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Javorčík PN, Harms A. Isolation and sequencing of a novel inovirus, "Copypasta," from Rhine River water. Microbiol Resour Announc 2024; 13:e0118023. [PMID: 38265206 PMCID: PMC10868210 DOI: 10.1128/mra.01180-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/06/2024] [Indexed: 01/25/2024] Open
Abstract
We present a new inovirus named Copypasta isolated from the Rhine River that infects Escherichia coli and shows the expected filamentous morphology. Copypasta has a circular single-stranded DNA genome that is 6,408 nt long and harbors 12 protein-coding genes.
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Affiliation(s)
- P. Nathael Javorčík
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
| | - Alexander Harms
- Institute of Food, Nutrition and Health, D-HEST, ETH Zurich, Zurich, Switzerland
- Biozentrum, University of Basel, Basel, Switzerland
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2
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Pozhydaieva N, Wolfram-Schauerte M, Keuthen H, Höfer K. The enigmatic epitranscriptome of bacteriophages: putative RNA modifications in viral infections. Curr Opin Microbiol 2024; 77:102417. [PMID: 38217927 DOI: 10.1016/j.mib.2023.102417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/15/2024]
Abstract
RNA modifications play essential roles in modulating RNA function, stability, and fate across all kingdoms of life. The entirety of the RNA modifications within a cell is defined as the epitranscriptome. While eukaryotic RNA modifications are intensively studied, understanding bacterial RNA modifications remains limited, and knowledge about bacteriophage RNA modifications is almost nonexistent. In this review, we shed light on known mechanisms of bacterial RNA modifications and propose how this knowledge might be extended to bacteriophages. We build hypotheses on enzymes potentially responsible for regulating the epitranscriptome of bacteriophages and their host. This review highlights the exciting prospects of uncovering the unexplored field of bacteriophage epitranscriptomics and its potential role to shape bacteriophage-host interactions.
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Affiliation(s)
| | | | - Helene Keuthen
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katharina Höfer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
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3
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Nguyen HM, Watanabe S, Sharmin S, Kawaguchi T, Tan XE, Wannigama DL, Cui L. RNA and Single-Stranded DNA Phages: Unveiling the Promise from the Underexplored World of Viruses. Int J Mol Sci 2023; 24:17029. [PMID: 38069353 PMCID: PMC10707117 DOI: 10.3390/ijms242317029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
RNA and single-stranded DNA (ssDNA) phages make up an understudied subset of bacteriophages that have been rapidly expanding in the last decade thanks to advancements in metaviromics. Since their discovery, applications of genetic engineering to ssDNA and RNA phages have revealed their immense potential for diverse applications in healthcare and biotechnology. In this review, we explore the past and present applications of this underexplored group of phages, particularly their current usage as therapeutic agents against multidrug-resistant bacteria. We also discuss engineering techniques such as recombinant expression, CRISPR/Cas-based genome editing, and synthetic rebooting of phage-like particles for their role in tailoring phages for disease treatment, imaging, biomaterial development, and delivery systems. Recent breakthroughs in RNA phage engineering techniques are especially highlighted. We conclude with a perspective on challenges and future prospects, emphasizing the untapped diversity of ssDNA and RNA phages and their potential to revolutionize biotechnology and medicine.
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Affiliation(s)
- Huong Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Sultana Sharmin
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Tomofumi Kawaguchi
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata 990-2292, Yamagata, Japan;
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
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4
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Coclet C, Sorensen PO, Karaoz U, Wang S, Brodie EL, Eloe-Fadrosh EA, Roux S. Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. MICROBIOME 2023; 11:237. [PMID: 37891627 PMCID: PMC10604447 DOI: 10.1186/s40168-023-01666-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/07/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics' seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. RESULTS We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a "seed-bank" viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: "Kill-The-Winner" which proposes that lytic phages are actively infecting abundant bacteria, and "Piggyback-The-Persistent" which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. CONCLUSION Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry. Video Abstract.
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Affiliation(s)
- Clement Coclet
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Patrick O Sorensen
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shi Wang
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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5
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Jo SJ, Kwon J, Kim SG, Lee SJ. The Biotechnological Application of Bacteriophages: What to Do and Where to Go in the Middle of the Post-Antibiotic Era. Microorganisms 2023; 11:2311. [PMID: 37764155 PMCID: PMC10534921 DOI: 10.3390/microorganisms11092311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Amid the escalating challenges of antibiotic resistance, bacterial infections have emerged as a global threat. Bacteriophages (phages), viral entities capable of selectively infecting bacteria, are gaining momentum as promising alternatives to traditional antibiotics. Their distinctive attributes, including host specificity, inherent self-amplification, and potential synergy with antibiotics, render them compelling candidates. Phage engineering, a burgeoning discipline, involves the strategic modification of bacteriophages to enhance their therapeutic potential and broaden their applications. The integration of CRISPR-Cas systems facilitates precise genetic modifications, enabling phages to serve as carriers of functional genes/proteins, thereby enhancing diagnostics, drug delivery, and therapy. Phage engineering holds promise in transforming precision medicine, addressing antibiotic resistance, and advancing diverse applications. Emphasizing the profound therapeutic potential of phages, this review underscores their pivotal role in combatting bacterial diseases and highlights their significance in the post-antibiotic era.
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Affiliation(s)
- Su Jin Jo
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Jun Kwon
- Laboratory of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan City 54596, Republic of Korea
| | - Sang Guen Kim
- Department of Biological Sciences, Kyonggi University, Suwon 16227, Republic of Korea
| | - Seung-Jun Lee
- Department of Pharmaceutical Science and Engineering, Seowon University, 377-3 Musimseoro, Seowon-gu, Cheong-ju City 28674, Republic of Korea
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6
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Le Lay C, Hamm JN, Williams TJ, Shi M, Cavicchioli R, Holmes EC. Viral community composition of hypersaline lakes. Virus Evol 2023; 9:vead057. [PMID: 37692898 PMCID: PMC10492444 DOI: 10.1093/ve/vead057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/03/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023] Open
Abstract
Despite their widespread distribution and remarkable antiquity no RNA viruses definitively associated with the domain Archaea have been identified. In contrast, 17 families of DNA viruses are known to infect archaea. In an attempt to uncover more of the elusive archaeal virosphere, we investigated the metatranscriptomes of hypersaline lakes that are a rich source of archaea. We sequenced RNA extracted from water filter samples of Lake Tyrrell (Victoria, Australia) and cultures seeded from four lakes in Antarctica. To identify highly divergent viruses in these data, we employed a variety of search tools, including Hidden Markov models (HMMs) and position-specific scoring matrices (PSSMs). From this, we identified 12 highly divergent, RNA virus-like candidate sequences from the virus phyla Artverviricota, Duplornaviricota, Kitrinoviricota, Negarnaviricota, and Pisuviricota, including those with similarity to the RNA-dependent RNA polymerase (RdRp). An additional analysis with an artificial intelligence (AI)-based approach that utilises both sequence and structural information identified seven putative and highly divergent RdRp sequences of uncertain phylogenetic position. A sequence matching the Pisuviricota from Deep Lake in Antarctica had the strongest RNA virus signal. Analyses of the dinucleotide representation of the virus-like candidates in comparison to that of potential host species were in some cases compatible with an association to archaeal or bacterial hosts. Notably, however, the use of archaeal CRISPR spacers as a BLAST database failed to detect any RNA viruses. We also described DNA viruses from the families Pleolipoviridae, Sphaerolipoviridae, Halspiviridae, and the class Caudoviricetes. Although we were unable to provide definitive evidence the existence of an RNA virus of archaea in these hypersaline lakes, this study lays the foundations for further investigations of highly divergent RNA viruses in natural environments.
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Affiliation(s)
- Callum Le Lay
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg NL-1790 AB, The Netherlands
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7
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Walt HK, Kooienga E, Cammack JA, Tomberlin JK, Jordan HR, Meyer F, Hoffmann FG. Bioinformatic Surveillance Leads to Discovery of Two Novel Putative Bunyaviruses Associated with Black Soldier Fly. Viruses 2023; 15:1654. [PMID: 37631997 PMCID: PMC10460066 DOI: 10.3390/v15081654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
The black soldier fly (Hermetia illucens, BSF) has emerged as an industrial insect of high promise because of its ability to convert organic waste into nutritious feedstock, making it an environmentally sustainable alternative protein source. As global interest rises, rearing efforts have also been upscaled, which is highly conducive to pathogen transmission. Viral epidemics have stifled mass-rearing efforts of other insects of economic importance, such as crickets, silkworms, and honeybees, but little is known about the viruses that associate with BSF. Although BSFs are thought to be unusually resistant to pathogens because of their expansive antimicrobial gene repertoire, surveillance techniques could be useful in identifying emerging pathogens and common BSF microbes. In this study, we used high-throughput sequencing data to survey BSF larvae and frass samples, and we identified two novel bunyavirus-like sequences. Our phylogenetic analysis grouped one in the family Nairoviridae and the other with two unclassified bunyaviruses. We describe these putative novel viruses as BSF Nairovirus-like 1 and BSF uncharacterized bunyavirus-like 1. We identified candidate segments for the full BSF Nairovirus-like 1 genome using a technique based on transcript co-occurrence and only a partial genome for BSF uncharacterized bunyavirus-like 1. These results emphasize the value of routine BSF colony surveillance and add to the number of viruses associated with BSF.
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Affiliation(s)
- Hunter K. Walt
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA;
| | - Emilia Kooienga
- Department of Biology, Mississippi State University, Starkville, MS 39762, USA (H.R.J.)
| | - Jonathan A. Cammack
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.A.C.); (J.K.T.)
- EVO Conversion Systems, LLC, College Station, TX 77845, USA
| | - Jeffery K. Tomberlin
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.A.C.); (J.K.T.)
| | - Heather R. Jordan
- Department of Biology, Mississippi State University, Starkville, MS 39762, USA (H.R.J.)
| | - Florencia Meyer
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA;
| | - Federico G. Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS 39762, USA;
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39762, USA
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Ntemafack A, Dzelamonyuy A, Nchinda G, Bopda Waffo A. Evolutionary Qβ Phage Displayed Nanotag Library and Peptides for Biosensing. Viruses 2023; 15:1414. [PMID: 37515102 PMCID: PMC10386108 DOI: 10.3390/v15071414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
We selected a novel biotin-binding peptide for sensing biotin, biotinylated proteins, and nucleotides. From a 15-mer library displayed on the RNA coliphage Qβ, a 15-amino acid long peptide (HGHGWQIPVWPWGQG) hereby referred to as a nanotag was identified to selectively bind biotin. The target selection was achieved through panning with elution by infection. The selected peptide was tested as a transducer for an immunogenic epitope of the foot-and-mouth disease virus (FMDV) on Qβ phage platform separated by a linker. The biotin-tag showed no significant influence on the affinity of the epitope to its cognate antibody (SD6). The nanotag-bound biotin selectively fused either to the C- or N-terminus of the epitope. The epitope would not bind or recognize SD6 while positioned at the N-terminus of the nanotag. Additionally, the biotin competed linearly with the SD6 antibody in a competitive ELISA. Competition assays using the selected recombinant phage itself as a probe or transducer enable the operationalization of this technology as a biosensor toolkit to sense and quantify SD6 analyte. Herein, the published Strep II nanotag (DVEWLDERVPLVET) was used as a control and has similar functionalities to our proposed novel biotin-tag thereby providing a new platform for developing devices for diagnostic purposes.
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Affiliation(s)
- Augustin Ntemafack
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA
| | - Aristide Dzelamonyuy
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA
| | - Godwin Nchinda
- Laboratory of Vaccinology and Biobanking, CIRCB BP 3077 Messa, Yaoundé P.O. Box 3077, Cameroon
- Department of Pharmaceutical Microbiology and Biotechnology, Nnamdi Azikiwe University, Awka 420110, Nigeria
- African Center of Excellence for Clinical and Translational Sciences (ACECTS), Yaoundé P.O. Box 13591, Cameroon
| | - Alain Bopda Waffo
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA
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Dominguez-Huerta G, Wainaina JM, Zayed AA, Culley AI, Kuhn JH, Sullivan MB. The RNA virosphere: How big and diverse is it? Environ Microbiol 2023; 25:209-215. [PMID: 36511833 PMCID: PMC9852017 DOI: 10.1111/1462-2920.16312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Guillermo Dominguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
| | - James M Wainaina
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
| | - Alexander I Culley
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio, USA
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10
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Chitcharoen S, Sivapornnukul P, Payungporn S. Revolutionized virome research using systems microbiology approaches. Exp Biol Med (Maywood) 2022; 247:1135-1147. [PMID: 35723062 PMCID: PMC9335507 DOI: 10.1177/15353702221102895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.
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Affiliation(s)
- Suwalak Chitcharoen
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand,Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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11
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Andrade-Martínez JS, Camelo Valera LC, Chica Cárdenas LA, Forero-Junco L, López-Leal G, Moreno-Gallego JL, Rangel-Pineros G, Reyes A. Computational Tools for the Analysis of Uncultivated Phage Genomes. Microbiol Mol Biol Rev 2022; 86:e0000421. [PMID: 35311574 PMCID: PMC9199400 DOI: 10.1128/mmbr.00004-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes. Novel phage genomes have been reported from a diverse range of biomes at an increasing rate, which has prompted the development of computational tools that support the multilevel characterization of these novel phages based solely on their genome sequences. The impact of these technologies has been so large that, together with MAGs (Metagenomic Assembled Genomes), we now have UViGs (Uncultivated Viral Genomes), which are now officially recognized by the International Committee for the Taxonomy of Viruses (ICTV), and new taxonomic groups can now be created based exclusively on genomic sequence information. Even though the available tools have immensely contributed to our knowledge of phage diversity and ecology, the ongoing surge in software programs makes it challenging to keep up with them and the purpose each one is designed for. Therefore, in this review, we describe a comprehensive set of currently available computational tools designed for the characterization of phage genome sequences, focusing on five specific analyses: (i) assembly and identification of phage and prophage sequences, (ii) phage genome annotation, (iii) phage taxonomic classification, (iv) phage-host interaction analysis, and (v) phage microdiversity.
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Affiliation(s)
- Juan Sebastián Andrade-Martínez
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Carolina Camelo Valera
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Luis Alberto Chica Cárdenas
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Forero-Junco
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Gamaliel López-Leal
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - J. Leonardo Moreno-Gallego
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Guillermo Rangel-Pineros
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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12
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Evaluation of UV-C Radiation Efficiency in the Decontamination of Inanimate Surfaces and Personal Protective Equipment Contaminated with Phage ϕ6. Microorganisms 2022; 10:microorganisms10030593. [PMID: 35336168 PMCID: PMC8954440 DOI: 10.3390/microorganisms10030593] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 12/23/2022] Open
Abstract
To help halt the global spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), appropriate disinfection techniques are required. Over the last years, the interest in Ultraviolet-C (UV-C) radiation as a method to disinfect inanimate surfaces and personal protective equipment (PPE) has increased, mainly to efficiently disinfect and prevent SARS-CoV-2 from spreading and allow for the safe reuse of said equipment. The bacteriophage ϕ6 (or simply phage ϕ6) is an RNA virus with a phospholipid envelope and is commonly used in environmental studies as a surrogate for human RNA-enveloped viruses, including SARS-CoV-2. The present study investigated the use of two new UV irradiation systems ((2)2.4W and (8)5.5W)) constituted by conventional mercury UV-C lamps with a strong emission peak at ~254 nm to potentially inactivate phage ϕ6 on different surfaces (glass, plastic, stainless steel, and wood) and personal protective equipment, PPE, (surgical and filtering facepiece 2, FFP2, masks, a clear acetate visor, and disposable protective clothing). The results showed that both UV-C systems were effective in inactivating phage ϕ6, but the UV-C sterilizing chamber (8)5.5W had the best disinfection performance on the tested surfaces. The inactivation effectiveness is material-dependent on all surfaces, reaching the detection limit of the method at different times (between 60 and 240 s of irradiation). The glass surface needed less time to reduce the virus (30 s) when compared with plastic, stainless, and wood surfaces (60 s). The virus inactivation was more effective in the disposable surgical and FFP2 masks (60 and 120 s, respectively) than in the disposable vest and clear acetate visor (240 s). Overall, this study suggests that UV-C lamps with peak emission at ~254 nm could provide rapid, efficient, and sustainable sanitization procedures to different materials and surfaces. However, dosage and irradiation time are important parameters to be considered during their implementation as a tool in the fight against human coronaviruses, namely against SARS-CoV-2.
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13
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Ravn Warncke S, Rohde Knudsen C. Detection methods targeting the positive- and negative-sense RNA transcripts from plus-stranded RNA viruses. APMIS 2021; 130:284-292. [PMID: 34939239 PMCID: PMC9306919 DOI: 10.1111/apm.13202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/16/2021] [Indexed: 11/27/2022]
Abstract
The largest group of viruses in the Baltimore classification system comprises viruses with a positive-sense, single-stranded RNA genome. Once the viral genome is released into the cytoplasm of a specific host cell following virus entry, it functions directly as a mRNA and the virus-encoded proteins that are essential for genome replication, are produced by the translation apparatus of the host cell. The positive-sense genome is replicated in two stages, initially the positive strand is copied to make a negative-sense RNA, which then functions as the template for transcription of many new positive-sense genomes. Virus infections can be detected at different stages throughout the infection cycle for diagnostic and scientific purposes. Here, the advantages and disadvantages of some of the relevant methods for genome detection will be briefly reviewed with special emphasis on techniques allowing strand-specific RNA detection. Furthermore, tools of the future are considered.
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Affiliation(s)
- Signe Ravn Warncke
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000, Aarhus C, Denmark
| | - Charlotte Rohde Knudsen
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000, Aarhus C, Denmark
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14
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Arghiani N, Shah K. Modulating microRNAs in cancer: Next-generation therapies. Cancer Biol Med 2021; 19:j.issn.2095-3941.2021.0294. [PMID: 34846108 PMCID: PMC8958885 DOI: 10.20892/j.issn.2095-3941.2021.0294] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenously expressed non-coding regulators of the genome with an ability to mediate a variety of biological and pathological processes. There is growing evidence demonstrating frequent dysregulation of microRNAs in cancer cells, which is associated with tumor initiation, development, migration, invasion, resisting cell death, and drug resistance. Studies have shown that modulation of these small RNAs is a novel and promising therapeutic tool in the treatment of a variety of diseases, especially cancer, due to their broad influence on multiple cellular processes. However, suboptimal delivery of the appropriate miRNA to the cancer sites, quick degradation by nucleases in the blood circulation, and off target effects have limited their research and clinical applications. Therefore, there is a pressing need to improve the therapeutic efficacy of miRNA modulators, while at the same time reducing their toxicities. Several delivery vehicles for miRNA modulators have been shown to be effective in vitro and in vivo. In this review, we will discuss the role and importance of miRNAs in cancer and provide perspectives on currently available carriers for miRNA modulation. We will also summarize the challenges and prospects for the clinical translation of miRNA-based therapeutic strategies.
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Affiliation(s)
- Nahid Arghiani
- Center for Stem Cell and Translational Immunotherapy (CSTI), Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Khalid Shah
- Center for Stem Cell and Translational Immunotherapy (CSTI), Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
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15
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Cultivation of a Lytic Double-Stranded RNA Bacteriophage Infecting Microvirgula aerodenitrificans Reveals a Mutualistic Parasitic Lifestyle. J Virol 2021; 95:e0039921. [PMID: 34133887 DOI: 10.1128/jvi.00399-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophages are considered the most abundant entities on earth. However, there are merely seven sequenced double-stranded RNA (dsRNA) phages, compared to thousands of sequenced double-stranded DNA (dsDNA) phages. Interestingly, dsRNA viruses are quite common in fungi and usually have a lifestyle of commensalism or mutualism. Thus, the classical protocol of using double-layer agar plates to characterize phage plaques might be significantly biased in the isolation of dsRNA phages beyond strictly lytic lifestyles. Thus, we applied a protocol for isolating fungal viruses to identify RNA phages in bacteria and successfully isolated a novel dsRNA phage, phiNY, from Microvirgula aerodenitrificans. phiNY has a genome consisting of three dsRNA segments, and its genome sequence has no nucleotide sequence similarity with any other phage. Although phiNY encodes a lytic protein of glycoside hydrolase, and phage particles are consistently released during bacterial growth, phiNY replication did not block bacterial growth, nor did it form any plaques on agar plates. More strikingly, the phiNY-infected strain grew faster than the phiNY-negative strain, indicating a mutualistic parasitic lifestyle. Thus, this study not only reveals a new mutualistic parasitic dsRNA phage but also implies that other virus isolation methods would be valuable to identify phages with nonlytic lifestyles. IMPORTANCE Viruses with dsRNA genomes are quite diverse and infect organisms in all three domains of life. Although dsRNA viruses that infect humans, plants, and fungi are quite common, dsRNA viruses that infect bacteria, known as bacteriophages, are quite understudied, and only seven dsRNA phages have been sequenced so far. One possible explanation for the rare isolation of dsRNA phages might be the protocol of the double-layer agar plate assay. Phages without strictly lytic lifestyles might not form plaques. Thus, we applied the protocol of isolating fungal viruses to identify RNA phages inside bacteria and successfully isolated a novel dsRNA phage, phiNY, with a mutualistic parasitic lifestyle. This study implies that dsRNA phages without strictly lytic lifestyles might be common in nature and deserve more investigations.
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16
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Correa AMS, Howard-Varona C, Coy SR, Buchan A, Sullivan MB, Weitz JS. Revisiting the rules of life for viruses of microorganisms. Nat Rev Microbiol 2021; 19:501-513. [PMID: 33762712 DOI: 10.1038/s41579-021-00530-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 02/01/2023]
Abstract
Viruses that infect microbial hosts have traditionally been studied in laboratory settings with a focus on either obligate lysis or persistent lysogeny. In the environment, these infection archetypes are part of a continuum that spans antagonistic to beneficial modes. In this Review, we advance a framework to accommodate the context-dependent nature of virus-microorganism interactions in ecological communities by synthesizing knowledge from decades of virology research, eco-evolutionary theory and recent technological advances. We discuss that nuanced outcomes, rather than the extremes of the continuum, are particularly likely in natural communities given variability in abiotic factors, the availability of suboptimal hosts and the relevance of multitrophic partnerships. We revisit the 'rules of life' in terms of how long-term infections shape the fate of viruses and microbial cells, populations and ecosystems.
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Affiliation(s)
| | | | - Samantha R Coy
- BioSciences Department, Rice University, Houston, TX, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA. .,Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,School of Physics, Georgia Institute of Technology, Atlanta, GA, USA.
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17
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Mahony J, van Sinderen D. Virome studies of food production systems: time for 'farm to fork' analyses. Curr Opin Biotechnol 2021; 73:22-27. [PMID: 34252795 DOI: 10.1016/j.copbio.2021.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022]
Abstract
The food industry is under increasing pressure to produce high quality, traceable and minimally processed foods that are produced using sustainable approaches and ingredients. In line with the latter, there is an increased pressure for plant-based products to replace animal-derived products. Until recently, research efforts have mainly focused on dairy and meat products owing to their economic importance. The shift towards plant-based diets and food production requires a corresponding shift in research efforts to define the microbial requirements for and composition of (novel) plant-based foods, the (micro)organisms that are beneficial to such production systems, and the abundance and role of (bacterio)phages in shaping the microbial landscape of these foods. In this review, we explore current efforts in the area of virome analysis of foods and food production environments and highlight the need for more unified approaches to understand the contribution of phages in food safety and quality, and to develop novel tools to enhance the traceability of foods.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland.
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18
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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: 33] [Impact Index Per Article: 11.0] [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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19
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Abd-Allah IM, El-Housseiny GS, Yahia IS, Aboshanab KM, Hassouna NA. Rekindling of a Masterful Precedent; Bacteriophage: Reappraisal and Future Pursuits. Front Cell Infect Microbiol 2021; 11:635597. [PMID: 34136415 PMCID: PMC8201069 DOI: 10.3389/fcimb.2021.635597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/13/2021] [Indexed: 12/30/2022] Open
Abstract
Antibiotic resistance is exuberantly becoming a deleterious health problem world-wide. Seeking innovative approaches is necessary in order to circumvent such a hazard. An unconventional fill-in to antibiotics is bacteriophage. Bacteriophages are viruses capable of pervading bacterial cells and disrupting their natural activity, ultimately resulting in their defeat. In this article, we will run-through the historical record of bacteriophage and its correlation with bacteria. We will also delineate the potential of bacteriophage as a therapeutic antibacterial agent, its supremacy over antibiotics in multiple aspects and the challenges that could arise on the way to its utilization in reality. Pharmacodynamics, pharmacokinetics and genetic engineering of bacteriophages and its proteins will be briefly discussed as well. In addition, we will highlight some of the in-use applications of bacteriophages, and set an outlook for their future ones. We will also overview some of the miscellaneous abilities of these tiny viruses in several fields other than the clinical one. This is an attempt to encourage tackling a long-forgotten hive. Perhaps, one day, the smallest of the creatures would be of the greatest help.
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Affiliation(s)
- Israa M. Abd-Allah
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Ghadir S. El-Housseiny
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Ibrahim S. Yahia
- Research Center for Advanced Materials Science (RCAMS), Advanced Functional Materials & Optoelectronic Laboratory (AFMOL), Department of Physics, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Nanoscience Laboratory for Environmental and Bio-Medical Applications (NLEBA), Semiconductor Lab., Metallurgical Lab, Physics Department, Faculty of Education, Ain Shams University, Cairo, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Nadia A. Hassouna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
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20
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Marian M, Fujikawa T, Shimizu M. Genome analysis provides insights into the biocontrol ability of Mitsuaria sp. strain TWR114. Arch Microbiol 2021; 203:3373-3388. [PMID: 33880605 DOI: 10.1007/s00203-021-02327-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022]
Abstract
Mitsuaria sp. TWR114 is a biocontrol agent against tomato bacterial wilt (TBW). We aimed to gain genomic insights relevant to the biocontrol mechanisms and colonization ability of this strain. The draft genome size was found to be 5,632,523 bp, with a GC content of 69.5%, assembled into 1144 scaffolds. Genome annotation predicted a total of 4675 protein coding sequences (CDSs), 914 pseudogenes, 49 transfer RNAs, 3 noncoding RNAs, and 2 ribosomal RNAs. Genome analysis identified multiple CDSs associated with various pathways for the metabolism and transport of amino acids and carbohydrates, motility and chemotactic capacities, protection against stresses (oxidative, antibiotic, and phage), production of secondary metabolites, peptidases, quorum-quenching enzymes, and indole-3-acetic acid, as well as protein secretion systems and their related appendages. The genome resource will extend our understanding of the genomic features related to TWR114's biocontrol and colonization abilities and facilitate its development as a new biopesticide against TBW.
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Affiliation(s)
- Malek Marian
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.,College of Agriculture, Ibaraki University, Ami, Inashiki, Ibaraki, 300-0393, Japan
| | - Takashi Fujikawa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8605, Japan
| | - Masafumi Shimizu
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.
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21
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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; 218:211916. [PMID: 33760921 PMCID: PMC8006857 DOI: 10.1084/jem.20201044] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [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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22
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Hassan AY, Lin JT, Ricker N, Anany H. The Age of Phage: Friend or Foe in the New Dawn of Therapeutic and Biocontrol Applications? Pharmaceuticals (Basel) 2021; 14:199. [PMID: 33670836 PMCID: PMC7997343 DOI: 10.3390/ph14030199] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023] Open
Abstract
Extended overuse and misuse of antibiotics and other antibacterial agents has resulted in an antimicrobial resistance crisis. Bacteriophages, viruses that infect bacteria, have emerged as a legitimate alternative antibacterial agent with a wide scope of applications which continue to be discovered and refined. However, the potential of some bacteriophages to aid in the acquisition, maintenance, and dissemination of negatively associated bacterial genes, including resistance and virulence genes, through transduction is of concern and requires deeper understanding in order to be properly addressed. In particular, their ability to interact with mobile genetic elements such as plasmids, genomic islands, and integrative conjugative elements (ICEs) enables bacteriophages to contribute greatly to bacterial evolution. Nonetheless, bacteriophages have the potential to be used as therapeutic and biocontrol agents within medical, agricultural, and food processing settings, against bacteria in both planktonic and biofilm environments. Additionally, bacteriophages have been deployed in developing rapid, sensitive, and specific biosensors for various bacterial targets. Intriguingly, their bioengineering capabilities show great promise in improving their adaptability and effectiveness as biocontrol and detection tools. This review aims to provide a balanced perspective on bacteriophages by outlining advantages, challenges, and future steps needed in order to boost their therapeutic and biocontrol potential, while also providing insight on their potential role in contributing to bacterial evolution and survival.
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Affiliation(s)
- Ahmad Y. Hassan
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada;
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Janet T. Lin
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Hany Anany
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada;
- Department of Food Science, Ontario Agricultural College, University of Guelph, Guelph, ON N1G 2W1, Canada
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23
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Martínez Arbas S, Narayanasamy S, Herold M, Lebrun LA, Hoopmann MR, Li S, Lam TJ, Kunath BJ, Hicks ND, Liu CM, Price LB, Laczny CC, Gillece JD, Schupp JM, Keim PS, Moritz RL, Faust K, Tang H, Ye Y, Skupin A, May P, Muller EEL, Wilmes P. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nat Microbiol 2021; 6:123-135. [PMID: 33139880 PMCID: PMC7752763 DOI: 10.1038/s41564-020-00794-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 09/11/2020] [Indexed: 02/07/2023]
Abstract
Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE-host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR-Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid-host and phage-host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant 'Candidatus Microthrix parvicella' population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.
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Affiliation(s)
- Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Megeno S.A., Esch-sur-Alzette, Luxembourg
| | - Malte Herold
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura A Lebrun
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Sujun Li
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Tony J Lam
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Benoît J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Nathan D Hicks
- TGen North, Flagstaff, AZ, USA
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Cindy M Liu
- TGen North, Flagstaff, AZ, USA
- Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Lance B Price
- TGen North, Flagstaff, AZ, USA
- Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Cedric C Laczny
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | | | - Paul S Keim
- TGen North, Flagstaff, AZ, USA
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Karoline Faust
- Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Haixu Tang
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Yuzhen Ye
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Neuroscience, University of California, La Jolla, CA, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Emilie E L Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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24
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Zhang W, Wu Q. Applications of phage-derived RNA-based technologies in synthetic biology. Synth Syst Biotechnol 2020; 5:343-360. [PMID: 33083579 PMCID: PMC7564126 DOI: 10.1016/j.synbio.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
As the most abundant biological entities with incredible diversity, bacteriophages (also known as phages) have been recognized as an important source of molecular machines for the development of genetic-engineering tools. At the same time, phages are crucial for establishing and improving basic theories of molecular biology. Studies on phages provide rich sources of essential elements for synthetic circuit design as well as powerful support for the improvement of directed evolution platforms. Therefore, phages play a vital role in the development of new technologies and central scientific concepts. After the RNA world hypothesis was proposed and developed, novel biological functions of RNA continue to be discovered. RNA and its related elements are widely used in many fields such as metabolic engineering and medical diagnosis, and their versatility led to a major role of RNA in synthetic biology. Further development of RNA-based technologies will advance synthetic biological tools as well as provide verification of the RNA world hypothesis. Most synthetic biology efforts are based on reconstructing existing biological systems, understanding fundamental biological processes, and developing new technologies. RNA-based technologies derived from phages will offer abundant sources for synthetic biological components. Moreover, phages as well as RNA have high impact on biological evolution, which is pivotal for understanding the origin of life, building artificial life-forms, and precisely reprogramming biological systems. This review discusses phage-derived RNA-based technologies terms of phage components, the phage lifecycle, and interactions between phages and bacteria. The significance of RNA-based technology derived from phages for synthetic biology and for understanding the earliest stages of biological evolution will be highlighted.
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Affiliation(s)
- Wenhui Zhang
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- Corresponding author. MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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25
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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: 40] [Impact Index Per Article: 10.0] [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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26
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Dong X, Edmondson R, Yang F, Tang Y, Wang P, Sun YP, Yang L. Carbon dots for effective photodynamic inactivation of virus. RSC Adv 2020; 10:33944-33954. [PMID: 35519058 PMCID: PMC9056736 DOI: 10.1039/d0ra05849a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/02/2020] [Indexed: 12/23/2022] Open
Abstract
The antiviral function of carbon dots (CDots) with visible light exposure was evaluated, for which the model bacteriophages MS2 as a surrogate of small RNA viruses were used. The results show clearly that the visible light-activated CDots are highly effective in diminishing the infectivity of MS2 in both low and high titer samples to the host E. coli cells, and the antiviral effects are dot concentration- and treatment time-dependent. The action of CDots apparently causes no significant damage to the structural integrity and morphology of the MS2 phage or the breakdown of the capsid proteins, but does result in the protein carbonylation (a commonly used indicator for protein oxidation) and the degradation of viral genomic RNA. Mechanistically the results may be understood in the framework of photodynamic effects that are associated with the unique excited state properties and processes of CDots. Opportunities for potentially broad applications of CDots coupled with visible/natural light in the prevention and control of viral transmission and spread are highlighted and discussed. The antiviral function of carbon dots (CDots) with visible light exposure was evaluated, for which the model bacteriophages MS2 as a surrogate of small RNA viruses were used.![]()
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Affiliation(s)
- Xiuli Dong
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University Durham NC 27707 USA +1-919-530-6705 +1-919-530-6704
| | | | - Fan Yang
- Department of Chemistry, Laboratory for Emerging Materials and Technology, Clemson University Clemson SC 29634 USA +1-864-656-5026
| | - Yongan Tang
- Department of Mathematics and Physics, North Carolina Central University Durham NC 27707 USA
| | - Ping Wang
- Department of Chemistry, Laboratory for Emerging Materials and Technology, Clemson University Clemson SC 29634 USA +1-864-656-5026
| | - Ya-Ping Sun
- Department of Chemistry, Laboratory for Emerging Materials and Technology, Clemson University Clemson SC 29634 USA +1-864-656-5026
| | - Liju Yang
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), North Carolina Central University Durham NC 27707 USA +1-919-530-6705 +1-919-530-6704
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Khan Mirzaei M, Xue J, Costa R, Ru J, Schulz S, Taranu ZE, Deng L. Challenges of Studying the Human Virome - Relevant Emerging Technologies. Trends Microbiol 2020; 29:171-181. [PMID: 32622559 DOI: 10.1016/j.tim.2020.05.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 01/17/2023]
Abstract
In this review we provide an overview of current challenges and advances in bacteriophage research within the growing field of viromics. In particular, we discuss, from a human virome study perspective, the current and emerging technologies available, their limitations in terms of de novo discoveries, and possible solutions to overcome present experimental and computational biases associated with low abundance of viral DNA or RNA. We summarize recent breakthroughs in metagenomics assembling tools and single-cell analysis, which have the potential to increase our understanding of phage biology, diversity, and interactions with both the microbial community and the human body. We expect that these recent and future advances in the field of viromics will have a strong impact on how we develop phage-based therapeutic approaches.
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Affiliation(s)
- Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Rita Costa
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Sarah Schulz
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany
| | - Zofia E Taranu
- Aquatic Contaminants Research Division (ACRD), Environment and Climate Change Canada (ECCC), Montréal, QC H2Y 2E7, Canada
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich and Technical University of Munich, Neuherberg, Bavaria 85764, Germany.
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Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Arch Virol 2020; 165:1253-1260. [PMID: 32162068 DOI: 10.1007/s00705-020-04577-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.
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29
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Sustained RNA virome diversity in Antarctic penguins and their ticks. ISME JOURNAL 2020; 14:1768-1782. [PMID: 32286545 PMCID: PMC7305176 DOI: 10.1038/s41396-020-0643-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/16/2020] [Accepted: 03/20/2020] [Indexed: 01/07/2023]
Abstract
Despite its isolation and extreme climate, Antarctica is home to diverse fauna and associated microorganisms. It has been proposed that the most iconic Antarctic animal, the penguin, experiences low pathogen pressure, accounting for their disease susceptibility in foreign environments. There is, however, a limited understanding of virome diversity in Antarctic species, the extent of in situ virus evolution, or how it relates to that in other geographic regions. To assess whether penguins have limited microbial diversity we determined the RNA viromes of three species of penguins and their ticks sampled on the Antarctic peninsula. Using total RNA sequencing we identified 107 viral species, comprising likely penguin associated viruses (n = 13), penguin diet and microbiome associated viruses (n = 82), and tick viruses (n = 8), two of which may have the potential to infect penguins. Notably, the level of virome diversity revealed in penguins is comparable to that seen in Australian waterbirds, including many of the same viral families. These data run counter to the idea that penguins are subject to lower pathogen pressure. The repeated detection of specific viruses in Antarctic penguins also suggests that rather than being simply spill-over hosts, these animals may act as key virus reservoirs.
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30
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Wassenaar TM, Jun S, Robeson M, Ussery DW. Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species. Microbiologyopen 2020; 9:e973. [PMID: 31742930 PMCID: PMC7002107 DOI: 10.1002/mbo3.973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022] Open
Abstract
The intraspecies genomic diversity of the single-strand RNA (+) virus species hepatitis A virus (Hepatovirus), hepatitis C virus (Hepacivirus), and hepatitis E virus (Orthohepevirus) was compared. These viral species all can cause liver inflammation (hepatitis), but share no gene similarity. The codon usage of human hepatitis A virus (HAV) is suboptimal for replication in its host, a characteristic it shares with taxonomically related rodent, simian, and bat hepatitis A virus species. We found this codon usage to be strikingly similar to that of Triatoma virus that infects blood-sucking kissing bugs. The codon usage of that virus is well adapted to its insect host. The codon usage of HAV is also similar to other invertebrate viruses of various taxonomic families. An evolutionary ancestor of HAV and related virus species is hypothesized to be an insect virus that underwent a host jump to infect mammals. The similarity between HAV and invertebrate viruses goes beyond codon usage, as they also share amino acid composition characteristics, while not sharing direct sequence homology. In contrast, hepatitis C virus and hepatitis E virus are highly similar in codon usage preference, nucleotide composition, and amino acid composition, and share these characteristics with Human pegivirus A, West Nile virus, and Zika virus. We present evidence that these observations are only partly explained by differences in nucleotide composition of the complete viral codon regions. We consider the combination of nucleotide composition, amino acid composition, and codon usage preference suitable to provide information on possible evolutionary similarities between distant virus species that cannot be investigated by phylogeny.
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Affiliation(s)
| | - Se‐Ran Jun
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockARUSA
| | - Michael Robeson
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockARUSA
| | - David W. Ussery
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockARUSA
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31
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Balcázar JL. Implications of bacteriophages on the acquisition and spread of antibiotic resistance in the environment. Int Microbiol 2020; 23:475-479. [PMID: 32002743 DOI: 10.1007/s10123-020-00121-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/30/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022]
Abstract
Although bacteriophages (or simply phages) are the most abundant biological entities and have the potential to transfer genetic material between bacterial hosts, their contribution to the acquisition and spread of antibiotic resistance genes in the environment has not been extensively studied. The environment is continually exposed to a wide variety of pollutants from anthropogenic sources, which may promote horizontal gene transfer events, including those mediated by phages. Considering the significant and growing concern of antibiotic resistance, phages should be taken into consideration during the implementation of mitigation measures. This review is focused on the emergence and spread of antibiotic resistance in the environment, with a special emphasis on the role of phages.
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Affiliation(s)
- José Luis Balcázar
- Catalan Institute for Water Research (ICRA), 17003, Girona, Spain.
- University of Girona, 17004, Girona, Spain.
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32
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Pinheiro LAM, Pereira C, Barreal ME, Gallego PP, Balcão VM, Almeida A. Use of phage ϕ6 to inactivate Pseudomonas syringae pv. actinidiae in kiwifruit plants: in vitro and ex vivo experiments. Appl Microbiol Biotechnol 2019; 104:1319-1330. [DOI: 10.1007/s00253-019-10301-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/14/2019] [Accepted: 12/08/2019] [Indexed: 12/22/2022]
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33
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Pinheiro LAM, Pereira C, Frazão C, Balcão VM, Almeida A. Efficiency of Phage φ6 for Biocontrol of Pseudomonas syringae pv. syringae: An in Vitro Preliminary Study. Microorganisms 2019; 7:E286. [PMID: 31450735 PMCID: PMC6780397 DOI: 10.3390/microorganisms7090286] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 07/31/2019] [Accepted: 08/21/2019] [Indexed: 12/14/2022] Open
Abstract
Pseudomonas syringae is a plant-associated bacterial species that has been divided into more than 60 pathovars, with the Pseudomonas syringae pv. syringae being the main causative agent of diseases in a wide variety of fruit trees. The most common treatments for biocontrol of P. syringae pv. syringae infections has involved copper derivatives and/or antibiotics. However, these treatments should be avoided due to their high toxicity to the environment and promotion of bacterial resistance. Therefore, it is essential to search for new approaches for controlling P. syringae pv. syringae. Phage therapy can be a useful alternative tool to the conventional treatments to control P. syringae pv. syringae infections in plants. In the present study, the efficacy of bacteriophage (or phage) φ6 (a commercially available phage) was evaluated in the control of P. syringae pv. syringae. As the plants are exposed to the natural variability of physical and chemical parameters, the influence of pH, temperature, solar radiation and UV-B irradiation on phage φ6 viability was also evaluated in order to develop an effective phage therapy protocol. The host range analysis revealed that the phage, besides its host (P. syringae pv. syringae), also infects the Pseudomonas syringae pv. actinidiae CRA-FRU 12.54 and P. syringae pv. actinidiae CRA-FRU 14.10 strains, not infecting strains from the other tested species. Both multiplicities of infection (MOIs) tested, 1 and 100, were effective to inactivate the bacterium, but the MOI 1 (maximum reduction of 3.9 log CFU/mL) was more effective than MOI 100 (maximum reduction of 2.6 log CFU/mL). The viability of phage φ6 was mostly affected by exposure to UV-B irradiation (decrease of 7.3 log PFU/mL after 8 h), exposure to solar radiation (maximum reduction of 2.1 PFU/mL after 6 h), and high temperatures (decrease of 8.5 PFU/mL after 6 days at 37 °C, but a decrease of only 2.0 log PFU/mL after 67 days at 15 °C and 25 °C). The host range, high bacterial control and low rates of development of phage-resistant bacterial clones (1.20 × 10-3) suggest that this phage can be used to control P. syringae pv. syringae infections in plants, but also to control infections by P. syringae pv. actinidiae, the causal agent of bacterial canker of kiwifruit. Although the stability of phage φ6 was affected by UV-B and solar radiation, this can be overcome by the application of phage suspensions at the end of the day or at night.
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Affiliation(s)
- Larindja A M Pinheiro
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carla Pereira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Carolina Frazão
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Victor M Balcão
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- PhageLab-Laboratory of Biofilms and Bacteriophages, University of Sorocaba, 18023-000 Sorocaba, São Paulo, Brazil
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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Somovilla P, Manrubia S, Lázaro E. Evolutionary Dynamics in the RNA Bacteriophage Qβ Depends on the Pattern of Change in Selective Pressures. Pathogens 2019; 8:pathogens8020080. [PMID: 31216651 PMCID: PMC6631425 DOI: 10.3390/pathogens8020080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/14/2019] [Accepted: 06/16/2019] [Indexed: 12/14/2022] Open
Abstract
The rate of change in selective pressures is one of the main factors that determines the likelihood that populations can adapt to stress conditions. Generally, the reduction in the population size that accompanies abrupt environmental changes makes it difficult to generate and select adaptive mutations. However, in systems with high genetic diversity, as happens in RNA viruses, mutations with beneficial effects under new conditions can already be present in the population, facilitating adaptation. In this work, we have propagated an RNA bacteriophage (Qβ) at temperatures higher than the optimum, following different patterns of change. We have determined the fitness values and the consensus sequences of all lineages throughout the evolutionary process in order to establish correspondences between fitness variations and adaptive pathways. Our results show that populations subjected to a sudden temperature change gain fitness and fix mutations faster than those subjected to gradual changes, differing also in the particular selected mutations. The life-history of populations prior to the environmental change has great importance in the dynamics of adaptation. The conclusion is that in the bacteriophage Qβ, the standing genetic diversity together with the rate of temperature change determine both the rapidity of adaptation and the followed evolutionary pathways.
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Affiliation(s)
- Pilar Somovilla
- Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain.
- Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain.
| | - Susanna Manrubia
- Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain.
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| | - Ester Lázaro
- Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain.
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