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Luca L, Pauliuc D, Oroian M. Honey microbiota, methods for determining the microbiological composition and the antimicrobial effect of honey - A review. Food Chem X 2024; 23:101524. [PMID: 38947342 PMCID: PMC11214184 DOI: 10.1016/j.fochx.2024.101524] [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: 03/28/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024] Open
Abstract
Honey is a natural product used since ancient times due to its taste, aroma, and therapeutic properties (antibacterial, antiviral, anti-inflammatory, and antioxidant activity). The purpose of this review is to present the species of microorganisms that can survive in honey and the effect they can have on bees and consumers. The techniques for identifying the microorganisms present in honey are also described in this study. Honey contains bacteria, yeasts, molds, and viruses, and some of them may present beneficial properties for humans. The antimicrobial effect of honey is due to its acidity and high viscosity, high sugar concentration, low water content, the presence of hydrogen peroxide and non-peroxidase components, particularly methylglyoxal (MGO), phenolic acids, flavonoids, proteins, peptides, and non-peroxidase glycopeptides. Honey has antibacterial action (it has effectiveness against bacteria, e.g. Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Acinetobacter, etc.), antifungal (effectiveness against Candida spp., Aspergillus spp., Fusarium spp., Rhizopus spp., and Penicillium spp.), antiviral (effectiveness against SARS-CoV-2, Herpes simplex virus type 1, Influenza virus A and B, Varicella zoster virus), and antiparasitic action (effectiveness against Plasmodium berghei, Giardia and Trichomonas, Toxoplasma gondii) demonstrated by numerous studies that are comprised and discussed in this review.
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Affiliation(s)
- Liliana Luca
- Suceava-Botoșani Regional Innovative Bioeconomy Cluster Association, 720229 Suceava, Romania
| | - Daniela Pauliuc
- Faculty of Food Engineering, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mircea Oroian
- Faculty of Food Engineering, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
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2
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Ramos EDSF, Tozetto-Mendoza TR, Bortoletto P, Ferreira NE, Honorato L, Barbosa EMG, Luchs A, Linhares IM, Spandorfer SD, Leal E, da Costa AC, Witkin SS, Mendes-Correa MC. Characterization of CRESS-DNA viruses in human vaginal secretions: An exploratory metagenomic investigation. J Med Virol 2024; 96:e29750. [PMID: 38953413 DOI: 10.1002/jmv.29750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/16/2024] [Accepted: 06/09/2024] [Indexed: 07/04/2024]
Abstract
The Phylum Cressdnaviricota consists of a large number of circular Rep-encoding single-stranded (CRESS)-DNA viruses. Recently, metagenomic analyzes revealed their ubiquitous distribution in a diverse range of eukaryotes. Data relating to CRESS-DNA viruses in humans remains scarce. Our study investigated the presence and genetic diversity of CRESS-DNA viruses in human vaginal secretions. Vaginal swabs were collected from 28 women between 29 and 43 years old attending a fertility clinic in New York City. An exploratory metagenomic analysis was performed and detection of CRESS-DNA viruses was confirmed through analysis of near full-length sequences of the viral isolates. A phylogenetic tree was based on the REP open reading frame sequences of the CRESS-DNA virus genome. Eleven nearly complete CRESS-DNA viral genomes were identified in 16 (57.1%) women. There were no associations between the presence of these viruses and any demographic or clinical parameters. Phylogenetic analysis indicated that one of the sequences belonged to the genus Gemycircularvirus within the Genomoviridae family, while ten sequences represented previously unclassified species of CRESS-DNA viruses. Novel species of CRESS-DNA viruses are present in the vaginal tract of adult women. Although they be transient commensal agents, the potential clinical implications for their presence at this site cannot be dismissed.
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Affiliation(s)
- Endrya do Socorro Foro Ramos
- Laboratório de diversidade Viral, Instituto de Ciências Biológicas, Departamento de Virologia, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Tania Regina Tozetto-Mendoza
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pietro Bortoletto
- Fertility department, Boston IVF-The Eugin Group, Waltham, Massachusetts, USA
- Medicine department, Harvard Medical School, Boston, Massachusetts, USA
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Noely Evangelista Ferreira
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Layla Honorato
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erick Matheus Garcia Barbosa
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Luchs
- Virology department, Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Sao Paulo, Brazil
| | - Iara M Linhares
- Department of Gynecology and Obstetrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Steven D Spandorfer
- Department of Gynecology and Obstetrics, Center for Reproductive Medicine and Infertility, Weill Cornell Medicine, New York City, New York, USA
| | - Elcio Leal
- Laboratório de diversidade Viral, Instituto de Ciências Biológicas, Departamento de Virologia, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Antonio Charlys da Costa
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Steven S Witkin
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York City, New York, USA
| | - Maria Cassia Mendes-Correa
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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3
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Jansz N, Faulkner GJ. Viral genome sequencing methods: benefits and pitfalls of current approaches. Biochem Soc Trans 2024; 52:1431-1447. [PMID: 38747720 DOI: 10.1042/bst20231322] [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: 02/22/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 06/27/2024]
Abstract
Whole genome sequencing of viruses provides high-resolution molecular insights, enhancing our understanding of viral genome function and phylogeny. Beyond fundamental research, viral sequencing is increasingly vital for pathogen surveillance, epidemiology, and clinical applications. As sequencing methods rapidly evolve, the diversity of viral genomics applications and catalogued genomes continues to expand. Advances in long-read, single molecule, real-time sequencing methodologies present opportunities to sequence contiguous, haplotype resolved viral genomes in a range of research and applied settings. Here we present an overview of nucleic acid sequencing methods and their applications in studying viral genomes. We emphasise the advantages of different viral sequencing approaches, with a particular focus on the benefits of third-generation sequencing technologies in elucidating viral evolution, transmission networks, and pathogenesis.
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Affiliation(s)
- Natasha Jansz
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
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4
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Sidharthan VK, Reddy V, Kiran G, Rajeswari V, Baranwal VK, Kumar MK, Kumar KS. Probing of plant transcriptomes reveals the hidden genetic diversity of the family Secoviridae. Arch Virol 2024; 169:150. [PMID: 38898334 DOI: 10.1007/s00705-024-06076-6] [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: 11/19/2023] [Accepted: 05/07/2024] [Indexed: 06/21/2024]
Abstract
Secoviruses are single-stranded RNA viruses that infect plants. In the present study, we identified 61 putative novel secoviral genomes in various plant species by mining publicly available plant transcriptome data. These viral sequences represent the genomes of 13 monopartite and 48 bipartite secovirids. The genome sequences of 52 secovirids were coding-complete, and nine were partial. Except for small open reading frames (ORFs) determined in waikaviral genomes and RNA2 of torradoviruses, all of the recovered genomes/genome segments contained a large ORF encoding a polyprotein. Based on genome organization and phylogeny, all but three of the novel secoviruses were assigned to different genera. The genome organization of two identified waika-like viruses resembled that of the recently identified waika-like virus Triticum aestivum secovirus. Phylogenetic analysis revealed a pattern of host-virus co-evolution in a few waika- and waika-like viruses and increased phylogenetic diversity of nepoviruses. The study provides a basis for further investigation of the biological properties of these novel secoviruses.
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Affiliation(s)
- V Kavi Sidharthan
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India.
| | - Vijayprakash Reddy
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
| | - G Kiran
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
| | - V Rajeswari
- School of Agricultural Sciences, Malla Reddy University, Hyderabad, India
| | - V K Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - M Kiran Kumar
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
| | - K Sudheer Kumar
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
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5
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Medina JE, Castañeda S, Camargo M, Garcia-Corredor DJ, Muñoz M, Ramírez JD. Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle. Vet Res Commun 2024:10.1007/s11259-024-10403-2. [PMID: 38865041 DOI: 10.1007/s11259-024-10403-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/01/2024] [Indexed: 06/13/2024]
Abstract
Cattle have a significant impact on human societies in terms of both economics and health. Viral infections pose a relevant problem as they directly or indirectly disrupt the balance within cattle populations. This has negative consequences at the economic level for producers and territories, and also jeopardizes human health through the transmission of zoonotic diseases that can escalate into outbreaks or pandemics. To establish prevention strategies and control measures at various levels (animal, farm, region, or global), it is crucial to identify the viral agents present in animals. Various techniques, including virus isolation, serological tests, and molecular techniques like PCR, are typically employed for this purpose. However, these techniques have two major drawbacks: they are ineffective for non-culturable viruses, and they only detect a small fraction of the viruses present. In contrast, metagenomics offers a promising approach by providing a comprehensive and unbiased analysis for detecting all viruses in a given sample. It has the potential to identify rare or novel infectious agents promptly and establish a baseline of healthy animals. Nevertheless, the routine application of viral metagenomics for epidemiological surveillance and diagnostics faces challenges related to socioeconomic variables, such as resource availability and space dedicated to metagenomics, as well as the lack of standardized protocols and resulting heterogeneity in presenting results. This review aims to provide an overview of the current knowledge and prospects for using viral metagenomics to detect and identify viruses in cattle raised for livestock, while discussing the epidemiological and clinical implications.
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Affiliation(s)
- Julián Esteban Medina
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Mosquera, Cundinamarca, Colombia
| | - Diego J Garcia-Corredor
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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6
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An Q, Wang Y, Tian Z, Han J, Li J, Liao F, Yu F, Zhao H, Wen Y, Zhang H, Deng Z. Molecular and structural basis of an ATPase-nuclease dual-enzyme anti-phage defense complex. Cell Res 2024:10.1038/s41422-024-00981-w. [PMID: 38834762 DOI: 10.1038/s41422-024-00981-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
Coupling distinct enzymatic effectors emerges as an efficient strategy for defense against phage infection in bacterial immune responses, such as the widely studied nuclease and cyclase activities in the type III CRISPR-Cas system. However, concerted enzymatic activities in other bacterial defense systems are poorly understood. Here, we biochemically and structurally characterize a two-component defense system DUF4297-HerA, demonstrating that DUF4297-HerA confers resistance against phage infection by cooperatively cleaving dsDNA and hydrolyzing ATP. DUF4297 alone forms a dimer, and HerA alone exists as a nonplanar split spiral hexamer, both of which exhibit extremely low enzymatic activity. Interestingly, DUF4297 and HerA assemble into an approximately 1 MDa supramolecular complex, where two layers of DUF4297 (6 DUF4297 molecules per layer) linked via inter-layer dimerization of neighboring DUF4297 molecules are stacked on top of the HerA hexamer. Importantly, the complex assembly promotes dimerization of DUF4297 molecules in the upper layer and enables a transition of HerA from a nonplanar hexamer to a planar hexamer, thus activating their respective enzymatic activities to abrogate phage infection. Together, our findings not only characterize a novel dual-enzyme anti-phage defense system, but also reveal a unique activation mechanism by cooperative complex assembly in bacterial immunity.
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Affiliation(s)
- Qiyin An
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong Wang
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenhua Tian
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Han
- Department of Human Anatomy, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jinyue Li
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Fumeng Liao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Feiyang Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Haiyan Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yancheng Wen
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian, China
| | - Heng Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zengqin Deng
- Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.
- Hubei Jiangxia Laboratory, Wuhan, Hubei, China.
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7
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Chong LC, Khan AM. A Systematic Bioinformatics Approach for Mapping the Minimal Set of a Viral Peptidome. Curr Protoc 2024; 4:e1056. [PMID: 38856995 DOI: 10.1002/cpz1.1056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Sequence changes in viral genomes generate protein sequence diversity that enables viruses to evade the host immune system, hindering the development of effective preventive and therapeutic interventions. The massive proliferation of sequence data provides unprecedented opportunities to study viral adaptation and evolution. An alignment-free approach removes various restrictions posed by an alignment-dependent approach for studying sequence diversity. The publicly available tool, UNIQmin, offers an alignment-free approach for studying viral sequence diversity at any given rank of taxonomy lineage and is big data ready. The tool performs an exhaustive search to determine the minimal set of sequences required to capture the peptidome diversity within a given dataset. This compression is possible through the removal of identical sequences and unique sequences that do not contribute effectively to the peptidome diversity pool. Herein, we describe a detailed four-part protocol utilizing UNIQmin to generate the minimal set for the purpose of viral diversity analyses, alignment-free at any rank of the taxonomy lineage, using the recent global public health threat Monkeypox virus (MPX) sequence data as a case study. The protocol enables a systematic bioinformatics approach to study sequence diversity across taxonomic lineages, which is crucial for our future preparedness against viral epidemics. This is particularly important when data are abundant, freely available, and alignment is not an option. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Tool installation and input file preparation Basic Protocol 2: Generation of a minimal set of sequences for a given dataset Basic Protocol 3: Comparative minimal set analysis across taxonomic lineage ranks Basic Protocol 4: Factors affecting the minimal set of sequences.
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Affiliation(s)
- Li Chuin Chong
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Turkey
- Current affiliation: Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a Medical School Hannover (MHH) and Helmholtz Centre for Infection Research (HZI) joint venture, Hannover, Germany
| | - Asif M Khan
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Turkey
- Current affiliation: College of Computing and Information Technology, University of Doha for Science and Technology, Doha, Qatar
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8
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Alfonso P, Butković A, Fernández R, Riesgo A, Elena SF. Unveiling the hidden viromes across the animal tree of life: insights from a taxonomic classification pipeline applied to invertebrates of 31 metazoan phyla. mSystems 2024; 9:e0012424. [PMID: 38651902 PMCID: PMC11097642 DOI: 10.1128/msystems.00124-24] [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: 01/26/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Invertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq data sets from diverse environments in the marine-terrestrial and marine-freshwater gradients. This study aims to (i) estimate virome compositions at the family level for the first time across the animal tree of life, including the first exploration of the virome in several phyla, (ii) quantify the diversity of invertebrate viromes and characterize the structure of invertebrate-virus infection networks, and (iii) investigate host phylum and habitat influence on virome differences. Results showed that a set of few viral families of eukaryotes, comprising Retroviridae, Flaviviridae, and several families of giant DNA viruses, were ubiquitous and highly abundant. Nevertheless, some differences emerged between phyla, revealing for instance a less diverse virome in Ctenophora compared to the other animal phyla. Compositional analysis of the viromes showed that the host phylum explained over five times more variance in composition than its habitat. Moreover, significant similarities were observed between the viromes of some phylogenetically related phyla, which could highlight the influence of co-evolution in shaping invertebrate viromes.IMPORTANCEThis study significantly enhances our understanding of the global animal virome by characterizing the viromes of previously unexamined invertebrate lineages from a large number of animal phyla. It showcases the great diversity of viromes within each phylum and investigates the role of habitat shaping animal viral communities. Furthermore, our research identifies dominant virus families in invertebrates and distinguishes phyla with analogous viromes. This study sets the road toward a deeper understanding of the virome across the animal tree of life.
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Affiliation(s)
- Pau Alfonso
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, València, Spain
| | - Anamarija Butković
- Institut Pasteur, Université Paris Cité, CNRS UMR6047 Archaeal Virology Unit, Paris, France
| | - Rosa Fernández
- Instituto de Biología Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Ana Riesgo
- Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
- Department of Life Sciences, Natural History Museum of London, London, United Kingdom
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, València, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, USA
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Wang X, Tang Y, Yue X, Wang S, Yang K, Xu Y, Shen Q, Friman VP, Wei Z. The role of rhizosphere phages in soil health. FEMS Microbiol Ecol 2024; 100:fiae052. [PMID: 38678007 PMCID: PMC11065364 DOI: 10.1093/femsec/fiae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.
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Affiliation(s)
- Xiaofang Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yike Tang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiufeng Yue
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuo Wang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Keming Yang
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Ville-Petri Friman
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Zhong Wei
- Jiangsu provincial key lab for solid organic waste utilization, Key lab of organic-based fertilizers of China,Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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10
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Cook R, Telatin A, Hsieh SY, Newberry F, Tariq MA, Baker DJ, Carding SR, Adriaenssens EM. Nanopore and Illumina sequencing reveal different viral populations from human gut samples. Microb Genom 2024; 10. [PMID: 38683195 DOI: 10.1099/mgen.0.001236] [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: 05/01/2024] Open
Abstract
The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.
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Affiliation(s)
- Ryan Cook
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | | | | | - Fiona Newberry
- Department of Biosciences, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Mohammad A Tariq
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne, NE1 8ST, UK
| | - Dave J Baker
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | - Simon R Carding
- Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
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11
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Chen J, Sun C, Dong Y, Jin M, Lai S, Jia L, Zhao X, Wang H, Gao NL, Bork P, Liu Z, Chen W, Zhao X. Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305818. [PMID: 38240578 PMCID: PMC10987132 DOI: 10.1002/advs.202305818] [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: 08/18/2023] [Revised: 12/01/2023] [Indexed: 04/04/2024]
Abstract
Current metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus-like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short- and long-read. Applied to 135 samples, a Chinese Gut Virome Catalog (CHGV) is assembled consisting of 21,499 non-redundant viral operational taxonomic units (vOTUs) that are significantly longer than those obtained by short-read sequencing and contained ≈35% (7675) complete genomes, which is ≈nine times more than those in the Gut Virome Database (GVD, ≈4%, 1,443). Interestingly, the majority (≈60%, 13,356) of the CHGV vOTUs are obtained by either long-read or hybrid assemblies, with little overlap with those assembled from only the short-read data. With this dataset, vast diversity of the gut virome is elucidated, including the identification of 32% (6,962) novel vOTUs compare to public gut virome databases, dozens of phages that are more prevalent than the crAssphages and/or Gubaphages, and several viral clades that are more diverse than the two. Finally, the functional capacities are also characterized of the CHGV encoded proteins and constructed a viral-host interaction network to facilitate future research and applications.
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Affiliation(s)
- Jingchao Chen
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Yanqi Dong
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Menglu Jin
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
| | - Senying Lai
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Longhao Jia
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Xueyang Zhao
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
| | - Huarui Wang
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Na L. Gao
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- Department of Laboratory MedicineZhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan430071China
| | - Peer Bork
- European Molecular Biology LaboratoryStructural and Computational Biology Unit69117HeidelbergGermany
- Max Delbrück Centre for Molecular Medicine13125BerlinGermany
- Yonsei Frontier Lab (YFL)Yonsei University03722SeoulSouth Korea
- Department of BioinformaticsBiocenterUniversity of Würzburg97070WürzburgGermany
| | - Zhi Liu
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and Technology430074WuhanChina
| | - Wei‐Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
- Institution of Medical Artificial IntelligenceBinzhou Medical UniversityYantai264003China
| | - Xing‐Ming Zhao
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligenceand MOE Frontiers Center for Brain ScienceFudan UniversityShanghai200433China
- State Key Laboratory of Medical NeurobiologyInstitute of Brain ScienceFudan UniversityShanghai200433China
- International Human Phenome Institutes (Shanghai)Shanghai200433China
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12
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Couto RDS, Abreu WU, Rodrigues LRR, Marinho LF, Morais VDS, Villanova F, Pandey RP, Deng X, Delwart E, da Costa AC, Leal E. Genomoviruses in Liver Samples of Molossus molossus Bats. Microorganisms 2024; 12:688. [PMID: 38674632 PMCID: PMC11052389 DOI: 10.3390/microorganisms12040688] [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: 02/24/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
CRESS-DNA encompasses a broad spectrum of viruses documented across diverse organisms such as animals, plants, diatoms, fungi, and marine invertebrates. Despite this prevalence, the full extent of these viruses' impact on the environment and their respective hosts remains incompletely understood. Furthermore, an increasing number of viruses within this category lack detailed characterization. This investigation focuses on unveiling and characterizing viruses affiliated with the Genomoviridae family identified in liver samples from the bat Molossus molossus. Leveraging viral metagenomics, we identified seven sequences (MmGmV-PA) featuring a circular DNA genome housing two ORFs encoding replication-associated protein (Rep) and capsid protein (Cap). Predictions based on conserved domains typical of the Genomoviridae family were established. Phylogenetic analysis revealed the segregation of these sequences into two clades aligning with the genera Gemycirculavirus (MmGmV-06-PA and MmGmV-07-PA) and Gemykibivirus (MmGmV-01-PA, MmGmV-02-PA, MmGmV-03-PA, MmGmV-05-PA, and MmGmV-09-PA). At the species level, pairwise comparisons based on complete nucleotide sequences indicated the potential existence of three novel species. In summary, our study significantly contributes to an enhanced understanding of the diversity of Genomoviridae within bat samples, shedding light on previously undiscovered viral entities and their potential ecological implications.
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Affiliation(s)
- Roseane da Silva Couto
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
| | - Wandercleyson Uchôa Abreu
- Programa de Pos-Graduação REDE Bionorte, Polo Pará, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | - Luís Reginaldo Ribeiro Rodrigues
- Laboratory of Genetics & Biodiversity, Institute of Educational Sciences, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | | | - Vanessa dos Santos Morais
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
| | - Ramendra Pati Pandey
- School of Health Sciences & Technology, UPES University, Dehradun 248007, Uttarakhand, India;
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94143, USA;
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA;
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
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13
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Tarakanov RI, Evseev PV, Vo HTN, Troshin KS, Gutnik DI, Ignatov AN, Toshchakov SV, Miroshnikov KA, Jafarov IH, Dzhalilov FSU. Xanthomonas Phage PBR31: Classifying the Unclassifiable. Viruses 2024; 16:406. [PMID: 38543771 PMCID: PMC10975493 DOI: 10.3390/v16030406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/24/2024] [Accepted: 03/04/2024] [Indexed: 05/23/2024] Open
Abstract
The ability of bacteriophages to destroy bacteria has made them the subject of extensive research. Interest in bacteriophages has recently increased due to the spread of drug-resistant bacteria, although genomic research has not kept pace with the growth of genomic data. Genomic analysis and, especially, the taxonomic description of bacteriophages are often difficult due to the peculiarities of the evolution of bacteriophages, which often includes the horizontal transfer of genes and genomic modules. The latter is particularly pronounced for temperate bacteriophages, which are capable of integration into the bacterial chromosome. Xanthomonas phage PBR31 is a temperate bacteriophage, which has been neither described nor classified previously, that infects the plant pathogen Xanthomonas campestris pv. campestris. Genomic analysis, including phylogenetic studies, indicated the separation of phage PBR31 from known classified bacteriophages, as well as its distant relationship with other temperate bacteriophages, including the Lederbervirus group. Bioinformatic analysis of proteins revealed distinctive features of PBR31, including the presence of a protein similar to the small subunit of D-family DNA polymerase and advanced lysis machinery. Taxonomic analysis showed the possibility of assigning phage PBR31 to a new taxon, although the complete taxonomic description of Xanthomonas phage PBR31 and other related bacteriophages is complicated by the complex evolutionary history of the formation of its genome. The general biological features of the PBR31 phage were analysed for the first time. Due to its presumably temperate lifestyle, there is doubt as to whether the PBR31 phage is appropriate for phage control purposes. Bioinformatics analysis, however, revealed the presence of cell wall-degrading enzymes that can be utilised for the treatment of bacterial infections.
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Affiliation(s)
- Rashit I. Tarakanov
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (K.S.T.)
| | - Peter V. Evseev
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (K.S.T.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Laboratory of Molecular Microbiology, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Ha T. N. Vo
- Faculty of Agronomy, Nong Lam University, Quarter 6, Thu Duc District, Ho Chi Minh City 721400, Vietnam
| | - Konstantin S. Troshin
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (K.S.T.)
| | - Daria I. Gutnik
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia;
| | - Aleksandr N. Ignatov
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str. 6, 117198 Moscow, Russia;
| | - Stepan V. Toshchakov
- Center for Genome Research, National Research Center “Kurchatov Institute”, Kurchatov Sq., 1, 123098 Moscow, Russia
| | - Konstantin A. Miroshnikov
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (K.S.T.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Ibrahim H. Jafarov
- Azerbaijan Scientific Research Institute for Plant Protection and Industrial Crops, AZ 4200 Ganja, Azerbaijan
| | - Fevzi S.-U. Dzhalilov
- Department of Plant Protection, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia; (R.I.T.); (K.S.T.)
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14
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Bozdag GO, Szeinbaum N, Conlin PL, Chen K, Fos SM, Garcia A, Penev PI, Schaible GA, Trubl G. Chapter 5: Major Biological Innovations in the History of Life on Earth. ASTROBIOLOGY 2024; 24:S107-S123. [PMID: 38498818 PMCID: PMC11071111 DOI: 10.1089/ast.2021.0119] [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: 07/27/2021] [Accepted: 11/14/2023] [Indexed: 03/20/2024]
Abstract
All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA-the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. This chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell-the eukaryotic cell-which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.
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Affiliation(s)
- G. Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L. Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin–Madison, Wisconsin, USA
| | - Petar I. Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - George A. Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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15
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Wang H, Ülgen M, Trajkovski M. Importance of temperature on immuno-metabolic regulation and cancer progression. FEBS J 2024; 291:832-845. [PMID: 36152006 DOI: 10.1111/febs.16632] [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: 06/23/2022] [Revised: 09/01/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022]
Abstract
Cancer immunotherapies emerge as promising strategies for restricting tumour growth. The tumour microenvironment (TME) has a major impact on the anti-tumour immune response and on the efficacy of the immunotherapies. Recent studies have linked changes in the ambient temperature with particular immuno-metabolic reprogramming and anti-cancer immune response in laboratory animals. Here, we describe the energetic balance of the organism during change in temperature, and link this to the immune alterations that could be of relevance for cancer, as well as for other human diseases. We highlight the contribution of the gut microbiota in modifying this interaction. We describe the overall metabolic response and underlying mechanisms of tumourigenesis in mouse models at varying ambient temperatures and shed light on their potential importance in developing therapeutics against cancer.
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Affiliation(s)
- Haiping Wang
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Centre Medical Universitaire (CMU), University of Geneva, Geneva, Switzerland
- Faculty of Medicine, Diabetes Center, University of Geneva, Geneva, Switzerland
| | - Melis Ülgen
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Centre Medical Universitaire (CMU), University of Geneva, Geneva, Switzerland
- Faculty of Medicine, Diabetes Center, University of Geneva, Geneva, Switzerland
| | - Mirko Trajkovski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Centre Medical Universitaire (CMU), University of Geneva, Geneva, Switzerland
- Faculty of Medicine, Diabetes Center, University of Geneva, Geneva, Switzerland
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16
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Liu L, Chen J, Jiang J, Liang J, Song Y, Chen Q, Yan F, Bai Z, Song Z, Liu J. Detection of Candidatus Liberibacter asiaticus and five viruses in individual Asian citrus psyllid in China. FRONTIERS IN PLANT SCIENCE 2024; 15:1357163. [PMID: 38379950 PMCID: PMC10877018 DOI: 10.3389/fpls.2024.1357163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024]
Abstract
Introduction Asian citrus psyllid (ACP, Diaphorina citri) is an important transmission vector of "Candidatus Liberibacter asiaticus" (CLas), the causal agent of Huanglongbing (HLB), the most destructive citrus disease in the world. As there are currently no HLB-resistant rootstocks or varieties, the control of ACP is an important way to prevent HLB. Some viruses of insect vectors can be used as genetically engineered materials to control insect vectors. Methods To gain knowledge on viruses in ACP in China, the prevalence of five RNA and DNA viruses was successfully determined by optimizing reverse transcription polymerase chain reaction (RT-PCR) in individual adult ACPs. The five ACP-associated viruses were identified as follows: diaphorina citri bunyavirus 2, which was newly identified by high-throughput sequencing in our lab, diaphorina citri reovirus (DcRV), diaphorina citri picorna-like virus (DcPLV), diaphorina citri bunyavirus (DcBV), and diaphorina citri densovirus-like virus (DcDV). Results DcPLV was the most prevalent and widespread ACP-associated virus, followed by DcBV, and it was detected in more than 50% of all samples tested. DcPLV was also demonstrated to propagate vertically and found more in salivary glands among different tissues. Approximately 60% of all adult insect samples were co-infected with more than one insect pathogen, including the five ACP-associated viruses and CLas. Discussion This is the first time these viruses, including the newly identified ACP-associated virus, have been detected in individual adult ACPs from natural populations in China's five major citrus-producing provinces. These results provide valuable information about the prevalence of ACP-associated viruses in China, some of which have the potential to be used as biocontrol agents. In addition, analysis of the change in prevalence of pathogens in a single insect vector is the basis for understanding the interactions between CLas, ACP, and insect viruses.
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Affiliation(s)
- Luqin Liu
- Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing, China
| | - Jing Chen
- Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing, China
| | - Junyao Jiang
- Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing, China
| | - Jiamei Liang
- Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing, China
| | - Yaqin Song
- Guangxi Academy of Specialty Crops, Guangxi Citrus Breeding and Cultivation Research Center of Engineering Technology, Guangxi, China
| | - Qi Chen
- Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing, China
| | - Fuling Yan
- Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing, China
| | - Ziqin Bai
- Fruit Research Institute, Guizhou Provincial Academy of Agricultural Sciences, Guizhou, China
| | - Zhen Song
- Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing, China
| | - Jinxiang Liu
- Citrus Research Institute, Southwest University/National Citrus Engineering Research Center, Chongqing, China
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17
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Cisneros-Martínez AM, Rodriguez-Cruz UE, Alcaraz LD, Becerra A, Eguiarte LE, Souza V. Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico. PLoS One 2024; 19:e0291402. [PMID: 38300968 PMCID: PMC10833507 DOI: 10.1371/journal.pone.0291402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Due to the enormous diversity of non-culturable viruses, new viruses must be characterized using culture-independent techniques. The associated host is an important phenotypic feature that can be inferred from metagenomic viral contigs thanks to the development of several bioinformatic tools. Here, we compare the performance of recently developed virus-host prediction tools on a dataset of 1,046 virus-host pairs and then apply the best-performing tools to a metagenomic dataset derived from a highly diverse transiently hypersaline site known as the Archaean Domes (AD) within the Cuatro Ciénegas Basin, Coahuila, Mexico. Among host-dependent methods, alignment-based approaches had a precision of 66.07% and a sensitivity of 24.76%, while alignment-free methods had an average precision of 75.7% and a sensitivity of 57.5%. RaFAH, a virus-dependent alignment-based tool, had the best overall performance (F1_score = 95.7%). However, when predicting the host of AD viruses, methods based on public reference databases (such as RaFAH) showed lower inter-method agreement than host-dependent methods run against custom databases constructed from prokaryotes inhabiting AD. Methods based on custom databases also showed the greatest agreement between the source environment and the predicted host taxonomy, habitat, lifestyle, or metabolism. This highlights the value of including custom data when predicting hosts on a highly diverse metagenomic dataset, and suggests that using a combination of methods and qualitative validations related to the source environment and predicted host biology can increase the number of correct predictions. Finally, these predictions suggest that AD viruses infect halophilic archaea as well as a variety of bacteria that may be halophilic, halotolerant, alkaliphilic, thermophilic, oligotrophic, sulfate-reducing, or marine, which is consistent with the specific environment and the known geological and biological evolution of the Cuatro Ciénegas Basin and its microorganisms.
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Affiliation(s)
- Alejandro Miguel Cisneros-Martínez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ulises E. Rodriguez-Cruz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis D. Alcaraz
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Arturo Becerra
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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18
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Urayama SI, Fukudome A, Hirai M, Okumura T, Nishimura Y, Takaki Y, Kurosawa N, Koonin EV, Krupovic M, Nunoura T. Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan. Nat Microbiol 2024; 9:514-523. [PMID: 38233646 PMCID: PMC10847044 DOI: 10.1038/s41564-023-01579-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024]
Abstract
Metatranscriptome sequencing expanded the known diversity of the bacterial RNA virome, suggesting that additional riboviruses infecting bacterial hosts remain to be discovered. Here we employed double-stranded RNA sequencing to recover complete genome sequences of two ribovirus groups from acidic hot springs in Japan. One group, denoted hot spring riboviruses (HsRV), consists of viruses with distinct RNA-directed RNA polymerases (RdRPs) that seem to be intermediates between typical ribovirus RdRPs and viral reverse transcriptases. This group forms a distinct phylum, Artimaviricota, or even kingdom within the realm Riboviria. We identified viruses encoding HsRV-like RdRPs in marine water, river sediments and salt marshes, indicating that this group is widespread beyond extreme ecosystems. The second group, denoted hot spring partiti-like viruses (HsPV), forms a distinct branch within the family Partitiviridae. The genome architectures of HsRV and HsPV and their identification in bacteria-dominated habitats suggest that these viruses infect thermoacidophilic bacteria.
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Affiliation(s)
- Syun-Ichi Urayama
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, Tsukuba, Japan.
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan.
| | - Akihito Fukudome
- Howard Hughes Medical Institute, Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Tomoyo Okumura
- Marine Core Research Institute, Kochi University, Nankoku, Kochi, Japan
| | - Yosuke Nishimura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC, Yokosuka, Japan
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Norio Kurosawa
- Faculty of Science and Engineering, Soka University, Hachioji, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC, Yokosuka, Japan
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19
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Liu K, Wang C, Zhou X, Guo X, Yang Y, Liu W, Zhao R, Song H. Bacteriophage therapy for drug-resistant Staphylococcus aureus infections. Front Cell Infect Microbiol 2024; 14:1336821. [PMID: 38357445 PMCID: PMC10864608 DOI: 10.3389/fcimb.2024.1336821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Drug-resistant Staphylococcus aureus stands as a prominent pathogen in nosocomial and community-acquired infections, capable of inciting various infections at different sites in patients. This includes Staphylococcus aureus bacteremia (SaB), which exhibits a severe infection frequently associated with significant mortality rate of approximately 25%. In the absence of better alternative therapies, antibiotics is still the main approach for treating infections. However, excessive use of antibiotics has, in turn, led to an increase in antimicrobial resistance. Hence, it is imperative that new strategies are developed to control drug-resistant S. aureus infections. Bacteriophages are viruses with the ability to infect bacteria. Bacteriophages, were used to treat bacterial infections before the advent of antibiotics, but were subsequently replaced by antibiotics due to limited theoretical understanding and inefficient preparation processes at the time. Recently, phages have attracted the attention of many researchers again because of the serious problem of antibiotic resistance. This article provides a comprehensive overview of phage biology, animal models, diverse clinical case treatments, and clinical trials in the context of drug-resistant S. aureus phage therapy. It also assesses the strengths and limitations of phage therapy and outlines the future prospects and research directions. This review is expected to offer valuable insights for researchers engaged in phage-based treatments for drug-resistant S. aureus infections.
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Affiliation(s)
- Kaixin Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Chao Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xudong Zhou
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- College of Public Health, China Medical University, Shenyang, China
| | - Xudong Guo
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yi Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Wanying Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Rongtao Zhao
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- College of Public Health, Zhengzhou University, Zhengzhou, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- College of Public Health, China Medical University, Shenyang, China
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20
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Lindner BG, Gerhardt K, Feistel DJ, Rodriguez-R LM, Hatt JK, Konstantinidis KT. A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection. Int J Food Microbiol 2024; 410:110488. [PMID: 38035404 DOI: 10.1016/j.ijfoodmicro.2023.110488] [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: 05/17/2023] [Revised: 09/15/2023] [Accepted: 11/11/2023] [Indexed: 12/02/2023]
Abstract
Metagenomics, i.e., shotgun sequencing of the total microbial community DNA from a sample, has become a mature technique but its application to pathogen detection in clinical, environmental, and food samples is far from common or standardized. In this review, we summarize ongoing developments in metagenomic sequence analysis that facilitate its wider application to pathogen detection. We examine theoretical frameworks for estimating the limit of detection for a particular level of sequencing effort, current approaches for achieving species and strain analytical resolution, and discuss some relevant modern tools for these tasks. While these recent advances are significant and establish metagenomics as a powerful tool to provide insights not easily attained by culture-based approaches, metagenomics is unlikely to emerge as a widespread, routine monitoring tool in the near future due to its inherently high detection limits, cost, and inability to easily distinguish between viable and non-viable cells. Instead, metagenomics seems best poised for applications involving special circumstances otherwise challenging for culture-based and molecular (e.g., PCR-based) approaches such as the de novo detection of novel pathogens, cases of co-infection by more than one pathogen, and situations where it is important to assess the genomic composition of the pathogenic population(s) and/or its impact on the indigenous microbiome.
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Affiliation(s)
- Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kenji Gerhardt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Dorian J Feistel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Luis M Rodriguez-R
- Department of Microbiology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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21
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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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22
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Labutin A, Heckel G. Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage. Virus Evol 2024; 10:veae002. [PMID: 38361825 PMCID: PMC10868551 DOI: 10.1093/ve/veae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/08/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from forty-two locations in the contact region between clades for TULV infection by reverse transcription (RT)-PCR. Sequencing yielded twenty-three TULV Central North and twenty-one TULV Central South genomes, which differed by 14.9-18.5 per cent at the nucleotide and 2.2-3.7 per cent at the amino acid (AA) level without evidence of recombination or reassortment between clades. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis, and genomic single nucleotide polymorphisms showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species, which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.
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Affiliation(s)
- Anton Labutin
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
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23
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Turner D, Adriaenssens EM, Lehman SM, Moraru C, Kropinski AM. Bacteriophage Taxonomy: A Continually Evolving Discipline. Methods Mol Biol 2024; 2734:27-45. [PMID: 38066361 DOI: 10.1007/978-1-0716-3523-0_3] [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] [Indexed: 12/18/2023]
Abstract
While taxonomy is an often underappreciated branch of science, it serves very important roles. Bacteriophage taxonomy has evolved from a discipline based mainly on morphology, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the sequence-based approach that is taken today. The Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a holistic approach to classifying prokaryote viruses by measuring overall DNA and protein similarity and phylogeny before making decisions about the taxonomic position of a new virus. The huge number of complete genomes being deposited with the National Center for Biotechnology Information (NCBI) and other public databases has resulted in a reassessment of the taxonomy of many viruses, and the future will see the introduction of new viral families and higher orders.
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Affiliation(s)
- Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, UK
| | | | - Susan M Lehman
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Cristina Moraru
- Department of The Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Andrew M Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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24
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Rodríguez-Negrete EA, Grande-Pérez A. Quantification of Virion-Sense and Complementary-Sense DNA Strands of Circular Single-Stranded DNA Viruses. Methods Mol Biol 2024; 2724:93-109. [PMID: 37987901 DOI: 10.1007/978-1-0716-3485-1_8] [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: 11/22/2023]
Abstract
Circular ssDNA viruses are ubiquitous and can be found in both prokaryotes and eukaryotes. To understand the interaction of ssDNA viruses with their hosts, it is important to characterize the dynamics of viral sense (VS) and complementary-sense (CS) viral strands during the infection process. Here, we present a simple and rapid protocol that allows sensitive and accurate determination of the VS and CS strands generated during viral infection.The method consists of a two-step qPCR in which the first step uses a strand-specific (CS or VS) labeled primer and T4 DNA polymerase that lacks strand displacement activity and makes a single copy per VS or CS strand. Next, the T4 DNA polymerase and unincorporated oligonucleotides are removed by a silica membrane spin column. Finally, the purified VS or CS strands are quantified by qPCR in a second step in which amplification uses a tag primer and a specific primer. Absolute quantification of VS and CS strands is obtained by extrapolating the Cq data to a standard curve of ssDNA, which can be generated by phagemid expression. Quantification of VS and CS strands of two geminiviruses in infections of Solanum lycopersicum (tomato) and Nicotiana benthamiana plants using this method is shown.
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Affiliation(s)
- Edgar A Rodríguez-Negrete
- Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa, Mexico
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain.
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.
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25
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Ghafari M, Sõmera M, Sarmiento C, Niehl A, Hébrard E, Tsoleridis T, Ball J, Moury B, Lemey P, Katzourakis A, Fargette D. Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses. PLoS Pathog 2024; 20:e1011911. [PMID: 38206964 PMCID: PMC10807823 DOI: 10.1371/journal.ppat.1011911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/24/2024] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that the Sobemovirus genus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence nearly 9,000 years ago, a time coinciding with the Neolithic period in the Near East. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species. We identified major radiation events beginning between 4,600 to 2,000 years ago, which aligns with the Neolithic period in various regions, suggesting a period of rapid diversification from then to the present. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.
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Affiliation(s)
- Mahan Ghafari
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Annette Niehl
- Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Eugénie Hébrard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Theocharis Tsoleridis
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Jonathan Ball
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Denis Fargette
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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26
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Chen JT, Zhan JB, Zhu MC, Li KJ, Liu MQ, Hu B, Cai K, Xiong HR, Chen SL, Tan WL, Chen LJ, Hou W. Diversity and genetic characterization of orthohantavirus from small mammals and humans during 2012-2022 in Hubei Province, Central China. Acta Trop 2024; 249:107046. [PMID: 37866727 DOI: 10.1016/j.actatropica.2023.107046] [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: 07/15/2023] [Revised: 10/03/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Hemorrhagic fever with renal syndrome (HFRS) is a significant public health problem in Hubei Province, China, where a novel strain of orthohantavirus, HV004, was reported in 2012. However, no systematic study has investigated the prevalence and variation of orthohantavirus in rodents and humans. Herein, 2137 small mammals were collected from ten HFRS epidemic areas in Hubei Province from 2012 to 2022, and 143 serum samples from patients with suspected hemorrhagic fever were collected from two hospitals from 2017 to 2021. Orthohantavirus RNA was recovered from 134 lung tissue samples from five rodent species, with a 6.27 % prevalence, and orthohantavirus was detected in serum samples from 25 patients. Genetic analyses revealed that orthohantavirus hantanense (HTNV), orthohantavirus seoulense (SEOV), and orthohantavirus dabieshanense (DBSV) are co-circulating in rodents in Hubei, and HTNV and SEOV were identified in patient serum. Phylogenetic analysis showed that most of the HTNV sequences were clustered with HV004, indicating that HV004-like orthohantavirus was the main HNTV subtype in rodents. Two genetic reassortments and six recombination events were observed in Hubei orthohantaviruses. In summary, this study identified the diversity of orthohantaviruses circulating in Hubei over the past decade, with the HV004-like subtype being the main genotype in rodents and patients. These findings highlight the need for continued attention and focus on orthohantaviruses, especially concerning newly identified strains.
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Affiliation(s)
- Jin-Tao Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Jian-Bo Zhan
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control & Prevention, 6 Zhuodaoquan Road, Wuhan, Hubei 430079, China
| | - Ming-Chao Zhu
- Department of Clinical Laboratory, The First People's Hospital of Tianmen, 1 Jingling Renming Road, Tianmen, Hubei 431700, China
| | - Kai-Ji Li
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Man-Qing Liu
- Division of Virology, Wuhan Center for Disease Control & Prevention, 288 Machang Road, Wuhan, Hubei 430015, China
| | - Bin Hu
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control & Prevention, 6 Zhuodaoquan Road, Wuhan, Hubei 430079, China
| | - Kun Cai
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control & Prevention, 6 Zhuodaoquan Road, Wuhan, Hubei 430079, China
| | - Hai-Rong Xiong
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Shu-Liang Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Wei-Long Tan
- Department of Infection Disease, Nanjing Bioengineering (Gene) Technology Center for Medicines, 293 Zhongshan East Road, Nanjing, Jiangsu 210002, China
| | - Liang-Jun Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China.
| | - Wei Hou
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China; School of Public Health, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China; School of Ecology and Environment, Tibet University, 36 Jiangsu Road, Lhasa 850000, China.
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27
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Zhou Y, Wang Y, Prangishvili D, Krupovic M. Exploring the Archaeal Virosphere by Metagenomics. Methods Mol Biol 2024; 2732:1-22. [PMID: 38060114 DOI: 10.1007/978-1-0716-3515-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
During the past decade, environmental research has demonstrated that archaea are abundant and widespread in nature and play important ecological roles at a global scale. Currently, however, the majority of archaeal lineages cannot be cultivated under laboratory conditions and are known exclusively or nearly exclusively through metagenomics. A similar trend extends to the archaeal virosphere, where isolated representatives are available for a handful of model archaeal virus-host systems. Viral metagenomics provides an alternative way to circumvent the limitations of culture-based virus discovery and offers insight into the diversity, distribution, and environmental impact of uncultured archaeal viruses. Presently, metagenomics approaches have been successfully applied to explore the viromes associated with various lineages of extremophilic and mesophilic archaea, including Asgard archaea (Asgardarchaeota), ANME-1 archaea (Methanophagales), thaumarchaea (Nitrososphaeria), altiarchaea (Altiarchaeota), and marine group II archaea (Poseidoniales). Here, we provide an overview of methods widely used in archaeal virus metagenomics, covering metavirome preparation, genome annotation, phylogenetic and phylogenomic analyses, and archaeal host assignment. We hope that this summary will contribute to further exploration and characterization of the enigmatic archaeal virome lurking in diverse environments.
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Affiliation(s)
- Yifan Zhou
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
| | - David Prangishvili
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France.
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28
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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29
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Medina JE, Castañeda S, Páez-Triana L, Camargo M, Garcia-Corredor DJ, Gómez M, Luna N, Ramírez AL, Pulido-Medellín M, Muñoz M, Ramírez JD. High prevalence of Enterovirus E, Bovine Kobuvirus, and Astrovirus revealed by viral metagenomics in fecal samples from cattle in Central Colombia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 117:105543. [PMID: 38135265 DOI: 10.1016/j.meegid.2023.105543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023]
Abstract
Livestock plays a crucial role in ensuring food security and driving the global economy. However, viral infections can have far-reaching consequences beyond economic productivity, affecting the health of cattle, as well as posing risks to human health and other animals. Identifying viruses present in fecal samples, a primary route of pathogen transmission, is essential for developing effective prevention, control, and surveillance strategies. Viral metagenomic approaches offer a broader perspective and hold great potential for detecting previously unknown viruses or uncovering previously undescribed agents. Ubaté Province is Colombia's dairy capital and a key center for livestock production in the country. Therefore, the purpose of this study was to characterize viral communities in fecal samples from cattle in this region. A total of 42 samples were collected from three municipalities in Ubaté Province, located in central Colombia, using a convenient non-probabilistic sampling method. We utilized metagenomic sequencing with Oxford Nanopore Technologies (ONT), combined with diversity and phylogenetic analysis. The findings revealed a consistent and stable viral composition across the municipalities, primarily comprising members of the Picornaviridae family. At the species level, the most frequent viruses were Enterovirus E (EVE) and Bovine Astrovirus (BoAstV). Significantly, this study reported, for the first time in Colombia, the presence of viruses with veterinary importance occurring at notable frequencies: EVE (59%), Bovine Kobuvirus (BKV) (52%), and BoAstV (19%). Additionally, the study confirmed the existence of Circular replicase-encoding single-stranded (CRESS) Virus in animal feces. These sequences were phylogenetically grouped with samples obtained from Asia and Latin America, underscoring the importance of having adequate representation across the continent. The virome of bovine feces in Ubaté Province is characterized by the predominance of potentially pathogenic viruses such as BoAstV and EVE that have been reported with substantial frequency and quantities. Several of these viruses were identified in Colombia for the first time. This study showcases the utility of using metagenomic sequencing techniques in epidemiological surveillance. It also paves the way for further research on the influence of these agents on bovine health and their frecuency across the country.
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Affiliation(s)
- Julián Esteban Medina
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luisa Páez-Triana
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Funza, Cundinamarca, Colombia
| | - Diego J Garcia-Corredor
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marcela Gómez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Grupo de Investigación en Ciencias Básicas (NÚCLEO) Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Angie L Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Martín Pulido-Medellín
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
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Brait N, Hackl T, Morel C, Exbrayat A, Gutierrez S, Lequime S. A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data. Virus Evol 2023; 10:vead088. [PMID: 38516656 PMCID: PMC10956553 DOI: 10.1093/ve/vead088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/24/2023] [Accepted: 12/22/2023] [Indexed: 03/23/2024] Open
Abstract
Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.
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Affiliation(s)
- Nadja Brait
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9747 AG, The Netherlands
| | | | - Côme Morel
- ASTRE research unit, Cirad, INRAe, Université de Montpellier, Montpellier 34398, France
| | - Antoni Exbrayat
- ASTRE research unit, Cirad, INRAe, Université de Montpellier, Montpellier 34398, France
| | - Serafin Gutierrez
- ASTRE research unit, Cirad, INRAe, Université de Montpellier, Montpellier 34398, France
| | - Sebastian Lequime
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9747 AG, The Netherlands
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31
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Lievens EJP, Agarkova IV, Dunigan DD, Van Etten JL, Becks L. Efficient assays to quantify the life history traits of algal viruses. Appl Environ Microbiol 2023; 89:e0165923. [PMID: 38092674 PMCID: PMC10734466 DOI: 10.1128/aem.01659-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 12/22/2023] Open
Abstract
IMPORTANCE Viruses play a crucial role in microbial ecosystems by liberating nutrients and regulating the growth of their hosts. These effects are governed by viral life history traits, i.e., by the traits determining viral reproduction and survival. Understanding these traits is essential to predicting viral effects, but measuring them is generally labor intensive. In this study, we present efficient methods to quantify the full life cycle of lytic viruses. We developed these methods for viruses infecting unicellular Chlorella algae but expect them to be applicable to other lytic viruses that can be quantified by flow cytometry. By making viral phenotypes accessible, our methods will support research into the diversity and ecological effects of microbial viruses.
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Affiliation(s)
- Eva J. P. Lievens
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Irina V. Agarkova
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - David D. Dunigan
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - James L. Van Etten
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Lutz Becks
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Konstanz, Germany
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32
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Zell R, Groth M, Selinka L, Selinka HC. Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany. Pathogens 2023; 12:1458. [PMID: 38133341 PMCID: PMC10745976 DOI: 10.3390/pathogens12121458] [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: 11/18/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Plant-infecting RNA viruses from 30 families and floating genera, as well as a great number of uncultured as yet-unclassified plant-associated viruses have been described. Even so, the plant RNA virosphere is still underexplored. RNA extracted from enriched virus particles of 50 L water samples from the Teltow Canal and the Havel River in Berlin, Germany, was sequenced using Illumina next-generation sequencing. Sequences were searched for plant viruses with BLAST and DIAMOND. Phylogenetic analyses were conducted with IQ-TREE 2. Altogether, 647 virus sequences greater than 1 kb were detected and further analyzed. These data revealed the presence of accepted and novel viruses related to Albetovirus, Alphaflexiviridae, Aspiviridae, Bromoviridae, Endornaviridae, Partitiviridae, Potyviridae, Solemoviridae, Tombusviridae and Virgaviridae. The vast majority of the sequences were novel and could not be taxonomically assigned. Several tombus- and endorna-like viruses make use of alternative translation tables that suggest unicellular green algae, ciliates, or diplomonades as their hosts. The identification of 27 albeto-like satellite viruses increases available sequence data five-fold. Sixteen new poty-like viruses align with other poty-like viruses in a link that combines the Astroviridae and Potyviridae families. Further, the identification of viruses with peptidase A6-like and peptidase A21-like capsid proteins suggests horizontal gene transfer in the evolution of these viruses.
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Affiliation(s)
- Roland Zell
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07745 Jena, Germany
| | - Marco Groth
- CF Next Generation Sequencing, Leibniz Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Lukas Selinka
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07745 Jena, Germany
| | - Hans-Christoph Selinka
- Section II 1.4 Microbiological Risks, Department of Environmental Hygiene, German Environment Agency, 14195 Berlin, Germany
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Lopez-Simon J, Vila-Nistal M, Rosenova A, De Corte D, Baltar F, Martinez-Garcia M. Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles. Nat Commun 2023; 14:8295. [PMID: 38097581 PMCID: PMC10721903 DOI: 10.1038/s41467-023-44028-x] [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: 05/30/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses play an important role in the marine ecosystem. However, our comprehension of viruses inhabiting the dark ocean, and in particular, under the Antarctic Ice Shelves, remains limited. Here, we mine single-cell genomic, transcriptomic, and metagenomic data to uncover the viral diversity, biogeography, activity, and their role as metabolic facilitators of microbes beneath the Ross Ice Shelf. This is the largest Antarctic ice shelf with a major impact on global carbon cycle. The viral community found in the cavity under the ice shelf mainly comprises endemic viruses adapted to polar and mesopelagic environments. The low abundance of genes related to lysogenic lifestyle (<3%) does not support a predominance of the Piggyback-the-Winner hypothesis, consistent with a low-productivity habitat. Our results indicate a viral community actively infecting key ammonium and sulfur-oxidizing chemolithoautotrophs (e.g. Nitrosopumilus spp, Thioglobus spp.), supporting a "kill-the-winner" dynamic. Based on genome analysis, these viruses carry specific auxiliary metabolic genes potentially involved in nitrogen, sulfur, and phosphorus acquisition. Altogether, the viruses under Antarctic ice shelves are putatively involved in programming the metabolism of ecologically relevant microbes that maintain primary production in these chemosynthetically-driven ecosystems, which have a major role in global nutrient cycles.
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Affiliation(s)
- Javier Lopez-Simon
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain
| | - Marina Vila-Nistal
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain
| | - Aleksandra Rosenova
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain
| | - Daniele De Corte
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Ocean Technology and Engineering, National Oceanography Centre, Southampton, UK
| | - Federico Baltar
- Department of Functional & Evolutionary Ecology, University of Vienna, Djerassi-Platz 1, 1030, Vienna, Austria.
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, 03690, Spain.
- Instituto Multidisciplinar para el Estudio del Medio Ramon Margalef, University of Alicante, San Vicente del Raspeig, Alicante, 03690, Spain.
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Bejerman N, Dietzgen R, Debat H. Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses. Viruses 2023; 15:2402. [PMID: 38140643 PMCID: PMC10747219 DOI: 10.3390/v15122402] [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: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented viruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the family Rhabdoviridae, and they should be classified in a novel genus within this family for which we suggest the name "Trirhavirus". Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (family Fimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genus Cytorhabdovirus into three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of the genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.
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Affiliation(s)
- Nicolas Bejerman
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
| | - Ralf Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Humberto Debat
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
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Sidharthan VK, Ashajyothi M. Neolamarckia cadamba hosts a putative novel deltapartitivirus: a revelation by transcriptome data-mining. Virusdisease 2023; 34:550-553. [PMID: 38046061 PMCID: PMC10686936 DOI: 10.1007/s13337-023-00845-8] [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: 06/18/2023] [Accepted: 08/28/2023] [Indexed: 12/05/2023] Open
Abstract
Neolamarckia cadamba (Roxb.) Bosser is a medicinally important, fast-growing, timber-yielding tree species. In the present study, the virome of N. cadamba was explored using the publicly available N. cadamba transcriptome datasets and a putative novel virus, tentatively named as cadamba cryptic virus 1 (CdbCV1), was identified. CdbCV1 contained two genome segments, each coding for a single protein. CdbCV1 RNA1 (1564 nt) encoded for an RNA dependent RNA polymerase (RdRp) protein while CdbCV1 RNA2 (1492 nt) encoded for a coat protein (CP). Phylogenetic and sequence similarity analyses revealed the relatedness of CdbCV1 to pepper cryptic virus 1 and pittosporum cryptic virus 1. Based on the species demarcation criteria, genome organization and phylogeny, CdbCV1 can be regarded a new member of the genus Deltapartitivirus. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00845-8.
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Affiliation(s)
| | - Mushineni Ashajyothi
- Plant Protection Lab, ICAR–Central Agroforestry Research Institute, Jhansi, 284003 India
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36
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Konstantinidis KT. Sequence-discrete species for prokaryotes and other microbes: A historical perspective and pending issues. MLIFE 2023; 2:341-349. [PMID: 38818268 PMCID: PMC10989153 DOI: 10.1002/mlf2.12088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/04/2023] [Accepted: 10/08/2023] [Indexed: 06/01/2024]
Abstract
Whether prokaryotes, and other microorganisms, form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying, regulating, and communicating about these organisms. In the past decade, comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters, albeit organisms of intermediate relatedness between the identified clusters are also frequently found. Accumulating evidence suggests, however, that the latter "intermediate" organisms show enough ecological and/or functional distinctiveness to be considered different species. Notably, the area of discontinuity between clusters often-but not always-appears to be around 85%-95% genome-average nucleotide identity, consistently among different taxa. More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well. This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters. The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination, which mediates (successful) horizontal gene transfer, around 95% nucleotide identity. Deviations from the 95% threshold (e.g., species showing lower intraspecies diversity) may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer. While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency (i.e., higher recombination within vs. between groups) is appealing, the supporting evidence remains anecdotal. The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.
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Affiliation(s)
- Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological SciencesGeorgia Institute of TechnologyAtlantaGeorgiaUSA
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37
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Nery FMB, Batista JG, Melo FFS, Ribeiro SG, Boiteux LS, Melo FL, Silva JGI, Reis LDNA, Pereira-Carvalho RC. Novel plant-associated genomoviruses from the Brazilian Cerrado biome. Arch Virol 2023; 168:286. [PMID: 37940763 DOI: 10.1007/s00705-023-05892-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 08/19/2023] [Indexed: 11/10/2023]
Abstract
The discovery rate of new plant viruses has increased due to studies involving high-throughput sequencing (HTS), particularly for single-stranded DNA viruses of the family Genomoviridae. We carried out an HTS-based survey of genomoviruses in a wide range of native and exotic trees grown in the Brazilian Cerrado biome, and the complete genome sequences of two novel members of the family Genomoviridae from two distinct genera were determined. Specific primers were designed to detect these genomoviruses in individual samples. A new gemykolovirus (Tecoma stans associated gemykolovirus) was detected in Tecoma stans, and a new gemykibivirus (Ouratea duparquetiana associated gemykibivirus) was detected in Ouratea duparquetiana. A gemykrogvirus related to Gila monster associated gemykrogvirus (80% pairwise identity) was also detected in foliar samples of Trembleya parviflora. Our pilot study paves the way for a better characterization of this diverse collection of genomoviruses as well as their interactions with the associated tree species.
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Affiliation(s)
- Flávia Milene B Nery
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Josiane G Batista
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Felipe Fochat S Melo
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Simone G Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-017, Brazil
| | - Leonardo S Boiteux
- Embrapa Vegetable Crops (Hortaliças), National Center for Vegetable Crops Research (CNPH), Brasília, DF, 70275-970, Brazil
| | - Fernando L Melo
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Juliana Gabrielle I Silva
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Luciane de Nazaré A Reis
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Rita C Pereira-Carvalho
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
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38
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Cissell EC, McCoy SJ. Top-heavy trophic structure within benthic viral dark matter. Environ Microbiol 2023; 25:2303-2320. [PMID: 37381050 DOI: 10.1111/1462-2920.16457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/16/2023] [Indexed: 06/30/2023]
Abstract
A better understanding of system-specific viral ecology in diverse environments is needed to predict patterns of virus-host trophic structure in the Anthropocene. This study characterised viral-host trophic structure within coral reef benthic cyanobacterial mats-a globally proliferating cause and consequence of coral reef degradation. We employed deep longitudinal multi-omic sequencing to characterise the viral assemblage (ssDNA, dsDNA, and dsRNA viruses) and profile lineage-specific host-virus interactions within benthic cyanobacterial mats sampled from Bonaire, Caribbean Netherlands. We recovered 11,012 unique viral populations spanning at least 10 viral families across the orders Caudovirales, Petitvirales, and Mindivirales. Gene-sharing network analyses provided evidence for extensive genomic novelty of mat viruses from reference and environmental viral sequences. Analysis of coverage ratios of viral sequences and computationally predicted hosts spanning 15 phyla and 21 classes revealed virus-host abundance (from DNA) and activity (from RNA) ratios consistently exceeding 1:1, suggesting a top-heavy intra-mat trophic structure with respect to virus-host interactions. Overall, our article contributes a curated database of viral sequences found in Caribbean coral reef benthic cyanobacterial mats (vMAT database) and provides multiple lines of field-based evidence demonstrating that viruses are active members of mat communities, with broader implications for mat functional ecology and demography.
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Affiliation(s)
- Ethan C Cissell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sophie J McCoy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Aylward FO, Abrahão JS, Brussaard CPD, Fischer MG, Moniruzzaman M, Ogata H, Suttle CA. Taxonomic update for giant viruses in the order Imitervirales (phylum Nucleocytoviricota). Arch Virol 2023; 168:283. [PMID: 37904060 PMCID: PMC11230039 DOI: 10.1007/s00705-023-05906-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Large DNA viruses in the phylum Nucleocytoviricota, sometimes referred to as "giant viruses" owing to their large genomes and virions, have been the subject of burgeoning interest over the last decade. Here, we describe recently adopted taxonomic updates for giant viruses within the order Imitervirales. The families Allomimiviridae, Mesomimiviridae, and Schizomimiviridae have been created to accommodate the increasing diversity of mimivirus relatives that have sometimes been referred to in the literature as "extended Mimiviridae". In addition, the subfamilies Aliimimivirinae, Megamimivirinae, and Klosneuvirinae have been established to refer to subgroups of the Mimiviridae. Binomial names have also been adopted for all recognized species in the order. For example, Acanthamoeba polyphaga mimivirus is now classified in the species Mimivirus bradfordmassiliense.
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Affiliation(s)
- Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
- Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, Blacksburg, VA, USA.
| | - Jonatas S Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Matthias G Fischer
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, FL, 33149, USA
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, 611-0011, Japan
| | - Curtis A Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
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40
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Mallawaarachchi V, Roach MJ, Decewicz P, Papudeshi B, Giles SK, Grigson SR, Bouras G, Hesse RD, Inglis LK, Hutton ALK, Dinsdale EA, Edwards RA. Phables: from fragmented assemblies to high-quality bacteriophage genomes. Bioinformatics 2023; 39:btad586. [PMID: 37738590 PMCID: PMC10563150 DOI: 10.1093/bioinformatics/btad586] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/14/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023] Open
Abstract
MOTIVATION Microbial communities have a profound impact on both human health and various environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of challenges in viral assembly, fragmentation of genomes can occur, and existing tools may recover incomplete genome fragments. Therefore, the identification and characterization of novel phage genomes remain a challenge, leading to the need of improved approaches for phage genome recovery. RESULTS We introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make. AVAILABILITY AND IMPLEMENTATION Phables is available on GitHub at https://github.com/Vini2/phables.
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Affiliation(s)
- Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Michael J Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Przemyslaw Decewicz
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Sarah K Giles
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Susanna R Grigson
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- The Department of Surgery—Otolaryngology Head and Neck Surgery, Central Adelaide Local Health Network, Adelaide, South Australia 5000, Australia
| | - Ryan D Hesse
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Laura K Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Abbey L K Hutton
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Elizabeth A Dinsdale
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
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41
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Gomes RAL, Zerbini FM. ConCreT, a 2D convolutional neural network for taxonomic classification applied to viruses in the phylum Cressdnaviricota. J Virol Methods 2023; 320:114789. [PMID: 37536450 DOI: 10.1016/j.jviromet.2023.114789] [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: 05/03/2023] [Revised: 07/19/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Taxonomic assignments allow scientists to communicate better with each other. In virology, taxonomy is continually improving towards a more precise and comprehensive framework. With the huge numbers of new viruses being described in metagenomic studies, automated taxonomy tools are urgently needed. A number of such tools have been proposed, and those applying machine learning (ML), mainly in the deep learning branch, stand out with accurate results. Still, there is a demand for tools that are less computationally intensive and that can classify viruses down to the ranks of genus and species. Cressdnaviruses are good subjects for testing such tools, due to their small, circular genomes and the existence of several families and genera with a highly imbalanced number of species. We developed a 2D convolutional neural network for virus taxonomy and tested it for classification of viruses from the phylum Cressdnaviricota. We obtained >98 % accuracy in the final pipeline tested, which we named ConCreT (Convolutional Neural Network for Cressdnavirus Taxonomy). The mixture of augmentation for more imbalanced groups with no augmentation for more balanced ones achieved the best score in the final test.
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Affiliation(s)
- Ruither A L Gomes
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; National Institute for Science and Technology on Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; National Institute for Science and Technology on Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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Cai H, Zhou Y, Li X, Xu T, Ni Y, Wu S, Yu Y, Wang Y. Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake. Viruses 2023; 15:2038. [PMID: 37896815 PMCID: PMC10611076 DOI: 10.3390/v15102038] [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: 09/13/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Viruses in aquatic ecosystems exhibit remarkable abundance and diversity. However, scattered studies have been conducted to mine uncultured viruses and identify them taxonomically in lake water. Here, whole genomes (29-173 kbp) of seven uncultured dsDNA bacteriophages were discovered in Dishui Lake, the largest artificial lake in Shanghai. We analyzed their genomic signatures and found a series of viral auxiliary metabolic genes closely associated with protein synthesis and host metabolism. Dishui Lake phages shared more genes with uncultivated environmental viruses than with reference viruses based on the gene-sharing network classification. Phylogeny of proteomes and comparative genomics delineated three new genera within two known viral families of Kyanoviridae and Autographiviridae, and four new families in Caudoviricetes for these seven novel phages. Their potential hosts appeared to be from the dominant bacterial phyla in Dishui Lake. Altogether, our study provides initial insights into the composition and diversity of bacteriophage communities in Dishui Lake, contributing valuable knowledge to the ongoing research on the roles played by viruses in freshwater ecosystems.
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Affiliation(s)
- Haoyun Cai
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yifan Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Xiefei Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Tianqi Xu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Shuang Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai 201306, China
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Kirchberger PC, Ochman H. Microviruses: A World Beyond phiX174. Annu Rev Virol 2023; 10:99-118. [PMID: 37774127 DOI: 10.1146/annurev-virology-100120-011239] [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] [Indexed: 10/01/2023]
Abstract
Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.
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Affiliation(s)
- Paul C Kirchberger
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA;
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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Kavi Sidharthan V, Diksha D, Singh R, Choudhary S, Naika MBN, Baranwal VK. Identification of two putative novel deltapartitiviruses and an enamovirus in coriander transcriptomes. Arch Microbiol 2023; 205:342. [PMID: 37755536 DOI: 10.1007/s00203-023-03681-y] [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: 05/18/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023]
Abstract
Coriander is a herbaceous spice and condiment crop also known for its medicinal properties. The present study identified two putative novel deltapartitiviruses and an enamovirus tentatively named as Coriandrum sativum deltapartitivirus 1, 2 (CsDPV1, 2) and Coriandrum sativum enamovirus (CsEV) in the publicly available transcriptome-assembled contigs derived from coriander grown in India. CsDPV1 and 2 contained tripartite and bipartite genomes, respectively, with each genome segment encoding a single open reading frame (ORF). CsEV contained five ORFs encoding proteins P0, P1, P2, P3 and P5. Phylogenetic analysis revealed three distinct subgroups of deltapartitiviruses wherein CsDPV1 and 2 grouped in subgroup 3 and 1, respectively, whilst CsEV formed a distinct sub-clade within enamoviruses. Further, the presence of CsDPV2 in fruit samples of one of the cultivars from where the virus was identified was confirmed through RT-PCR assay and Sanger sequencing. The study highlights the need for further studies on understanding the importance and the biological properties of identified novel viruses.
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Affiliation(s)
| | - Damini Diksha
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ravindra Singh
- ICAR-National Research Centre on Seed Spices, Tabiji, Ajmer, Rajasthan, India
| | - Sharda Choudhary
- ICAR-National Research Centre on Seed Spices, Tabiji, Ajmer, Rajasthan, India
| | - Mahantesha B N Naika
- Department of Biotechnology and Crop Improvement, K. R. C. College of Horticulture, University of Horticultural Sciences, Arabhavi, Bagalkot, Karnataka, India
| | - V K Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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45
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Fonseca PLC, Gaur RK, Aguiar ERGR. Editorial: Using virus specific-signatures during infection to characterize host-pathogen interactions. Front Genet 2023; 14:1290714. [PMID: 37811151 PMCID: PMC10556736 DOI: 10.3389/fgene.2023.1290714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Affiliation(s)
- Paula Luize Camargos Fonseca
- Genetics Department, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rajarshi Kumar Gaur
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, India
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46
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Mallawaarachchi V, Roach MJ, Decewicz P, Papudeshi B, Giles SK, Grigson SR, Bouras G, Hesse RD, Inglis LK, Hutton ALK, Dinsdale EA, Edwards RA. Phables: from fragmented assemblies to high-quality bacteriophage genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535632. [PMID: 37066369 PMCID: PMC10104058 DOI: 10.1101/2023.04.04.535632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Microbial communities influence both human health and different environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies, and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of the challenges in viral assembly, fragmentation of genomes can occur, leading to the need for new approaches in viral identification. Therefore, the identification and characterisation of novel phages remain a challenge. We introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make. Phables is available on GitHub at https://github.com/Vini2/phables.
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Affiliation(s)
- 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
| | - Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Sarah K Giles
- 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, The University of Adelaide, North Tce, Adelaide, SA, 5000, Australia
| | - Ryan D Hesse
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Laura K Inglis
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Abbey L K Hutton
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - 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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47
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Papa G, Abbà S, Galetto L, Parise C, Marzachì C, Negri I. Distribution and prevalence of viral genomes in Italian populations of the invasive brown marmorated stink bug Halyomorpha halys. J Invertebr Pathol 2023; 200:107977. [PMID: 37591337 DOI: 10.1016/j.jip.2023.107977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/28/2023] [Accepted: 08/11/2023] [Indexed: 08/19/2023]
Abstract
Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species that causes significant agricultural losses, especially to orchard fruits, vegetables, herbaceous and ornamental plants. It is also a nuisance pest that seeks shelter in indoor spaces during the winter months. Harnessing the H. halys virome can result in new environmentally sustainable approaches to contain its populations and its relatated agricultural damages. In this study, RNA-Seq data were used to explore the virome associated to ten field populations collected in the Lombardy region in Northern Italy. We identified six complete viral genomes, three of which were previously unknown, belonging to the orders Reovirales, Articulavirales, Ghabrivirales, Durnavirales, and Picornavirales. The prevalence of the six viruses was evaluated by Real-time reverse transcription-quantitative PCR on eighty individuals. Halyomorpha halys ifla-like virus 2 turned out to be the most geographically widespread virus, as it was found in more than 50% of the analyzed insects and in nine out of the ten sampling locations. Moreover, in some individuals, this iflavirus was found in association with each of the other viruses in various combinations that involved up to four viruses. Further studies on such virus-virus interactions and their relationships with the insect host may open the possibility to exploit these naturally occurring viruses as specific and targeted biocontrol agents of H. halys.
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Affiliation(s)
- Giulia Papa
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore Via Emilia Parmense 84, 29122 Piacenza, Italy; Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Simona Abbà
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy.
| | - Luciana Galetto
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Cecilia Parise
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy; Università degli Studi di Torino, DISAFA, Largo Paolo Braccini 2, 10095 Grugliasco, TO, Italy
| | - Cristina Marzachì
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Ilaria Negri
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore Via Emilia Parmense 84, 29122 Piacenza, Italy.
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48
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Eke M, Tougeron K, Hamidovic A, Tinkeu LSN, Hance T, Renoz F. Deciphering the functional diversity of the gut microbiota of the black soldier fly (Hermetia illucens): recent advances and future challenges. Anim Microbiome 2023; 5:40. [PMID: 37653468 PMCID: PMC10472620 DOI: 10.1186/s42523-023-00261-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023] Open
Abstract
Bioconversion using insects is a promising strategy to convert organic waste (catering leftovers, harvest waste, food processing byproducts, etc.) into biomass that can be used for multiple applications, turned into high added-value products, and address environmental, societal and economic concerns. Due to its ability to feed on a tremendous variety of organic wastes, the black soldier fly (Hermetia illucens) has recently emerged as a promising insect for bioconversion of organic wastes on an industrial scale. A growing number of studies have highlighted the pivotal role of the gut microbiota in the performance and health of this insect species. This review aims to provide a critical overview of current knowledge regarding the functional diversity of the gut microbiota of H. illucens, highlighting its importance for bioconversion, food safety and the development of new biotechnological tools. After providing an overview of the different strategies that have been used to outline the microbial communities of H. illucens, we discuss the diversity of these gut microbes and the beneficial services they can provide to their insect host. Emphasis is placed on technical strategies and aspects of host biology that require special attention in the near future of research. We also argue that the singular digestive capabilities and complex gut microbiota of H. illucens make this insect species a valuable model for addressing fundamental questions regarding the interactions that insects have evolved with microorganisms. By proposing new avenues of research, this review aims to stimulate research on the microbiota of a promising insect to address the challenges of bioconversion, but also fundamental questions regarding bacterial symbiosis in insects.
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Affiliation(s)
- Maurielle Eke
- Biodiversity Research Centre, Earth and Life Institute, UCLouvain, 1348, Louvain-la-Neuve, Belgium
- Department of Biological Sciences, University of Ngaoundéré, PO BOX 454, Ngaoundéré, Cameroon
| | - Kévin Tougeron
- UMR CNRS 7058 EDYSAN (Ecologie et Dynamique des Systèmes Anthropisés), Université de Picardie Jules Verne, Amiens, 80039 France
- Research Institute in Bioscience, Université de Mons, Mons, 7000 Belgium
| | - Alisa Hamidovic
- Biodiversity Research Centre, Earth and Life Institute, UCLouvain, 1348, Louvain-la-Neuve, Belgium
| | - Leonard S. Ngamo Tinkeu
- Department of Biological Sciences, University of Ngaoundéré, PO BOX 454, Ngaoundéré, Cameroon
| | - Thierry Hance
- Biodiversity Research Centre, Earth and Life Institute, UCLouvain, 1348, Louvain-la-Neuve, Belgium
| | - François Renoz
- Biodiversity Research Centre, Earth and Life Institute, UCLouvain, 1348, Louvain-la-Neuve, Belgium
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8634 Japan
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49
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Zhang ZF, Liu LR, Pan YP, Pan J, Li M. Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments. MICROBIOME 2023; 11:188. [PMID: 37612768 PMCID: PMC10464287 DOI: 10.1186/s40168-023-01630-x] [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: 04/15/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques. RESULTS Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle. CONCLUSIONS The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.
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Affiliation(s)
- Zhi-Feng Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Present Address: Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Li-Rui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yue-Ping Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
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50
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Wang T, Luo L, Xiong Y, Wang C, Shao H, Wang M, Guo C. Characterization and genomic analysis of an oceanic cyanophage infecting marine Synechococcus reveal a novel genus. Front Microbiol 2023; 14:1231279. [PMID: 37601358 PMCID: PMC10436341 DOI: 10.3389/fmicb.2023.1231279] [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: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 08/22/2023] Open
Abstract
Cyanophages play a crucial role in the biogeochemical cycles of aquatic ecosystems by affecting the population dynamics and community structure of cyanobacteria. In this study, a novel cyanophage, Nanhaivirus ms29, that infects Synechococcus sp. MW02 was isolated from the ocean basin in the South China Sea. It was identified as a T4-like phage using transmission electron microscopy. Phylogenetic analysis demonstrated that this cyanophage is distinct from other known T4-like cyanophage, belonging to a novel genus named Nanhaivirus within the family Kyanoviridae, according to the most recent classification proposed by the International Committee on Taxonomy of Viruses (ICTV). The genome of this novel cyanophage is composed of 178,866 bp of double-stranded DNA with a G + C content of 42.5%. It contains 217 potential open reading frames (ORFs) and 6 tRNAs. As many as 30 auxiliary metabolic genes (AMGs) were identified in the genome, which related to photosynthesis, carbon metabolism, nutrient uptake and stress tolerance, possibly reflecting a genomic adaption to the oligotrophic environment. Read-mapping analysis showed that Nanhaivirus ms29 mainly distributed in temperate and tropical epipelagic waters. This study enriches of the virus gene database of cyanophages and provides valuable insights into the phylogeny of cyanophages and their interactions with their hosts.
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Affiliation(s)
- Tiancong Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Lin Luo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yao Xiong
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Chuxiao Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Ocean University of China, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Ocean University of China, Qingdao, China
- Haide College, Ocean University of China, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Cui Guo
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Ocean University of China, Qingdao, China
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