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Cook R, Crisci MA, Pye HV, Telatin A, Adriaenssens EM, Santini JM. Decoding huge phage diversity: a taxonomic classification of Lak megaphages. J Gen Virol 2024; 105. [PMID: 38814706 DOI: 10.1099/jgv.0.001997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
Abstract
High-throughput sequencing for uncultivated viruses has accelerated the understanding of global viral diversity and uncovered viral genomes substantially larger than any that have so far been cultured. Notably, the Lak phages are an enigmatic group of viruses that present some of the largest known phage genomes identified in human and animal microbiomes, and are dissimilar to any cultivated viruses. Despite the wealth of viral diversity that exists within sequencing datasets, uncultivated viruses have rarely been used for taxonomic classification. We investigated the evolutionary relationships of 23 Lak phages and propose a taxonomy for their classification. Predicted protein analysis revealed the Lak phages formed a deeply branching monophyletic clade within the class Caudoviricetes which contained no other phage genomes. One of the interesting features of this clade is that all current members are characterised by an alternative genetic code. We propose the Lak phages belong to a new order, the 'Grandevirales'. Protein and nucleotide-based analyses support the creation of two families, three sub-families, and four genera within the order 'Grandevirales'. We anticipate that the proposed taxonomy of Lak megaphages will simplify the future classification of related viral genomes as they are uncovered. Continued efforts to classify divergent viruses are crucial to aid common analyses of viral genomes and metagenomes.
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Affiliation(s)
- Ryan Cook
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Marco A Crisci
- Department of Structural and Molecular Biology, Division of Biosciences, UCL, London, UK
| | - Hannah V Pye
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Andrea Telatin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Joanne M Santini
- Department of Structural and Molecular Biology, Division of Biosciences, UCL, London, UK
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Babkin IV, Tikunov AY, Baykov IK, Morozova VV, Tikunova NV. Genome Analysis of Epsilon CrAss-like Phages. Viruses 2024; 16:513. [PMID: 38675856 PMCID: PMC11054128 DOI: 10.3390/v16040513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon crAss-like phage genomes was found. Comparative analysis indicated that epsilon crAss-like phages are divided into two putative genera, which were proposed to be named Epsilonunovirus and Epsilonduovirus; CrAssE-Sib belongs to the former. The crAssE-Sib genome contains a diversity-generating retroelement (DGR) cassette with all essential elements, including the reverse transcriptase (RT) and receptor binding protein (RBP) genes. However, this RT contains the GxxxSP motif in its fourth domain instead of the usual GxxxSQ motif found in all known phage and bacterial DGRs. RBP encoded by CrAssE-Sib and other Epsilonunoviruses has an unusual structure, and no similar phage proteins were found. In addition, crAssE-Sib and other Epsilonunoviruses encode conserved prophage repressor and anti-repressors that could be involved in lysogenic-to-lytic cycle switches. Notably, DNA primase sequences of epsilon crAss-like phages are not included in the monophyletic group formed by the DNA primases of all other crAss-like phages. Therefore, epsilon crAss-like phage substantially differ from other crAss-like phages, indicating the need to classify these phages into a separate family.
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Affiliation(s)
- Igor V. Babkin
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Artem Y. Tikunov
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Ivan K. Baykov
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
- Shared Research Facility “Siberian Circular Photon Source” (SRF “SKIF”) of Boreskov Institute of Catalysis SB RAS, 630090 Novosibirsk, Russia
| | - Vera V. Morozova
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
| | - Nina V. Tikunova
- Federal State Public Scientific Institution «Institute of Chemical Biology and Fundamental Medicine», Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.Y.T.); (I.K.B.); (V.V.M.)
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Remesh AT, Viswanathan R. CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09584-5. [PMID: 38413544 DOI: 10.1007/s12560-024-09584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.
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Cingolani G, Lokareddy R, Hou CF, Forti F, Iglesias S, Li F, Pavlenok M, Niederweis M, Briani F. Integrative structural analysis of Pseudomonas phage DEV reveals a genome ejection motor. RESEARCH SQUARE 2024:rs.3.rs-3941185. [PMID: 38463957 PMCID: PMC10925440 DOI: 10.21203/rs.3.rs-3941185/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
DEV is an obligatory lytic Pseudomonas phage of the N4-like genus, recently reclassified as Schitoviridae. The DEV genome encodes 91 ORFs, including a 3,398 amino acid virion-associated RNA polymerase. Here, we describe the complete architecture of DEV, determined using a combination of cryo-electron microscopy localized reconstruction, biochemical methods, and genetic knockouts. We built de novo structures of all capsid factors and tail components involved in host attachment. We demonstrate that DEV long tail fibers are essential for infection of Pseudomonas aeruginosa and dispensable for infecting mutants with a truncated lipopolysaccharide devoid of the O-antigen. We identified DEV ejection proteins and, unexpectedly, found that the giant DEV RNA polymerase, the hallmark of the Schitoviridae family, is an ejection protein. We propose that DEV ejection proteins form a genome ejection motor across the host cell envelope and that these structural principles are conserved in all Schitoviridae.
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Mahony J. Biological and bioinformatic tools for the discovery of unknown phage-host combinations. Curr Opin Microbiol 2024; 77:102426. [PMID: 38246125 DOI: 10.1016/j.mib.2024.102426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/21/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
The field of microbial ecology has been transformed by metagenomics in recent decades and has culminated in vast datasets that facilitate the bioinformatic dissection of complex microbial communities. Recently, attention has turned from defining the microbiota composition to the interactions and relationships that occur between members of the microbiota. Within complex microbiota, the identification of bacteriophage-host combinations has been a major challenge. Recent developments in artificial intelligence tools to predict protein structure and function as well as the relationships between bacteria and their infecting bacteriophages allow a strategic approach to identifying and validating phage-host relationships. However, biological validation of these predictions remains essential and will serve to improve the existing predictive tools. In this review, I provide an overview of the most recent developments in both bioinformatic and experimental approaches to predicting and experimentally validating unknown phage-host combinations.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, T12 YT20 Cork, Ireland.
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Koonin EV, Kuhn JH, Dolja VV, Krupovic M. Megataxonomy and global ecology of the virosphere. THE ISME JOURNAL 2024; 18:wrad042. [PMID: 38365236 PMCID: PMC10848233 DOI: 10.1093/ismejo/wrad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 02/18/2024]
Abstract
Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. Comparative analysis of these viruses using advanced computational methods culminated in the reconstruction of the evolution of major groups of viruses and enabled the construction of a virus megataxonomy, which has been formally adopted by the International Committee on Taxonomy of Viruses. This comprehensive taxonomy consists of six virus realms, which are aspired to be monophyletic and assembled based on the conservation of hallmark proteins involved in capsid structure formation or genome replication. The viruses in different major taxa substantially differ in host range and accordingly in ecological niches. In this review article, we outline the latest developments in virus megataxonomy and the recent discoveries that will likely lead to reassessment of some major taxa, in particular, split of three of the current six realms into two or more independent realms. We then discuss the correspondence between virus taxonomy and the distribution of viruses among hosts and ecological niches, as well as the abundance of viruses versus cells in different habitats. The distribution of viruses across environments appears to be primarily determined by the host ranges, i.e. the virome is shaped by the composition of the biome in a given habitat, which itself is affected by abiotic factors.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, United States
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 75015 Paris, France
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Iglesias SM, Lokareddy RK, Yang R, Li F, Yeggoni DP, David Hou CF, Leroux MN, Cortines JR, Leavitt JC, Bird M, Casjens SR, White S, Teschke CM, Cingolani G. Molecular Architecture of Salmonella Typhimurium Virus P22 Genome Ejection Machinery. J Mol Biol 2023; 435:168365. [PMID: 37952769 PMCID: PMC10842050 DOI: 10.1016/j.jmb.2023.168365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Bacteriophage P22 is a prototypical member of the Podoviridae superfamily. Since its discovery in 1952, P22 has become a paradigm for phage transduction and a model for icosahedral viral capsid assembly. Here, we describe the complete architecture of the P22 tail apparatus (gp1, gp4, gp10, gp9, and gp26) and the potential location and organization of P22 ejection proteins (gp7, gp20, and gp16), determined using cryo-EM localized reconstruction, genetic knockouts, and biochemical analysis. We found that the tail apparatus exists in two equivalent conformations, rotated by ∼6° relative to the capsid. Portal protomers make unique contacts with coat subunits in both conformations, explaining the 12:5 symmetry mismatch. The tail assembles around the hexameric tail hub (gp10), which folds into an interrupted β-propeller characterized by an apical insertion domain. The tail hub connects proximally to the dodecameric portal protein and head-to-tail adapter (gp4), distally to the trimeric tail needle (gp26), and laterally to six trimeric tailspikes (gp9) that attach asymmetrically to gp10 insertion domain. Cryo-EM analysis of P22 mutants lacking the ejection proteins gp7 or gp20 and biochemical analysis of purified recombinant proteins suggest that gp7 and gp20 form a molecular complex associated with the tail apparatus via the portal protein barrel. We identified a putative signal transduction pathway from the tailspike to the tail needle, mediated by three flexible loops in the tail hub, that explains how lipopolysaccharide (LPS) is sufficient to trigger the ejection of the P22 DNA in vitro.
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Affiliation(s)
- Stephano M Iglesias
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Ruoyu Yang
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA
| | - Fenglin Li
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA
| | - Daniel P Yeggoni
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA
| | - Chun-Feng David Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA
| | - Makayla N Leroux
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA
| | - Juliana R Cortines
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA; Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21590-902, Brazil
| | - Justin C Leavitt
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Mary Bird
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA
| | - Sherwood R Casjens
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Simon White
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA; Department of Chemistry, University of Connecticut, 91 N. Eagleville Road, Storrs, CT 06269, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locus Street, Philadelphia, PA 19107, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA.
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Zhu D, Cao D, Zhang X. Virus structures revealed by advanced cryoelectron microscopy methods. Structure 2023; 31:1348-1359. [PMID: 37797619 DOI: 10.1016/j.str.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
Before the resolution revolution, cryoelectron microscopy (cryo-EM) single-particle analysis (SPA) already achieved resolutions beyond 4 Å for certain icosahedral viruses, enabling ab initio atomic model building of these viruses. As the only samples that achieved such high resolution at that time, cryo-EM method development was closely intertwined with the improvement of reconstructions of symmetrical viruses. Viral morphology exhibits significant diversity, ranging from small to large, uniform to non-uniform, and from containing single symmetry to multiple symmetries. Furthermore, viruses undergo conformational changes during their life cycle. Several methods, such as asymmetric reconstruction, Ewald sphere correction, cryoelectron tomography (cryo-ET), and sub-tomogram averaging (STA), have been developed and applied to determine virus structures in vivo and in vitro. This review outlines current advanced cryo-EM methods for high-resolution structure determination of viruses and summarizes accomplishments obtained with these approaches. Moreover, persisting challenges in comprehending virus structures are discussed and we propose potential solutions.
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Affiliation(s)
- Dongjie Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Zheng J, Chen W, Xiao H, Yang F, Song J, Cheng L, Liu H. Asymmetric Structure of Podophage GP4 Reveals a Novel Architecture of Three Types of Tail Fibers. J Mol Biol 2023; 435:168258. [PMID: 37660940 DOI: 10.1016/j.jmb.2023.168258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
Bacteriophage tail fibers (or called tail spikes) play a critical role in the early stage of infection by binding to the bacterial surface. Podophages with known structures usually possess one or two types of fibers. Here, we resolved an asymmetric structure of the podophage GP4 to near-atomic resolution by cryo-EM. Our structure revealed a symmetry-mismatch relationship between the components of the GP4 tail with previously unseen topologies. In detail, two dodecameric adaptors (adaptors I and II), a hexameric nozzle, and a tail needle form a conserved tail body connected to a dodecameric portal occupying a unique vertex of the icosahedral head. However, five chain-like extended fibers (fiber I) and five tulip-like short fibers (fiber II) are anchored to a 15-fold symmetric fiber-tail adaptor, encircling the adaptor I, and six bamboo-like trimeric fibers (fiber III) are connected to the nozzle. Five fibers I, each composed of five dimers of the protein gp80 linked by an elongated rope protein, are attached to the five edges of the tail vertex of the icosahedral head. In this study, we identified a new structure of the podophage with three types of tail fibers, and such phages with different types of fibers may have a broad host range and/or infect host cells with considerably high efficiency, providing evolutionary advantages in harsh environments.
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Affiliation(s)
- Jing Zheng
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China
| | - Wenyuan Chen
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China
| | - Hao Xiao
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China; State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Fan Yang
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China
| | - Jingdong Song
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Lingpeng Cheng
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China.
| | - Hongrong Liu
- Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China.
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Papudeshi B, Vega AA, Souza C, Giles SK, Mallawaarachchi V, Roach MJ, An M, Jacobson N, McNair K, Fernanda Mora M, Pastrana K, Boling L, Leigh C, Harker C, Plewa WS, Grigson SR, Bouras G, Decewicz P, Luque A, Droit L, Handley SA, Wang D, Segall AM, Dinsdale EA, Edwards RA. Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2. Microb Genom 2023; 9:001100. [PMID: 37665209 PMCID: PMC10569736 DOI: 10.1099/mgen.0.001100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. 'tikkala' strain Bc01, Kolpuevirus sp. 'frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome.
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Affiliation(s)
- Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Alejandro A. Vega
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Cole Souza
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Sarah K. Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Michelle An
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Nicole Jacobson
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Katelyn McNair
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
| | - Maria Fernanda Mora
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Karina Pastrana
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Lance Boling
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Christopher Leigh
- Adelaide Microscopy, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Clarice Harker
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Will S. Plewa
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Susanna R. Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Przemysław Decewicz
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, Warsaw, 02-096, Poland
| | - Antoni Luque
- Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
- Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Drive, San Diego, CA, 992182, USA
- Present address: Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Scott A. Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anca M. Segall
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Elizabeth A. Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA, 5042, Australia
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Ramos-Barbero MD, Gómez-Gómez C, Sala-Comorera L, Rodríguez-Rubio L, Morales-Cortes S, Mendoza-Barberá E, Vique G, Toribio-Avedillo D, Blanch AR, Ballesté E, Garcia-Aljaro C, Muniesa M. Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution. Nat Commun 2023; 14:4295. [PMID: 37463935 PMCID: PMC10354031 DOI: 10.1038/s41467-023-40098-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
Crassvirales (crAss-like phages) are an abundant group of human gut-specific bacteriophages discovered in silico. The use of crAss-like phages as human fecal indicators is proposed but the isolation of only seven cultured strains of crAss-like phages to date has greatly hindered their study. Here, we report the isolation and genetic characterization of 25 new crAss-like phages (termed crAssBcn) infecting Bacteroides intestinalis, belonging to the order Crassvirales, genus Kehishuvirus and, based on their genomic variability, classified into six species. CrAssBcn phage genomes are similar to ΦCrAss001 but show genomic and aminoacidic differences when compared to other crAss-like phages of the same family. CrAssBcn phages are detected in fecal metagenomes around the world at a higher frequency than ΦCrAss001. This study increases the known crAss-like phage isolates and their abundance and heterogeneity open the question of what member of the Crassvirales group should be selected as human fecal marker.
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Affiliation(s)
- María Dolores Ramos-Barbero
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Clara Gómez-Gómez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Lorena Rodríguez-Rubio
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Sara Morales-Cortes
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Elena Mendoza-Barberá
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Gloria Vique
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Daniel Toribio-Avedillo
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Anicet R Blanch
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Elisenda Ballesté
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Cristina Garcia-Aljaro
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain
| | - Maite Muniesa
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, E-08028, Barcelona, Spain.
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