic virome significantly increased during the second semester of life, probably because of an increased environmental exposure of infants with age. Our findings suggest an early and permanent contact of infants with a diverse array of bacteriophages and eukaryotic viruses, whose composition changes over time. The bacteriophages and eukaryotic viruses found in these children could represent a metastable virome, whose potential influence on the development of the infant's immune system or on the health of the infants later in life, remains to be investigated.
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Affiliation(s)
- Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Patricia Morán
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Angélica Serrano-Vázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Pavel Iša
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Liliana Rojas-Velázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Horacio Pérez-Juárez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Cecilia Ximenez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (CFA); (CX); (JT)
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111
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Guerin E, Shkoporov AN, Stockdale SR, Comas JC, Khokhlova EV, Clooney AG, Daly KM, Draper LA, Stephens N, Scholz D, Ross RP, Hill C. Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens. MICROBIOME 2021; 9:89. [PMID: 33845877 PMCID: PMC8042965 DOI: 10.1186/s40168-021-01036-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/12/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND The gut phageome comprises a complex phage community of thousands of individual strains, with a few highly abundant bacteriophages. CrAss-like phages, which infect bacteria of the order Bacteroidales, are the most abundant bacteriophage family in the human gut and make an important contribution to an individual's core virome. Based on metagenomic data, crAss-like phages form a family, with four sub-families and ten candidate genera. To date, only three representatives isolated in pure culture have been reported: ΦcrAss001 and two closely related phages DAC15 and DAC17; all are members of the less abundant candidate genus VI. The persistence at high levels of both crAss-like phage and their Bacteroidales hosts in the human gut has not been explained mechanistically, and this phage-host relationship can only be properly studied with isolated phage-host pairs from as many genera as possible. RESULTS Faeces from a healthy donor with high levels of crAss-like phage was used to initiate a faecal fermentation in a chemostat, with selected antibiotics chosen to inhibit rapidly growing bacteria and selectively enrich for Gram-negative Bacteroidales. This had the objective of promoting the simultaneous expansion of crAss-like phages on their native hosts. The levels of seven different crAss-like phages expanded during the fermentation, indicating that their hosts were also present in the fermenter. The enriched supernatant was then tested against individual Bacteroidales strains isolated from the same faecal sample. This resulted in the isolation of a previously uncharacterised crAss-like phage of candidate genus IV of the proposed Alphacrassvirinae sub-family, ΦcrAss002, that infects the gut commensal Bacteroides xylanisolvens. ΦcrAss002 does not form plaques or spots on lawns of sensitive cells, nor does it lyse liquid cultures, even at high titres. In keeping with the co-abundance of phage and host in the human gut, ΦcrAss002 and Bacteroides xylanisolvens can also co-exist at high levels when co-cultured in laboratory media. CONCLUSIONS We report the isolation and characterisation of ΦcrAss002, the first representative of the proposed Alphacrassvirinae sub-family of crAss-like phages. ΦcrAss002 cannot form plaques or spots on bacterial lawns but can co-exist with its host, Bacteroides xylanisolvens, at very high levels in liquid culture without impacting on bacterial numbers. Video abstract.
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Affiliation(s)
- Emma Guerin
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | | | | | | | | | - Adam G Clooney
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Karen M Daly
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Niamh Stephens
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dimitri Scholz
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
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112
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Fernández L, Duarte AC, Rodríguez A, García P. The relationship between the phageome and human health: are bacteriophages beneficial or harmful microbes? Benef Microbes 2021; 12:107-120. [PMID: 33789552 DOI: 10.3920/bm2020.0132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the context of the global antibiotic resistance crisis, bacteriophages are increasingly becoming promising antimicrobial agents against multi-resistant bacteria. Indeed, a huge effort is being made to bring phage-derived products to the market, a process that will also require revising the current regulations in order to facilitate their approval. However, despite the evidence supporting the safety of phages for humans, the general public would still be reluctant to use 'viruses' for therapeutic purposes. In this scenario, we consider that it is important to discuss the role of these microorganisms in the equilibrium of the microbiota and how this relates to human health. To do that, this review starts by examining the role of phages as key players in bacterial communities (including those that naturally inhabit the human body), modulating the species composition and contributing to maintain a 'healthy' status quo. Additionally, in specific situations, e.g. an infectious disease, bacteriophages can be used as target-specific antimicrobials against pathogenic bacteria (phage therapy), while being harmless to the desirable microbiota. Apart from that, incipient research shows the potential application of these viruses to treat diseases caused by bacterial dysbiosis. This latter application would be comparable to the use of probiotics or prebiotics, since bacteriophages can indirectly improve the growth of beneficial bacteria in the gastrointestinal tract by removing undesirable competitors. On the other hand, possible adverse effects do not appear to be an impediment to promote phage therapy. Nonetheless, it is important to remember their potentially negative impact, mainly concerning their immunogenicity or their potential spread of virulence and antibiotic resistance genes, especially by temperate phages. Overall, we believe that phages should be largely considered beneficial microbes, although it is paramount not to overlook their potential risks.
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Affiliation(s)
- L Fernández
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
| | - A C Duarte
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
| | - A Rodríguez
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
| | - P García
- Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Asturias, Spain.,DairySafe Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Av. del Hospital Universitario s/n, 33011 Oviedo, Spain
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113
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Cook R, Hooton S, Trivedi U, King L, Dodd CER, Hobman JL, Stekel DJ, Jones MA, Millard AD. Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens. MICROBIOME 2021; 9:65. [PMID: 33743832 PMCID: PMC7981956 DOI: 10.1186/s40168-021-01010-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/02/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle in the UK producing 7-8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a 5-month period using short and long-read sequencing. RESULTS Hybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~ 98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a 5-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community, including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut. CONCLUSIONS The cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment. Video abstract.
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Affiliation(s)
- Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Steve Hooton
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Liz King
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Christine E R Dodd
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Michael A Jones
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK.
| | - Andrew D Millard
- Dept Genetics and Genome Biology, University of Leicester, University Road, Leicester, Leicestershire, LE1 7RH, UK.
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114
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Turner D, Kropinski AM, Adriaenssens EM. A Roadmap for Genome-Based Phage Taxonomy. Viruses 2021; 13:v13030506. [PMID: 33803862 PMCID: PMC8003253 DOI: 10.3390/v13030506] [Citation(s) in RCA: 259] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy.
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Affiliation(s)
- Dann Turner
- Department of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK;
| | - Andrew M. Kropinski
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
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115
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Fitzgerald CB, Shkoporov AN, Upadrasta A, Khokhlova EV, Ross RP, Hill C. Probing the "Dark Matter" of the Human Gut Phageome: Culture Assisted Metagenomics Enables Rapid Discovery and Host-Linking for Novel Bacteriophages. Front Cell Infect Microbiol 2021; 11:616918. [PMID: 33791236 PMCID: PMC8005731 DOI: 10.3389/fcimb.2021.616918] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/29/2021] [Indexed: 12/16/2022] Open
Abstract
Recent years have been marked by the growing interest towards virulent and temperate bacteriophage populations inhabiting the human lower gastrointestinal tract – the gut phageome. A number of studies demonstrated high levels of specificity and temporal stability of individual gut phageomes, as well as their specific alterations in disease cohorts, in parallel with changes in the bacteriome. It has been speculated that phages might have an active role in shaping the taxonomic composition and functional properties of the human gut bacteriome. An overwhelming majority of gut bacteriophages, however, remain uncultured, unclassified, and their specific hosts and infection strategies are still unknown. They are often referred to as “the viral dark matter”. A possible breakthrough in understanding of the phageome can only become possible when a significant proportion of the “the viral dark matter” is identified and linked to bacterial hosts. Here, we describe a method that enables rapid discovery and host-linking of novel bacteriophages in the gut via a combination of serial enrichment cultures and shotgun metagenomics of viral DNA. Using this approach dozens of novel and previously known bacteriophages were detected, including the ones infecting difficult-to-culture anaerobic bacteria. The majority of phages failed to produce lysis and propagate on host cultures in traditional assays. The newly identified phages include representatives of Siphoviridae, Myoviridae, Podoviridae, and crAss-like viruses, infecting diverse bacterial taxa of Bacteroidetes, Firmicutes, Actinobacteria, Verrucomicrobia and Proteobacteria phyla. The proposed new method has a potential for high-throughput screening applications for mass discovery of new phages in different environments.
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Affiliation(s)
| | | | | | | | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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116
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Callanan J, Stockdale SR, Shkoporov A, Draper LA, Ross RP, Hill C. Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review. Microorganisms 2021; 9:524. [PMID: 33806607 PMCID: PMC8000950 DOI: 10.3390/microorganisms9030524] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/17/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022] Open
Abstract
The human gut is colonised by a vast array of microbes that include bacteria, viruses, fungi, and archaea. While interest in these microbial entities has largely focused on the bacterial constituents, recently the viral component has attracted more attention. Metagenomic advances, compared to classical isolation procedures, have greatly enhanced our understanding of the composition, diversity, and function of viruses in the human microbiome (virome). We highlight that viral extraction methodologies are crucial in terms of identifying and characterising communities of viruses infecting eukaryotes and bacteria. Different viral extraction protocols, including those used in some of the most significant human virome publications to date, have introduced biases affecting their a overall conclusions. It is important that protocol variations should be clearly highlighted across studies, with the ultimate goal of identifying and acknowledging biases associated with different protocols and, perhaps, the generation of an unbiased and standardised method for examining this portion of the human microbiome.
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Affiliation(s)
| | | | | | | | | | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, T12 YT20 Cork, Ireland; (J.C.); (S.R.S.); (A.S.); (L.A.D.); (R.P.R.)
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117
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Koonin EV, Dolja VV, Krupovic M. The healthy human virome: from virus-host symbiosis to disease. Curr Opin Virol 2021; 47:86-94. [PMID: 33652230 DOI: 10.1016/j.coviro.2021.02.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 02/07/2023]
Abstract
Viruses are ubiquitous, essential components of any ecosystem, and of multicellular organism holobionts. Numerous viruses cause acute infection, killing the host or being cleared by immune system. In many other cases, viruses coexist with the host as symbionts, either temporarily or for the duration of the host's life. Apparently, virus-host relationships span the entire range from aggressive parasitism to mutualism. Here we attempt to delineate the healthy human virome, that is, the entirety of viruses that are present in a healthy human body. The bulk of the healthy virome consists of bacteriophages infecting bacteria in the intestine and other locations. However, a variety of viruses, such as anelloviruses and herpesviruses, and the numerous endogenous retroviruses, persist by replicating in human cells, and these are our primary focus. Crucially, the boundary between symbiotic and pathogenic viruses is fluid such that members of the healthy virome can become pathogens under changing conditions.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
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118
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Marbouty M, Thierry A, Millot GA, Koszul R. MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut. eLife 2021; 10:60608. [PMID: 33634788 PMCID: PMC7963479 DOI: 10.7554/elife.60608] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 02/20/2021] [Indexed: 12/15/2022] Open
Abstract
Bacteriophages play important roles in regulating the intestinal human microbiota composition, dynamics, and homeostasis, and characterizing their bacterial hosts is needed to understand their impact. We applied a metagenomic Hi-C approach on 10 healthy human gut samples to unveil a large infection network encompassing more than 6000 interactions bridging a metagenomic assembled genomes (MAGs) and a phage sequence, allowing to study in situ phage-host ratio. Whereas three-quarters of these sequences likely correspond to dormant prophages, 5% exhibit a much higher coverage than their associated MAG, representing potentially actively replicating phages. We detected 17 sequences of members of the crAss-like phage family, whose hosts diversity remained until recently relatively elusive. For each of them, a unique bacterial host was identified, all belonging to different genus of Bacteroidetes. Therefore, metaHiC deciphers infection network of microbial population with a high specificity paving the way to dynamic analysis of mobile genetic elements in complex ecosystems.
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Affiliation(s)
- Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Paris, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Paris, France
| | - Gaël A Millot
- Institut Pasteur, Bioinformatics and Biostatistics Hub, CNRS, USR 3756, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Paris, France
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119
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Moon K, Cho JC. Metaviromics coupled with phage-host identification to open the viral 'black box'. J Microbiol 2021; 59:311-323. [PMID: 33624268 DOI: 10.1007/s12275-021-1016-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 12/22/2022]
Abstract
Viruses are found in almost all biomes on Earth, with bacteriophages (phages) accounting for the majority of viral particles in most ecosystems. Phages have been isolated from natural environments using the plaque assay and liquid medium-based dilution culturing. However, phage cultivation is restricted by the current limitations in the number of culturable bacterial strains. Unlike prokaryotes, which possess universally conserved 16S rRNA genes, phages lack universal marker genes for viral taxonomy, thus restricting cultureindependent analyses of viral diversity. To circumvent these limitations, shotgun viral metagenome sequencing (i.e., metaviromics) has been developed to enable the extensive sequencing of a variety of viral particles present in the environment and is now widely used. Using metaviromics, numerous studies on viral communities have been conducted in oceans, lakes, rivers, and soils, resulting in many novel phage sequences. Furthermore, auxiliary metabolic genes such as ammonic monooxygenase C and β-lactamase have been discovered in viral contigs assembled from viral metagenomes. Current attempts to identify putative bacterial hosts of viral metagenome sequences based on sequence homology have been limited due to viral sequence variations. Therefore, culture-independent approaches have been developed to predict bacterial hosts using single-cell genomics and fluorescentlabeling. This review focuses on recent viral metagenome studies conducted in natural environments, especially in aquatic ecosystems, and their contributions to phage ecology. Here, we concluded that although metaviromics is a key tool for the study of viral ecology, this approach must be supplemented with phage-host identification, which in turn requires the cultivation of phage-bacteria systems.
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Affiliation(s)
- Kira Moon
- Biological Resources Utilization Division, Honam National Institute of Biological Resources, Mokpo, 58762, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
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120
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Yutin N, Benler S, Shmakov SA, Wolf YI, Tolstoy I, Rayko M, Antipov D, Pevzner PA, Koonin EV. Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features. Nat Commun 2021; 12:1044. [PMID: 33594055 PMCID: PMC7886860 DOI: 10.1038/s41467-021-21350-w] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
CrAssphage is the most abundant human-associated virus and the founding member of a large group of bacteriophages, discovered in animal-associated and environmental metagenomes, that infect bacteria of the phylum Bacteroidetes. We analyze 4907 Circular Metagenome Assembled Genomes (cMAGs) of putative viruses from human gut microbiomes and identify nearly 600 genomes of crAss-like phages that account for nearly 87% of the DNA reads mapped to these cMAGs. Phylogenetic analysis of conserved genes demonstrates the monophyly of crAss-like phages, a putative virus order, and of 5 branches, potential families within that order, two of which have not been identified previously. The phage genomes in one of these families are almost twofold larger than the crAssphage genome (145-192 kilobases), with high density of self-splicing introns and inteins. Many crAss-like phages encode suppressor tRNAs that enable read-through of UGA or UAG stop-codons, mostly, in late phage genes. A distinct feature of the crAss-like phages is the recurrent switch of the phage DNA polymerase type between A and B families. Thus, comparative genomic analysis of the expanded assemblage of crAss-like phages reveals aspects of genome architecture and expression as well as phage biology that were not apparent from the previous work on phage genomics.
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Affiliation(s)
- Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Sean Benler
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Sergei A Shmakov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Igor Tolstoy
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Mike Rayko
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Dmitry Antipov
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California-San Diego, La Jolla, CA, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.
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121
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Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD. Massive expansion of human gut bacteriophage diversity. Cell 2021; 184:1098-1109.e9. [PMID: 33606979 PMCID: PMC7895897 DOI: 10.1016/j.cell.2021.01.029] [Citation(s) in RCA: 268] [Impact Index Per Article: 89.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/02/2020] [Accepted: 01/19/2021] [Indexed: 12/25/2022]
Abstract
Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence in the human gut remains largely unknown. Here, we introduce the Gut Phage Database, a collection of ∼142,000 non-redundant viral genomes (>10 kb) obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria. Host assignment revealed that viral diversity is highest in the Firmicutes phyla and that ∼36% of viral clusters (VCs) are not restricted to a single species, creating gene flow networks across phylogenetically distinct bacterial species. Epidemiological analysis uncovered 280 globally distributed VCs found in at least 5 continents and a highly prevalent phage clade with features reminiscent of p-crAssphage. This high-quality, large-scale catalog of phage genomes will improve future virome studies and enable ecological and evolutionary analysis of human gut bacteriophages.
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Affiliation(s)
- Luis F Camarillo-Guerrero
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
| | - Alexandre Almeida
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SA, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Guillermo Rangel-Pineros
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SA, UK; Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogota 111711, Colombia
| | - Robert D Finn
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
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122
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Does over a century of aerobic phage work provide a solid framework for the study of phages in the gut? Anaerobe 2021; 68:102319. [PMID: 33465423 DOI: 10.1016/j.anaerobe.2021.102319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
Bacterial viruses (bacteriophages, phages) of the gut have increasingly become a focus in microbiome studies, with an understanding that they are likely key players in health and disease. However, characterization of the virome remains largely based on bioinformatic approaches, with the impact of these viromes inferred based on a century of knowledge from aerobic phage work. Studying the phages infecting anaerobes is difficult, as they are often technically demanding to isolate and propagate. In this review, we primarily discuss the phages infecting three well-studied anaerobes in the gut: Bifidobacterium, Clostridia and Bacteroides, with a particular focus on the challenges in isolating and characterizing these phages. We contrast the lessons learned from these to other anaerobic work on phages infecting facultative anaerobes of the gut: Enterococcus and Lactobacillus. Phages from the gut do appear to adhere to the lessons learned from aerobic work, but the additional challenges of working on them has required ingenious new approaches to enable their study. This, in turn, has uncovered remarkable biology likely underpinning phage-host relationships in many stable environments.
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123
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Li Y, Gordon E, Shean RC, Idle A, Deng X, Greninger AL, Delwart E. CrAssphage and its bacterial host in cat feces. Sci Rep 2021; 11:815. [PMID: 33436756 PMCID: PMC7804022 DOI: 10.1038/s41598-020-80076-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/14/2020] [Indexed: 12/17/2022] Open
Abstract
CrAssphages are a diverse group of related phages detected in human feces where they are the most prevalent and abundant prokaryotic virus. CrAssphages' cellular host has been identified as the anaerobic Bacteroides intestinalis. CrAssphage has also been reported in non-human primates and environmental samples and has been proposed as a marker of human fecal contamination. Here we describe crAssphage DNA in a feline fecal sample. 95% of the ~ 100 Kb genome could be assembled and classified in genus 1 of the recently proposed Alphacrassvirinae subfamily. The cat origin of the fecal sample was confirmed by partial mitochondrial DNA sequencing. High levels of Bacteroides intestinalis DNA could also be detected in this cat's feces. Fecal samples longitudinally collected over a 4-week period showed the continuous shedding of crAssphage DNA. We therefore report the first genome sequence-confirmed detection of crAssphage in fecal samples of a non-primate mammal.
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Affiliation(s)
- Yanpeng Li
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94118, USA
| | - Emilia Gordon
- The British Columbia Society for the Prevention of Cruelty to Animals, Vancouver, BC, V5T 1R1, Canada
| | - Ryan C Shean
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, 98195, USA
| | - Amanda Idle
- The British Columbia Society for the Prevention of Cruelty to Animals, Vancouver, BC, V5T 1R1, Canada
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94118, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, 98195, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118, USA.
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94118, USA.
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124
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Drobysheva AV, Panafidina SA, Kolesnik MV, Klimuk EI, Minakhin L, Yakunina MV, Borukhov S, Nilsson E, Holmfeldt K, Yutin N, Makarova KS, Koonin EV, Severinov KV, Leiman PG, Sokolova ML. Structure and function of virion RNA polymerase of a crAss-like phage. Nature 2021; 589:306-309. [PMID: 33208949 DOI: 10.1038/s41586-020-2921-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/08/2020] [Indexed: 01/29/2023]
Abstract
CrAss-like phages are a recently described expansive group of viruses that includes the most abundant virus in the human gut1-3. The genomes of all crAss-like phages encode a large virion-packaged protein2,4 that contains a DFDxD sequence motif, which forms the catalytic site in cellular multisubunit RNA polymerases (RNAPs)5. Here, using Cellulophaga baltica crAss-like phage phi14:2 as a model system, we show that this protein is a DNA-dependent RNAP that is translocated into the host cell along with the phage DNA and transcribes early phage genes. We determined the crystal structure of this 2,180-residue enzyme in a self-inhibited state, which probably occurs before virion packaging. This conformation is attained with the help of a cleft-blocking domain that interacts with the active site and occupies the cavity in which the RNA-DNA hybrid binds. Structurally, phi14:2 RNAP is most similar to eukaryotic RNAPs that are involved in RNA interference6,7, although most of the phi14:2 RNAP structure (nearly 1,600 residues) maps to a new region of the protein fold space. Considering this structural similarity, we propose that eukaryal RNA interference polymerases have their origins in phage, which parallels the emergence of the mitochondrial transcription apparatus8.
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Affiliation(s)
- Arina V Drobysheva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Sofia A Panafidina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Matvei V Kolesnik
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evgeny I Klimuk
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Leonid Minakhin
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Maria V Yakunina
- Peter the Great St Petersburg Polytechnic University, St Petersburg, Russia
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ, USA
| | - Emelie Nilsson
- Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Karin Holmfeldt
- Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Konstantin V Severinov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
| | - Maria L Sokolova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.
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125
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Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat Microbiol 2021; 6:960-970. [PMID: 34168315 PMCID: PMC8241571 DOI: 10.1038/s41564-021-00928-6] [Citation(s) in RCA: 218] [Impact Index Per Article: 72.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023]
Abstract
Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.
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126
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Yan Q, Wang Y, Chen X, Jin H, Wang G, Guan K, Zhang Y, Zhang P, Ayaz T, Liang Y, Wang J, Cui G, Sun Y, Xiao M, Kang J, Zhang W, Zhang A, Li P, Liu X, Ulllah H, Ma Y, Li S, Ma T. Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis. Virus Evol 2021; 7:veab022. [PMID: 33959381 PMCID: PMC8087960 DOI: 10.1093/ve/veab022] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Trillions of viruses inhabit the gastrointestinal tract. Some of them have been well-studied on their roles in infection and human health, but the majority remains unsurveyed. It has been established that the composition of the gut virome is highly variable based on the changes of diet, physical state, and environmental factors. However, the effect of host genetic factors, for example ethnic origin, on the gut virome is rarely investigated. Here, we characterized and compared the gut virome in a cohort of local Chinese residents and visiting Pakistani individuals, each group containing twenty-four healthy adults and six children. Using metagenomic shotgun sequencing and assembly of fecal samples, a huge number of viral operational taxonomic units (vOTUs) were identified for profiling the DNA and RNA viromes. National background contributed a primary variation to individuals' gut virome. Compared with the Chinese adults, the Pakistan adults showed higher macrodiversity and different compositional and functional structures in their DNA virome and lower diversity and altered composition in their RNA virome. The virome variations of Pakistan children were not only inherited from that of the adults but also tended to share similar characteristics with the Chinese cohort. We also analyzed and compared the bacterial microbiome between two cohorts and further revealed numerous connections between viruses and bacterial host. Statistically, the gut DNA and RNA viromes were covariant to some extent (P < 0.001), and they both correlated the holistic bacterial composition and vice versa. This study provides an overview of the gut viral community in Chinese and visiting Pakistanis and proposes a considerable role of ethnic origin in shaping the virome.
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Affiliation(s)
- Qiulong Yan
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yu Wang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- Institute of Translational Medicine, Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing 210029, China
| | - Xiuli Chen
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Hao Jin
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
- College of Food Science and Engineering, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Saihan District, Hohhot 010018, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Kuiqing Guan
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Yue Zhang
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Pan Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai 200032, China
| | - Taj Ayaz
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yanshan Liang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Junyi Wang
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Guangyi Cui
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
| | - Yuanyuan Sun
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Manchun Xiao
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Jian Kang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Wei Zhang
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Aiqin Zhang
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Peng Li
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Xueyang Liu
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Hayan Ulllah
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Yufang Ma
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
| | - Shenghui Li
- Shenzhen Puensum Genetech Institute, 345 Dongbin Road, Nanshan District, Shenzhen 518052, China
| | - Tonghui Ma
- School of Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing 210029, China
- College of Basic Medical Sciences, Dalian Medical University, No.9 West Section Lvshun South Road, Dalian 116044, China
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Abstract
The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the 'virome'. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 1031 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 1013 particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral 'dark matter'. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host-virome interactions in health and disease.
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128
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Coughlan S, Das A, O’Herlihy E, Shanahan F, O’Toole P, Jeffery I. The gut virome in Irritable Bowel Syndrome differs from that of controls. Gut Microbes 2021; 13:1-15. [PMID: 33602058 PMCID: PMC7899630 DOI: 10.1080/19490976.2021.1887719] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/28/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
Irritable Bowel Syndrome (IBS), the most common gastrointestinal disorder, is diagnosed solely on symptoms. Potentially diagnostic alterations in the bacterial component of the gut microbiome (the bacteriome) are associated with IBS, but despite the known role of the virome (particularly bacteriophages), in shaping the gut bacteriome, few studies have investigated the virome in IBS. We performed metagenomic sequencing of fecal Virus-Like Particles (VLPs) from 55 patients with IBS and 51 control individuals. We detected significantly lower alpha diversity of viral clusters comprising both known and novel viruses (viral 'dark matter') in IBS and a significant difference in beta diversity compared to controls, but not between IBS symptom subtypes. The three most abundant bacteriophage clusters belonged to the Siphoviridae, Myoviridae, and Podoviridae families (Order Caudovirales). A core virome (defined as a cluster present in at least 50% of samples) of 5 and 12 viral clusters was identified in IBS and control subjects, respectively. We also identified a subset of viral clusters that showed differential abundance between IBS and controls. The virome did not co-vary significantly with the bacteriome, with IBS clinical subtype, or with Bile Acid Malabsorption status. However, differences in the virome could be related back to the bacteriome as analysis of CRISPR spacers indicated that the virome alterations were at least partially related to the alterations in the bacteriome. We found no evidence for a shift from lytic to lysogenic replication of core viral clusters, a phenomenon reported for the gut virome of patients with Inflammatory Bowel Disease. Collectively, our data show alterations in the virome of patients with IBS, regardless of clinical subtype, which may facilitate development of new microbiome-based therapeutics.
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Affiliation(s)
- S. Coughlan
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - A. Das
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - E. O’Herlihy
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
| | - F. Shanahan
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
| | - P.W. O’Toole
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
| | - I.B. Jeffery
- 4D Pharma Cork Limited, Cavanagh Pharmacy Building, University College Cork, National University of Ireland, Cork, Ireland
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129
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Luque A, Benler S, Lee DY, Brown C, White S. The Missing Tailed Phages: Prediction of Small Capsid Candidates. Microorganisms 2020; 8:E1944. [PMID: 33302408 PMCID: PMC7762592 DOI: 10.3390/microorganisms8121944] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/04/2020] [Accepted: 12/05/2020] [Indexed: 12/17/2022] Open
Abstract
Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common icosahedral capsid architectures T = 1 and T = 3 is puzzling. Here, we extracted geometrical features from high-resolution tailed phage capsid reconstructions and built a statistical model based on physical principles to predict the capsid diameter and genome length of the missing small-tailed phage capsids. We applied the model to 3348 isolated tailed phage genomes and 1496 gut metagenome-assembled tailed phage genomes. Four isolated tailed phages were predicted to form T = 3 icosahedral capsids, and twenty-one metagenome-assembled tailed phages were predicted to form T < 3 capsids. The smallest capsid predicted was a T = 4/3 ≈ 1.33 architecture. No tailed phages were predicted to form the smallest icosahedral architecture, T = 1. We discuss the feasibility of the missing T = 1 tailed phage capsids and the implications of isolating and characterizing small-tailed phages for viral evolution and phage therapy.
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Affiliation(s)
- Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; (D.Y.L.); (C.B.)
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA
| | - Sean Benler
- National Center for Biotechnology Information (NCBI), Bethesda, MD 20894, USA;
| | - Diana Y. Lee
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; (D.Y.L.); (C.B.)
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
| | - Colin Brown
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; (D.Y.L.); (C.B.)
- Department of Physics, San Diego State University, San Diego, CA 92182, USA
| | - Simon White
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA;
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130
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Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut. Cell Host Microbe 2020; 28:724-740.e8. [PMID: 32841606 PMCID: PMC7443397 DOI: 10.1016/j.chom.2020.08.003] [Citation(s) in RCA: 303] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
The gut microbiome profoundly affects human health and disease, and their infecting viruses are likely as important, but often missed because of reference database limitations. Here, we (1) built a human Gut Virome Database (GVD) from 2,697 viral particle or microbial metagenomes from 1,986 individuals representing 16 countries, (2) assess its effectiveness, and (3) report a meta-analysis that reveals age-dependent patterns across healthy Westerners. The GVD contains 33,242 unique viral populations (approximately species-level taxa) and improves average viral detection rates over viral RefSeq and IMG/VR nearly 182-fold and 2.6-fold, respectively. GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from technical artifacts is larger than any "disease" effect at the population level, and document how viral diversity changes from human infancy into senescence. Together, this compact foundational resource, these standardization guidelines, and these meta-analysis findings provide a systematic toolkit to help maximize our understanding of viral roles in health and disease.
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Affiliation(s)
- Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Allison Howell
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA.
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131
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Monaghan TM, Sloan TJ, Stockdale SR, Blanchard AM, Emes RD, Wilcox M, Biswas R, Nashine R, Manke S, Gandhi J, Jain P, Bhotmange S, Ambalkar S, Satav A, Draper LA, Hill C, Kashyap RS. Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome. Gut Microbes 2020; 12:1752605. [PMID: 32459982 PMCID: PMC7781581 DOI: 10.1080/19490976.2020.1752605] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants. RESULTS We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3rd generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism. CONCLUSIONS We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations.
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Affiliation(s)
- Tanya M. Monaghan
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,CONTACT Tanya M. Monaghan NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Tim J. Sloan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Adam M. Blanchard
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Richard D. Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK,Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Mark Wilcox
- Leeds Teaching Hospitals NHS Trust and University of Leeds, UK
| | - Rima Biswas
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Rupam Nashine
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Sonali Manke
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Jinal Gandhi
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Pratishtha Jain
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrejal Bhotmange
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrikant Ambalkar
- Department of Clinical Microbiology and Infection, King’s Mill Hospital, Sherwood Forest Hospitals NHS Trust, Sutton in Ashfield, UK
| | | | | | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Rajpal Singh Kashyap
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India,Rajpal Singh Kashyap Biochemistry Research Centre, Central India Institute of Medical Sciences, 88/2 Bajaj Nagar, Nagpur, Maharashtra, India
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132
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crAssphage genomes identified in fecal samples of an adult and infants with evidence of positive genomic selective pressure within tail protein genes. Virus Res 2020; 292:198219. [PMID: 33137401 DOI: 10.1016/j.virusres.2020.198219] [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] [Received: 06/30/2020] [Revised: 10/06/2020] [Accepted: 10/26/2020] [Indexed: 01/21/2023]
Abstract
crAssphages are a broad group of diverse bacteriophages in the order Caudovirales that have been found to be highly abundant in the human gastrointestinal tract. Despite their high prevalence, we have an incomplete understanding of how crAssphages shape and respond to ecological and evolutionary dynamics in the gut. Here, we report genomes of crAssphages from feces of one South African woman and three infants. Across the complete genome sequences of the South African crAssphages described here, we identify particularly elevated positive selection in RNA polymerase and phage tail protein encoding genes, contrasted against purifying selection, genome-wide. We further validate these findings against a crAssphage genome from previous studies. Together, our results suggest hotspots of selection within crAssphage RNA polymerase and phage tail protein encoding genes are potentially mediated by interactions between crAssphages and their bacterial partners.
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133
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Yan A, Butcher J, Mack D, Stintzi A. Virome Sequencing of the Human Intestinal Mucosal-Luminal Interface. Front Cell Infect Microbiol 2020; 10:582187. [PMID: 33194818 PMCID: PMC7642909 DOI: 10.3389/fcimb.2020.582187] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/14/2020] [Indexed: 01/12/2023] Open
Abstract
While the human gut virome has been increasingly explored in recent years, nearly all studies have been limited to fecal sampling. The mucosal-luminal interface has been established as a viable sample type for profiling the microbial biogeography of the gastrointestinal tract. We have developed a protocol to extract nucleic acids from viruses at the mucosal-luminal interface of the proximal and distal colon. Colonic viromes from pediatric patients with Crohn's disease demonstrated high interpatient diversity and low but significant intrapatient variation between sites. Whole metagenomics was also performed to explore virome-bacteriome interactions and to compare the viral communities observed in virome and whole metagenomic sequencing. A site-specific study of the human gut virome is a necessary step to advance our understanding of virome-bacteriome-host interactions in human diseases.
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Affiliation(s)
- Austin Yan
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - James Butcher
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - David Mack
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Inflammatory Bowel Disease Centre and CHEO Research Institute, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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134
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Crank K, Li X, North D, Ferraro GB, Iaconelli M, Mancini P, La Rosa G, Bibby K. CrAssphage abundance and correlation with molecular viral markers in Italian wastewater. WATER RESEARCH 2020; 184:116161. [PMID: 32810770 DOI: 10.1016/j.watres.2020.116161] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 05/18/2023]
Abstract
Current fecal indicators for environmental health monitoring are primarily based on fecal indicator bacteria (FIB) which do not accurately represent viral pathogens. There is a need for highly abundant, human-associated viral fecal indicators to represent viral pathogens in sewage-contaminated water. In the present study, we evaluate the abundance of the emerging viral fecal indicator crAssphage in 156 Italian wastewater samples collected between 2014 and 2018. Samples were collected using two separate viral concentration methods, glycine-CF and PEG-dextran and qPCR assays were run for crAssphage (CPQ56) and Human Polyomavirus (HPyV) and endpoint PCR assays were run for Human Bocavirus (HBoc) and Hepatitis E Virus (HepE). CrAssphage was detected in 96% of samples and no statistically significant difference was observed in crAssphage abundance between concentration methods (p = 0.39). CrAssphage concentrations also did not correlate with location (latitude) or size (load and capacity) of the wastewater treatment plant. HPyV detection rates with the glycine-CF and PEG-dextran methods were 64% and 100%, respectively, and the concentrations of HPyV were statistically significantly influenced by the concentration method (p < 0.0001). CrAssphage was measured at significantly higher concentrations than HPyV for both concentration methods (p < 0.0001). The observed concentration ranges were 3.84-7.29 log10GC/100 mL for crAssphage and 3.45-5.17 log10GC/100 mL for HPyV. There was a strong positive correlation between crAssphage and HPyV abundance for both concentration methods; however, the slope of the correlation depended on the concentration method. CrAssphage presence correlated with the presence of HBoc in samples concentrated with glycine-CF, but did not correlate with the presence of HBoc concentrated with the PEG-dextran method or with the presence of HepE. Overall, these results demonstrate that crAssphage is an abundant viral fecal indicator in wastewater with statistically significant correlation with human viral pathogens (e.g., HPyV) and viral concentration methods influence the interpretation of fecal viral indicator detection.
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Affiliation(s)
- Katherine Crank
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Xiang Li
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA; School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Devin North
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | - Marcello Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Pamela Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA.
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135
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Rossi A, Treu L, Toppo S, Zschach H, Campanaro S, Dutilh BE. Evolutionary Study of the Crassphage Virus at Gene Level. Viruses 2020; 12:v12091035. [PMID: 32957679 PMCID: PMC7551546 DOI: 10.3390/v12091035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
crAss-like viruses are a putative family of bacteriophages recently discovered. The eponym of the clade, crAssphage, is an enteric bacteriophage estimated to be present in at least half of the human population and it constitutes up to 90% of the sequences in some human fecal viral metagenomic datasets. We focused on the evolutionary dynamics of the genes encoded on the crAssphage genome. By investigating the conservation of the genes, a consistent variation in the evolutionary rates across the different functional groups was found. Gene duplications in crAss-like genomes were detected. By exploring the differences among the functional categories of the genes, we confirmed that the genes encoding capsid proteins were the most ubiquitous, despite their overall low sequence conservation. It was possible to identify a core of proteins whose evolutionary trees strongly correlate with each other, suggesting their genetic interaction. This group includes the capsid proteins, which are thus established as extremely suitable for rebuilding the phylogenetic tree of this viral clade. A negative correlation between the ubiquity and the conservation of viral protein sequences was shown. Together, this study provides an in-depth picture of the evolution of different genes in crAss-like viruses.
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Affiliation(s)
- Alessandro Rossi
- Department of Biology, University of Padova, 35131 Padova, Italy; (A.R.); (S.C.)
| | - Laura Treu
- Department of Biology, University of Padova, 35131 Padova, Italy; (A.R.); (S.C.)
- Correspondence: ; Tel.: +39-049-827-6165
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, 35131 Padova, Italy;
| | - Henrike Zschach
- Department of Biology, University of Copenhagen, 1017 Copenhagen, Denmark;
| | - Stefano Campanaro
- Department of Biology, University of Padova, 35131 Padova, Italy; (A.R.); (S.C.)
- CRIBI Biotechnology Center, University of Padua, 35131 Padova, Italy
| | - Bas E. Dutilh
- Institute of Biodynamics and Biocomplexity, University of Utrecht, 3508 Utrecht, The Netherlands;
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136
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Guerin E, Hill C. Shining Light on Human Gut Bacteriophages. Front Cell Infect Microbiol 2020; 10:481. [PMID: 33014897 PMCID: PMC7511551 DOI: 10.3389/fcimb.2020.00481] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/04/2020] [Indexed: 12/15/2022] Open
Abstract
The human gut is a complex environment that contains a multitude of microorganisms that are collectively termed the microbiome. Multiple factors have a role to play in driving the composition of human gut bacterial communities either toward homeostasis or the instability that is associated with many disease states. One of the most important forces are likely to be bacteriophages, bacteria-infecting viruses that constitute by far the largest portion of the human gut virome. Despite this, bacteriophages (phages) are the one of the least studied residents of the gut. This is largely due to the challenges associated with studying these difficult to culture entities. Modern high throughput sequencing technologies have played an important role in improving our understanding of the human gut phageome but much of the generated sequencing data remains uncharacterised. Overcoming this requires database-independent bioinformatic pipelines and even those phages that are successfully characterized only provide limited insight into their associated biological properties, and thus most viral sequences have been characterized as “viral dark matter.” Fundamental to understanding the role of phages in shaping the human gut microbiome, and in turn perhaps influencing human health, is how they interact with their bacterial hosts. An essential aspect is the isolation of novel phage-bacteria host pairs by direct isolation through various screening methods, which can transform in silico phages into a biological reality. However, this is also beset with multiple challenges including culturing difficulties and the use of traditional methods, such as plaquing, which may bias which phage-host pairs that can be successfully isolated. Phage-bacteria interactions may be influenced by many aspects of complex human gut biology which can be difficult to reproduce under laboratory conditions. Here we discuss some of the main findings associated with the human gut phageome to date including composition, our understanding of phage-host interactions, particularly the observed persistence of virulent phages and their hosts, as well as factors that may influence these highly intricate relationships. We also discuss current methodologies and bottlenecks hindering progression in this field and identify potential steps that may be useful in overcoming these hurdles.
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Affiliation(s)
- Emma Guerin
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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137
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Hryckowian AJ, Merrill BD, Porter NT, Van Treuren W, Nelson EJ, Garlena RA, Russell DA, Martens EC, Sonnenburg JL. Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions. Cell Host Microbe 2020; 28:371-379.e5. [PMID: 32652063 PMCID: PMC8045012 DOI: 10.1016/j.chom.2020.06.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/22/2020] [Accepted: 06/12/2020] [Indexed: 12/21/2022]
Abstract
Our emerging view of the gut microbiome largely focuses on bacteria, while less is known about other microbial components, such as bacteriophages (phages). Though phages are abundant in the gut, very few phages have been isolated from this ecosystem. Here, we report the genomes of 27 phages from the United States and Bangladesh that infect the prevalent human gut bacterium Bacteroides thetaiotaomicron. These phages are mostly distinct from previously sequenced phages with the exception of two, which are crAss-like phages. We compare these isolates to existing human gut metagenomes, revealing similarities to previously inferred phages and additional unexplored phage diversity. Finally, we use host tropisms of these phages to identify alleles of phage structural genes associated with infectivity. This work provides a detailed view of the gut's "viral dark matter" and a framework for future efforts to further integrate isolation- and sequencing-focused efforts to understand gut-resident phages.
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Affiliation(s)
- Andrew J Hryckowian
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Bryan D Merrill
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nathan T Porter
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - William Van Treuren
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eric J Nelson
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca A Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Eric C Martens
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Justin L Sonnenburg
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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138
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Lourenço M, Chaffringeon L, Lamy-Besnier Q, Pédron T, Campagne P, Eberl C, Bérard M, Stecher B, Debarbieux L, De Sordi L. The Spatial Heterogeneity of the Gut Limits Predation and Fosters Coexistence of Bacteria and Bacteriophages. Cell Host Microbe 2020; 28:390-401.e5. [DOI: 10.1016/j.chom.2020.06.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/30/2020] [Accepted: 06/02/2020] [Indexed: 02/08/2023]
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139
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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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140
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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: 47] [Impact Index Per Article: 11.8] [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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141
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Abstract
Shotgun metagenomic sequencing has revolutionized our ability to detect and characterize the diversity and function of complex microbial communities. In this review, we highlight the benefits of using metagenomics as well as the breadth of conclusions that can be made using currently available analytical tools, such as greater resolution of species and strains across phyla and functional content, while highlighting challenges of metagenomic data analysis. Major challenges remain in annotating function, given the dearth of functional databases for environmental bacteria compared to model organisms, and the technical difficulties of metagenome assembly and phasing in heterogeneous environmental samples. In the future, improvements and innovation in technology and methodology will lead to lowered costs. Data integration using multiple technological platforms will lead to a better understanding of how to harness metagenomes. Subsequently, we will be able not only to characterize complex microbiomes but also to manipulate communities to achieve prosperous outcomes for health, agriculture, and environmental sustainability.
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Affiliation(s)
- Felicia N New
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, USA;
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, USA;
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142
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Wang W, Ren J, Tang K, Dart E, Ignacio-Espinoza JC, Fuhrman JA, Braun J, Sun F, Ahlgren NA. A network-based integrated framework for predicting virus-prokaryote interactions. NAR Genom Bioinform 2020; 2:lqaa044. [PMID: 32626849 PMCID: PMC7324143 DOI: 10.1093/nargab/lqaa044] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 03/12/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences; however, it remains challenging to identify the host(s) of these new viruses. We developed VirHostMatcher-Net, a flexible, network-based, Markov random field framework for predicting virus–prokaryote interactions using multiple, integrated features: CRISPR sequences and alignment-free similarity measures (\documentclass[12pt]{minimal}
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}{}$s_2^*$\end{document} and WIsH). Evaluation of this method on a benchmark set of 1462 known virus–prokaryote pairs yielded host prediction accuracy of 59% and 86% at the genus and phylum levels, representing 16–27% and 6–10% improvement, respectively, over previous single-feature prediction approaches. We applied our host prediction tool to crAssphage, a human gut phage, and two metagenomic virus datasets: marine viruses and viral contigs recovered from globally distributed, diverse habitats. Host predictions were frequently consistent with those of previous studies, but more importantly, this new tool made many more confident predictions than previous tools, up to nearly 3-fold more (n > 27 000), greatly expanding the diversity of known virus–host interactions.
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Affiliation(s)
- Weili Wang
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Jie Ren
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Kujin Tang
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Emily Dart
- Biology Department, Clark University, Worcester, MA 01610, USA
| | | | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jonathan Braun
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Fengzhu Sun
- Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
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143
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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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144
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Morrison CM, Betancourt WQ, Quintanar DR, Lopez GU, Pepper IL, Gerba CP. Potential indicators of virus transport and removal during soil aquifer treatment of treated wastewater effluent. WATER RESEARCH 2020; 177:115812. [PMID: 32311575 DOI: 10.1016/j.watres.2020.115812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 05/03/2023]
Abstract
Increased water demands have led to a notable interest in the use of treated wastewater for reuse. Typically, this results from the implementation of advanced treatment of final effluent from wastewater treatment plants prior to reuse for potable or non-potable purposes. Soil aquifer treatment (SAT) is a natural treatment process in which water from sources of varying quality is infiltrated into the soil to further improve its quality. The goal of this study was to determine the log10 reduction values (LRVs) of viruses naturally present in treated effluent and evaluate two potential indicators of virus removal and transport, pepper mild mottle virus (PMMoV) and crAssphage, during SAT of treated effluent. Groundwater was sampled at three wells with different attributes within the Sweetwater Recharge Facility (SWRF) in Tucson, AZ. These sites vary greatly in operational parameters such as effluent infiltration rates and wetting/drying cycles, which may influence virus removal efficiency. Detection of adenovirus, enterovirus, PMMoV, and crAssphage were determined by qPCR/RT-qPCR and log10 reduction values (LRVs) were determined. PMMoV and crAssphage were detected in groundwater associated with a set of recharge basins that exhibited shorter wetting/drying cycles and faster infiltration rates. LRVs for crAssphage and PMMoV at this site ranged from 3.9 to 5.8, respectively. Moreover, PMMoV was detected downflow of the SAT sites, indicating the potential degradation of microbial groundwater quality in the region surrounding managed aquifer recharge facilities. Overall, PMMoV and crAssphage showed potential as conservative process indicators of virus removal during SAT, particularly for attribution of LRV credits. Moreover, the detection of these viruses indicated the potential influence of wetting/drying cycles on virus removal by SAT, a parameter that has not yet been studied with respect to biological contaminants.
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Affiliation(s)
- Christina M Morrison
- Department of Environmental Science, Water and Energy Sustainable Technology (WEST) Center University of Arizona, Tucson, AZ, USA.
| | - Walter Q Betancourt
- Department of Environmental Science, Water and Energy Sustainable Technology (WEST) Center University of Arizona, Tucson, AZ, USA
| | | | - Gerardo U Lopez
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Ian L Pepper
- Department of Environmental Science, Water and Energy Sustainable Technology (WEST) Center University of Arizona, Tucson, AZ, USA
| | - Charles P Gerba
- Department of Environmental Science, Water and Energy Sustainable Technology (WEST) Center University of Arizona, Tucson, AZ, USA
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145
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Park GW, Ng TFF, Freeland AL, Marconi VC, Boom JA, Staat MA, Montmayeur AM, Browne H, Narayanan J, Payne DC, Cardemil CV, Treffiletti A, Vinjé J. CrAssphage as a Novel Tool to Detect Human Fecal Contamination on Environmental Surfaces and Hands. Emerg Infect Dis 2020; 26:1731-1739. [PMID: 32511090 PMCID: PMC7392416 DOI: 10.3201/eid2608.200346] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
CrAssphage is a recently discovered human gut–associated bacteriophage. To validate the potential use of crAssphage for detecting human fecal contamination on environmental surfaces and hands, we tested stool samples (n = 60), hand samples (n = 30), and environmental swab samples (n = 201) from 17 norovirus outbreaks for crAssphage by real-time PCR. In addition, we tested stool samples from healthy persons (n = 173), respiratory samples (n = 113), and animal fecal specimens (n = 68) and further sequenced positive samples. Overall, we detected crAssphage in 71.4% of outbreak stool samples, 48%–68.5% of stool samples from healthy persons, 56.2% of environmental swabs, and 60% of hand rinse samples, but not in human respiratory samples or animal fecal samples. CrAssphage sequences could be grouped into 2 major genetic clusters. Our data suggest that crAssphage could be used to detect human fecal contamination on environmental surfaces and hands.
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146
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Morozova V, Fofanov M, Tikunova N, Babkin I, Morozov VV, Tikunov A. First crAss-Like Phage Genome Encoding the Diversity-Generating Retroelement (DGR). Viruses 2020; 12:v12050573. [PMID: 32456083 PMCID: PMC7290462 DOI: 10.3390/v12050573] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/20/2022] Open
Abstract
A new crAss-like genome encoding diversity-generating retroelement (DGR) was found in the fecal virome of a healthy volunteer. The genome of the phage referred to as the crAssphage LMMB, belonged to the candidate genus I of the AlphacrAssvirinae subfamily. The DGR-cassette of the crAssphage LMMB contained all the essential elements: the gene encoding reverse transcriptase (RT), the target gene (TG) encoding the tail-collar fiber protein, and variable and template repeats (VR and TR) with IMH (initiation of mutagenic homing) and IMH* sequences at the 3′-end of the VR and TR, respectively. Architecture of the DGR-cassette was TG-VR(IMH)-TR(IMH*)-RT and an accessory variable determinant (avd) was absent from the cassette. Analysis of 91 genomes and genome fragments from genus I of the AlphacrAssvirinae showed that 15 (16%) of the genomes had DGRs with the same architecture as the crAssphage LMMB, while 66 of the genomes contained incomplete DGR-cassettes or some elements of the DGR.
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147
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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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148
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Matijašić M, Meštrović T, Paljetak HČ, Perić M, Barešić A, Verbanac D. Gut Microbiota beyond Bacteria-Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD. Int J Mol Sci 2020; 21:E2668. [PMID: 32290414 PMCID: PMC7215374 DOI: 10.3390/ijms21082668] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well as numerous disease etiologies. Dominated by bacteria, the microbiota also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in the past two decades, these non-bacterial microorganisms, their functional roles, and their interaction with one another or with host immune system have not been as widely explored. This review covers the recent findings on the non-bacterial communities of the human gastrointestinal microbiota and their involvement in health and disease, with particular focus on the pathophysiology of inflammatory bowel disease.
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Affiliation(s)
- Mario Matijašić
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | | | - Hana Čipčić Paljetak
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Mihaela Perić
- Center for Translational and Clinical Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Anja Barešić
- Division of Electronics, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Donatella Verbanac
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
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149
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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: 115] [Impact Index Per Article: 28.8] [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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150
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Koonin EV, Yutin N. The crAss-like Phage Group: How Metagenomics Reshaped the Human Virome. Trends Microbiol 2020; 28:349-359. [PMID: 32298613 DOI: 10.1016/j.tim.2020.01.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 02/07/2023]
Abstract
Metagenomics is currently the primary means for identifying new viruses. One of the most impactful metagenomic discoveries is that of crAssphage, the most abundant human-associated virus that is found in about 50% of human gut viromes where it can comprise up to 90% of the virus sequences. Although initial genome analysis of crAssphage failed to detect related phages, or functionally annotate most of the genes, subsequent reanalysis with powerful computational methods and larger databases led to the identification of an expansive group of crAss-like phages. The functions of most crAssphage proteins were predicted, including unusual ones such as giant RNA polymerase polyproteins. The host range of the crAss-like phages consists of various members of the bacterial phylum Bacteroidetes as demonstrated by CRISPR spacer analysis and by analysis of genes acquired by phages from the hosts. New metagenomic studies vastly expanded the crAss-like phage group and demonstrated its global spread and ancient association with primates. The first members of the crAss-like group was recently isolated and shown to infect the bacterium Bacteroides intestinales. Characterization of this phage validated the predicted podovirus-like virion structure and the identity of the major capsid protein and other predicted virion proteins, including three RNA polymerase subunits.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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