1
|
Magar S, Kolte V, Sharma G, Govindarajan S. Exploring pangenomic diversity and CRISPR-Cas evasion potential in jumbo phages: a comparative genomics study. Microbiol Spectr 2024:e0420023. [PMID: 39264185 DOI: 10.1128/spectrum.04200-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 08/07/2024] [Indexed: 09/13/2024] Open
Abstract
Jumbo phages are characterized by their remarkably large-sized genome and unique life cycles. Jumbo phages belonging to Chimalliviridae family protect the replicating phage DNA from host immune systems like CRISPR-Cas and restriction-modification system through a phage nucleus structure. Several recent studies have provided new insights into jumbo phage infection biology, but the pan-genome diversity of jumbo phages and their relationship with CRISPR-Cas targeting beyond Chimalliviridae are not well understood. In this study, we used pan-genome analysis to identify orthologous gene families shared among 331 jumbo phages with complete genomes. We show that jumbo phages lack a universally conserved set of core genes but identified seven "soft-core genes" conserved in over 50% of these phages. These genes primarily govern DNA-related activities, such as replication, repair, or nucleotide synthesis. Jumbo phages exhibit a wide array of accessory and unique genes, underscoring their genetic diversity. Phylogenetic analyses of the soft-core genes revealed frequent horizontal gene transfer events between jumbo phages, non-jumbo phages, and occasionally even giant eukaryotic viruses, indicating a polyphyletic evolutionary nature. We categorized jumbo phages into 11 major viral clusters (VCs) spanning 130 sub-clusters, with the majority being multi-genus jumbo phage clusters. Moreover, through the analysis of hallmark genes related to CRISPR-Cas targeting, we predict that many jumbo phages can evade host immune systems using both known and yet-to-be-identified mechanisms. In summary, our study enhances our understanding of jumbo phages, shedding light on their pan-genome diversity and remarkable genome protection capabilities. IMPORTANCE Jumbo phages are large bacterial viruses known for more than 50 years. However, only in recent years, a significant number of complete genome sequences of jumbo phages have become available. In this study, we employed comparative genomic approaches to investigate the genomic diversity and genome protection capabilities of the 331 jumbo phages. Our findings revealed that jumbo phages exhibit high genetic diversity, with only a few genes being relatively conserved across jumbo phages. Interestingly, our data suggest that jumbo phages employ yet-to-be-identified strategies to protect their DNA from the host immune system, such as CRISPR-Cas.
Collapse
Affiliation(s)
- Sharayu Magar
- Department of Biological Sciences, SRM University AP, Amaravati, Andhra Pradesh, India
| | - Vaishnavi Kolte
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Gaurav Sharma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Hyderabad, India
| | | |
Collapse
|
2
|
Yang Y, Shao Q, Guo M, Han L, Zhao X, Wang A, Li X, Wang B, Pan JA, Chen Z, Fokine A, Sun L, Fang Q. Capsid structure of bacteriophage ΦKZ provides insights into assembly and stabilization of jumbo phages. Nat Commun 2024; 15:6551. [PMID: 39095371 PMCID: PMC11297242 DOI: 10.1038/s41467-024-50811-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic pathogen leading to acute or chronic infection in immunocompromised individuals. It holds potential to be used as an antimicrobial agent and as a model for uncovering basic phage biology. Although previous low-resolution structural studies have indicated that jumbo phages may have more complicated capsid structures than smaller phages such as HK97, the detailed structures and the assembly mechanism of their capsids remain largely unknown. Here, we report a 3.5-Å-resolution cryo-EM structure of the ΦKZ capsid. The structure unveiled ten minor capsid proteins, with some decorating the outer surface of the capsid and the others forming a complex network attached to the capsid's inner surface. This network seems to play roles in driving capsid assembly and capsid stabilization. Similar mechanisms of capsid assembly and stabilization are probably employed by many other jumbo viruses.
Collapse
Affiliation(s)
- Yashan Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Qianqian Shao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Mingcheng Guo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Lin Han
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xinyue Zhao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Aohan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Xiangyun Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Bo Wang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zhenguo Chen
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Lei Sun
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Qianglin Fang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China.
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China.
| |
Collapse
|
3
|
Villicaña C, Rubí-Rangel LM, Amarillas L, Lightbourn-Rojas LA, Carrillo-Fasio JA, León-Félix J. Isolation and Characterization of Two Novel Genera of Jumbo Bacteriophages Infecting Xanthomonas vesicatoria Isolated from Agricultural Regions in Mexico. Antibiotics (Basel) 2024; 13:651. [PMID: 39061333 PMCID: PMC11273794 DOI: 10.3390/antibiotics13070651] [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: 06/04/2024] [Revised: 06/27/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Bacterial spot is a serious disease caused by several species of Xanthomonas affecting pepper and tomato production worldwide. Since the strategies employed for disease management have been inefficient and pose a threat for environmental and human health, the development of alternative methods is gaining relevance. The aim of this study is to isolate and characterize lytic phages against Xanthomonas pathogens. Here, we isolate two jumbo phages, named XaC1 and XbC2, from water obtained from agricultural irrigation channels by the enrichment technique using X. vesicatoria as a host. We determined that both phages were specific for inducing the lysis of X. vesicatoria strains, but not of other xanthomonads. The XaC1 and XbC2 phages showed a myovirus morphology and were classified as jumbo phages due to their genomes being larger than 200 kb. Phylogenetic and comparative analysis suggests that XaC1 and XbC2 represent both different and novel genera of phages, where XaC1 possesses a low similarity to other phage genomes reported before. Finally, XaC1 and XbC2 exhibited thermal stability up to 45 °C and pH stability from 5 to 9. All these results indicate that the isolated phages are promising candidates for the development of formulations against bacterial spot, although further characterization is required.
Collapse
Affiliation(s)
- Claudia Villicaña
- CONAHCYT—Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo, A. C., Culiacán 80110, Sinaloa, Mexico;
| | - Lucía M. Rubí-Rangel
- Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo, A. C., Culiacán 80110, Sinaloa, Mexico;
| | - Luis Amarillas
- Laboratorio de Genética, Instituto de Investigación Lightbourn, A. C., Cd. Jimenez 33981, Chihuahua, Mexico; (L.A.)
| | | | - José Armando Carrillo-Fasio
- Laboratorio de Nematología Agrícola, Centro de Investigación en Alimentación y Desarrollo, A. C., Culiacán 80110, Sinaloa, Mexico;
| | - Josefina León-Félix
- Laboratorio de Biología Molecular y Genómica Funcional, Centro de Investigación en Alimentación y Desarrollo, A. C., Culiacán 80110, Sinaloa, Mexico;
| |
Collapse
|
4
|
Kozlova AP, Muntyan VS, Vladimirova ME, Saksaganskaia AS, Kabilov MR, Gorbunova MK, Gorshkov AN, Grudinin MP, Simarov BV, Roumiantseva ML. Soil Giant Phage: Genome and Biological Characteristics of Sinorhizobium Jumbo Phage. Int J Mol Sci 2024; 25:7388. [PMID: 39000497 PMCID: PMC11242549 DOI: 10.3390/ijms25137388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
This paper presents the first in-depth research on the biological and genomic properties of lytic rhizobiophage AP-J-162 isolated from the soils of the mountainous region of Dagestan (North Caucasus), which belongs to the centers of origin of cultivated plants, according to Vavilov N.I. The rhizobiophage host strains are nitrogen-fixing bacteria of the genus Sinorhizobium spp., symbionts of leguminous forage grasses. The phage particles have a myovirus virion structure. The genome of rhizobiophage AP-J-162 is double-stranded DNA of 471.5 kb in length; 711 ORFs are annotated and 41 types of tRNAs are detected. The closest phylogenetic relative of phage AP-J-162 is Agrobacterium phage Atu-ph07, but no rhizobiophages are known. The replicative machinery, capsid, and baseplate proteins of phage AP-J-162 are structurally similar to those of Escherichia phage T4, but there is no similarity between their tail protein subunits. Amino acid sequence analysis shows that 339 of the ORFs encode hypothetical or functionally relevant products, while the remaining 304 ORFs are unique. Additionally, 153 ORFs are similar to those of Atu_ph07, with one-third of the ORFs encoding different enzymes. The biological properties and genomic characteristics of phage AP-J-162 distinguish it as a unique model for exploring phage-microbe interactions with nitrogen-fixing symbiotic microorganisms.
Collapse
Affiliation(s)
- Alexandra P Kozlova
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Victoria S Muntyan
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Maria E Vladimirova
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Alla S Saksaganskaia
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Marsel R Kabilov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Maria K Gorbunova
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Andrey N Gorshkov
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 Saint Petersburg, Russia
| | - Mikhail P Grudinin
- Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 Saint Petersburg, Russia
| | - Boris V Simarov
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| | - Marina L Roumiantseva
- Laboratory of Genetics and Selection of Microorganisms, Federal State Budget Scientific Institution All-Russia Research Institute for Agricultural Microbiology (FSBSI ARRIAM), 196608 Saint Petersburg, Russia
| |
Collapse
|
5
|
Ranta K, Skurnik M, Kiljunen S. fENko-Kae01 is a flagellum-specific jumbo phage infecting Klebsiella aerogenes. BMC Microbiol 2024; 24:234. [PMID: 38951769 PMCID: PMC11218385 DOI: 10.1186/s12866-024-03387-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Klebsiella aerogenes is an opportunistic pathogen that causes a wide variety of infections. Due to the rising problem of antibiotic resistance, novel antibiotics and strategies to combat bacterial infections are needed. Host-specific bacteriophages are natural enemies of bacteria and can be used in phage therapy as an alternative form of treatment against bacterial infections. Jumbo phages are defined as phages with genomes larger than 200 kb. Relatively few studies have been done on jumbo phages compared to smaller phages. RESULTS A novel phage, fENko-Kae01, was isolated from a commercial phage cocktail. Genomic analysis revealed that fENko-Kae01 is a lytic jumbo phage with a 360 kb genome encoding 578 predicted genes. No highly similar phage genomes were identified and fENko-Kae01 may be a completely new genus representative. No known genes associated with lysogenic life cycle, bacterial virulence, or antibiotic resistance were identified. The phage had myovirus morphology and a narrow host range. Phage resistant bacterial mutants emerged under phage selection. Whole genome sequencing revealed that the biogenesis of the flagellum was affected in four mutants and the lack of functional flagellum was confirmed in motility assays. Furthermore, phage fENKo-Kae01 failed to adsorb on the non-motile mutants indicating that the bacterial flagellum is the phage-binding receptor. CONCLUSIONS fENko-Kae01 is a novel jumbo bacteriophage that is considered safe for phage therapy. fENko-Kae01 uses the flagellum as the phage-binding receptor and may represent a completely novel genus.
Collapse
Affiliation(s)
- Kira Ranta
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Human Microbiome Research Program, Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikael Skurnik
- Human Microbiome Research Program, Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Saija Kiljunen
- Human Microbiome Research Program, Research Program Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
6
|
Guzel M, Yucefaydali A, Yetiskin S, Deniz A, Yaşar Tel O, Akçelik M, Soyer Y. Genomic analysis of Salmonella bacteriophages revealed multiple endolysin ORFs and importance of ligand-binding site of receptor-binding protein. FEMS Microbiol Ecol 2024; 100:fiae079. [PMID: 38816206 PMCID: PMC11180984 DOI: 10.1093/femsec/fiae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/02/2024] [Accepted: 05/29/2024] [Indexed: 06/01/2024] Open
Abstract
Salmonella is a prevalent foodborne pathogen causing millions of global cases annually. Antimicrobial resistance is a growing public health concern, leading to search for alternatives like bacteriophages. A total of 97 bacteriophages, isolated from cattle farms (n = 48), poultry farms (n = 37), and wastewater (n = 5) samples in Türkiye, were subjected to host-range analysis using 36 Salmonella isolates with 18 different serotypes. The broadest host range belonged to an Infantis phage (MET P1-091), lysing 28 hosts. A total of 10 phages with the widest host range underwent further analysis, revealing seven unique genomes (32-243 kb), including a jumbophage (>200 kb). Except for one with lysogenic properties, none of them harbored virulence or antibiotic resistance genes, making them potential Salmonella reducers in different environments. Examining open reading frames (ORFs) of endolysin enzymes revealed surprising findings: five of seven unique genomes contained multiple endolysin ORFs. Despite sharing same endolysin sequences, phages exhibited significant differences in host range. Detailed analysis unveiled diverse receptor-binding protein sequences, with similar structures but distinct ligand-binding sites. These findings emphasize the importance of ligand-binding sites of receptor-binding proteins. Additionally, bacterial reduction curve and virulence index revealed that Enteritidis phages inhibit bacterial growth even at low concentrations, unlike Infantis and Kentucky phages.
Collapse
Affiliation(s)
- Mustafa Guzel
- Department of Biotechnology, Middle East Technical University, Ankara 06800, Türkiye
- Department of Food Engineering, Hitit University, Corum 19030, Türkiye
| | - Aysenur Yucefaydali
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
| | - Segah Yetiskin
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
| | - Aysu Deniz
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
| | - Osman Yaşar Tel
- Faculty of Veterinary Medicine, Harran University, Şanlıurfa 63300, Türkiye
| | - Mustafa Akçelik
- Department of Biology, Ankara University, Ankara 06100, Türkiye
| | - Yeşim Soyer
- Department of Biotechnology, Middle East Technical University, Ankara 06800, Türkiye
- Department of Food Engineering, Faculty of Engineering, Middle East Technical University, Ankara 06800, Türkiye
| |
Collapse
|
7
|
Wu Q, An N, Fang Z, Li S, Xiang L, Liu Q, Tan L, Weng Q. Characteristics and whole-genome analysis of a novel Pseudomonas syringae pv. tomato bacteriophage D6 isolated from a karst cave. Virus Genes 2024; 60:295-308. [PMID: 38594490 PMCID: PMC11139720 DOI: 10.1007/s11262-024-02064-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
Pseudomonas syringae is a gram-negative plant pathogen that infects plants such as tomato and poses a threat to global crop production. In this study, a novel lytic phage infecting P. syringae pv. tomato DC3000, named phage D6, was isolated and characterized from sediments in a karst cave. The latent period of phage D6 was found to be 60 min, with a burst size of 16 plaque-forming units per cell. Phage D6 was stable at temperatures between 4 and 40 °C but lost infectivity when heated to 70 °C. Its infectivity was unaffected at pH 6-10 but became inactivated at pH ≤ 5 or ≥ 12. The genome of phage D6 is a linear double-stranded DNA of 307,402 bp with a G + C content of 48.43%. There is a codon preference between phage D6 and its host, and the translation of phage D6 gene may not be entirely dependent on the tRNA library provided by the host. A total of 410 open reading frames (ORFs) and 14 tRNAs were predicted in its genome, with 92 ORFs encoding proteins with predicted functions. Phage D6 showed low genomic similarity to known phage genomes in the GenBank and Viral sequence databases. Genomic and phylogenetic analyses revealed that phage D6 is a novel phage. The tomato plants were first injected with phage D6, and subsequently with Pst DC3000, using the foliar spraying and root drenching inoculum approach. Results obtained after 14 days indicated that phage D6 inoculation decreased P. syringae-induced symptoms in tomato leaves and inhibited the pathogen's growth in the leaves. The amount of Pst DC3000 was reduced by 150- and 263-fold, respectively. In conclusion, the lytic phage D6 identified in this study belongs to a novel phage within the Caudoviricetes class and has potential for use in biological control of plant diseases.
Collapse
Affiliation(s)
- Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Ni An
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Shixia Li
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Lan Xiang
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, People's Republic of China.
- Qiannan Normal College for Nationalities, Duyun, 558000, People's Republic of China.
| |
Collapse
|
8
|
George NA, Zhou Z, Anantharaman K, Hug LA. Discarded diversity: Novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596742. [PMID: 38854013 PMCID: PMC11160803 DOI: 10.1101/2024.05.30.596742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background Viruses are the most abundant microbial entity on the planet, impacting microbial community structure and ecosystem services. Despite outnumbering Bacteria and Archaea by an order of magnitude, viruses have been comparatively underrepresented in reference databases. Metagenomic examinations have illustrated that viruses of Bacteria and Archaea have been specifically understudied in engineered environments. Here we employed metagenomic and computational biology methods to examine the diversity, host interactions, and genetic systems of viruses predicted from 27 samples taken from three municipal landfills across North America. Results We identified numerous viruses that are not represented in reference databases, including the third largest bacteriophage genome identified to date (~678 kbp), and note a cosmopolitan diversity of viruses in landfills that are distinct from viromes in other systems. Host-virus interactions were examined via host CRISPR spacer to viral protospacer mapping which captured hyper-targeted viral populations and six viral populations predicted to infect across multiple phyla. Virally-encoded auxiliary metabolic genes (AMGs) were identified with the potential to augment hosts' methane, sulfur, and contaminant degradation metabolisms, including AMGs not previously reported in literature. CRISPR arrays and CRISPR-Cas systems were identified from predicted viral genomes, including the two largest bacteriophage genomes to contain these genetic features. Some virally encoded Cas effector proteins appear distinct relative to previously reported Cas systems and are interesting targets for potential genome editing tools. Conclusions Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for diverse viruses and atypical virus-host dynamics.
Collapse
Affiliation(s)
- Nikhil A. George
- Department of Biology, University of Waterloo, Waterloo ON, Canada
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin – Madison, Madison, WI, USA
| | | | - Laura A. Hug
- Department of Biology, University of Waterloo, Waterloo ON, Canada
| |
Collapse
|
9
|
Kang Y, Wang J, Wang Y, Li Z. Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171766. [PMID: 38513871 DOI: 10.1016/j.scitotenv.2024.171766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Hospital wastewater (HWW) is known to host taxonomically diverse microbial communities, yet limited information is available on the phages infecting these microorganisms. To fill this knowledge gap, we conducted an in-depth analysis using 377 publicly available HWW metagenomic datasets from 16 countries across 4 continents in the NCBI SRA database to elucidate phage-host dynamics and phage contributions to resistance gene transmission. We first assembled a metagenomic HWW phage catalog comprising 13,812 phage operational taxonomic units (pOTUs). The majority of these pOTUs belonged to the Caudoviricetes order, representing 75.29 % of this catalog. Based on the lifestyle of phages, we found that potentially virulent phages predominated in HWW. Specifically, 583 pOTUs have been predicted to have the capability to lyse 81 potentially pathogenic bacteria, suggesting the promising role of HWW phages as a viable alternative to antibiotics. Among all pOTUs, 1.56 % of pOTUs carry 108 subtypes of antibiotic resistance genes (ARGs), 0.96 % of pOTUs carry 76 subtypes of metal resistance genes (MRGs), and 0.96 % of pOTUs carry 22 subtypes of non-phage mobile genetic elements (MGEs). Predictions indicate that certain phages carrying ARGs, MRGs, and non-phage MGEs could infect bacteria hosts, even potential pathogens. This suggests that phages in HWW may contribute to the dissemination of resistance-associated genes in the environment. This meta-analysis provides the first global catalog of HWW phages, revealing their correlations with microbial hosts and pahge-associated ARGs, MRG, and non-phage MGEs. The insights gained from this research hold promise for advancing the applications of phages in medical and industrial contexts.
Collapse
Affiliation(s)
- Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- North China University of Science and Technology, Basic Medical College, Tangshan, Hebei 063210, P.R. China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102200, China.
| |
Collapse
|
10
|
Naknaen A, Samernate T, Saeju P, Nonejuie P, Chaikeeratisak V. Nucleus-forming jumbophage PhiKZ therapeutically outcompetes non-nucleus-forming jumbophage Callisto. iScience 2024; 27:109790. [PMID: 38726363 PMCID: PMC11079468 DOI: 10.1016/j.isci.2024.109790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/21/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
With the recent resurgence of phage therapy in modern medicine, jumbophages are currently under the spotlight due to their numerous advantages as anti-infective agents. However, most significant discoveries to date have primarily focused on nucleus-forming jumbophages, not their non-nucleus-forming counterparts. In this study, we compare the biological characteristics exhibited by two genetically diverse jumbophages: 1) the well-studied nucleus-forming jumbophage, PhiKZ; and 2) the newly discovered non-nucleus-forming jumbophage, Callisto. Single-cell infection studies further show that Callisto possesses different replication machinery, resulting in a delay in phage maturation compared to that of PhiKZ. The therapeutic potency of both phages was examined in vitro and in vivo, demonstrating that PhiKZ holds certain superior characteristics over Callisto. This research sheds light on the importance of the subcellular infection machinery and the organized progeny maturation process, which could potentially provide valuable insight in the future development of jumbophage-based therapeutics.
Collapse
Affiliation(s)
- Ampapan Naknaen
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Thanadon Samernate
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Panida Saeju
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | | |
Collapse
|
11
|
Cook R, Crisci MA, Pye HV, Telatin A, Adriaenssens EM, Santini JM. Decoding huge phage diversity: a taxonomic classification of Lak megaphages. J Gen Virol 2024; 105:001997. [PMID: 38814706 PMCID: PMC11165621 DOI: 10.1099/jgv.0.001997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024] Open
Abstract
High-throughput sequencing for uncultivated viruses has accelerated the understanding of global viral diversity and uncovered viral genomes substantially larger than any that have so far been cultured. Notably, the Lak phages are an enigmatic group of viruses that present some of the largest known phage genomes identified in human and animal microbiomes, and are dissimilar to any cultivated viruses. Despite the wealth of viral diversity that exists within sequencing datasets, uncultivated viruses have rarely been used for taxonomic classification. We investigated the evolutionary relationships of 23 Lak phages and propose a taxonomy for their classification. Predicted protein analysis revealed the Lak phages formed a deeply branching monophyletic clade within the class Caudoviricetes which contained no other phage genomes. One of the interesting features of this clade is that all current members are characterised by an alternative genetic code. We propose the Lak phages belong to a new order, the 'Grandevirales'. Protein and nucleotide-based analyses support the creation of two families, three sub-families, and four genera within the order 'Grandevirales'. We anticipate that the proposed taxonomy of Lak megaphages will simplify the future classification of related viral genomes as they are uncovered. Continued efforts to classify divergent viruses are crucial to aid common analyses of viral genomes and metagenomes.
Collapse
Affiliation(s)
- Ryan Cook
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Marco A. Crisci
- Department of Structural and Molecular Biology, Division of Biosciences, UCL, London, UK
| | - Hannah V. Pye
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Joanne M. Santini
- Department of Structural and Molecular Biology, Division of Biosciences, UCL, London, UK
| |
Collapse
|
12
|
Flores VS, Amgarten DE, Iha BKV, Ryon KA, Danko D, Tierney BT, Mason C, da Silva AM, Setubal JC. Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium. Sci Rep 2024; 14:7913. [PMID: 38575625 PMCID: PMC10994904 DOI: 10.1038/s41598-024-58226-0] [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: 06/08/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Bacteriophages are recognized as the most abundant members of microbiomes and have therefore a profound impact on microbial communities through the interactions with their bacterial hosts. The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics, throwing light into these hitherto largely unexplored urban environments. MetaSUB focused primarily on the bacterial community. In this work, we explored MetaSUB metagenomic data in order to recover and analyze bacteriophage genomes. We recovered and analyzed 1714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. The recovered genomes were predicted to belong to temperate (69%) and lytic (31%) phages. Thirty-three of these genomes have more than 200 kbp, and one of them reaches 572 kbp, placing it among the largest phage genomes ever found. In general, the phages tended to be site-specific or nearly so, but 194 genomes could be identified in every city from which phage genomes were retrieved. We predicted hosts for 48% of the phages and observed general agreement between phage abundance and the respective bacterial host abundance, which include the most common nosocomial multidrug-resistant pathogens. A small fraction of the phage genomes are carriers of antibiotic resistance genes, and such genomes tended to be particularly abundant in the sites where they were found. We also detected CRISPR-Cas systems in five phage genomes. This study expands the previously reported MetaSUB results and is a contribution to the knowledge about phage diversity, global distribution, and phage genome content.
Collapse
Affiliation(s)
- Vinicius S Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Deyvid E Amgarten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Bruno Koshin Vázquez Iha
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | | | | | - Braden T Tierney
- Weill Cornell Medicine, New York, NY, USA
- Harvard Medical School, Cambridge, MA, USA
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
| |
Collapse
|
13
|
Acton L, Pye HV, Thilliez G, Kolenda R, Matthews M, Turner AK, Yasir M, Holden E, Al-Khanaq H, Webber M, Adriaenssens EM, Kingsley RA. Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica. J Virol 2024; 98:e0147623. [PMID: 38376991 PMCID: PMC10949491 DOI: 10.1128/jvi.01476-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing, and agriculture. In this study, we isolated 12 bacteriophages termed SPLA phage which infect the foodborne pathogen Salmonella enterica. To determine phage host range, a diverse collection of Enterobacteriaceae and Salmonella enterica was used and genes involved in infection by six SPLA phages were identified using Salmonella Typhimurium strain ST4/74. Candidate host receptors included lipopolysaccharide (LPS), cellulose, and BtuB. Lipopolysaccharide was identified as a susceptibility factor for phage SPLA1a and mutations in LPS biosynthesis genes spontaneously emerged during culture with S. Typhimurium. Conversely, LPS was a resistance factor for phage SPLA5b which suggested that emergence of LPS mutations in culture with SPLA1a represented collateral sensitivity to SPLA5b. We show that bacteria-phage co-culture with SPLA1a and SPLA5b was more successful in limiting the emergence of phage resistance compared to single phage co-culture. Identification of host susceptibility and resistance genes and understanding infection dynamics are critical steps in the rationale design of phage cocktails against specific bacterial pathogens.IMPORTANCEAs antibiotic resistance continues to emerge in bacterial pathogens, bacterial viruses (phage) represent a potential alternative or adjunct to antibiotics. One challenge for their implementation is the predisposition of bacteria to rapidly acquire resistance to phages. We describe a functional genomics approach to identify mechanisms of susceptibility and resistance for newly isolated phages that infect and lyse Salmonella enterica and use this information to identify phage combinations that exploit collateral sensitivity, thus increasing efficacy. Collateral sensitivity is a phenomenon where resistance to one class of antibiotics increases sensitivity to a second class of antibiotics. We report a functional genomics approach to rationally design a phage combination with a collateral sensitivity dynamic which resulted in increased efficacy. Considering such evolutionary trade-offs has the potential to manipulate the outcome of phage therapy in favor of resolving infection without selecting for escape mutants and is applicable to other virus-host interactions.
Collapse
Affiliation(s)
- Luke Acton
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | - Hannah V. Pye
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | - Gaëtan Thilliez
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Rafał Kolenda
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Michaela Matthews
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - A. Keith Turner
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Muhammad Yasir
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Emma Holden
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Haider Al-Khanaq
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Mark Webber
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| | | | - Robert A. Kingsley
- Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
| |
Collapse
|
14
|
Chen L, Banfield JF. COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes. Nat Microbiol 2024; 9:737-750. [PMID: 38321183 PMCID: PMC10914622 DOI: 10.1038/s41564-023-01598-2] [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: 06/06/2023] [Accepted: 12/19/2023] [Indexed: 02/08/2024]
Abstract
Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.
Collapse
Affiliation(s)
- LinXing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Environmental Science Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| |
Collapse
|
15
|
Gios E, Mosley OE, Hoggard M, Handley KM. High niche specificity and host genetic diversity of groundwater viruses. THE ISME JOURNAL 2024; 18:wrae035. [PMID: 38452204 PMCID: PMC10980836 DOI: 10.1093/ismejo/wrae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analysed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units. At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host's intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g. dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.
Collapse
Affiliation(s)
- Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- NINA, Norwegian Institute for Nature Research, Trondheim 7034, Norway
| | - Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- NatureMetrics Ltd, Surrey Research Park, Guildford GU2 7HJ, United Kingdom
| | - Michael Hoggard
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| |
Collapse
|
16
|
Rossi FPN, Flores VS, Uceda-Campos G, Amgarten DE, Setubal JC, da Silva AM. Comparative Analyses of Bacteriophage Genomes. Methods Mol Biol 2024; 2802:427-453. [PMID: 38819567 DOI: 10.1007/978-1-0716-3838-5_14] [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] [Indexed: 06/01/2024]
Abstract
Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in phage-centered research motivated by their enormous potential as antimicrobials to cope with multidrug-resistant pathogens. An ever-growing number of complete phage genomes are becoming available, derived either from newly isolated phages (cultivated phages) or recovered from metagenomic sequencing data (uncultivated phages). Robust comparative analysis is crucial for a comprehensive understanding of genotypic variations of phages and their related evolutionary processes, and to investigate the interaction mechanisms between phages and their hosts. In this chapter, we present a protocol for phage comparative genomics employing tools selected out of the many currently available, focusing on complete genomes of phages classified in the class Caudoviricetes. This protocol provides accurate identification of similarities, differences, and patterns among new and previously known complete phage genomes as well as phage clustering and taxonomic classification.
Collapse
Affiliation(s)
| | - Vinicius Sousa Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Guillermo Uceda-Campos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | | | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil.
| |
Collapse
|
17
|
Muscatt G, Cook R, Millard A, Bending GD, Jameson E. Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile. mBio 2023; 14:e0224623. [PMID: 38032184 PMCID: PMC10746233 DOI: 10.1128/mbio.02246-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems.
Collapse
Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, Leicester Centre for Phage Research, University of Leicester, Leicester, United Kingdom
| | - Gary D. Bending
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| |
Collapse
|
18
|
Montso PK, Kropinski AM, Mokoena F, Pierneef RE, Mlambo V, Ateba CN. Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces. Sci Rep 2023; 13:21426. [PMID: 38052835 PMCID: PMC10698182 DOI: 10.1038/s41598-023-48788-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
The increasing prevalence of antimicrobial-resistant (AMR) pathogens has become a major global health concern. To address this challenge, innovative strategies such as bacteriophage therapy must be optimised. Genomic characterisation is a crucial step in identifying suitable phage candidates for combating AMR pathogens. The aim of this study was to characterise seven phages that infect the Escherichia coli O177 strain using a whole genome sequencing. The analysis of genome sequences revealed that these phages had linear dsDNA, with genome sizes spanning from 136, 483 to 166,791 bp and GC content varying from 35.39 to 43.63%. Taxonomically, the phages were classified under three different subfamilies (Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae) and three genera (Phapecoctavirus, Tequatrovirus, and Vequintavirus) within the class Caudoviricetes. In silico PhageAI analysis predicted that all the phages were virulent, with confidence levels between 96.07 and 97.26%. The phage genomes contained between 66 and 82 ORFs, which encode hypothetical and putative functional proteins. In addition, the phage genomes contained core genes associated with molecular processes such as DNA replication, transcription modulation, nucleotide metabolism, phage structure (capsid and tail), and lysis. None of the genomes carried genes associated with undesirable traits such as integrase, antimicrobial resistance, virulence, and toxins. The study revealed high genome and proteome homology among E. coli O177 phages and other known Escherichia phages. The results suggest that the seven phages are new members of the genera Phapecoctavirus, Tequatrovirus, and Vequintavirus under the subfamilies Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae, respectively.
Collapse
Affiliation(s)
- Peter Kotsoana Montso
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
| | - Andrew M Kropinski
- Department Food Science, and Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Fortunate Mokoena
- Department of Biochemistry, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Rian Ewald Pierneef
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0001, South Africa
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, 0001, South Africa
- SARChI Chair: Marine Microbiomics, Microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
| | - Victor Mlambo
- Faculty of Agriculture and Natural Sciences, School of Agricultural Sciences, University of Mpumalanga, Mbombela, 1200, South Africa
| | - Collins Njie Ateba
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| |
Collapse
|
19
|
Valadez-Cano C, Reyes-Prieto A, Lawrence J. Novel virulent and temperate cyanophages predicted to infect Microcoleus associated with anatoxin-producing benthic mats. Environ Microbiol 2023; 25:3319-3332. [PMID: 37849433 DOI: 10.1111/1462-2920.16527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023]
Abstract
Cyanophages are crucial for regulating cyanobacterial populations, but their influence on anatoxin-producing Microcoleus mat dynamics remains unexplored. Here, we use metagenomics to explore phage presence in benthic mats from the Wolastoq|Saint John River (New Brunswick, Canada) and the Eel River (California, USA). We recovered multiple viral-like sequences associated with different putative bacterial hosts, including two cyanophage genomes with apparently different replication strategies. A temperate cyanophage was found integrated in the genomes of Microcoleus sp. 3 recovered from the Eel River and is phylogenetically related to Phormidium phages. We also recovered novel virulent cyanophage genomes from Wolastoq and Eel River mats that were dominated by anatoxin-producing Microcoleus species predicted to be the host. Despite the geographical distance, these genomes have similar sizes (circa 239 kbp) and share numerous orthologous genes with high sequence identity. A considerable reduction of the anatoxin-producing Microcoleus species in Wolastoq mats following the emergence of the virulent phage suggests that phage infections have an important role in limiting the abundance of this toxigenic cyanobacterium and releasing anatoxins into the surrounding water. Our results constitute the first report of cyanophages predicted to infect mat-forming Microcoleus species associated with anatoxin production.
Collapse
Affiliation(s)
- Cecilio Valadez-Cano
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Janice Lawrence
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| |
Collapse
|
20
|
da Silva JD, Melo LDR, Santos SB, Kropinski AM, Xisto MF, Dias RS, da Silva Paes I, Vieira MS, Soares JJF, Porcellato D, da Silva Duarte V, de Paula SO. Genomic and proteomic characterization of vB_SauM-UFV_DC4, a novel Staphylococcus jumbo phage. Appl Microbiol Biotechnol 2023; 107:7231-7250. [PMID: 37741937 PMCID: PMC10638138 DOI: 10.1007/s00253-023-12743-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/03/2023] [Accepted: 08/21/2023] [Indexed: 09/25/2023]
Abstract
Staphylococcus aureus is one of the most relevant mastitis pathogens in dairy cattle, and the acquisition of antimicrobial resistance genes presents a significant health issue in both veterinary and human fields. Among the different strategies to tackle S. aureus infection in livestock, bacteriophages have been thoroughly investigated in the last decades; however, few specimens of the so-called jumbo phages capable of infecting S. aureus have been described. Herein, we report the biological, genomic, and structural proteomic features of the jumbo phage vB_SauM-UFV_DC4 (DC4). DC4 exhibited a remarkable killing activity against S. aureus isolated from the veterinary environment and stability at alkaline conditions (pH 4 to 12). The complete genome of DC4 is 263,185 bp (GC content: 25%), encodes 263 predicted CDSs (80% without an assigned function), 1 tRNA (Phe-tRNA), multisubunit RNA polymerase, and an RNA-dependent DNA polymerase. Moreover, comparative analysis revealed that DC4 can be considered a new viral species belonging to a new genus DC4 and showed a similar set of lytic proteins and depolymerase activity with closely related jumbo phages. The characterization of a new S. aureus jumbo phage increases our understanding of the diversity of this group and provides insights into the biotechnological potential of these viruses. KEY POINTS: • vB_SauM-UFV_DC4 is a new viral species belonging to a new genus within the class Caudoviricetes. • vB_SauM-UFV_DC4 carries a set of RNA polymerase subunits and an RNA-directed DNA polymerase. • vB_SauM-UFV_DC4 and closely related jumbo phages showed a similar set of lytic proteins.
Collapse
Affiliation(s)
- Jéssica Duarte da Silva
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Luís D R Melo
- Centre of Biological Engineering - CEB, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Sílvio B Santos
- Centre of Biological Engineering - CEB, University of Minho, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Portugal
| | - Andrew M Kropinski
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mariana Fonseca Xisto
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Roberto Sousa Dias
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Isabela da Silva Paes
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Marcella Silva Vieira
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - José Júnior Ferreira Soares
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
| | - Vinícius da Silva Duarte
- Department of Microbiology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil.
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway.
| | - Sérgio Oliveira de Paula
- Department of General Biology, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, Viçosa, Minas Gerais, 36570-900, Brazil
| |
Collapse
|
21
|
Kallies R, Hu D, Abdulkadir N, Schloter M, Rocha U. Identification of Huge Phages from Wastewater Metagenomes. Viruses 2023; 15:2330. [PMID: 38140571 PMCID: PMC10747093 DOI: 10.3390/v15122330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. We screened 165 wastewater metagenomes for the presence of viral sequences. After identifying over 600 potential huge phage genomes, we reduced the dataset using manual curation by excluding viral contigs that did not contain viral protein-coding genes or consisted of concatemers of several small phage genomes. This dataset showed seven fully annotated huge phage genomes. The phages grouped into distinct phylogenetic clades, likely forming new genera and families. A phylogenomic analysis between our huge phages and phages with smaller genomes, i.e., less than 200 kb, supported the hypothesis that huge phages have undergone convergent evolution. The genomes contained typical phage protein-coding genes, sequential gene cassettes for metabolic pathways, and complete inventories of tRNA genes covering all standard and rare amino acids. Our study showed a pipeline for huge phage analyses that may lead to new enzymes for therapeutic or biotechnological applications.
Collapse
Affiliation(s)
- René Kallies
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Die Hu
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Nafi’u Abdulkadir
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Michael Schloter
- Department of Environmental Health, Helmholtz Munich, Ingolstaedter Landstr. 1, D-85758 Neuherberg, Germany;
| | - Ulisses Rocha
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| |
Collapse
|
22
|
Rigou S, Schmitt A, Alempic JM, Lartigue A, Vendloczki P, Abergel C, Claverie JM, Legendre M. Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses. Mol Biol Evol 2023; 40:msad244. [PMID: 37950899 PMCID: PMC10664404 DOI: 10.1093/molbev/msad244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/13/2023] Open
Abstract
Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery of Pithovirus sibericum, recovered from a 30,000-yr-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here, we report the isolation and genome sequencing of 2 Pithoviridae from soil samples, in addition to 3 other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomic study of the Pithoviridae family to decipher the organization and evolution of their genomes. Our study reveals a nonuniform genome organization in 2 main regions: 1 concentrating core genes and another gene duplications. We also found that Pithoviridae genomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events, and genomic rearrangements that contribute to their evolution.
Collapse
Affiliation(s)
- Sofia Rigou
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Alain Schmitt
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Jean-Marie Alempic
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Audrey Lartigue
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Peter Vendloczki
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Chantal Abergel
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Jean-Michel Claverie
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| | - Matthieu Legendre
- Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille 13288 Cedex 9, France
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Alotaibi R, Eifan S, Hanif A, Nour I, Alkathiri A. Prevalence and Genetic Diversity of Cross-Assembly Phages in Wastewater Treatment Plants in Riyadh, Saudi Arabia. Microorganisms 2023; 11:2167. [PMID: 37764011 PMCID: PMC10535421 DOI: 10.3390/microorganisms11092167] [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: 07/27/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The most common DNA virus found in wastewaters globally is the cross-assembly phage (crAssphage). King Saud University wastewater treatment plant (KSU-WWTP); Manfoha wastewater treatment plant (MN-WWTP); and the Embassy wastewater treatment plant (EMB-WWTP) in Riyadh, Saudi Arabia were selected, and 36 untreated sewage water samples during the year 2022 were used in the current study. The meteorological impact on crAssphage prevalence was investigated. CrAssphage prevalence was recorded using PCR and Sanger sequencing. The molecular diversity of crAssphage sequences was studied for viral gene segments from the major capsid protein (MCP) and membrane protein containing the peptidoglycan-binding domain (MP-PBD). KSU-WWTP and EMB-WWTP showed a higher prevalence of crAssphage (83.3%) than MN-WWTP (75%). Phylogenetic analysis of MCP and MP-PBD segments depicted a close relationship to the Japanese isolates. The MCP gene from the current study's isolate WW/2M/SA/2022 depicted zero evolutionary divergence from 3057_98020, 2683_104905, and 4238_99953 isolates (d = 0.000) from Japan. A significant influence of temporal variations on the prevalence of crAssphage was detected in the three WWTPs. CrAssphage displayed the highest prevalence at high temperatures (33-44 °C), low relative humidity (6-14%), and moderate wind speed (16-21 Km/h). The findings provided pioneering insights into crAssphage prevalence and its genetic diversity in WWTPs in Riyadh, Saudi Arabia.
Collapse
Affiliation(s)
| | | | - Atif Hanif
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | | | | |
Collapse
|
25
|
Harding KR, Kyte N, Fineran PC. Jumbo phages. Curr Biol 2023; 33:R750-R751. [PMID: 37490856 DOI: 10.1016/j.cub.2023.05.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
In this Quick guide, Harding et al. introduce jumbo phages - the overlooked giants of the phage universe.
Collapse
Affiliation(s)
- Kate R Harding
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin 9054, New Zealand
| | - Natalie Kyte
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, Dunedin 9054, New Zealand; Bioprotection Aotearoa, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin 9054, New Zealand.
| |
Collapse
|
26
|
Grenfell AW, Intile PJ, McFarlane JA, Leung DC, Abdalla K, Wold MC, Kees ED, Gralnick JA. The Outer Membrane Cytochrome OmcA Is Essential for Infection of Shewanella oneidensis by a Zebrafish-Associated Bacteriophage. J Bacteriol 2023; 205:e0046922. [PMID: 37227287 PMCID: PMC10294696 DOI: 10.1128/jb.00469-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/25/2023] [Indexed: 05/26/2023] Open
Abstract
The microbiota-the mixture of microorganisms in the intestinal tract of animals-plays an important role in host biology. Bacteriophages are a prominent, though often overlooked, component of the microbiota. The mechanisms that phage use to infect susceptible cells associated with animal hosts, and the broader role they could play in determining the substituents of the microbiota, are poorly understood. In this study, we isolated a zebrafish-associated bacteriophage, which we named Shewanella phage FishSpeaker. This phage infects Shewanella oneidensis strain MR-1, which cannot colonize zebrafish, but it is unable to infect Shewanella xiamenensis strain FH-1, a strain isolated from the zebrafish gut. Our data suggest that FishSpeaker uses the outer membrane decaheme cytochrome OmcA, which is an accessory component of the extracellular electron transfer (EET) pathway in S. oneidensis, as well as the flagellum to recognize and infect susceptible cells. In a zebrafish colony that lacks detectable FishSpeaker, we found that most Shewanella spp. are sensitive to infection and that some strains are resistant to infection. Our results suggest that phage could act as a selectivity filter for zebrafish-associated Shewanella and show that the EET machinery can be targeted by phage in the environment. IMPORTANCE Phage exert selective pressure on bacteria that influences and shapes the composition of microbial populations. However, there is a lack of native, experimentally tractable systems for studying how phage influence microbial population dynamics in complex communities. Here, we show that a zebrafish-associated phage requires both the outer membrane-associated extracellular electron transfer protein OmcA and the flagellum to infect Shewanella oneidensis strain MR-1. Our results suggest that the newly discovered phage-FishSpeaker-could exert selective pressure that restricts which Shewanella spp. colonize zebrafish. Moreover, the requirement of OmcA for infection by FishSpeaker suggests that the phage preferentially infects cells that are oxygen limited, a condition required for OmcA expression and an ecological feature of the zebrafish gut.
Collapse
Affiliation(s)
- Andrew W. Grenfell
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Peter J. Intile
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - John A. McFarlane
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Dani C. Leung
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Khalid Abdalla
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Michael C. Wold
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Eric D. Kees
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Jeffrey A. Gralnick
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| |
Collapse
|
27
|
Hou Y, Wu Z, Ren L, Chen Y, Zhang YA, Zhou Y. Characterization and application of a lytic jumbo phage ZPAH34 against multidrug-resistant Aeromonas hydrophila. Front Microbiol 2023; 14:1178876. [PMID: 37415809 PMCID: PMC10321303 DOI: 10.3389/fmicb.2023.1178876] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/18/2023] [Indexed: 07/08/2023] Open
Abstract
Aeromonas hydrophila is an emerging foodborne pathogen causing human gastroenteritis. Aeromonas species isolated from food such as seafood presented multidrug-resistance (MDR), raising serious concerns regarding food safety and public health. The use of phages to infect bacteria is a defense against drug-resistant pathogens. In this study, phage ZPAH34 isolated from the lake sample exerted lytic activity against MDR A. hydrophila strain ZYAH75 and inhibited the biofilm on different food-contacting surfaces. ZPAH34 has a large dsDNA genome of 234 kb which belongs to a novel jumbo phage. However, its particle size is the smallest of known jumbo phages so far. Based on phylogenetic analysis, ZPAH34 was used to establish a new genus Chaoshanvirus. Biological characterization revealed that ZPAH34 exhibited wide environmental tolerance, and a high rapid adsorb and reproductive capacity. Food biocontrol experiments demonstrated that ZPAH34 reduces the viable count of A. hydrophila on fish fillets (2.31 log) and lettuce (3.28 log) with potential bactericidal effects. This study isolated and characterized jumbo phage ZPAH34 not only enriched the understanding of phage biological entity diversity and evolution because of its minimal virion size with large genome but also was the first usage of jumbo phage in food safety to eliminate A. hydrophila.
Collapse
Affiliation(s)
- Yuting Hou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhihao Wu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Li Ren
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Yuan Chen
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Yong-An Zhang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yang Zhou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Shenzhen Institute of Nutrition and Health, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| |
Collapse
|
28
|
Hu M, Xing B, Yang M, Han R, Pan H, Guo H, Liu Z, Huang T, Du K, Jiang S, Zhang Q, Lu W, Huang X, Zhou C, Li J, Song W, Deng Z, Xiao M. Characterization of a novel genus of jumbo phages and their application in wastewater treatment. iScience 2023; 26:106947. [PMID: 37324530 PMCID: PMC10265529 DOI: 10.1016/j.isci.2023.106947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/22/2023] [Accepted: 05/20/2023] [Indexed: 06/17/2023] Open
Abstract
Phages widely exist in numerous environments from wastewater to deep ocean, representing a huge virus diversity, yet remain poorly characterized. Among them, jumbo phages are of particular interests due to their large genome (>200 kb) and unusual biology. To date, only six strains of jumbo phages infecting Klebsiella pneumoniae have been described. Here, we report the isolation and characterization of two jumbo phages from hospital wastewater representing the sixth genus: φKp5130 and φKp9438. Both phages showed lytic activity against broad range of clinical antibiotic-resistant K. pneumoniae strains and distinct physiology including long latent period, small burst size, and high resistance to thermal and pH stress. The treatment of sewage water with the phages cocktail resulted in dramatic decline in K. pneumoniae population. Overall, this study provides detailed molecular and genomics characterization of two novel jumbo phages, expands viral diversity, and provides novel candidate phages to facilitate environmental wastewater treatment.
Collapse
Affiliation(s)
- Ming Hu
- Department of Special Medicine, Basic Medicine College, Qingdao University, Qingdao 266071, China
| | - Bo Xing
- BGI-Shenzhen, Shenzhen 518083, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minghua Yang
- BGI-Shenzhen, Shenzhen 518083, China
- BGI College, Zhengzhou University, Zhengzhou 450000, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Rui Han
- BGI-Beijing, Beijing 102601, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huazheng Pan
- Department of The Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Hui Guo
- Department of The Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Zhen Liu
- Department of Special Medicine, Basic Medicine College, Qingdao University, Qingdao 266071, China
| | - Tao Huang
- Department of Kidney Transplantation, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Kang Du
- University of Science and Technology of China, Hefei 230026, China
| | | | - Qian Zhang
- Department of Prosthodontics, The Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Wenjing Lu
- Department of Dermatology, Qilu Hospital of Shandong University (Qingdao), Qingdao 266000, China
| | - Xun Huang
- Infection Control Center, Xiangya Hospital, Central South University, Changsha 410011, China
| | - Congzhao Zhou
- University of Science and Technology of China, Hefei 230026, China
| | - Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenchen Song
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Ziqing Deng
- BGI-Shenzhen, Shenzhen 518083, China
- BGI-Beijing, Beijing 102601, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| |
Collapse
|
29
|
Alexyuk P, Bogoyavlenskiy A, Alexyuk M, Akanova K, Moldakhanov Y, Berezin V. Isolation and Characterization of Jumbo Coliphage vB_EcoM_Lh1B as a Promising Therapeutic Agent against Chicken Colibacillosis. Microorganisms 2023; 11:1524. [PMID: 37375026 DOI: 10.3390/microorganisms11061524] [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: 05/14/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Colibacillosis in chickens can cause the death of young stock, decrease weight gain and lead to significant economic losses. Currently, antibiotic therapy is the main method of treatment of infected animals, but unchecked use of antibiotics has led to widespread antibiotic resistance among microorganisms. Therefore, it is necessary to develop alternative methods of treating bacterial infections that are fully consistent with the One Health concept and introduce them into practice. Phage therapy meets the specified requirements perfectly. This study describes the isolation and characterization of the lytic jumbo phage vB_EcoM_Lh1B and evaluates its potential use in controlling antibiotic-resistant E. coli infection in poultry. The complete phage genome is 240,200 bp long. Open reading frame (ORF) prediction shows that the phage genome does not contain genes encoding antibiotic resistance and lysogeny factors. Based on phylogenetic and electron microscopic analysis, vB_EcoM_Lh1B belongs to the group of myoviruses of the Seoulvirus genus of the Caudoviricetes class. The bacteriophage has good resistance to a wide range of pH and temperatures and has the ability to suppress 19 out of 30 studied pathogenic E. coli strains. The biological and lytic properties of the isolated vB_EcoM_Lh1B phage make it a promising target of further study as a therapeutic agent against E. coli infections in poultry.
Collapse
Affiliation(s)
- Pavel Alexyuk
- Laboratory of Antiviral Protection, Department of Virology, Research and Production Center for Microbiology and Virology, Bogenbai Batyr Street 105, Almaty 050010, Kazakhstan
| | - Andrey Bogoyavlenskiy
- Laboratory of Antiviral Protection, Department of Virology, Research and Production Center for Microbiology and Virology, Bogenbai Batyr Street 105, Almaty 050010, Kazakhstan
| | - Madina Alexyuk
- Laboratory of Antiviral Protection, Department of Virology, Research and Production Center for Microbiology and Virology, Bogenbai Batyr Street 105, Almaty 050010, Kazakhstan
| | - Kuralay Akanova
- Laboratory of Antiviral Protection, Department of Virology, Research and Production Center for Microbiology and Virology, Bogenbai Batyr Street 105, Almaty 050010, Kazakhstan
| | - Yergali Moldakhanov
- Laboratory of Antiviral Protection, Department of Virology, Research and Production Center for Microbiology and Virology, Bogenbai Batyr Street 105, Almaty 050010, Kazakhstan
| | - Vladimir Berezin
- Laboratory of Antiviral Protection, Department of Virology, Research and Production Center for Microbiology and Virology, Bogenbai Batyr Street 105, Almaty 050010, Kazakhstan
| |
Collapse
|
30
|
Naknaen A, Samernate T, Wannasrichan W, Surachat K, Nonejuie P, Chaikeeratisak V. Combination of genetically diverse Pseudomonas phages enhances the cocktail efficiency against bacteria. Sci Rep 2023; 13:8921. [PMID: 37264114 DOI: 10.1038/s41598-023-36034-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/28/2023] [Indexed: 06/03/2023] Open
Abstract
Phage treatment has been used as an alternative to antibiotics since the early 1900s. However, bacteria may acquire phage resistance quickly, limiting the use of phage treatment. The combination of genetically diverse phages displaying distinct replication machinery in phage cocktails has therefore become a novel strategy to improve therapeutic outcomes. Here, we isolated and studied lytic phages (SPA01 and SPA05) that infect a wide range of clinical Pseudomonas aeruginosa isolates. These relatively small myophages have around 93 kbp genomes with no undesirable genes, have a 30-min latent period, and reproduce a relatively high number of progenies, ranging from 218 to 240 PFU per infected cell. Even though both phages lyse their hosts within 4 h, phage-resistant bacteria emerge during the treatment. Considering SPA01-resistant bacteria cross-resist phage SPA05 and vice versa, combining SPA01 and SPA05 for a cocktail would be ineffective. According to the decreased adsorption rate of the phages in the resistant isolates, one of the anti-phage mechanisms may occur through modification of phage receptors on the target cells. All resistant isolates, however, are susceptible to nucleus-forming jumbophages (PhiKZ and PhiPA3), which are genetically distinct from phages SPA01 and SPA05, suggesting that the jumbophages recognize a different receptor during phage entry. The combination of these phages with the jumbophage PhiKZ outperforms other tested combinations in terms of bactericidal activity and effectively suppresses the emergence of phage resistance. This finding reveals the effectiveness of the diverse phage-composed cocktail for reducing bacterial growth and prolonging the evolution of phage resistance.
Collapse
Affiliation(s)
- Ampapan Naknaen
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Thanadon Samernate
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Wichanan Wannasrichan
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
- Cell and Biomolecular Imaging Research Unit (CBIRU), Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
| |
Collapse
|
31
|
Jo D, Kim H, Lee Y, Kim J, Ryu S. Characterization and genomic study of EJP2, a novel jumbo phage targeting antimicrobial resistant Escherichia coli. Front Microbiol 2023; 14:1194435. [PMID: 37250060 PMCID: PMC10213699 DOI: 10.3389/fmicb.2023.1194435] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
The emergence of antimicrobial resistance (AMR) Escherichia coli has noticeably increased in recent years worldwide and causes serious public health concerns. As alternatives to antibiotics, bacteriophages are regarded as promising antimicrobial agents. In this study, we isolated and characterized a novel jumbo phage EJP2 that specifically targets AMR E. coli strains. EJP2 belonged to the Myoviridae family with an icosahedral head (120.9 ± 2.9 nm) and a non-contractile tail (111.1 ± 0.6 nm), and contained 349,185 bp double-stranded DNA genome with 540 putative ORFs, suggesting that EJP2 could be classified as jumbo phage. The functions of genes identified in EJP2 genome were mainly related to nucleotide metabolism, DNA replication, and recombination. Comparative genomic analysis revealed that EJP2 was categorized in the group of Rak2-related virus and presented low sequence similarity at the nucleotide and amino acid level compared to other E. coli jumbo phages. EJP2 had a broad host spectrum against AMR E. coli as well as pathogenic E. coli and recognized LPS as a receptor for infection. Moreover, EJP2 treatment could remove over 80% of AMR E. coli biofilms on 96-well polystyrene, and exhibit synergistic antimicrobial activity with cefotaxime against AMR E. coli. These results suggest that jumbo phage EJP2 could be used as a potential biocontrol agent to combat the AMR issue in food processing and clinical environments.
Collapse
|
32
|
Zaki BM, Mohamed AA, Dawoud A, Essam K, Hammouda ZK, Abdelsattar AS, El-Shibiny A. Isolation, screening and characterization of phage. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 200:13-60. [PMID: 37739553 DOI: 10.1016/bs.pmbts.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Bacterial resistance threatens public health due to a lack of novel antibacterial classes since the 21st century. Bacteriophages, the most ubiquitous microorganism on Earth and natural predators of bacteria, have the potential to save the world from the post-antibiotic era. Therefore, phage isolation and characterization are in high demand to find suitable phages for therapeutic and bacterial control applications. The chapter presents brief guidance supported by recommendations on the isolation of phages, and initial screening of phage antimicrobial efficacy, in addition to, conducting comprehensive characterization addressing morphological, biological, genomic, and taxonomic features.
Collapse
Affiliation(s)
- Bishoy Maher Zaki
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Amira A Mohamed
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Kareem Essam
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Zainab K Hammouda
- Microbiology and Immunology Department, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza, Egypt; Faculty of Environmental Agricultural Sciences, Arish University, Arish, Egypt
| |
Collapse
|
33
|
Śliwka P, Weber-Dąbrowska B, Żaczek M, Kuźmińska-Bajor M, Dusza I, Skaradzińska A. Characterization and Comparative Genomic Analysis of Three Virulent E. coli Bacteriophages with the Potential to Reduce Antibiotic-Resistant Bacteria in the Environment. Int J Mol Sci 2023; 24:ijms24065696. [PMID: 36982770 PMCID: PMC10059673 DOI: 10.3390/ijms24065696] [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: 01/21/2023] [Revised: 02/26/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
The emerging global crisis of antibiotic resistance demands new alternative antibacterial solutions. Although bacteriophages have been used to combat bacterial infections for over a century, a dramatic boost in phage studies has recently been observed. In the development of modern phage applications, a scientific rationale is strongly required and newly isolated phages need to be examined in detail. In this study, we present the full characterization of bacteriophages BF9, BF15, and BF17, with lytic activity against extended-spectrum β-lactamases (ESBLs)- and AmpC β-lactamases (AmpC)-producing Escherichia coli, the prevalence of which has increased significantly in livestock in recent decades, representing a great hazard to food safety and a public health risk. Comparative genomic and phylogenetic analysis indicated that BF9, BF15, and BF17 represent the genera Dhillonvirus, Tequatrovirus, and Asteriusvirus, respectively. All three phages significantly reduced in vitro growth of their bacterial host and retained the ability to lyse bacteria after preincubation at wide ranges of temperature (−20–40 °C) and pH (5–9). The results described herein indicate the lytic nature of BF9, BF15, and BF17, which, along with the absence of genes encoding toxins and bacterial virulence factors, represents an undoubted asset in terms of future phage application.
Collapse
Affiliation(s)
- Paulina Śliwka
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
| | - Maciej Żaczek
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wrocław, Poland
| | - Marta Kuźmińska-Bajor
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
| | - Izabela Dusza
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
| | - Aneta Skaradzińska
- Department of Biotechnology and Food Microbiology, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
- Correspondence: ; Tel.: +48-71-320-7791
| |
Collapse
|
34
|
Isolation and characterization of Aeromonas hydrophila lytic phage, and evaluation of a phage cocktail against A. hydrophila contamination in fish fillet. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
35
|
Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities. mSystems 2023; 8:e0070122. [PMID: 36622155 PMCID: PMC9948695 DOI: 10.1128/msystems.00701-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Microbiomes are intricately intertwined with human health, geochemical cycles, and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven to be powerful model systems for the study of microbial interactions. To provide a more comprehensive view of the genomic potential and temporal dynamics of cheese rind communities, we combined longitudinal, multi-platform metagenomics of three ripening washed-rind cheeses with whole-genome sequencing of community isolates. Sequencing-based approaches revealed a highly reproducible microbial succession in each cheese and the coexistence of closely related Psychrobacter species and enabled the prediction of plasmid and phage diversity and their host associations. In combination with culture-based approaches, we established a genomic catalog and a paired 16-member in vitro washed-rind cheese system. The combination of multi-platform metagenomic time-series data and an in vitro model provides a rich resource for further investigation of cheese rind microbiomes both computationally and experimentally. IMPORTANCE Metagenome sequencing can provide great insights into microbiome composition and function and help researchers develop testable hypotheses. Model microbiomes, such as those composed of cheese rind bacteria and fungi, allow the testing of these hypotheses in a controlled manner. Here, we first generated an extensive longitudinal metagenomic data set. This data set reveals successional dynamics, yields a phyla-spanning bacterial genomic catalog, associates mobile genetic elements with their hosts, and provides insights into functional enrichment of Psychrobacter in the cheese environment. Next, we show that members of the washed-rind cheese microbiome lend themselves to in vitro community reconstruction. This paired metagenomic data and in vitro system can thus be used as a platform for generating and testing hypotheses related to the dynamics within, and the functions associated with, cheese rind microbiomes.
Collapse
|
36
|
Kim Y, Lee SM, Nong LK, Kim J, Kim SB, Kim D. Characterization of Klebsiella pneumoniae bacteriophages, KP1 and KP12, with deep learning-based structure prediction. Front Microbiol 2023; 13:990910. [PMID: 36762092 PMCID: PMC9902359 DOI: 10.3389/fmicb.2022.990910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/19/2022] [Indexed: 01/26/2023] Open
Abstract
Concerns over Klebsiella pneumoniae resistance to the last-line antibiotic treatment have prompted a reconsideration of bacteriophage therapy in public health. Biotechnological application of phages and their gene products as an alternative to antibiotics necessitates the understanding of their genomic context. This study sequenced, annotated, characterized, and compared two Klebsiella phages, KP1 and KP12. Physiological validations identified KP1 and KP12 as members of Myoviridae family. Both phages showed that their activities were stable in a wide range of pH and temperature. They exhibit a host specificity toward K. pneumoniae with a broad intraspecies host range. General features of genome size, coding density, percentage GC content, and phylogenetic analyses revealed that these bacteriophages are distantly related. Phage lytic proteins (endolysin, anti-/holin, spanin) identified by the local alignment against different databases, were subjected to further bioinformatic analyses including three-dimensional (3D) structure prediction by AlphaFold. AlphaFold models of phage lysis proteins were consistent with the published X-ray crystal structures, suggesting the presence of T4-like and P1/P2-like bacteriophage lysis proteins in KP1 and KP12, respectively. By providing the primary sequence information, this study contributes novel bacteriophages for research and development pipelines of phage therapy that ultimately, cater to the unmet clinical and industrial needs against K. pneumoniae pathogens.
Collapse
Affiliation(s)
- Youngju Kim
- Optipharm Inc., Cheongju-si, Chungcheongbuk-do, Republic of Korea,Department of Microbiology and Molecular Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jaehyung Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea,*Correspondence: Donghyuk Kim,
| |
Collapse
|
37
|
Zhang Z, Liang L, Li D, Li Y, Sun Q, Li Y, Yang H. Bacillus subtilis phage phi18: genomic analysis and receptor identification. Arch Virol 2023; 168:17. [PMID: 36593367 DOI: 10.1007/s00705-022-05686-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/22/2022] [Indexed: 01/04/2023]
Abstract
Bacillus subtilis strains play a pivotal role in the fermentation industry. B. subtilis phages can cause severe damage by infecting bacterial cells used in industrial fermentation processes. In this work, we isolated and characterized a Bacillus subtilis-infecting phage, termed phi18. Transmission electron microscopy revealed that phage phi18 particles have typical myovirus morphology, with an icosahedral head connected to a contractile tail. Genomic analysis revealed that the phage genome is a linear double-stranded DNA molecule of 147,298 bp with terminal redundancy of 14,434 bp, and 226 protein coding genes and four tRNA genes were predicted in the genome. Phage-resistant mutants were selected from a mariner transposon-insertion library of B. subtilis 168 in which two bacterial genes, tagE and pgcA, which are required for the glycosylation of wall teichoic acid (WTA), were found to be disrupted, suggesting that WTA is the receptor for phage phi18. Comparative genomic analysis showed that phage phi18 is a new member of the genus Okubovirus of the family Herelleviridae. Finally, general characteristics of the phage-resistant mutants, including biofilm formation, growth, and sporulation, were examined. The results showed that the phage-resistant mutants grew as rapidly as the parental strain B. subtilis 168 at 42 °C, suggesting that these phage-resistant mutants may be used as starters in fermentation processes.
Collapse
Affiliation(s)
- Zhiqiang Zhang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Li Liang
- Shandong Vland Biotech Co., Ltd, Shandong, 251700, China
| | - Donghang Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yutong Li
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Qinghui Sun
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Control of Tropical Diseases, School of Tropical Medicine, Hainan Medical University, Hainan, 571199, China
| | - Ye Li
- Institute of Environment and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Hainan University, Hainan, 571199, China
| | - Hongjiang Yang
- Key Laboratory of Industrial Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
| |
Collapse
|
38
|
Liu Z, Xiang Y. Structural studies of the nucleus-like assembly of jumbo bacteriophage 201φ2-1. Front Microbiol 2023; 14:1170112. [PMID: 37138628 PMCID: PMC10149743 DOI: 10.3389/fmicb.2023.1170112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023] Open
Abstract
The jumbo phages encode proteins that assemble to form a nucleus-like compartment in infected cells. Here we report the cryo-EM structure and biochemistry characterization of gp105, a protein that is encoded by the jumbo phage 201φ2-1 and is involved in the formation of the nucleus-like compartment in phage 201φ2-1 infected Pseudomonas chlororaphis. We found that, although most gp105 molecules are in the monomeric state in solution, a small portion of gp105 assemble to form large sheet-like assemblies and small cube-like particles. Reconstruction of the cube-like particles showed that the particle consists of six flat head-to-tail tetramers arranged into an octahedral cube. The four molecules at the contact interface of two head-to-tail tetramers are 2-fold symmetry-related and constitute a concave tetramer. Further reconstructions without applying symmetry showed that molecules in the particles around the distal ends of a 3-fold axis are highly dynamic and have the tendency to open up the assembly. Local classifications and refinements of the concave tetramers in the cube-like particle resulted in a map of the concave tetramer at a resolution of 4.09 Å. Structural analysis of the concave tetramer indicates that the N and C terminal fragments of gp105 are important for mediating the intermolecular interactions, which was further confirmed by mutagenesis studies. Biochemistry assays showed that, in solution, the cube-like particles of gp105 are liable to either disassemble to form the monomers or recruit more molecules to form the high molecular weight lattice-like assembly. We also found that monomeric gp105s can self-assemble to form large sheet-like assemblies in vitro, and the assembly of gp105 in vitro is a reversible dynamic process and temperature-dependent. Taken together, our results revealed the dynamic assembly of gp105, which helps to understand the development and function of the nucleus-like compartment assembled by phage-encoded proteins.
Collapse
|
39
|
Zhao J, Wang Z, Li C, Shi T, Liang Y, Jiao N, Zhang Y. Significant Differences in Planktonic Virus Communities Between "Cellular Fraction" (0.22 ~ 3.0 µm) and "Viral Fraction" (< 0.22 μm) in the Ocean. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02167-6. [PMID: 36585490 DOI: 10.1007/s00248-022-02167-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Compared to free-living viruses (< 0.22 m) in the ocean, planktonic viruses in the "cellular fraction" (0.22 ~ 3.0 μm) are now far less well understood, and the differences between them remain largely unexplored. Here, we revealed that even in the same seawater samples, the "cellular fraction" comprised significantly distinct virus communities from the free virioplankton, with only 13.87% overlap in viral contigs at the species level. Compared to the viral genomes deposited in NCBI RefSeq database, 99% of the assembled viral genomes in the "cellular fraction" represented novel genera. Notably, the assembled (near-) complete viral genomes within the "cellular fraction" were significantly larger than that in the "viral fraction," and the "cellular fraction" contained three times more species of giant viruses or jumbo phages with genomes > 200 kb than the "viral fraction." The longest complete genomes of jumbo phage (~ 252 kb) and giant virus (~ 716 kb) were both detected only in the "cellular fraction." Moreover, a relatively higher proportion of proviruses were predicted within the "cellular fraction" than "viral fraction." Besides the substantial divergence in viral community structure, the different fractions also contained their unique viral auxiliary metabolic genes; e.g., those potentially participating in inorganic carbon fixation in deep sea were detected only in the "cellular-fraction" viromes. In addition, there was a considerable divergence in the community structure of both "cellular fraction" and "viral fraction" viromes between the surface and deep-sea habitats, suggesting that they might have similar environmental adaptation properties. The findings deepen our understanding of the complexity of viral community structure and function in the ocean.
Collapse
Affiliation(s)
- Jiulong Zhao
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zengmeng Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengcheng Li
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Tongmei Shi
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yantao Liang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
| | - Yongyu Zhang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
40
|
Zhu Y, Shang J, Peng C, Sun Y. Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework. Front Microbiol 2022; 13:1032186. [PMID: 36590402 PMCID: PMC9800612 DOI: 10.3389/fmicb.2022.1032186] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to (viral) metagenomic sequencing, a large number of new bacteriophages have been discovered. However, lacking a standard and automatic virus classification pipeline, the taxonomic characterization of new viruses seriously lag behind the sequencing efforts. In particular, according to the latest version of ICTV, several large phage families in the previous classification system are removed. Therefore, a comprehensive review and comparison of taxonomic classification tools under the new standard are needed to establish the state-of-the-art. In this work, we retrained and tested four recently published tools on newly labeled databases. We demonstrated their utilities and tested them on multiple datasets, including the RefSeq, short contigs, simulated metagenomic datasets, and low-similarity datasets. This study provides a comprehensive review of phage family classification in different scenarios and a practical guidance for choosing appropriate taxonomic classification pipelines. To our best knowledge, this is the first review conducted under the new ICTV classification framework. The results show that the new family classification framework overall leads to better conserved groups and thus makes family-level classification more feasible.
Collapse
|
41
|
Ouyang R, Costa AR, Cassidy CK, Otwinowska A, Williams VCJ, Latka A, Stansfeld PJ, Drulis-Kawa Z, Briers Y, Pelt DM, Brouns SJJ, Briegel A. High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers. Nat Commun 2022; 13:7241. [PMID: 36433970 PMCID: PMC9700779 DOI: 10.1038/s41467-022-34972-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, microbiological and machine learning approaches to explore the capsid, tail, and tail fibers of ϕKp24. We determine the structure of the capsid and tail at 4.1 Å and 3.0 Å resolution. We observe the tail fibers are branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide ϕKp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types of Klebsiella pneumoniae. Our study provides structural and functional insight into how ϕKp24 adapts to the variable surfaces of capsulated bacterial pathogens, which is useful for the development of phage therapy approaches against pan-drug resistant K. pneumoniae strains.
Collapse
Affiliation(s)
- Ruochen Ouyang
- grid.43169.390000 0001 0599 1243MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xianning West Road 28, Xi’an, 710049 China ,grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ana Rita Costa
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands ,grid.5292.c0000 0001 2097 4740Kavli Institute of Nanoscience, Delft, The Netherlands
| | - C. Keith Cassidy
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, UK
| | - Aleksandra Otwinowska
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland
| | - Vera C. J. Williams
- grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Agnieszka Latka
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland ,grid.5342.00000 0001 2069 7798Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Phill J. Stansfeld
- grid.7372.10000 0000 8809 1613School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
| | - Zuzanna Drulis-Kawa
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland
| | - Yves Briers
- grid.5342.00000 0001 2069 7798Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Daniël M. Pelt
- grid.5132.50000 0001 2312 1970Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333CA Leiden, The Netherlands
| | - Stan J. J. Brouns
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands ,grid.5292.c0000 0001 2097 4740Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Ariane Briegel
- grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| |
Collapse
|
42
|
Uchiyama J, Takemura-Uchiyama I, Gotoh K, Kato SI, Sakaguchi Y, Murakami H, Fukuyama T, Kaneki M, Matsushita O, Matsuzaki S. Phylogenic analysis of new viral cluster of large phages with unusual DNA genomes containing uracil in place of thymine in gene-sharing network, using phages S6 and PBS1 and relevant uncultured phages derived from sewage metagenomics. Virus Res 2022; 319:198881. [PMID: 35934259 DOI: 10.1016/j.virusres.2022.198881] [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: 03/29/2022] [Revised: 06/28/2022] [Accepted: 07/28/2022] [Indexed: 11/19/2022]
Abstract
Bacteriophages (phages) are the most diverse and abundant life-form on Earth. Jumbophages are phages with double-stranded DNA genomes longer than 200 kbp. Among these, some jumbophages with uracil in place of thymine as a nucleic acid base, which we have tentatively termed "dU jumbophages" in this study, have been reported. Because the dU jumbophages are considered to be a living fossil from the RNA world, the evolutionary traits of dU jumbophages are of interest. In this study, we examined the phylogeny of dU jumbophages. First, tBLASTx analysis of newly sequenced dU jumbophages such as Bacillus phage PBS1 and previously isolated Staphylococcus phage S6 showed similarity to the other dU jumbophages. Second, we detected the two partial genome sequences of uncultured phages possibly relevant to dU jumbophages, scaffold_002 and scaffold_007, from wastewater metagenomics. Third, according to the gene-sharing network analysis, the dU jumbophages, including phages PBS1 and S6, and uncultured phage scaffold_002 formed a cluster, which suggested a new viral subfamily/family. Finally, analyses of the phylogenetic relationship with other phages showed that the dU jumbophage cluster, which had two clades of phages infecting Gram-negative and Gram-positive bacteria, diverged from the single ancestral phage. These findings together with previous reports may imply that dU jumbophages evolved from the same origin before divergence of Gram-negative and Gram-positive bacteria.
Collapse
Affiliation(s)
- Jumpei Uchiyama
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan.
| | - Iyo Takemura-Uchiyama
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Kazuyoshi Gotoh
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Shin-Ichiro Kato
- Research Institute of Molecular Genetics, Kochi University, Kochi 783-0093, Japan
| | - Yoshihiko Sakaguchi
- Department of Microbiology, Kitasato University School of Medicine, Kanagawa 252-0374, Japan
| | - Hironobu Murakami
- School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Tomoki Fukuyama
- School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Mao Kaneki
- School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Osamu Matsushita
- Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Shigenobu Matsuzaki
- Department of Medical Laboratory Science, Faculty of Health Sciences, Kochi Gakuen University, Kochi 780-0955, Japan
| |
Collapse
|
43
|
Iyer LM, Burroughs AM, Anantharaman V, Aravind L. Apprehending the NAD +-ADPr-Dependent Systems in the Virus World. Viruses 2022; 14:1977. [PMID: 36146784 PMCID: PMC9503650 DOI: 10.3390/v14091977] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022] Open
Abstract
NAD+ and ADP-ribose (ADPr)-containing molecules are at the interface of virus-host conflicts across life encompassing RNA processing, restriction, lysogeny/dormancy and functional hijacking. We objectively defined the central components of the NAD+-ADPr networks involved in these conflicts and systematically surveyed 21,191 completely sequenced viral proteomes representative of all publicly available branches of the viral world to reconstruct a comprehensive picture of the viral NAD+-ADPr systems. These systems have been widely and repeatedly exploited by positive-strand RNA and DNA viruses, especially those with larger genomes and more intricate life-history strategies. We present evidence that ADP-ribosyltransferases (ARTs), ADPr-targeting Macro, NADAR and Nudix proteins are frequently packaged into virions, particularly in phages with contractile tails (Myoviruses), and deployed during infection to modify host macromolecules and counter NAD+-derived signals involved in viral restriction. Genes encoding NAD+-ADPr-utilizing domains were repeatedly exchanged between distantly related viruses, hosts and endo-parasites/symbionts, suggesting selection for them across the virus world. Contextual analysis indicates that the bacteriophage versions of ADPr-targeting domains are more likely to counter soluble ADPr derivatives, while the eukaryotic RNA viral versions might prefer macromolecular ADPr adducts. Finally, we also use comparative genomics to predict host systems involved in countering viral ADP ribosylation of host molecules.
Collapse
Affiliation(s)
| | | | | | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| |
Collapse
|
44
|
Alanazi F, Nour I, Hanif A, Al-Ashkar I, Aljowaie RM, Eifan S. Novel findings in context of molecular diversity and abundance of bacteriophages in wastewater environments of Riyadh, Saudi Arabia. PLoS One 2022; 17:e0273343. [PMID: 35980993 PMCID: PMC9387821 DOI: 10.1371/journal.pone.0273343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/05/2022] [Indexed: 11/18/2022] Open
Abstract
The diversity among bacteriophages depends on different factors like ecology, temperature conditions and genetic pool. Current study focused on isolation, identification and diversity of phages from 34 sewage water samples collected from two different wastewater treatment plants (WWTPs), King Saud University wastewater treatment plants (KSU-WWTP) and Manfoha wastewater treatment plants (MN-WWTP) in Riyadh, Saudi Arabia. Samples were analyzed by PCR and Next Generation Sequencing (NGS). Siphoviridae, Podoviridae and Myoviridae families were detected by family-specific PCR and highest prevalence of Myoviridae 29.40% was found at MN-WWTP followed by 11.76% at KSU-WWTP. Siphoviridae was detected 11.76% at MN-WWTP and 5.88% at KSU-WWTP. Lowest prevalence for Podoviridae family (5.88%) was recorded at MN-WWTP. Significant influence of temporal variations on prevalence of Myoviridae and Siphoviridae was detected in both WWTP and MN-WWTP, respectively. Highest phage prevalence was obtained in August (75%), followed by September (50%). Highest phage prevalence was recorded at a temperature range of 29–33°C. Significant influence of temperature on the prevalence of Myoviridae phages was detected at MN-WWTP. Four bacteriophages with various abundance levels were identified by NGS. Cronobacter virus Esp2949-1 was found first time with highest abundance (4.41%) in wastewater of Riyadh. Bordetella virus BPP1 (4.14%), Dickeya virus Limestone (1.55%) and Ralstonia virus RSA1 (1.04%) were also detected from samples of MN-WWTP. Highest occurrence of Bordetella virus BPP1 (67%) and (33.33%) was recorded at KSU-WWTP and MN-WWTP, respectively. Highest Bordetella virus BPP1 occurrence was recorded in September (50%) followed by August (40%). The findings of study showed new insights of phage diversity from wastewater sources and further large-scale data studies are suggested for comprehensive understanding.
Collapse
Affiliation(s)
- Fahad Alanazi
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Islam Nour
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Atif Hanif
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ibrahim Al-Ashkar
- Department of Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Reem M. Aljowaie
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh Eifan
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- * E-mail:
| |
Collapse
|
45
|
Rossi A, Morlino MS, Gaspari M, Basile A, Kougias P, Treu L, Campanaro S. Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction. MICROBIOME 2022; 10:125. [PMID: 35965344 PMCID: PMC9377139 DOI: 10.1186/s40168-022-01316-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-investigated. A viral induction experiment was conducted on separate batches undergoing a series of DNA-damaging stresses, in order to coerce temperate viruses to enter the lytic cycle. RESULTS The sequencing of the metagenome revealed a viral community almost entirely composed of tailed bacteriophages of the order Caudovirales. Following a binning procedure 1,092 viral and 120 prokaryotic genomes were reconstructed, 64 of which included an integrated prophage in their sequence. Clustering of coverage profiles revealed the presence of species, both viral and microbial, sharing similar reactions to shocks. A group of viral genomes, which increase under organic overload and decrease under basic pH, uniquely encode the yopX gene, which is involved in the induction of temperate prophages. Moreover, the in-silico functional analysis revealed an enrichment of sialidases in viral genomes. These genes are associated with tail proteins and, as such, are hypothesised to be involved in the interaction with the host. Archaea registered the most pronounced changes in relation to shocks and featured behaviours not shared with other species. Subsequently, data from 123 different samples of the global anaerobic digestion database was used to determine coverage profiles of host and viral genomes on a broader scale. CONCLUSIONS Viruses are key components in anaerobic digestion environments, shaping the microbial guilds which drive the methanogenesis process. In turn, environmental conditions are pivotal in shaping the viral community and the rate of induction of temperate viruses. This study provides an initial insight into the complexity of the anaerobic digestion virome and its relation with the microbial community and the diverse environmental parameters. Video Abstract.
Collapse
Affiliation(s)
- Alessandro Rossi
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Maria Gaspari
- Department of Hydraulics, Soil Science and Agricultural Engineering, Faculty of Agriculture, Aristotle University of Thessaloniki, GR-54124, Thessaloniki, Greece
| | - Arianna Basile
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| | - Panagiotis Kougias
- Soil and Water Resources Institute, Hellenic Agricultural Organisation Demeter, Thermi, 57001, Thessaloniki, Greece
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
- CRIBI biotechnology center, University of Padua, via U. Bassi 58/b, 35131, Padova, Italy
| |
Collapse
|
46
|
Interactions between Jumbo Phage SA1 and Staphylococcus: A Global Transcriptomic Analysis. Microorganisms 2022; 10:microorganisms10081590. [PMID: 36014008 PMCID: PMC9414953 DOI: 10.3390/microorganisms10081590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 01/21/2023] Open
Abstract
Staphylococcus aureus (S. aureus) is an important zoonotic pathogen that poses a serious health concern to humans and cattle worldwide. Although it has been proven that lytic phages may successfully kill S. aureus, the interaction between the host and the phage has yet to be thoroughly investigated, which will likely limit the clinical application of phage. Here, RNA sequencing (RNA-seq) was used to examine the transcriptomics of jumbo phage SA1 and Staphylococcus JTB1-3 during a high multiplicity of infection (MOI) and RT-qPCR was used to confirm the results. The RNA-seq analysis revealed that phage SA1 took over the transcriptional resources of the host cells and that the genes were categorized as early, middle, and late, based on the expression levels during infection. A minor portion of the resources of the host was employed to enable phage replication after infection because only 35.73% (997/2790) of the host genes were identified as differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the phage infection mainly affected the nucleotide metabolism, protein metabolism, and energy-related metabolism of the host. Moreover, the expression of the host genes involved in anti-phage systems, virulence, and drug resistance significantly changed during infection. This research gives a fresh understanding of the relationship between jumbo phages and their Gram-positive bacteria hosts and provides a reference for studying phage treatment and antibiotics.
Collapse
|
47
|
Aylward FO, Moniruzzaman M. Viral Complexity. Biomolecules 2022; 12:1061. [PMID: 36008955 PMCID: PMC9405923 DOI: 10.3390/biom12081061] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 12/18/2022] Open
Abstract
Although traditionally viewed as streamlined and simple, discoveries over the last century have revealed that viruses can exhibit surprisingly complex physical structures, genomic organization, ecological interactions, and evolutionary histories. Viruses can have physical dimensions and genome lengths that exceed many cellular lineages, and their infection strategies can involve a remarkable level of physiological remodeling of their host cells. Virus-virus communication and widespread forms of hyperparasitism have been shown to be common in the virosphere, demonstrating that dynamic ecological interactions often shape their success. And the evolutionary histories of viruses are often fraught with complexities, with chimeric genomes including genes derived from numerous distinct sources or evolved de novo. Here we will discuss many aspects of this viral complexity, with particular emphasis on large DNA viruses, and provide an outlook for future research.
Collapse
Affiliation(s)
- Frank O. Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, Blacksburg, VA 24061, USA
| | - Mohammad Moniruzzaman
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Coral Gables, FL 33149, USA;
| |
Collapse
|
48
|
Schulz F, Abergel C, Woyke T. Giant virus biology and diversity in the era of genome-resolved metagenomics. Nat Rev Microbiol 2022; 20:721-736. [PMID: 35902763 DOI: 10.1038/s41579-022-00754-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/09/2022]
Abstract
The discovery of giant viruses, with capsids as large as some bacteria, megabase-range genomes and a variety of traits typically found only in cellular organisms, was one of the most remarkable breakthroughs in biology. Until recently, most of our knowledge of giant viruses came from ~100 species-level isolates for which genome sequences were available. However, these isolates were primarily derived from laboratory-based co-cultivation with few cultured protists and algae and, thus, did not reflect the true diversity of giant viruses. Although virus co-cultures enabled valuable insights into giant virus biology, many questions regarding their origin, evolution and ecological importance remain unanswered. With advances in sequencing technologies and bioinformatics, our understanding of giant viruses has drastically expanded. In this Review, we summarize our understanding of giant virus diversity and biology based on viral isolates as laboratory cultivation has enabled extensive insights into viral morphology and infection strategies. We then explore how cultivation-independent approaches have heightened our understanding of the coding potential and diversity of the Nucleocytoviricota. We discuss how metagenomics has revolutionized our perspective of giant viruses by revealing their distribution across our planet's biomes, where they impact the biology and ecology of a wide range of eukaryotic hosts and ultimately affect global nutrient cycles.
Collapse
Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Chantal Abergel
- Aix Marseille University, CNRS, IGS UMR7256, IMM FR3479, IM2B, IO, Marseille, France
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,University of California Merced, Merced, CA, USA.
| |
Collapse
|
49
|
Albrycht K, Rynkiewicz AA, Harasymczuk M, Barylski J, Zielezinski A. Daily Reports on Phage-Host Interactions. Front Microbiol 2022; 13:946070. [PMID: 35910653 PMCID: PMC9329054 DOI: 10.3389/fmicb.2022.946070] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding phage-host relationships is crucial for the study of virus biology and the application of phages in biotechnology and medicine. However, information concerning the range of hosts for bacterial and archaeal viruses is scattered across numerous databases and is difficult to obtain. Therefore, here we present PHD (Phage & Host Daily), a web application that offers a comprehensive, up-to-date catalog of known phage-host associations that allows users to select viruses targeting specific bacterial and archaeal taxa of interest. Our service combines the latest information on virus-host interactions from seven source databases with current taxonomic classification retrieved directly from the groups and institutions responsible for its maintenance. The web application also provides summary statistics on host and virus diversity, their pairwise interactions, and the host range of deposited phages. PHD is updated daily and available at http://phdaily.info or http://combio.pl/phdaily.
Collapse
Affiliation(s)
- Kamil Albrycht
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Adam A. Rynkiewicz
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Michal Harasymczuk
- Department of Traumatology, Orthopaedics and Hand Surgery, University of Medical Sciences, Poznan, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Andrzej Zielezinski
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| |
Collapse
|
50
|
Queiroz VF, Rodrigues RAL, Boratto PVDM, La Scola B, Andreani J, Abrahão JS. Amoebae: Hiding in Plain Sight: Unappreciated Hosts for the Very Large Viruses. Annu Rev Virol 2022; 9:79-98. [DOI: 10.1146/annurev-virology-100520-125832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For decades, viruses have been isolated primarily from humans and other organisms. Interestingly, one of the most complex sides of the virosphere was discovered using free-living amoebae as hosts. The discovery of giant viruses in the early twenty-first century opened a new chapter in the field of virology. Giant viruses are included in the phylum Nucleocytoviricota and harbor large and complex DNA genomes (up to 2.7 Mb) encoding genes never before seen in the virosphere and presenting gigantic particles (up to 1.5 μm). Different amoebae have been used to isolate and characterize a plethora of new viruses with exciting details about novel viral biology. Through distinct isolation techniques and metagenomics, the diversity and complexity of giant viruses have astonished the scientific community. Here, we discuss the latest findings on amoeba viruses and how using these single-celled organisms as hosts has revealed entities that have remained hidden in plain sight for ages. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Victória Fulgêncio Queiroz
- Laboratório de Vírus, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Araújo Lima Rodrigues
- Laboratório de Vírus, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Bernard La Scola
- Department of Microbes, Evolution, Phylogeny and Infection, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Julien Andreani
- Department of Microbes, Evolution, Phylogeny and Infection, Institut de Recherche pour le Développement, Assistance Publique-Hôpitaux de Marseille, Aix-Marseille Université, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Laboratoire de Virologie, Centre Hospitalier Universitaire Grenoble-Alpes, Grenoble, France
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|