151
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Bueren EK, Weinheimer AR, Aylward FO, Hsu BB, Haak DC, Belden LK. Characterization of prophages in bacterial genomes from the honey bee ( Apis mellifera) gut microbiome. PeerJ 2023; 11:e15383. [PMID: 37312882 PMCID: PMC10259446 DOI: 10.7717/peerj.15383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/18/2023] [Indexed: 06/15/2023] Open
Abstract
The gut of the European honey bee (Apis mellifera) possesses a relatively simple bacterial community, but little is known about its community of prophages (temperate bacteriophages integrated into the bacterial genome). Although prophages may eventually begin replicating and kill their bacterial hosts, they can also sometimes be beneficial for their hosts by conferring protection from other phage infections or encoding genes in metabolic pathways and for toxins. In this study, we explored prophages in 17 species of core bacteria in the honey bee gut and two honey bee pathogens. Out of the 181 genomes examined, 431 putative prophage regions were predicted. Among core gut bacteria, the number of prophages per genome ranged from zero to seven and prophage composition (the compositional percentage of each bacterial genome attributable to prophages) ranged from 0 to 7%. Snodgrassella alvi and Gilliamella apicola had the highest median prophages per genome (3.0 ± 1.46; 3.0 ± 1.59), as well as the highest prophage composition (2.58% ± 1.4; 3.0% ± 1.59). The pathogen Paenibacillus larvae had a higher median number of prophages (8.0 ± 5.33) and prophage composition (6.40% ± 3.08) than the pathogen Melissococcus plutonius or any of the core bacteria. Prophage populations were highly specific to their bacterial host species, suggesting most prophages were acquired recently relative to the divergence of these bacterial groups. Furthermore, functional annotation of the predicted genes encoded within the prophage regions indicates that some prophages in the honey bee gut encode additional benefits to their bacterial hosts, such as genes in carbohydrate metabolism. Collectively, this survey suggests that prophages within the honey bee gut may contribute to the maintenance and stability of the honey bee gut microbiome and potentially modulate specific members of the bacterial community, particularly S. alvi and G. apicola.
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Affiliation(s)
- Emma K. Bueren
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Alaina R. Weinheimer
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Bryan B. Hsu
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - David C. Haak
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
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152
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Štrancar V, Marušić M, Tušar J, Praček N, Kolenc M, Šuster K, Horvat S, Janež N, Peterka M. Isolation and in vitro characterization of novel S. epidermidis phages for therapeutic applications. Front Cell Infect Microbiol 2023; 13:1169135. [PMID: 37293203 PMCID: PMC10244729 DOI: 10.3389/fcimb.2023.1169135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
S. epidermidis is an important opportunistic pathogen causing chronic prosthetic joint infections associated with biofilm growth. Increased tolerance to antibiotic therapy often requires prolonged treatment or revision surgery. Phage therapy is currently used as compassionate use therapy and continues to be evaluated for its viability as adjunctive therapy to antibiotic treatment or as an alternative treatment for infections caused by S. epidermidis to prevent relapses. In the present study, we report the isolation and in vitro characterization of three novel lytic S. epidermidis phages. Their genome content analysis indicated the absence of antibiotic resistance genes and virulence factors. Detailed investigation of the phage preparation indicated the absence of any prophage-related contamination and demonstrated the importance of selecting appropriate hosts for phage development from the outset. The isolated phages infect a high proportion of clinically relevant S. epidermidis strains and several other coagulase-negative species growing both in planktonic culture and as a biofilm. Clinical strains differing in their biofilm phenotype and antibiotic resistance profile were selected to further identify possible mechanisms behind increased tolerance to isolated phages.
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Affiliation(s)
- Vida Štrancar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Monika Marušić
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Jasmina Tušar
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Neža Praček
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Marko Kolenc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Šuster
- Valdoltra Orthopaedic Hospital, Ankaran, Slovenia
| | - Simon Horvat
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Nika Janež
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
| | - Matjaž Peterka
- Centre of Excellence for Biosensors, Instrumentation and Process Control, Ajdovščina, Slovenia
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153
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Arnau V, Díaz-Villanueva W, Mifsut Benet J, Villasante P, Beamud B, Mompó P, Sanjuan R, González-Candelas F, Domingo-Calap P, Džunková M. Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts. Viruses 2023; 15:v15051196. [PMID: 37243281 DOI: 10.3390/v15051196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids.
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Affiliation(s)
- Vicente Arnau
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), 46980 Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
| | - Wladimiro Díaz-Villanueva
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), 46980 Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
| | - Jorge Mifsut Benet
- Department of Space, Earth and Environment, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | | | - Beatriz Beamud
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), 46980 Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
| | - Paula Mompó
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
| | - Rafael Sanjuan
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), 46980 Valencia, Spain
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), 46980 Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), 46980 Valencia, Spain
| | - Mária Džunková
- Institute for Integrative Systems Biology, University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), 46980 Valencia, Spain
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154
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Lamy-Besnier Q, Bignaud A, Garneau JR, Titecat M, Conti DE, Von Strempel A, Monot M, Stecher B, Koszul R, Debarbieux L, Marbouty M. Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria. MICROBIOME 2023; 11:111. [PMID: 37208714 PMCID: PMC10197239 DOI: 10.1186/s40168-023-01541-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/04/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Bacteria and their viruses, bacteriophages, are the most abundant entities of the gut microbiota, a complex community of microorganisms associated with human health and disease. In this ecosystem, the interactions between these two key components are still largely unknown. In particular, the impact of the gut environment on bacteria and their associated prophages is yet to be deciphered. RESULTS To gain insight into the activity of lysogenic bacteriophages within the context of their host genomes, we performed proximity ligation-based sequencing (Hi-C) in both in vitro and in vivo conditions on the 12 bacterial strains of the OMM12 synthetic bacterial community stably associated within mice gut (gnotobiotic mouse line OMM12). High-resolution contact maps of the chromosome 3D organization of the bacterial genomes revealed a wide diversity of architectures, differences between environments, and an overall stability over time in the gut of mice. The DNA contacts pointed at 3D signatures of prophages leading to 16 of them being predicted as functional. We also identified circularization signals and observed different 3D patterns between in vitro and in vivo conditions. Concurrent virome analysis showed that 11 of these prophages produced viral particles and that OMM12 mice do not carry other intestinal viruses. CONCLUSIONS The precise identification by Hi-C of functional and active prophages within bacterial communities will unlock the study of interactions between bacteriophages and bacteria across conditions (healthy vs disease). Video Abstract.
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Affiliation(s)
- Quentin Lamy-Besnier
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Amaury Bignaud
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Julian R Garneau
- Institut Pasteur, Université Paris Cité, Plate-Forme Technologique Biomics, 75015, Paris, France
| | - Marie Titecat
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France
- Université de Lille, INSERM, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, Lille, 59000, France
| | - Devon E Conti
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Alexandra Von Strempel
- Max Von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Marc Monot
- Institut Pasteur, Université Paris Cité, Plate-Forme Technologique Biomics, 75015, Paris, France
| | - Bärbel Stecher
- Max Von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site LMU Munich, Munich, Germany
| | - Romain Koszul
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, 25-28 Rue du Dr Roux, 75015, Paris, France.
| | - Martial Marbouty
- Institut Pasteur, Université Paris Cité, Spatial Regulation of Genomes Group, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015, Paris, France.
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155
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Michelle JiaMin L, Mutusamy P, Karthikeyan P, Kumaresan R, Millard A, Parimannan S, Rajandas H. Genome Characterization of Enterococcus faecalis Bacteriophage EFKL. Microbiol Resour Announc 2023:e0016023. [PMID: 37133380 DOI: 10.1128/mra.00160-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
We characterized the complete genome of the lytic Enterococcus faecalis phage EFKL, which was isolated from a sewage treatment plant in Kuala Lumpur, Malaysia. The phage, which was classified in the genus Saphexavirus, has a 58,343-bp double-stranded DNA genome containing 97 protein-encoding genes and shares 80.60% nucleotide similarity with Enterococcus phage EF653P5 and Enterococcus phage EF653P3.
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Affiliation(s)
- Loh Michelle JiaMin
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | - Prasanna Mutusamy
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | | | | | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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156
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Flamholz ZN, Biller SJ, Kelly L. Large language models improve annotation of viral proteins. RESEARCH SQUARE 2023:rs.3.rs-2852098. [PMID: 37205395 PMCID: PMC10187409 DOI: 10.21203/rs.3.rs-2852098/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Viral sequences are poorly annotated in environmental samples, a major roadblock to understanding how viruses influence microbial community structure. Current annotation approaches rely on alignment-based sequence ho-mology methods, which are limited by available viral sequences and sequence divergence in viral proteins. Here, we show that protein language model representations capture viral protein function beyond the limits of remote sequence homology by targeting two axes of viral sequence annotation: systematic labeling of protein families and function identification for biologic discovery. Protein language model representations capture protein functional properties specific to viruses and expand the annotated fraction of ocean virome viral protein sequences by 37%. Among unannotated viral protein families, we identify a novel DNA editing protein family that defines a new mobile element in marine picocyanobacteria. Protein language models thus significantly enhance remote homology detection of viral proteins and can be utilized to enable new biological discovery across diverse functional categories.
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Affiliation(s)
- Zachary N. Flamholz
- Department of Systems and Computational Biology, Albert Einstein College of Medicine; Bronx, NY, USA
| | - Steve J. Biller
- Department of Biological Sciences, Wellesley College; Wellesley, MA USA
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine; Bronx, NY, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine; Bronx, NY, USA
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157
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Bakuradze N, Merabishvili M, Kusradze I, Ceyssens PJ, Onsea J, Metsemakers WJ, Grdzelishvili N, Natroshvili G, Tatrishvili T, Lazvliashvili D, Mitskevich N, Pirnay JP, Chanishvili N. Characterization of a Bacteriophage GEC_vB_Bfr_UZM3 Active against Bacteroides fragilis. Viruses 2023; 15:v15051042. [PMID: 37243129 DOI: 10.3390/v15051042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/15/2023] [Accepted: 04/15/2023] [Indexed: 05/28/2023] Open
Abstract
Bacteroides fragilis is a commensal gut bacterium that is associated with a number of blood and tissue infections. It has not yet been recognized as one of the drug-resistant human pathogens, but cases of the refractory infections, caused by strains that are not susceptible to the common antibiotic regimes established for B. fragilis, have been more frequently reported. Bacteriophages (phages) were found to be a successful antibacterial alternative to antibiotic therapy in many cases of multidrug-resistant (MDR) bacterial infections. We have characterized the bacteriophage GEC_vB_Bfr_UZM3 (UZM3), which was used for the treatment of a patient with a chronic osteomyelitis caused by a B. fragilis mixed infection. Studied biological and morphological properties of UZM3 showed that it seems to represent a strictly lytic phage belonging to a siphovirus morphotype. It is characterized by high stability at body temperature and in pH environments for about 6 h. Whole genome sequencing analysis of the phage UZM3 showed that it does not harbor any known virulence genes and can be considered as a potential therapeutic phage to be used against B. fragilis infections.
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Affiliation(s)
- Nata Bakuradze
- Laboratory of Microbial Biotechnology, Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi 0160, Georgia
- Department of Biology, Faculty of Exact and Natural Sciences, Javakhishvili Tbilisi State University, Tbilisi 0179, Georgia
- AIETI Medical School, Davit Tvildiani Medical University, Tbilisi 0159, Georgia
| | - Maia Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium
| | - Ia Kusradze
- Laboratory of General Microbiology, Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi 0160, Georgia
- Faculty of Medicine, European University, Tbilisi 0141, Georgia
| | | | - Jolien Onsea
- Department of Trauma Surgery, University Hospitals Leuven, 3000 Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Willem-Jan Metsemakers
- Department of Trauma Surgery, University Hospitals Leuven, 3000 Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Nino Grdzelishvili
- Laboratory of Microbial Biotechnology, Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi 0160, Georgia
- Faculty of Natural Science and Medicine, Ilia State University, Tbilisi 0162, Georgia
| | - Guliko Natroshvili
- Laboratory of Microbial Biotechnology, Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi 0160, Georgia
| | - Tamar Tatrishvili
- Laboratory of Microbial Biotechnology, Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi 0160, Georgia
- Faculty of Natural Science and Medicine, Ilia State University, Tbilisi 0162, Georgia
| | - Davit Lazvliashvili
- Laboratory of Microbial Biotechnology, Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi 0160, Georgia
- Faculty of Natural Science and Medicine, Ilia State University, Tbilisi 0162, Georgia
| | - Nunu Mitskevich
- Department of Biology, Faculty of Exact and Natural Sciences, Javakhishvili Tbilisi State University, Tbilisi 0179, Georgia
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium
| | - Nina Chanishvili
- Laboratory of Microbial Biotechnology, Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi 0160, Georgia
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158
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Moraru C. VirClust-A Tool for Hierarchical Clustering, Core Protein Detection and Annotation of ( Prokaryotic) Viruses. Viruses 2023; 15:v15041007. [PMID: 37112988 PMCID: PMC10143988 DOI: 10.3390/v15041007] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called "megataxonomy of viruses", recognizes six different viral realms, defined based on the presence of viral hallmark genes (VHGs). Within the realms, viruses are classified into hierarchical taxons, ideally defined by the phylogeny of their shared genes. To enable the detection of shared genes, viruses have first to be clustered, and there is currently a need for tools to assist with virus clustering and classification. Here, VirClust is presented. It is a novel, reference-free tool capable of performing: (i) protein clustering, based on BLASTp and Hidden Markov Models (HMMs) similarities; (ii) hierarchical clustering of viruses based on intergenomic distances calculated from their shared protein content; (iii) identification of core proteins and (iv) annotation of viral proteins. VirClust has flexible parameters both for protein clustering and for splitting the viral genome tree into smaller genome clusters, corresponding to different taxonomic levels. Benchmarking on a phage dataset showed that the genome trees produced by VirClust match the current ICTV classification at family, sub-family and genus levels. VirClust is freely available, as a web-service and stand-alone tool.
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Affiliation(s)
- Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky-Str. 9-11, 26111 Oldenburg, Germany
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159
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Shah SA, Deng L, Thorsen J, Pedersen AG, Dion MB, Castro-Mejía JL, Silins R, Romme FO, Sausset R, Jessen LE, Ndela EO, Hjelmsø M, Rasmussen MA, Redgwell TA, Leal Rodríguez C, Vestergaard G, Zhang Y, Chawes B, Bønnelykke K, Sørensen SJ, Bisgaard H, Enault F, Stokholm J, Moineau S, Petit MA, Nielsen DS. Expanding known viral diversity in the healthy infant gut. Nat Microbiol 2023; 8:986-998. [PMID: 37037943 PMCID: PMC10159846 DOI: 10.1038/s41564-023-01345-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/17/2023] [Indexed: 04/12/2023]
Abstract
The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother-child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.
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Affiliation(s)
- Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark.
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders G Pedersen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Moïra B Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
| | | | - Ronalds Silins
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Fie O Romme
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Romain Sausset
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Leon E Jessen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Eric Olo Ndela
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mathis Hjelmsø
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Morten A Rasmussen
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Tamsin A Redgwell
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Cristina Leal Rodríguez
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Gisle Vestergaard
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Yichang Zhang
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Francois Enault
- Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Quebec, Canada
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark.
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160
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Hwang Y, Roux S, Coclet C, Krause SJE, Girguis PR. Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats. Nat Microbiol 2023; 8:946-957. [PMID: 37024618 PMCID: PMC10159854 DOI: 10.1038/s41564-023-01347-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/25/2023] [Indexed: 04/08/2023]
Abstract
Many microbes in nature reside in dense, metabolically interdependent communities. We investigated the nature and extent of microbe-virus interactions in relation to microbial density and syntrophy by examining microbe-virus interactions in a biomass dense, deep-sea hydrothermal mat. Using metagenomic sequencing, we find numerous instances where phylogenetically distant (up to domain level) microbes encode CRISPR-based immunity against the same viruses in the mat. Evidence of viral interactions with hosts cross-cutting microbial domains is particularly striking between known syntrophic partners, for example those engaged in anaerobic methanotrophy. These patterns are corroborated by proximity-ligation-based (Hi-C) inference. Surveys of public datasets reveal additional viruses interacting with hosts across domains in diverse ecosystems known to harbour syntrophic biofilms. We propose that the entry of viral particles and/or DNA to non-primary host cells may be a common phenomenon in densely populated ecosystems, with eco-evolutionary implications for syntrophic microbes and CRISPR-mediated inter-population augmentation of resilience against viruses.
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Affiliation(s)
- Yunha Hwang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Simon Roux
- DOE (Department of Energy) Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Clément Coclet
- DOE (Department of Energy) Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sebastian J E Krause
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, CA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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161
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Newberry F, Shibu P, Smith-Zaitlik T, Eladawy M, McCartney AL, Hoyles L, Negus D. Lytic bacteriophage vB_KmiS-Kmi2C disrupts biofilms formed by members of the Klebsiella oxytoca complex, and represents a novel virus family and genus. J Appl Microbiol 2023; 134:lxad079. [PMID: 37070958 DOI: 10.1093/jambio/lxad079] [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: 01/13/2023] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
AIMS This study aimed to characterize the lytic phage vB_KmiS-Kmi2C, isolated from sewage water on a GES-positive strain of Klebsiella michiganensis. METHODS AND RESULTS Comparative phylogenetic and network-based analyses were used to characterize the genome of phage vB_KmiS-Kmi2C (circular genome of 42 234 bp predicted to encode 55 genes), demonstrating it shared little similarity with other known phages. The phage was lytic on clinical strains of K. oxytoca (n = 2) and K. michiganensis (n = 4), and was found to both prevent biofilm formation and disrupt established biofilms produced by these strains. CONCLUSIONS We have identified a phage capable of killing clinically relevant members of the K. oxytoca complex (KoC). The phage represents a novel virus family (proposed name Dilsviridae) and genus (proposed name Dilsvirus).
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Affiliation(s)
- Fiona Newberry
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Preetha Shibu
- Life Sciences, University of Westminster, W1W 6UW, UK
| | - Thomas Smith-Zaitlik
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Mohamed Eladawy
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
- Microbiology and Immunology Department, Faculty of Pharmacy, Mansoura University, Egypt
| | - Anne L McCartney
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - David Negus
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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162
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Jenson JM, Li T, Du F, Ea CK, Chen ZJ. Ubiquitin-like conjugation by bacterial cGAS enhances anti-phage defence. Nature 2023; 616:326-331. [PMID: 36848932 PMCID: PMC10097602 DOI: 10.1038/s41586-023-05862-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 02/17/2023] [Indexed: 03/01/2023]
Abstract
cGAS is an evolutionarily conserved enzyme that has a pivotal role in immune defence against infection1-3. In vertebrate animals, cGAS is activated by DNA to produce cyclic GMP-AMP (cGAMP)4,5, which leads to the expression of antimicrobial genes6,7. In bacteria, cyclic dinucleotide (CDN)-based anti-phage signalling systems (CBASS) have been discovered8-11. These systems are composed of cGAS-like enzymes and various effector proteins that kill bacteria on phage infection, thereby stopping phage spread. Of the CBASS systems reported, approximately 39% contain Cap2 and Cap3, which encode proteins with homology to ubiquitin conjugating (E1/E2) and deconjugating enzymes, respectively8,12. Although these proteins are required to prevent infection of some bacteriophages8, the mechanism by which the enzymatic activities exert an anti-phage effect is unknown. Here we show that Cap2 forms a thioester bond with the C-terminal glycine of cGAS and promotes conjugation of cGAS to target proteins in a process that resembles ubiquitin conjugation. The covalent conjugation of cGAS increases the production of cGAMP. Using a genetic screen, we found that the phage protein Vs.4 antagonized cGAS signalling by binding tightly to cGAMP (dissociation constant of approximately 30 nM) and sequestering it. A crystal structure of Vs.4 bound to cGAMP showed that Vs.4 formed a hexamer that was bound to three molecules of cGAMP. These results reveal a ubiquitin-like conjugation mechanism that regulates cGAS activity in bacteria and illustrates an arms race between bacteria and viruses through controlling CDN levels.
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Affiliation(s)
- Justin M Jenson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tuo Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Fenghe Du
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chee-Kwee Ea
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhijian J Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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163
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Sharma V, Hünnefeld M, Luthe T, Frunzke J. Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity. Sci Rep 2023; 13:4410. [PMID: 36932119 PMCID: PMC10023795 DOI: 10.1038/s41598-023-30829-z] [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: 06/25/2022] [Accepted: 03/02/2023] [Indexed: 03/19/2023] Open
Abstract
Actinobacteria represent one of the largest bacterial phyla harboring many species of high medical, biotechnological and ecological relevance. Prophage elements are major contributors to bacterial genome diversity and were shown to significantly shape bacterial fitness and host-microbe interactions. In this study, we performed a systematic analysis of prophage elements in 2406 complete actinobacterial genomes. Overall, 2106 prophage elements were predicted to be present in about 50% (1172/2406) of the analyzed datasets. Interestingly, these identified sequences compose a high prevalence of cryptic prophage elements, indicating genetic decay and domestication. Analysis of the sequence relationship of predicted prophages with known actinobacteriophage genomes revealed an exceptional high phylogenetic diversity of prophage elements. As a trend, we observed a higher prevalence of prophage elements in vicinity to the terminus. Analysis of the prophage-encoded gene functions revealed that prophage sequences significantly contribute to the bacterial antiviral immune system, but no biosynthetic gene clusters involved in the synthesis of known antiphage molecules were identified in prophage genomes. Overall, the current study highlights the remarkable diversity of prophages in actinobacterial genomes, with highly divergent prophages in actinobacterial genomes and thus provides an important basis for further investigation of phage-host interactions in this important bacterial phylum.
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Affiliation(s)
- Vikas Sharma
- Institute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany.
| | - Max Hünnefeld
- Institute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Tom Luthe
- Institute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany.
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164
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Nyerges A, Vinke S, Flynn R, Owen SV, Rand EA, Budnik B, Keen E, Narasimhan K, Marchand JA, Baas-Thomas M, Liu M, Chen K, Chiappino-Pepe A, Hu F, Baym M, Church GM. A swapped genetic code prevents viral infections and gene transfer. Nature 2023; 615:720-727. [PMID: 36922599 PMCID: PMC10151025 DOI: 10.1038/s41586-023-05824-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 02/10/2023] [Indexed: 03/17/2023]
Abstract
Engineering the genetic code of an organism has been proposed to provide a firewall from natural ecosystems by preventing viral infections and gene transfer1-6. However, numerous viruses and mobile genetic elements encode parts of the translational apparatus7-9, potentially rendering a genetic-code-based firewall ineffective. Here we show that such mobile transfer RNAs (tRNAs) enable gene transfer and allow viral replication in Escherichia coli despite the genome-wide removal of 3 of the 64 codons and the previously essential cognate tRNA and release factor genes. We then establish a genetic firewall by discovering viral tRNAs that provide exceptionally efficient codon reassignment allowing us to develop cells bearing an amino acid-swapped genetic code that reassigns two of the six serine codons to leucine during translation. This amino acid-swapped genetic code renders cells resistant to viral infections by mistranslating viral proteomes and prevents the escape of synthetic genetic information by engineered reliance on serine codons to produce leucine-requiring proteins. As these cells may have a selective advantage over wild organisms due to virus resistance, we also repurpose a third codon to biocontain this virus-resistant host through dependence on an amino acid not found in nature10. Our results may provide the basis for a general strategy to make any organism safely resistant to all natural viruses and prevent genetic information flow into and out of genetically modified organisms.
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Affiliation(s)
- Akos Nyerges
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Svenja Vinke
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Regan Flynn
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Siân V Owen
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eleanor A Rand
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bogdan Budnik
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Eric Keen
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St Louis, MO, USA
| | | | - Jorge A Marchand
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | | | - Min Liu
- GenScript USA Inc., Piscataway, NJ, USA
| | | | | | | | - Michael Baym
- Department of Biomedical Informatics and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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165
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Wu J, Liu Q, Li M, Xu J, Wang C, Zhang J, Xiao M, Bin Y, Xia J. PhaGAA: an integrated web server platform for phage genome annotation and analysis. Bioinformatics 2023; 39:7070502. [PMID: 36882183 PMCID: PMC10013646 DOI: 10.1093/bioinformatics/btad120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
MOTIVATION Phage genome annotation plays a key role in the design of phage therapy. To date, there have been various genome annotation tools for phages, but most of these tools focus on mono-functional annotation and have complex operational processes. Accordingly, comprehensive and user-friendly platforms for phage genome annotation are needed. RESULTS Here, we propose PhaGAA, an online integrated platform for phage genome annotation and analysis. By incorporating several annotation tools, PhaGAA is constructed to annotate the prophage genome at DNA and protein levels and provide the analytical results. Furthermore, PhaGAA could mine and annotate phage genomes from bacterial genome or metagenome. In summary, PhaGAA will be a useful resource for experimental biologists and help advance the phage synthetic biology in basic and application research. AVAILABILITY AND IMPLEMENTATION PhaGAA is freely available at http://phage.xialab.info/.
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Affiliation(s)
- Jiawei Wu
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, and Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Qingrui Liu
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, and Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Min Li
- BGI-Shenzhen, Shenzhen 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiliang Xu
- School of Computer Science and Technology, Anhui University, Hefei, Anhui 230601, China
| | - Chen Wang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, and Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Junyin Zhang
- School of Computer Science and Technology, Anhui University, Hefei, Anhui 230601, China
| | - Minfeng Xiao
- BGI-Shenzhen, Shenzhen 518083, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Yannan Bin
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, and Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Junfeng Xia
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, and Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
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166
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Beamud B, García-González N, Gómez-Ortega M, González-Candelas F, Domingo-Calap P, Sanjuan R. Genetic determinants of host tropism in Klebsiella phages. Cell Rep 2023; 42:112048. [PMID: 36753420 PMCID: PMC9989827 DOI: 10.1016/j.celrep.2023.112048] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/25/2022] [Accepted: 01/13/2023] [Indexed: 02/08/2023] Open
Abstract
Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates of Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show a narrow host range for most phages, with <2% of 6,319 phage-host combinations tested yielding detectable interactions. Bacterial capsule diversity is the main factor restricting phage host range. Consequently, phage-encoded depolymerases are key determinants of host tropism, and depolymerase sequence types are associated with the ability to infect specific capsular types across phage families. However, all phages with a broader host range found do not encode canonical depolymerases, suggesting alternative modes of entry. These findings expand our knowledge of the complex interactions between bacteria and their viruses and point out the feasibility of predicting the first steps of phage infection using bacterial and phage genome sequences.
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Affiliation(s)
- Beatriz Beamud
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Neris García-González
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Mar Gómez-Ortega
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
| | - Rafael Sanjuan
- Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
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167
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PCR Assay for Rapid Taxonomic Differentiation of Virulent Staphylococcus aureus and Klebsiella pneumoniae Bacteriophages. Int J Mol Sci 2023; 24:ijms24054483. [PMID: 36901913 PMCID: PMC10003202 DOI: 10.3390/ijms24054483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Phage therapy is now seen as a promising way to overcome the current global crisis in the spread of multidrug-resistant bacteria. However, phages are highly strain-specific, and in most cases one will have to isolate a new phage or search for a phage suitable for a therapeutic application in existing libraries. At an early stage of the isolation process, rapid screening techniques are needed to identify and type potential virulent phages. Here, we propose a simple PCR approach to differentiate between two families of virulent Staphylococcus phages (Herelleviridae and Rountreeviridae) and eleven genera of virulent Klebsiella phages (Przondovirus, Taipeivirus, Drulisvirus, Webervirus, Jiaodavirus, Sugarlandvirus, Slopekvirus, Jedunavirus, Marfavirus, Mydovirus and Yonseivirus). This assay includes a thorough search of a dataset comprising S. aureus (n = 269) and K. pneumoniae (n = 480) phage genomes available in the NCBI RefSeq/GenBank database for specific genes that are highly conserved at the taxonomic group level. The selected primers showed high sensitivity and specificity for both isolated DNA and crude phage lysates, which permits circumventing DNA purification protocols. Our approach can be extended and applied to any group of phages, given the large number of available genomes in the databases.
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168
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Oliveira LS, Reyes A, Dutilh BE, Gruber A. Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons. Viruses 2023; 15:519. [PMID: 36851733 PMCID: PMC9966878 DOI: 10.3390/v15020519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Profile hidden Markov models (HMMs) are a powerful way of modeling biological sequence diversity and constitute a very sensitive approach to detecting divergent sequences. Here, we report the development of protocols for the rational design of profile HMMs. These methods were implemented on TABAJARA, a program that can be used to either detect all biological sequences of a group or discriminate specific groups of sequences. By calculating position-specific information scores along a multiple sequence alignment, TABAJARA automatically identifies the most informative sequence motifs and uses them to construct profile HMMs. As a proof-of-principle, we applied TABAJARA to generate profile HMMs for the detection and classification of two viral groups presenting different evolutionary rates: bacteriophages of the Microviridae family and viruses of the Flavivirus genus. We obtained conserved models for the generic detection of any Microviridae or Flavivirus sequence, and profile HMMs that can specifically discriminate Microviridae subfamilies or Flavivirus species. In another application, we constructed Cas1 endonuclease-derived profile HMMs that can discriminate CRISPRs and casposons, two evolutionarily related transposable elements. We believe that the protocols described here, and implemented on TABAJARA, constitute a generic toolbox for generating profile HMMs for the highly sensitive and specific detection of sequence classes.
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Affiliation(s)
- Liliane S. Oliveira
- Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743 Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Arthur Gruber
- Department of Parasitology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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169
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Kosmopoulos JC, Campbell DE, Whitaker RJ, Wilbanks EG. Horizontal gene transfer and CRISPR targeting drive phage-bacterial host interactions and coevolution in pink berry marine microbial aggregates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527410. [PMID: 36798152 PMCID: PMC9934561 DOI: 10.1101/2023.02.06.527410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Bacteriophages (phages), viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. The study of phage-host interactions, however, is made difficult by a paucity of model systems from natural environments and known and cultivable phage-host pairs. Here, we investigate phage-host interactions in the "pink berry" consortia, naturally-occurring, low-diversity, macroscopic aggregates of bacteria found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPR), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect the known pink berry symbionts Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and belong to entirely novel viral taxa, except for one genome which represents the second member of the Knuthellervirus genus. We further observed increased nucleotide variation over a region of a conserved phage capsid gene that is commonly targeted by host CRISPR systems, suggesting that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary, emphasizing the role of phages in bacterial evolution in pink berries. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages, and provide evidence for phage-host co-evolution via multiple mechanisms in a natural microbial system. IMPORTANCE Phages (viruses that infect bacteria) are important components of all microbial systems, where they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and co-evolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms are CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate bacteria and phage populations from a simple marine microbial community known as "pink berries" found in salt marshes of Falmouth, Massachusetts, as a model of phage-host co-evolution. We identify eight novel phages, and characterize a case of putative CRISPR-driven phage evolution and an instance of HGT between phage and host, together suggesting that phages have large evolutionary impacts in a naturally-occuring microbial community.
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Affiliation(s)
- James C. Kosmopoulos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbial Diversity 2020, University of Chicago Marine Biological Laboratory, Woods Hole, MA, USA
| | - Danielle E. Campbell
- Microbial Diversity 2020, University of Chicago Marine Biological Laboratory, Woods Hole, MA, USA
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Address correspondence to or
| | - Rachel J. Whitaker
- Microbial Diversity 2020, University of Chicago Marine Biological Laboratory, Woods Hole, MA, USA
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - Elizabeth G. Wilbanks
- Microbial Diversity 2020, University of Chicago Marine Biological Laboratory, Woods Hole, MA, USA
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, California, USA
- Address correspondence to or
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170
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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: 9] [Impact Index Per Article: 4.5] [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.
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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,
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171
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Billaud M, Petit MA, Lossouarn J. The Clostridium-infecting filamentous phage CAK1 genome analysis allows to define a new potential clade of Tubulavirales. FEMS Microbiol Lett 2023; 370:fnad099. [PMID: 37791400 DOI: 10.1093/femsle/fnad099] [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: 07/27/2023] [Revised: 09/21/2023] [Accepted: 10/02/2023] [Indexed: 10/05/2023] Open
Abstract
What we know about Tubulavirales, i.e. filamentous phages, essentially comes from Gram-negative-infecting Inoviridae. However, metagenomics recently suggests filamentous phages are much more widespread and diverse. Here, we report the complete sequence and functional annotation of CAK1, a 6.6 kb filamentous phage that was shown to chronically infect Clostridium beijerinckii 30 years ago and only represents the second filamentous phage cultivated on a Gram-positive bacterium. CAK1 has a typical filamentous phage modular genome with no homologs in databases and we were interested to compare it with a pig gut filamentous phage metagenomics dataset that we previously assembled and for which many filamentous phages were predicted to infect Clostridium species by bioinformatics means. CAK1 is distantly related to nine of these sequences, two of which have been predicted as Clostridium-associated. In itself, this small cluster of CAK1-connected sequences sheds light on the diversity of filamentous phages that putatively infect Clostridium species, and probably many other Gram-positive genera.
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Affiliation(s)
- Maud Billaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
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172
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Bouras G, Nepal R, Houtak G, Psaltis AJ, Wormald PJ, Vreugde S. Pharokka: a fast scalable bacteriophage annotation tool. Bioinformatics 2023; 39:6858464. [PMID: 36453861 PMCID: PMC9805569 DOI: 10.1093/bioinformatics/btac776] [Citation(s) in RCA: 174] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/20/2022] [Accepted: 11/30/2022] [Indexed: 12/04/2022] Open
Abstract
SUMMARY In recent years, there has been an increasing interest in bacteriophages, which has led to growing numbers of bacteriophage genomic sequences becoming available. Consequently, there is a need for a rapid and consistent genomic annotation tool dedicated for bacteriophages. Existing tools either are not designed specifically for bacteriophages or are web- and email-based and require significant manual curation, which makes their integration into bioinformatic pipelines challenging. Pharokka was created to provide a tool that annotates bacteriophage genomes easily, rapidly and consistently with standards compliant outputs. Moreover, Pharokka requires only two lines of code to install and use and takes under 5 min to run for an average 50-kb bacteriophage genome. AVAILABILITY AND IMPLEMENTATION Pharokka is implemented in Python and is available as a bioconda package using 'conda install -c bioconda pharokka'. The source code is available on GitHub (https://github.com/gbouras13/pharokka). Pharokka has been tested on Linux-64 and MacOSX machines and on Windows using a Linux Virtual Machine.
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Affiliation(s)
| | - Roshan Nepal
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5070, Australia
- Department of Surgery—Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA 5070, Australia
| | - Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5070, Australia
- Department of Surgery—Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA 5070, Australia
| | - Alkis James Psaltis
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5070, Australia
- Department of Surgery—Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA 5070, Australia
| | - Peter-John Wormald
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5070, Australia
- Department of Surgery—Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA 5070, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5070, Australia
- Department of Surgery—Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, SA 5070, Australia
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173
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Li R, Wang Y, Hu H, Tan Y, Ma Y. Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut. Nat Commun 2022; 13:7978. [PMID: 36581612 PMCID: PMC9800368 DOI: 10.1038/s41467-022-35735-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
The human gut microbiome has been extensively explored, while the archaeal viruses remain largely unknown. Here, we present a comprehensive analysis of the archaeal viruses from the human gut metagenomes and the existing virus collections using the CRISPR spacer and viral signature-based approach. This results in 1279 viral species, of which, 95.2% infect Methanobrevibacteria_A, 56.5% shared high identity (>95%) with the archaeal proviruses, 37.2% have a host range across archaeal species, and 55.7% are highly prevalent in the human population (>1%). A methanogenic archaeal virus-specific gene for pseudomurein endoisopeptidase (PeiW) frequently occurs in the viral sequences (n = 150). Analysis of 33 Caudoviricetes viruses with a complete genome often discovers the genes (integrase, n = 29; mazE, n = 10) regulating the viral lysogenic-lytic cycle, implying the dominance of temperate viruses in the archaeal virome. Together, our work uncovers the unexplored diversity of archaeal viruses, revealing the novel facet of the human gut microbiome.
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Affiliation(s)
- Ran Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongming Wang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Han Hu
- Xbiome, Scientific Research Building, Tsinghua High-Tech Park, Shenzhen, China
| | - Yan Tan
- Xbiome, Scientific Research Building, Tsinghua High-Tech Park, Shenzhen, China
| | - Yingfei Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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174
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Brossard Stoos KA, Ren J, Shields-Cutler RR, Sams KL, Caldwell S, Ho MB, Rivara G, Whistler CA, Jones SH, Wiedmann M, DeMent J, Getchell RG, Marquis H. Coastal water bacteriophages infect various sets of Vibrio parahaemolyticus sequence types. Front Microbiol 2022; 13:1041942. [PMID: 36601403 PMCID: PMC9807174 DOI: 10.3389/fmicb.2022.1041942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Gastrointestinal illnesses associated with the consumption of shellfish contaminated with Vibrio parahaemolyticus have a negative impact on the shellfish industry due to recalls and loss of consumer confidence in products. This bacterial pathogen is very diverse and specific sequence types (STs), ST631 and ST36, have emerged as prevalent causes of Vibrio foodborne disease outbreaks in the US, though other STs have been implicated in sporadic cases. We investigated whether bacteriophages could be used as a proxy to monitor for the presence of distinct V. parahaemolyticus STs in coastal waters. Methods For this purpose, bacteriophages infecting V. parahaemolyticus were isolated from water samples collected on the Northeast Atlantic coast. The isolated phages were tested against a collection of 29 V. parahaemolyticus isolates representing 18 STs, including six clonal complexes (CC). Four distinct phages were identified based on their ability to infect different sets of V. parahaemolyticus isolates. Results and Discussion Overall, the 29 bacterial isolates segregated into one of eight patterns of susceptibility, ranging from resistance to all four phages to susceptibility to any number of phages. STs represented by more than one bacterial isolate segregated within the same pattern of susceptibility except for one V. parahaemolyticus ST. Other patterns of susceptibility included exclusively clinical isolates represented by distinct STs. Overall, this study suggests that phages populating coastal waters could be exploited to monitor for the presence of V. parahaemolyticus STs known to cause foodborne outbreaks.
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Affiliation(s)
- Kari A. Brossard Stoos
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States,Department of Health Promotion and Physical Education, Ithaca College, Ithaca, NY, United States,*Correspondence: Kari A. Brossard Stoos,
| | - Jennifer Ren
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | | | - Kelly L. Sams
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Shannon Caldwell
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Marvin B. Ho
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Gregg Rivara
- Cornell Cooperative Extension of Suffolk County, Southold, NY, United States
| | - Cheryl A. Whistler
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, NH, United States,Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Stephen H. Jones
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, NH, United States,Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Jamie DeMent
- Florida Department of Health, Tallahassee, FL, United States
| | - Rodman G. Getchell
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
| | - Hélène Marquis
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, United States
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175
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Ulrich L, Giez C, Steiner LX, Hentschel U, Lachnit T. Adaptive lifestyle of bacteria determines phage-bacteria interaction. Front Microbiol 2022; 13:1056388. [PMID: 36560945 PMCID: PMC9763317 DOI: 10.3389/fmicb.2022.1056388] [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: 09/28/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Bacteriophages and their interactions with microbes are not well understood. As a first step toward achieving a better understanding, we isolated and sequenced the Curvibacter phage PCA1 for the purpose of eliminating Curvibacter sp. AEP1.3, the main colonizer of Hydra vulgaris AEP. Our experiments showed that PCA1 phage caused a strong, virulent infection only in sessile Curvibacter sp. AEP1.3 but was unable to infect planktonic and host-associated bacterial cells of the same strain. In an effort to investigate this phenomenon, we compared sessile, planktonic, and host-associated bacteria via RNA sequencing and found that all three states differed significantly in their expression patterns. This finding led us to propose that the adaptive lifestyle of Curvibacter sp. AEP1.3 results in varying degrees of susceptibility to bacteriophage infection. This concept could be relevant for phage research and phage therapy in particular. Finally, we were able to induce phage infection in planktonic cells and pinpoint the infection process to a membrane protein. We further identified potential phage-binding protein candidates based on expression pattern analysis.
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Affiliation(s)
- Laura Ulrich
- Zoological Institute, Christian-Albrechts-Universität, Kiel, Germany
| | - Christoph Giez
- Zoological Institute, Christian-Albrechts-Universität, Kiel, Germany
| | - Leon X. Steiner
- RD3 Marine Ecology, RU Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Ute Hentschel
- RD3 Marine Ecology, RU Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Tim Lachnit
- Zoological Institute, Christian-Albrechts-Universität, Kiel, Germany,*Correspondence: Tim Lachnit,
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176
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Olo Ndela É, Cobigo LM, Roux S, Enault F. [A better understanding of Earth's viruses thanks to metagenomes]. Med Sci (Paris) 2022; 38:999-1007. [PMID: 36692279 DOI: 10.1051/medsci/2022166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite their large number, viruses present in the environment remain largely unknown. Metagenomic approaches, targeting viruses specifically or not, have allowed us a better understanding of the composition of natural viral communities, with Caudoviricetes, Microviridae, Cressdnaviricota or Phycodnaviridae being the most frequently found viral groups. Metagenomes are gradually revealing the extent of the diversity of these groups and their structure, highlighting the large number of species, genera and even viral families, most of which being seen for the first time. Within these groups, the gene content, infected hosts and inhabited ecosystems are often consistent with the evolutionary history traced with marker genes. Thus, the diversity of viruses and their genes is more a reflection of their ancient origin and long coevolution with their hosts than of their ability to mutate rapidly.
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Affiliation(s)
- Éric Olo Ndela
- Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France
| | - Louis-Marie Cobigo
- Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, États-Unis
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France
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177
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Baran N, Carlson MCG, Sabehi G, Peleg M, Kondratyeva K, Pekarski I, Lindell D. Widespread yet persistent low abundance of TIM5-like cyanophages in the oceans. Environ Microbiol 2022; 24:6476-6492. [PMID: 36116015 PMCID: PMC10087341 DOI: 10.1111/1462-2920.16210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/12/2022] [Indexed: 01/12/2023]
Abstract
Ocean ecosystems are inhabited by a diverse set of viruses that impact microbial mortality and evolution. However, the distribution and abundances of specific viral lineages, particularly those from the large bank of rare viruses, remains largely unknown. Here, we assessed the diversity and abundance of the TIM5-like cyanophages. The sequencing of three new TIM5-like cyanophage genomes and environmental amplicons of a signature gene from the Red Sea revealed highly conserved gene content and sequence similarity. We adapted the polony method, a solid-phase polymerase chain reaction assay, to quantify TIM5-like cyanophages during three 2000 km expeditions in the Pacific Ocean and four annual cycles in the Red Sea. TIM5-like cyanophages were widespread, detected at all latitudes and seasons surveyed throughout the photic zone. Yet they were generally rare, ranging between <100 and 4000 viruses·ml-1 . Occasional peaks in abundance of 10- to 100-fold were observed, reaching 71,000 viruses·ml-1 . These peaks were ephemeral and seasonally variable in the Red Sea. Infection levels, quantified during one such peak, were very low. These characteristics of low diversity and abundance, as well as variable outbreaks, distinguishes the TIM5-like lineage from other major cyanophage lineages and illuminates that rare virus lineages can be persistent and widespread in the oceans.
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Affiliation(s)
- Nava Baran
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Michael C G Carlson
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Gazalah Sabehi
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Margalit Peleg
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Kira Kondratyeva
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Irena Pekarski
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
| | - Debbie Lindell
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, Israel
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178
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Batinovic S, Stanton CR, Rice DTF, Rowe B, Beer M, Petrovski S. Tyroviruses are a new group of temperate phages that infect Bacillus species in soil environments worldwide. BMC Genomics 2022; 23:777. [PMID: 36443683 PMCID: PMC9703825 DOI: 10.1186/s12864-022-09023-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Bacteriophages are widely considered to be highly abundant and genetically diverse, with their role in the evolution and virulence of many pathogens becoming increasingly clear. Less attention has been paid on phages preying on Bacillus, despite the potential for some of its members, such as Bacillus anthracis, to cause serious human disease. RESULTS We have isolated five phages infecting the causative agent of anthrax, Bacillus anthracis. Using modern phylogenetic approaches we place these five new Bacillus phages, as well as 21 similar phage genomes retrieved from publicly available databases and metagenomic datasets into the Tyrovirus group, a newly proposed group named so due to the conservation of three distinct tyrosine recombinases. Genomic analysis of these large phages (~ 160-170 kb) reveals their DNA packaging mechanism and genomic features contributing to virion morphogenesis, host cell lysis and phage DNA replication processes. Analysis of the three tyrosine recombinases suggest Tyroviruses undergo a prophage lifecycle that may involve both host integration and plasmid stages. Further we show that Tyroviruses rely on divergent invasion mechanisms, with a subset requiring host S-layer for infection. CONCLUSIONS Ultimately, we expand upon our understanding on the classification, phylogeny, and genomic organisation of a new and substantial phage group that prey on critically relevant Bacillus species. In an era characterised by a rapidly evolving landscape of phage genomics the deposition of future Tyroviruses will allow the further unravelling of the global spread and evolutionary history of these Bacillus phages.
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Affiliation(s)
- Steven Batinovic
- grid.1018.80000 0001 2342 0938Department of Physiology, Anatomy, and Microbiology, La Trobe University, Bundoora, VIC Australia ,grid.268446.a0000 0001 2185 8709Present address: Division of Materials Science and Chemical Engineering, Yokohama National University, Yokohama, Kanagawa Japan
| | - Cassandra R. Stanton
- grid.1018.80000 0001 2342 0938Department of Physiology, Anatomy, and Microbiology, La Trobe University, Bundoora, VIC Australia
| | - Daniel T. F. Rice
- grid.1018.80000 0001 2342 0938Department of Physiology, Anatomy, and Microbiology, La Trobe University, Bundoora, VIC Australia
| | - Brittany Rowe
- grid.1018.80000 0001 2342 0938Department of Physiology, Anatomy, and Microbiology, La Trobe University, Bundoora, VIC Australia
| | - Michael Beer
- grid.431245.50000 0004 0385 5290Defence Science and Technology Group, Fishermans Bend, Victoria, Australia
| | - Steve Petrovski
- grid.1018.80000 0001 2342 0938Department of Physiology, Anatomy, and Microbiology, La Trobe University, Bundoora, VIC Australia
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179
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Genome Sequence of a Lytic Staphylococcus aureus Bacteriophage Isolated from Breast Milk. Microbiol Resour Announc 2022; 11:e0095322. [DOI: 10.1128/mra.00953-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We identified a double-stranded DNA (dsDNA) bacteriophage appearing to belong to
Herelleviridae
, genus
Kayvirus
. The bacteriophage, Biyabeda-mokiny 1, was isolated from breast milk using a clinical isolate of
Staphylococcus aureus
. The genome is 141,091 bp in length and encodes 230 putative coding sequences.
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180
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Genome Sequences of Two Lytic Staphylococcus aureus Bacteriophages Isolated from Wastewater. Microbiol Resour Announc 2022; 11:e0095422. [DOI: 10.1128/mra.00954-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Two lytic double-stranded DNA (dsDNA) bacteriophages, belonging to the family
Herelleviridae
, were isolated from wastewater in Western Australia. Biyabeda-mokiny 2 appears to belong to the genus
Kayvirus
, and Koomba-kaat 1 to
Silviavirus
.
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181
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Complete Genomes of Three Pseudomonas aeruginosa Bacteriophages, Kara-mokiny 1, Kara-mokiny 2, and Kara-mokiny 3. Microbiol Resour Announc 2022; 11:e0095522. [DOI: 10.1128/mra.00955-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Here, we present the complete genome sequence of
Pseudomonas aeruginosa
phages Kara-mokiny 1, Kara-mokiny 2, and Kara-mokiny 3. These phages have lytic capabilities against
P. aeruginosa
and belong to the myovirus morphotype. The genomes of Kara-mokiny 1 and Kara-mokiny 2 are 67,075 bp while that of Kara-mokiny 3 is 66,019 bp long.
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182
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Muscatt G, Hilton S, Raguideau S, Teakle G, Lidbury IDEA, Wellington EMH, Quince C, Millard A, Bending GD, Jameson E. Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere. MICROBIOME 2022; 10:181. [PMID: 36280853 PMCID: PMC9590211 DOI: 10.1186/s40168-022-01371-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/18/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions. RESULTS Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation. CONCLUSIONS Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.
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Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sebastien Raguideau
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Graham Teakle
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Ian D E A Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Christopher Quince
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK.
- School of Natural Sciences, Bangor University, Bangor, UK.
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183
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Ngo VQH, Enault F, Midoux C, Mariadassou M, Chapleur O, Mazéas L, Loux V, Bouchez T, Krupovic M, Bize A. Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics. Environ Microbiol 2022; 24:4853-4868. [PMID: 35848130 PMCID: PMC9796341 DOI: 10.1111/1462-2920.16120] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/01/2022] [Accepted: 06/29/2022] [Indexed: 01/01/2023]
Abstract
Diversity of viruses infecting non-extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head-tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near-complete genomes of spindle-shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head-tailed virus-like particles and the presence of spindle-shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens.
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Affiliation(s)
- Vuong Quoc Hoang Ngo
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - François Enault
- Université Clermont Auvergne, CNRS, LMGEClermont‐FerrandFrance
| | - Cédric Midoux
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance
- Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Mahendra Mariadassou
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance
- Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Olivier Chapleur
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Laurent Mazéas
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Valentin Loux
- Université Paris‐Saclay, INRAE, MaIAGEJouy‐en‐JosasFrance
- Université Paris‐Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics FacilityJouy‐en‐JosasFrance
| | - Théodore Bouchez
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, CNRS UMR6047, Archaeal Virology UnitParisFrance
| | - Ariane Bize
- Université Paris‐Saclay, INRAE, PRocédés biOtechnologiques au Service de l'EnvironnementAntonyFrance
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184
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Complete Genome Sequences of Five Phietaviruses Infecting Staphylococcus aureus. Microbiol Resour Announc 2022; 11:e0085522. [PMID: 36173192 PMCID: PMC9583785 DOI: 10.1128/mra.00855-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The annotated whole-genome sequences of five cultured phietaviruses infecting Staphylococcus aureus are presented. They are closely related to prophages that were previously sequenced as part of S. aureus genomes.
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185
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Potapov S, Krasnopeev A, Tikhonova I, Podlesnaya G, Gorshkova A, Belykh O. The Viral Fraction Metatranscriptomes of Lake Baikal. Microorganisms 2022; 10:1937. [PMID: 36296212 PMCID: PMC9611531 DOI: 10.3390/microorganisms10101937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022] Open
Abstract
This article characterises viral fraction metatranscriptomes (smaller than 0.2 µm) from the pelagic zone of oligotrophic Lake Baikal (Russia). The study revealed the dominance of transcripts of DNA viruses: bacteriophages and algal viruses. We identified transcripts similar to Pithovirus sibericum, a nucleocytoplasmic large DNA virus (NCLDV) isolated from the permafrost region of Eastern Siberia. Among the families detected were RNA viruses assigned to Retroviridae, Metaviridae, Potyviridae, Astroviridae, and Closteroviridae. Using the PHROG, SEED subsystems databases, and the VOGDB, we indicated that the bulk of transcripts belong to the functional replication of viruses. In a comparative unweighted pair group method with arithmetic mean (UPGMA) analysis, the transcripts from Lake Baikal formed a separate cluster included in the clade with transcripts from other freshwater lakes, as well as marine and oceanic waters, while there was no separation based on the trophic state of the water bodies, the size of the plankton fraction, or salinity.
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Affiliation(s)
- Sergey Potapov
- Limnological Institute SB RAS, 3, Ulan-Batorskaya, 664033 Irkutsk, Russia
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186
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Smith-Zaitlik T, Shibu P, McCartney AL, Foster G, Hoyles L, Negus D. Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36156193 DOI: 10.1099/mic.0.001247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several hypothetical homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Differences in the tail fibre protein may explain the non-identical host range of the two phages. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.
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Affiliation(s)
| | - Preetha Shibu
- Life Sciences, University of Westminster, London, UK.,Present address: Berkshire and Surrey Pathology Services, Frimley Health NHS Trust, Wexham Park Hospital, Slough, UK
| | - Anne L McCartney
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | | | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
| | - David Negus
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
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187
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Cook R, Darby T, Roach DR. Complete Genome Sequence of Pseudomonas aeruginosa Bacteriophage vB_PaeP_PaCe. Microbiol Resour Announc 2022; 11:e0046322. [PMID: 35862916 PMCID: PMC9387253 DOI: 10.1128/mra.00463-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
Here, we report the complete genome sequence of the virulent podovirus PaCe, which was isolated from wastewater in San Diego, California, using the host Pseudomonas aeruginosa. Its complete genome is 45,365 bp in length, with a GC content of 52.5%. PaCe belongs to the genus Bruynoghevirus in the class Caudoviricetes.
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Affiliation(s)
- Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Taylor Darby
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Dwayne R. Roach
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
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188
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Gendre J, Ansaldi M, Olivenza DR, Denis Y, Casadesús J, Ginet N. Genetic Mining of Newly Isolated Salmophages for Phage Therapy. Int J Mol Sci 2022; 23:8917. [PMID: 36012174 PMCID: PMC9409062 DOI: 10.3390/ijms23168917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/29/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
Salmonella enterica, a Gram-negative zoonotic bacterium, is mainly a food-borne pathogen and the main cause of diarrhea in humans worldwide. The main reservoirs are found in poultry farms, but they are also found in wild birds. The development of antibiotic resistance in S. enterica species raises concerns about the future of efficient therapies against this pathogen and revives the interest in bacteriophages as a useful therapy against bacterial infections. Here, we aimed to decipher and functionally annotate 10 new Salmonella phage genomes isolated in Spain in the light of phage therapy. We designed a bioinformatic pipeline using available building blocks to de novo assemble genomes and perform syntaxic annotation. We then used genome-wide analyses for taxonomic annotation enabled by vContact2 and VICTOR. We were also particularly interested in improving functional annotation using remote homologies detection and comparisons with the recently published phage-specific PHROG protein database. Finally, we searched for useful functions for phage therapy, such as systems encoded by the phage to circumvent cellular defenses with a particular focus on anti-CRISPR proteins. We, thus, were able to genetically characterize nine virulent phages and one temperate phage and identify putative functions relevant to the formulation of phage cocktails for Salmonella biocontrol.
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Affiliation(s)
- Julia Gendre
- Laboratoire de Chimie Bactérienne, (UMR7283)-CNRS/Aix-Marseille Université, 13009 Marseille, France
| | - Mireille Ansaldi
- Laboratoire de Chimie Bactérienne, (UMR7283)-CNRS/Aix-Marseille Université, 13009 Marseille, France
| | - David R. Olivenza
- Departamento de Genética, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Yann Denis
- Institut de Microbiologie de la Méditerranée, (FR3479)-CNRS/Aix-Marseille Université, 13009 Marseille, France
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Nicolas Ginet
- Laboratoire de Chimie Bactérienne, (UMR7283)-CNRS/Aix-Marseille Université, 13009 Marseille, France
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189
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Viral biogeography of the mammalian gut and parenchymal organs. Nat Microbiol 2022; 7:1301-1311. [PMID: 35918425 PMCID: PMC7614033 DOI: 10.1038/s41564-022-01178-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 06/21/2022] [Indexed: 01/13/2023]
Abstract
The mammalian virome has been linked to health and disease but our understanding of how it is structured along the longitudinal axis of the mammalian gastrointestinal tract (GIT) and other organs is limited. Here, we report a metagenomic analysis of the prokaryotic and eukaryotic virome occupying luminal and mucosa-associated habitats along the GIT, as well as parenchymal organs (liver, lung and spleen), in two representative mammalian species, the domestic pig and rhesus macaque (six animals per species). Luminal samples from the large intestine of both mammals harboured the highest loads and diversity of bacteriophages (class Caudoviricetes, family Microviridae and others). Mucosal samples contained much lower viral loads but a higher proportion of eukaryotic viruses (families Astroviridae, Caliciviridae, Parvoviridae). Parenchymal organs contained bacteriophages of gut origin, in addition to some eukaryotic viruses. Overall, GIT virome composition was specific to anatomical region and host species. Upper GIT and mucosa-specific viruses were greatly under-represented in distal colon samples (a proxy for faeces). Nonetheless, certain viral and phage species were ubiquitous in all samples from the oral cavity to the distal colon. The dataset and its accompanying methodology may provide an important resource for future work investigating the biogeography of the mammalian gut virome.
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190
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Paillet T, Lossouarn J, Figueroa C, Midoux C, Rué O, Petit MA, Dugat-Bony E. Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory. Viruses 2022; 14:1620. [PMID: 35893685 PMCID: PMC9331655 DOI: 10.3390/v14081620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
Smear-ripened cheeses host complex microbial communities that play a crucial role in the ripening process. Although bacteriophages have been frequently isolated from dairy products, their diversity and ecological role in such this type of cheese remain underexplored. In order to fill this gap, the main objective of this study was to isolate and characterize bacteriophages from the rind of a smear-ripened cheese. Thus, viral particles extracted from the cheese rind were tested through a spot assay against a collection of bacteria isolated from the same cheese and identified by sequencing the full-length small subunit ribosomal RNA gene. In total, five virulent bacteriophages infecting Brevibacterium aurantiacum, Glutamicibacter arilaitensis, Leuconostoc falkenbergense and Psychrobacter aquimaris species were obtained. All exhibit a narrow host range, being only able to infect a few cheese-rind isolates within the same species. The complete genome of each phage was sequenced using both Nanopore and Illumina technologies, assembled and annotated. A sequence comparison with known phages revealed that four of them may represent at least new genera. The distribution of the five virulent phages into the dairy-plant environment was also investigated by PCR, and three potential reservoirs were identified. This work provides new knowledge on the cheese rind viral community and an overview of the distribution of phages within a cheese factory.
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Affiliation(s)
- Thomas Paillet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France; (T.P.); (C.F.)
| | - Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78352 Jouy-en-Josas, France; (J.L.); (M.-A.P.)
| | - Clarisse Figueroa
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France; (T.P.); (C.F.)
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (C.M.); (O.R.)
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350 Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, PROSE, 92761 Antony, France
| | - Olivier Rué
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (C.M.); (O.R.)
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350 Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78352 Jouy-en-Josas, France; (J.L.); (M.-A.P.)
| | - Eric Dugat-Bony
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France; (T.P.); (C.F.)
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191
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Balcão VM, Moreli FC, Silva EC, Belline BG, Martins LF, Rossi FPN, Pereira C, Vila MMDC, da Silva AM. Isolation and Molecular Characterization of a Novel Lytic Bacteriophage That Inactivates MDR Klebsiella pneumoniae Strains. Pharmaceutics 2022; 14:pharmaceutics14071421. [PMID: 35890314 PMCID: PMC9324672 DOI: 10.3390/pharmaceutics14071421] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 02/07/2023] Open
Abstract
The worldwide increase in serious infections caused by multidrug-resistant (MDR) K. pneumoniae emphasizes the urgent need of new therapeutic strategies for the control of this pathogen. There is growing interest in the use of bacteriophages (or phages) to treat K. pneumoniae infections, and newly isolated phages are needed. Here, we report the isolation and physical/biological/molecular characterization of a novel lytic phage and its efficacy in the control of MDR K. pneumoniae. The phage vB_KpnS_Uniso31, referred to hereafter as phage Kpn31, was isolated from hospital wastewater using K. pneumoniae CCCD-K001 as the host. Phage Kpn31 presents a siphovirus-like morphotype and was classified as Demerecviridae; Sugarlandvirus based on its complete genome sequence. The 113,444 bp Kpn31 genome does not encode known toxins or antimicrobial resistance genes, nor does it encode depolymerases related sequences. Phage Kpn31 showed an eclipse time of 15 min and a burst size of 9.12 PFU/host cell, allowing us to conclude it replicates well in K. pneumoniae CCCD-K001 with a latency period of 30 min. Phage Kpn31 was shown to be effective against at least six MDR K. pneumoniae clinical isolates in in vitro antibacterial activity assays. Based on its features, phage Kpn31 has potential for controlling infections caused by MDR K. pneumoniae.
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Affiliation(s)
- Victor M Balcão
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
- Department of Biology and CESAM, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Fernanda C Moreli
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Erica C Silva
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Bianca G Belline
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Layla F Martins
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Fernando P N Rossi
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Carla Pereira
- Department of Biology and CESAM, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Marta M D C Vila
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Aline M da Silva
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
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192
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Abstract
The recovery of DNA from viromes is a major obstacle in the use of long-read sequencing to study their genomes. For this reason, the use of cellular metagenomes (>0.2-μm size range) emerges as an interesting complementary tool, since they contain large amounts of naturally amplified viral genomes from prelytic replication. We have applied second-generation (Illumina NextSeq; short reads) and third-generation (PacBio Sequel II; long reads) sequencing to compare the diversity and features of the viral community in a marine sample obtained from offshore waters of the western Mediterranean. We found that a major wedge of the expected marine viral diversity was directly recovered by the raw PacBio circular consensus sequencing (CCS) reads. More than 30,000 sequences were detected only in this data set, with no homologues in the long- and short-read assembly, and ca. 26,000 had no homologues in the large data set of the Global Ocean Virome 2 (GOV2), highlighting the information gap created by the assembly bias. At the level of complete viral genomes, the performance was similar in both approaches. However, the hybrid long- and short-read assembly provided the longest average length of the sequences and improved the host assignment. Although no novel major clades of viruses were found, there was an increase in the intraclade genomic diversity recovered by long reads that produced an enriched assessment of the real diversity and allowed the discovery of novel genes with biotechnological potential (e.g., endolysin genes). IMPORTANCE We explored the vast genetic diversity of environmental viruses by using a combination of cellular metagenome (as opposed to virome) sequencing using high-fidelity long-read sequences (in this case, PacBio CCS). This approach resulted in the recovery of a representative sample of the viral population, and it performed better (more phage contigs, larger average contig size) than Illumina sequencing applied to the same sample. By this approach, the many biases of assembly are avoided, as the CCS reads recovers (typically around 5 kb) complete genes and even operons, resulting in a better discovery of the viral gene diversity based on viral marker proteins. Thus, biotechnologically promising genes, such as endolysin genes, can be very efficiently searched with this approach. In addition, hybrid assembly produces more complete and longer contigs, which is particularly important for studying little-known viral groups such as the nucleocytoplasmic large DNA viruses (NCLDV).
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193
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Mestre MR, Gao LA, Shah SA, López-Beltrán A, González-Delgado A, Martínez-Abarca F, Iranzo J, Redrejo-Rodríguez M, Zhang F, Toro N. UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. Nucleic Acids Res 2022; 50:6084-6101. [PMID: 35648479 PMCID: PMC9226505 DOI: 10.1093/nar/gkac467] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/11/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022] Open
Abstract
Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.
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Affiliation(s)
- Mario Rodríguez Mestre
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - Linyi Alex Gao
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820 Gentofte, Denmark
| | - Adrián López-Beltrán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Alejandro González-Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Spain
| | - Francisco Martínez-Abarca
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Spain
| | - Jaime Iranzo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
| | - Modesto Redrejo-Rodríguez
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid, Spain
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Massachusetts Institute of Technology, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicolás Toro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Spain
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Andrade-Martínez JS, Camelo Valera LC, Chica Cárdenas LA, Forero-Junco L, López-Leal G, Moreno-Gallego JL, Rangel-Pineros G, Reyes A. Computational Tools for the Analysis of Uncultivated Phage Genomes. Microbiol Mol Biol Rev 2022; 86:e0000421. [PMID: 35311574 PMCID: PMC9199400 DOI: 10.1128/mmbr.00004-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes. Novel phage genomes have been reported from a diverse range of biomes at an increasing rate, which has prompted the development of computational tools that support the multilevel characterization of these novel phages based solely on their genome sequences. The impact of these technologies has been so large that, together with MAGs (Metagenomic Assembled Genomes), we now have UViGs (Uncultivated Viral Genomes), which are now officially recognized by the International Committee for the Taxonomy of Viruses (ICTV), and new taxonomic groups can now be created based exclusively on genomic sequence information. Even though the available tools have immensely contributed to our knowledge of phage diversity and ecology, the ongoing surge in software programs makes it challenging to keep up with them and the purpose each one is designed for. Therefore, in this review, we describe a comprehensive set of currently available computational tools designed for the characterization of phage genome sequences, focusing on five specific analyses: (i) assembly and identification of phage and prophage sequences, (ii) phage genome annotation, (iii) phage taxonomic classification, (iv) phage-host interaction analysis, and (v) phage microdiversity.
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Affiliation(s)
- Juan Sebastián Andrade-Martínez
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Carolina Camelo Valera
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Luis Alberto Chica Cárdenas
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Forero-Junco
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Gamaliel López-Leal
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - J. Leonardo Moreno-Gallego
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Guillermo Rangel-Pineros
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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195
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Biosca EG, Català-Senent JF, Figàs-Segura À, Bertolini E, López MM, Álvarez B. Genomic Analysis of the First European Bacteriophages with Depolymerase Activity and Biocontrol Efficacy against the Phytopathogen Ralstonia solanacearum. Viruses 2021; 13:v13122539. [PMID: 34960808 PMCID: PMC8703784 DOI: 10.3390/v13122539] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/28/2022] Open
Abstract
Ralstonia solanacearum is the causative agent of bacterial wilt, one of the most destructive plant diseases. While chemical control has an environmental impact, biological control strategies can allow sustainable agrosystems. Three lytic bacteriophages (phages) of R. solanacearum with biocontrol capacity in environmental water and plants were isolated from river water in Europe but not fully analysed, their genomic characterization being fundamental to understand their biology. In this work, the phage genomes were sequenced and subjected to bioinformatic analysis. The morphology was also observed by electron microscopy. Phylogenetic analyses were performed with a selection of phages able to infect R. solanacearum and the closely related phytopathogenic species R. pseudosolanacearum. The results indicated that the genomes of vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 range from 40,688 to 41,158 bp with almost 59% GC-contents, 52 ORFs in vRsoP-WF2 and vRsoP-WM2, and 53 in vRsoP-WR2 but, with only 22 or 23 predicted proteins with functional homologs in databases. Among them, two lysins and one exopolysaccharide (EPS) depolymerase, this type of depolymerase being identified in R. solanacearum phages for the first time. These three European phages belong to the same novel species within the Gyeongsanvirus, Autographiviridae family (formerly Podoviridae). These genomic data will contribute to a better understanding of the abilities of these phages to damage host cells and, consequently, to an improvement in the biological control of R. solanacearum.
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Affiliation(s)
- Elena G. Biosca
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Correspondence:
| | - José Francisco Català-Senent
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Centro de Investigación Príncipe Felipe, Unidad de Bioinformática y Bioestadística, 46012 Valencia, Spain
| | - Àngela Figàs-Segura
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
| | - Edson Bertolini
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil
| | - María M. López
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Valencia, Spain;
| | - Belén Álvarez
- Departamento de Microbiología y Ecología, Universitat de València (UV), 46100 Valencia, Spain; (J.F.C.-S.); (À.F.-S.); (E.B.); (B.Á.)
- Departamento de Investigación Aplicada y Extensión Agraria, Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), 28800 Alcalá de Henares, Spain
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196
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Olo Ndela E, Enault F, Toussaint A. Transposable Prophages in Leptospira: An Ancient, Now Diverse, Group Predominant in Causative Agents of Weil's Disease. Int J Mol Sci 2021; 22:13434. [PMID: 34948244 PMCID: PMC8705779 DOI: 10.3390/ijms222413434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 12/24/2022] Open
Abstract
The virome associated with the corkscrew shaped bacterium Leptospira, responsible for Weil's disease, is scarcely known, and genetic tools available for these bacteria remain limited. To reduce these two issues, potential transposable prophages were searched in Leptospiraceae genomes. The 236 predicted transposable prophages were particularly abundant in the most pathogenic leptospiral clade, being potentially involved in the acquisition of virulent traits. According to genomic similarities and phylogenies, these prophages are distantly related to known transposable phages and are organized into six groups, one of them encompassing prophages with unusual TA-TA ends. Interestingly, structural and transposition proteins reconstruct different relationships between groups, suggesting ancestral recombinations. Based on the baseplate phylogeny, two large clades emerge, with specific gene-contents and high sequence divergence reflecting their ancient origin. Despite their high divergence, the size and overall genomic organization of all prophages are very conserved, a testimony to the highly constrained nature of their genomes. Finally, similarities between these prophages and the three known non-transposable phages infecting L. biflexa, suggest gene transfer between different Caudovirales inside their leptospiral host, and the possibility to use some of the transposable prophages in that model strain.
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Affiliation(s)
- Eric Olo Ndela
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, F-63000 Clermont-Ferrand, France;
| | - François Enault
- Laboratoire Microorganismes: Genome Environment (LMGE), Université Clermont Auvergne, CNRS, F-63000 Clermont-Ferrand, France;
| | - Ariane Toussaint
- Microbiologie Cellulaire et Moléculaire, Université Libre de Bruxelles, IBMM-DBM, 12 Rue des Professeurs Jeneer et Brachet, B-6041 Gosselies, Belgium;
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197
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Shen A, Millard A. Phage Genome Annotation: Where to Begin and End. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:183-193. [PMID: 36159890 PMCID: PMC9041514 DOI: 10.1089/phage.2021.0015] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
With the renewed interest in phage research, coupled with the rising accessibility to affordable sequencing, ever increasing numbers of phage genomes are being sequenced. Therefore, there is an increased need to assemble and annotate phage genomes. There is a plethora of tools and platforms that allow phage genomes to be assembled and annotated. The choice of tools can often be bewildering for those new to phage genome assembly. Here we provide an overview of the assembly and annotation process from obtaining raw reads to genome submission, with worked examples, providing those new to genome assembly and annotation with a guided pathway to genome submission. We focus on the use of open access tools that can be incorporated into workflows to allow easy repetition of steps, highlighting multiple tools that can be used and common pitfalls that may occur.
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Affiliation(s)
- Anastasiya Shen
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, United Kingdom
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198
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Billaud M, Lamy-Besnier Q, Lossouarn J, Moncaut E, Dion MB, Moineau S, Traoré F, Le Chatelier E, Denis C, Estelle J, Achard C, Zemb O, Petit MA. Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages rarely carry antibiotic resistance genes. ISME COMMUNICATIONS 2021; 1:55. [PMID: 37938642 PMCID: PMC9723715 DOI: 10.1038/s43705-021-00054-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 05/09/2023]
Abstract
Understanding the transmission of antibiotic resistance genes (ARGs) is critical for human health. For this, it is necessary to identify which type of mobile genetic elements is able to spread them from animal reservoirs into human pathogens. Previous research suggests that in pig feces, ARGs may be encoded by bacteriophages. However, convincing proof for phage-encoded ARGs in pig viromes is still lacking, because of bacterial DNA contaminating issues. We collected 14 pig fecal samples and performed deep sequencing on both highly purified viral fractions and total microbiota, in order to investigate phage and prophage-encoded ARGs. We show that ARGs are absent from the genomes of active, virion-forming phages (below 0.02% of viral contigs from viromes), but present in three prophages, representing 0.02% of the viral contigs identified in the microbial dataset. However, the corresponding phages were not detected in the viromes, and their genetic maps suggest they might be defective. We conclude that among pig fecal samples, phages and prophages rarely carry ARG. Furthermore, our dataset allows for the first time a comprehensive view of the interplay between prophages and viral particles, and uncovers two large clades, inoviruses and Oengus-like phages.
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Affiliation(s)
- Maud Billaud
- Université Paris- Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- Pherecydes Pharma 22 Bd Benoni Goullin, Nantes, France
| | - Quentin Lamy-Besnier
- Université Paris- Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Julien Lossouarn
- Université Paris- Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Elisabeth Moncaut
- Université Paris- Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Moira B Dion
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
- Felix D'Hérelle Reference Center for Bacterial Viruses, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | | | | | | | - Jordi Estelle
- Université Paris-Saclay, INRAE, GABI, Jouy-en-Josas, France
| | - Caroline Achard
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet-Tolosan, France
| | - Olivier Zemb
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet-Tolosan, France
| | - Marie-Agnès Petit
- Université Paris- Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
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