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Paietta EN, Kraberger S, Lund MC, Vargas KL, Custer JM, Ehmke E, Yoder AD, Varsani A. Diverse Circular DNA Viral Communities in Blood, Oral, and Fecal Samples of Captive Lemurs. Viruses 2024; 16:1099. [PMID: 39066262 PMCID: PMC11281440 DOI: 10.3390/v16071099] [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: 06/11/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Few studies have addressed viral diversity in lemurs despite their unique evolutionary history on the island of Madagascar and high risk of extinction. Further, while a large number of studies on animal viromes focus on fecal samples, understanding viral diversity across multiple sample types and seasons can reveal complex viral community structures within and across species. Groups of captive lemurs at the Duke Lemur Center (Durham, NC, USA), a conservation and research center, provide an opportunity to build foundational knowledge on lemur-associated viromes. We sampled individuals from seven lemur species, i.e., collared lemur (Eulemur collaris), crowned lemur (Eulemur coronatus), blue-eyed black lemur (Eulemur flavifrons), ring-tailed lemur (Lemur catta), Coquerel's sifaka (Propithecus coquereli), black-and-white ruffed lemur (Varecia variegata variegata), and red ruffed lemur (Varecia rubra), across two lemur families (Lemuridae, Indriidae). Fecal, blood, and saliva samples were collected from Coquerel's sifaka and black-and-white ruffed lemur individuals across two sampling seasons to diversify virome biogeography and temporal sampling. Using viral metagenomic workflows, the complete genomes of anelloviruses (n = 4), cressdnaviruses (n = 47), caudoviruses (n = 15), inoviruses (n = 34), and microviruses (n = 537) were determined from lemur blood, feces, and saliva. Many virus genomes, especially bacteriophages, identified in this study were present across multiple lemur species. Overall, the work presented here uses a viral metagenomics approach to investigate viral communities inhabiting the blood, oral cavity, and feces of healthy captive lemurs.
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Affiliation(s)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Michael C. Lund
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Karla L. Vargas
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Erin Ehmke
- Duke Lemur Center, Duke University, Durham, NC 27708, USA
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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2
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Mäkelä K, Laanto E, Sundberg LR. Determinants in the phage life cycle: The dynamic nature of ssDNA phage FLiP and host interactions under varying environmental conditions and growth phases. Environ Microbiol 2024; 26:e16670. [PMID: 38952172 DOI: 10.1111/1462-2920.16670] [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: 12/20/2023] [Accepted: 05/24/2024] [Indexed: 07/03/2024]
Abstract
The influence of environmental factors on the interactions between phages and bacteria, particularly single-stranded DNA (ssDNA) phages, has been largely unexplored. In this study, we used Finnlakevirus FLiP, the first known ssDNA phage species with a lipid membrane, as our model phage. We examined the infectivity of FLiP with three Flavobacterium host strains, B330, B167 and B114. We discovered that FLiP infection is contingent on the host strain and conditions such as temperature and bacterial growth phase. FLiP can infect its hosts across a wide temperature range, but optimal phage replication varies with each host. We uncovered some unique aspects of phage infectivity: FLiP has limited infectivity in liquid-suspended cells, but it improves when cells are surface-attached. Moreover, FLiP infects stationary phase B167 and B114 cells more rapidly and efficiently than exponentially growing cells, a pattern not observed with the B330 host. We also present the first experimental evidence of endolysin function in ssDNA phages. The activity of FLiP's lytic enzymes was found to be condition-dependent. Our findings underscore the importance of studying phage ecology in contexts that are relevant to the environment, as both the host and the surrounding conditions can significantly alter the outcome of phage-host interactions.
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Affiliation(s)
- Kati Mäkelä
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Elina Laanto
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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3
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Bardy P, MacDonald CI, Kirchberger PC, Jenkins HT, Botka T, Byrom L, Alim NT, Traore DA, König HC, Nicholas TR, Chechik M, Hart SJ, Turkenburg JP, Blaza JN, Beatty JT, Fogg PC, Antson AA. A stargate mechanism of Microviridae genome delivery unveiled by cryogenic electron tomography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598214. [PMID: 38915634 PMCID: PMC11195240 DOI: 10.1101/2024.06.11.598214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Single-stranded DNA bacteriophages of the Microviridae family are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut microbiome, where their diversity has been linked to various chronic health disorders. Despite the clear importance of microviruses, little is known about the molecular mechanism of host infection. Here, we have characterized an exceptionally large microvirus, Ebor, and provide crucial insights into long-standing mechanistic questions. Cryogenic electron microscopy of Ebor revealed a capsid with trimeric protrusions that recognise lipopolysaccharides on the host surface. Cryogenic electron tomography of the host cell colonized with virus particles demonstrated that the virus initially attaches to the cell via five such protrusions, located at the corners of a single pentamer. This interaction triggers a stargate mechanism of capsid opening along the 5-fold symmetry axis, enabling delivery of the virus genome. Despite variations in specific virus-host interactions among different Microviridae family viruses, structural data indicate that the stargate mechanism of infection is universally employed by all members of the family. Startlingly, our data reveal a mechanistic link for the opening of relatively small capsids made out of a single jelly-roll fold with the structurally unrelated giant viruses.
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Affiliation(s)
- Pavol Bardy
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
| | - Conor I.W. MacDonald
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Paul C. Kirchberger
- Department of Microbiology & Molecular Genetics, Oklahoma State University, US
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
| | - Tibor Botka
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Lewis Byrom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Nawshin T.B. Alim
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - Daouda A.K. Traore
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG, Eindhoven, The Netherlands
| | - Hannah C. König
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - Tristan R. Nicholas
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
| | - Samuel J. Hart
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - James N. Blaza
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
| | - J. Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada
| | - Paul C.M. Fogg
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom. YO10 5NG
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4
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Xie K, Lin B, Sun X, Zhu P, Liu C, Liu G, Cao X, Pan J, Qiu S, Yuan X, Liang M, Jiang J, Yuan L. Identification and classification of the genomes of novel microviruses in poultry slaughterhouse. Front Microbiol 2024; 15:1393153. [PMID: 38756731 PMCID: PMC11096546 DOI: 10.3389/fmicb.2024.1393153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
Microviridae is a family of phages with circular ssDNA genomes and they are widely found in various environments and organisms. In this study, virome techniques were employed to explore potential members of Microviridae in a poultry slaughterhouse, leading to the identification of 98 novel and complete microvirus genomes. Using a similarity clustering network classification approach, these viruses were found to belong to at least 6 new subfamilies within Microviridae and 3 higher-level taxonomic units. Genome size, GC content and genome structure of these new taxa showed evident regularities, validating the rationality of our classification method. Our method can divide microviruses into about 45 additional detailed clusters, which may serve as a new standard for classifying Microviridae members. Furthermore, by addressing the scarcity of host information for microviruses, the current study significantly broadened their host range and discovered over 20 possible new hosts, including important pathogenic bacteria such as Helicobacter pylori and Vibrio cholerae, as well as different taxa demonstrated different host specificities. The findings of this study effectively expand the diversity of the Microviridae family, providing new insights for their classification and identification. Additionally, it offers a novel perspective for monitoring and controlling pathogenic microorganisms in poultry slaughterhouse environments.
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Affiliation(s)
- Keming Xie
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Benfu Lin
- Huadu District Animal Health Supervision Institution, Guangzhou, Guangdong, China
| | - Xinyu Sun
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Peng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Chang Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Guangfeng Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Xudong Cao
- Department of Chemical and Biological Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Jingqi Pan
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Suiping Qiu
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Xiaoqi Yuan
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Mengshi Liang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Jingzhe Jiang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China
| | - Lihong Yuan
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
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5
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Olivo D, Khalifeh A, Custer JM, Kraberger S, Varsani A. Diverse Small Circular DNA Viruses Identified in an American Wigeon Fecal Sample. Microorganisms 2024; 12:196. [PMID: 38258021 PMCID: PMC10821283 DOI: 10.3390/microorganisms12010196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
American wigeons (Mareca americana) are waterfowls that are widely distributed throughout North America. Research of viruses associated with American wigeons has been limited to orthomyxoviruses, coronaviruses, and circoviruses. To address this poor knowledge of viruses associated with American wigeons, we undertook a pilot study to identify small circular DNA viruses in a fecal sample collected in January 2021 in the city of Tempe, Arizona (USA). We identified 64 diverse circular DNA viral genomes using a viral metagenomic workflow biased towards circular DNA viruses. Of these, 45 belong to the phylum Cressdnaviricota based on their replication-associated protein sequence, with 3 from the Genomoviridae family and the remaining 42 which currently cannot be assigned to any established virus group. It is most likely that these 45 viruses infect various organisms that are associated with their diet or environment. The remaining 19 virus genomes are part of the Microviridae family and likely associated with the gut enterobacteria of American wigeons.
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Affiliation(s)
- Diego Olivo
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Anthony Khalifeh
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Joy M. Custer
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Simona Kraberger
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Arvind Varsani
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
- Structural Biology Research Unit, Department of Integrative, Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
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6
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Romeyer Dherbey J, Bertels F. The untapped potential of phage model systems as therapeutic agents. Virus Evol 2024; 10:veae007. [PMID: 38361821 PMCID: PMC10868562 DOI: 10.1093/ve/veae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/18/2023] [Accepted: 01/12/2024] [Indexed: 02/17/2024] Open
Abstract
With the emergence of widespread antibiotic resistance, phages are an appealing alternative to antibiotics in the fight against multidrug-resistant bacteria. Over the past few years, many phages have been isolated from various environments to treat bacterial pathogens. While isolating novel phages for treatment has had some success for compassionate use, developing novel phages into a general therapeutic will require considerable time and financial resource investments. These investments may be less significant for well-established phage model systems. The knowledge acquired from decades of research on their structure, life cycle, and evolution ensures safe application and efficient handling. However, one major downside of the established phage model systems is their inability to infect pathogenic bacteria. This problem is not insurmountable; phage host range can be extended through genetic engineering or evolution experiments. In the future, breeding model phages to infect pathogens could provide a new avenue to develop phage therapeutic agents.
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Affiliation(s)
- Jordan Romeyer Dherbey
- Microbial Population Biology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, Plön, Schleswig-Holstein 24306, Germany
| | - Frederic Bertels
- Microbial Population Biology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, Plön, Schleswig-Holstein 24306, Germany
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7
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Nguyen HM, Watanabe S, Sharmin S, Kawaguchi T, Tan XE, Wannigama DL, Cui L. RNA and Single-Stranded DNA Phages: Unveiling the Promise from the Underexplored World of Viruses. Int J Mol Sci 2023; 24:17029. [PMID: 38069353 PMCID: PMC10707117 DOI: 10.3390/ijms242317029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
RNA and single-stranded DNA (ssDNA) phages make up an understudied subset of bacteriophages that have been rapidly expanding in the last decade thanks to advancements in metaviromics. Since their discovery, applications of genetic engineering to ssDNA and RNA phages have revealed their immense potential for diverse applications in healthcare and biotechnology. In this review, we explore the past and present applications of this underexplored group of phages, particularly their current usage as therapeutic agents against multidrug-resistant bacteria. We also discuss engineering techniques such as recombinant expression, CRISPR/Cas-based genome editing, and synthetic rebooting of phage-like particles for their role in tailoring phages for disease treatment, imaging, biomaterial development, and delivery systems. Recent breakthroughs in RNA phage engineering techniques are especially highlighted. We conclude with a perspective on challenges and future prospects, emphasizing the untapped diversity of ssDNA and RNA phages and their potential to revolutionize biotechnology and medicine.
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Affiliation(s)
- Huong Minh Nguyen
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Sultana Sharmin
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Tomofumi Kawaguchi
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
| | - Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata 990-2292, Yamagata, Japan;
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan; (H.M.N.); (S.W.); (S.S.); (T.K.); (X.-E.T.)
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8
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Martinez ZA, Murray RM, Thomson MW. TRILL: ORCHESTRATING MODULAR DEEP-LEARNING WORKFLOWS FOR DEMOCRATIZED, SCALABLE PROTEIN ANALYSIS AND ENGINEERING. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563881. [PMID: 37986952 PMCID: PMC10659302 DOI: 10.1101/2023.10.24.563881] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Deep-learning models have been rapidly adopted by many fields, partly due to the deluge of data humanity has amassed. In particular, the petabases of biological sequencing data enable the unsupervised training of protein language models that learn the "language of life." However, due to their prohibitive size and complexity, contemporary deep-learning models are often unwieldy, especially for scientists with limited machine learning backgrounds. TRILL (TRaining and Inference using the Language of Life) is a platform for creative protein design and discovery. Leveraging several state-of-the-art models such as ESM-2, DiffDock, and RFDiffusion, TRILL allows researchers to generate novel proteins, predict 3-D structures, extract high-dimensional representations of proteins, functionally classify proteins and more. What sets TRILL apart is its ability to enable complex pipelines by chaining together models and effectively merging the capabilities of different models to achieve a sum greater than its individual parts. Whether using Google Colab with one GPU or a supercomputer with hundreds, TRILL allows scientists to effectively utilize models with millions to billions of parameters by using optimized training strategies such as ZeRO-Offload and distributed data parallel. Therefore, TRILL not only bridges the gap between complex deep-learning models and their practical application in the field of biology, but also simplifies the orchestration of these models into comprehensive workflows, democratizing access to powerful methods. Documentation: https://trill.readthedocs.io/en/latest/home.html.
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Affiliation(s)
- Zachary A Martinez
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125
| | - Richard M Murray
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125
| | - Matt W Thomson
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125
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9
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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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10
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Pan J, Ji L, Wu H, Wang X, Wang Y, Wu Y, Yang S, Shen Q, Liu Y, Zhang W, Zhang K, Shan T. Metagenomic analysis of herbivorous mammalian viral communities in the Northwest Plateau. BMC Genomics 2023; 24:568. [PMID: 37749507 PMCID: PMC10521573 DOI: 10.1186/s12864-023-09646-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Mammals are potential hosts for many infectious diseases. However, studies on the viral communities of herbivorous mammals in the Northwest Plateau are limited. Here, we studied the viral communities of herbivorous mammals in the Northwest Plateau using virus metagenomic analysis to analyze and compare the viral community composition of seven animal species. RESULTS By library construction and next-generation sequencing, contigs and singlets reads with similar viral sequences were classified into 24 viral families. Analyzed from the perspective of sampling areas, the virus community composition was relatively similar in two areas of Wuwei and Jinchang, Gansu Province. Analyzed from the perspective of seven animal species, the viral reads of seven animal species were mostly ssDNA and dominated by CRESS-DNA viruses. Phylogenetic analysis based on viral marker genes indicated that CRESS-DNA viruses and microviruses have high genetic diversity. In addition to DNA viruses, nodaviruses, pepper mild mottle viruses and picornaviruses were RNA viruses that we performed by phylogenetic analysis. The CRESS-DNA viruses and nodaviruses are believed to infect plants and insects, and microviruses can infect bacteria, identifying that they were likely from the diet of herbivorous mammals. Notably, two picornaviruses were identified from red deer and wild horse, showing that the picornavirus found in red deer had the relatively high similarity with human hepatitis A virus, and the picornavirus carried by wild horse could potentially form a new species within the Picornaviridae family. CONCLUSIONS This study explored the herbivorous mammalian virus community in the Northwest Plateau and the genetic characteristics of viruses that potentially threaten human health. It reveals the diversity and stability of herbivorous mammalian virus communities in the Northwest Plateau and helps to expand our knowledge of various herbivorous mammalian potentially pathogenic viruses.
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Grants
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No.2022YFC2603801 National Key Research and Development Programs of China
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
- No. 20220817004 Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents
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Affiliation(s)
- Jiamin Pan
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haisheng Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yan Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuwei Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
| | - Keshan Zhang
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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11
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Paietta EN, Kraberger S, Custer JM, Vargas KL, Espy C, Ehmke E, Yoder AD, Varsani A. Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA). Viruses 2023; 15:1821. [PMID: 37766228 PMCID: PMC10537320 DOI: 10.3390/v15091821] [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: 07/08/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The diversity of viruses identified from the various niches of the human oral cavity-from saliva to dental plaques to the surface of the tongue-has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral viral diversity is incomplete, with only a few studies utilizing passive drool collection in conjunction with metagenomic sequencing methods. For this pilot study, we obtained 14 samples from healthy staff members working at the Duke Lemur Center (Durham, NC, USA) to determine the viral diversity that can be identified in passive drool samples from humans. The complete genomes of 3 anelloviruses, 9 cressdnaviruses, 4 Caudoviricetes large bacteriophages, 29 microviruses, and 19 inoviruses were identified in this study using high-throughput sequencing and viral metagenomic workflows. The results presented here expand our understanding of the vertebrate-infecting and microbe-infecting viral diversity of the human oral virome in North Carolina (USA).
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Affiliation(s)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Karla L. Vargas
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Claudia Espy
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Erin Ehmke
- Duke Lemur Center, Duke University, Durham, NC 27705, USA;
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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12
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Lund MC, Larsen BB, Rowsey DM, Otto HW, Gryseels S, Kraberger S, Custer JM, Steger L, Yule KM, Harris RE, Worobey M, Van Doorslaer K, Upham NS, Varsani A. Using archived and biocollection samples towards deciphering the DNA virus diversity associated with rodent species in the families cricetidae and heteromyidae. Virology 2023; 585:42-60. [PMID: 37276766 DOI: 10.1016/j.virol.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Abstract
Rodentia is the most speciose order of mammals, and they are known to harbor a wide range of viruses. Although there has been significant research on zoonotic viruses in rodents, research on the diversity of other viruses has been limited, especially for rodents in the families Cricetidae and Heteromyidae. In fecal and liver samples of nine species of rodents, we identify 346 distinct circular DNA viral genomes. Of these, a large portion are circular, single-stranded DNA viruses in the families Anelloviridae (n = 3), Circoviridae (n = 5), Genomoviridae (n = 7), Microviridae (n = 297), Naryaviridae (n = 4), Vilyaviridae (n = 15) and in the phylum Cressdnaviricota (n = 13) that cannot be assigned established families. We also identified two large bacteriophages of 36 and 50 kb that are part of the class Caudoviricetes. Some of these viruses are clearly those that infect rodents, however, most of these likely infect various organisms associated with rodents, their environment or their diet.
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Affiliation(s)
- Michael C Lund
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98102, USA
| | - Dakota M Rowsey
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Sophie Gryseels
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium; Department of Biology, University of Antwerp, 2000, Antwerp, Belgium; OD Taxonomy and Phylogeny, Royal Belgian Museum of Natural Sciences, 1000, Brussels, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Laura Steger
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Kelsey M Yule
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Robin E Harris
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, AZ, 85724, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7701, South Africa.
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13
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Johansen J, Atarashi K, Arai Y, Hirose N, Sørensen SJ, Vatanen T, Knip M, Honda K, Xavier RJ, Rasmussen S, Plichta DR. Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan. Nat Microbiol 2023; 8:1064-1078. [PMID: 37188814 DOI: 10.1038/s41564-023-01370-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/23/2023] [Indexed: 05/17/2023]
Abstract
Distinct gut microbiome ecology may be implicated in the prevention of aging-related diseases as it influences systemic immune function and resistance to infections. Yet, the viral component of the microbiome throughout different stages in life remains unexplored. Here we present a characterization of the centenarian gut virome using previously published metagenomes from 195 individuals from Japan and Sardinia. Compared with gut viromes of younger adults (>18 yr) and older individuals (>60 yr), centenarians had a more diverse virome including previously undescribed viral genera, such as viruses associated with Clostridia. A population shift towards higher lytic activity was also observed. Finally, we investigated phage-encoded auxiliary functions that influence bacterial physiology, which revealed an enrichment of genes supporting key steps in sulfate metabolic pathways. Phage and bacterial members of the centenarian microbiome displayed an increased potential for converting methionine to homocysteine, sulfate to sulfide and taurine to sulfide. A greater metabolic output of microbial hydrogen sulfide in centenarians may in turn support mucosal integrity and resistance to pathobionts.
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Affiliation(s)
- Joachim Johansen
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Koji Atarashi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Yasumichi Arai
- Center for Supercentenarian Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Nobuyoshi Hirose
- Center for Supercentenarian Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tommi Vatanen
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikael Knip
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- New Children's Hospital, Helsinki University Hospital, Helsinki, Finland
- Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Kenya Honda
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Damian R Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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14
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Special Issue “Bacteriophage Genomics”: Editorial. Microorganisms 2023; 11:microorganisms11030693. [PMID: 36985265 PMCID: PMC10054338 DOI: 10.3390/microorganisms11030693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023] Open
Abstract
Virus genomics as a separate branch of biology has emerged relatively recently [...]
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15
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Harding C, Larsen BB, Otto HW, Potticary AL, Kraberger S, Custer JM, Suazo C, Upham NS, Worobey M, Van Doorslaer K, Varsani A. Diverse DNA virus genomes identified in fecal samples of Mexican free-tailed bats (Tadarida brasiliensis) captured in Chiricahua Mountains of southeast Arizona (USA). Virology 2023; 580:98-111. [PMID: 36801670 DOI: 10.1016/j.virol.2023.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
Bats (order Chiroptera) are some of the most abundant mammals on earth and their species ecology strongly influences zoonotic potential. While substantial research has been conducted on bat-associated viruses, particularly on those that can cause disease in humans and/or livestock, globally, limited research has focused on endemic bats in the USA. The southwest region of the US is of particular interest because of its high diversity of bat species. We identified 39 single-stranded DNA virus genomes in the feces of Mexican free-tailed bats (Tadarida brasiliensis) sampled in the Rucker Canyon (Chiricahua Mountains) of southeast Arizona (USA). Twenty-eight of these belong to the virus families Circoviridae (n = 6), Genomoviridae (n = 17), and Microviridae (n = 5). Eleven viruses cluster with other unclassified cressdnaviruses. Most of the viruses identified represent new species. Further research on identification of novel bat-associated cressdnaviruses and microviruses is needed to provide greater insights regarding their co-evolution and ecology relative to bats.
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Affiliation(s)
- Ciara Harding
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Ahva L Potticary
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; University of Georgia in the Department of Entomology, Athens, GA, 30602, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA
| | - Crystal Suazo
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, Genetics Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, AZ, 85724, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7701, South Africa.
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16
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Jimoh AO, Balle C, Brown B, Feng C, Havyarimana E, Konstantinus IN, Gill K, Bekker LG, Passmore JAS, Jaspan HB, Varsani A, Happel AU. Genome Sequences of Anelloviruses, a Genomovirus, Microviruses, Polyomaviruses, and an Unclassified Caudovirus Identified in Vaginal Secretions from South African Adolescents. Microbiol Resour Announc 2023; 12:e0114322. [PMID: 36533922 PMCID: PMC9872636 DOI: 10.1128/mra.01143-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/03/2022] [Indexed: 12/23/2022] Open
Abstract
Other than for papillomaviruses, there is a paucity of whole-genome sequences for bacteriophages and eukaryote-infecting viruses isolated from the female genital tract. Here, we report the genome sequences of 16 microviruses, 3 anelloviruses, 2 polyomaviruses, 1 genomovirus, and 1 caudovirus that were identified in vaginal secretion samples from adolescents in South Africa.
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Affiliation(s)
- Adijat O. Jimoh
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Genetics, Genomics, and Bioinformatics Department, National Biotechnology Development Agency, Abuja, Nigeria
| | - Christina Balle
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Bryan Brown
- Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Colin Feng
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Enock Havyarimana
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Iyaloo N. Konstantinus
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Namibia Institute of Pathology, Windhoek, Namibia
- NRF-DST Centre of Excellence in HIV Prevention, Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | | | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Jo-Ann S. Passmore
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Heather B. Jaspan
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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17
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Olo Ndela E, Roux S, Henke C, Sczyrba A, Sime Ngando T, Varsani A, Enault F. Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages. Virus Evol 2022; 9:veac123. [PMID: 36694818 PMCID: PMC9865509 DOI: 10.1093/ve/veac123] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/19/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022] Open
Abstract
Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, Amoyvirinae, has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics data sets from various aquatic ecosystems, of sixteen complete microvirus genomes significantly smaller (2.991-3.692 kb) than known ones. Phylogenetic analysis reveals that these sixteen genomes represent two related, yet distinct and diverse, novel groups of microviruses-amoyviruses being their closest known relatives. We propose that these small microviruses are members of two tentatively named subfamilies Reekeekeevirinae and Roodoodoovirinae. As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction software, we developed a new methodology to identify all genes based on protein conservation, amino acid composition, and selection pressure estimations. Surprisingly, only four to five genes could be identified per genome, with the number of overprinted genes lower than that in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two Microviridae groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small number of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and are further evidence that these viruses have explored a wide range of possibilities during their long evolution.
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Affiliation(s)
| | | | - Christian Henke
- Computational Metagenomics, Bielefeld University, Universitätsstraße 27, Bielefeld 30501, Germany,Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Alexander Sczyrba
- Computational Metagenomics, Bielefeld University, Universitätsstraße 27, Bielefeld 30501, Germany,Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Télesphore Sime Ngando
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, Clermont-Ferrand F-63000, France
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18
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Shaidullina A, Harms A. Toothpicks, logic, and next-generation sequencing: systematic investigation of bacteriophage-host interactions. Curr Opin Microbiol 2022; 70:102225. [PMID: 36327691 DOI: 10.1016/j.mib.2022.102225] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/27/2022] [Accepted: 10/01/2022] [Indexed: 01/25/2023]
Abstract
Bacteriophages are abundant and diverse predators that drive community dynamics in many ecosystems and hold great potential for biotechnology and as therapeutics for bacterial infections. Previous research has largely explored phage-host interactions one-by-one, which limited our ability to observe phenotypic patterns, to uncover their genetic basis, and to unravel the underlying molecular mechanisms. However, the famous 'toothpicks and logic' were recently joined by large-scale sequencing of phage genomes and bacterial genome-wide screens that enable us to systematically investigate phage-host interactions. In this article, we highlight recent breakthroughs from the molecular basis of phage host range and receptor recognition over new insights into bacterial immunity to the serendipitous discovery of a new bacterial surface glycan. Future work will enable the understanding, prediction, and engineering of more complicated phage traits for new applications and extend the scope of these studies from simple test tube experiments to natural communities of phages and hosts.
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19
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Lee H, Baxter AJ, Bator CM, Fane BA, Hafenstein SL. Cryo-EM Structure of Gokushovirus ΦEC6098 Reveals a Novel Capsid Architecture for a Single-Scaffolding Protein, Microvirus Assembly System. J Virol 2022; 96:e0099022. [PMID: 36255280 PMCID: PMC9645218 DOI: 10.1128/jvi.00990-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022] Open
Abstract
Ubiquitous and abundant in ecosystems and microbiomes, gokushoviruses constitute a Microviridae subfamily, distantly related to bacteriophages ΦX174, α3, and G4. A high-resolution cryo-EM structure of gokushovirus ΦEC6098 was determined, and the atomic model was built de novo. Although gokushoviruses lack external scaffolding and spike proteins, which extensively interact with the ΦX174 capsid protein, the core of the ΦEC6098 coat protein (VP1) displayed a similar structure. There are, however, key differences. At each ΦEC6098 icosahedral 3-fold axis, a long insertion loop formed mushroom-like protrusions, which have been noted in lower-resolution gokushovirus structures. Hydrophobic interfaces at the bottom of these protrusions may confer stability to the capsid shell. In ΦX174, the N-terminus of the capsid protein resides directly atop the 3-fold axes of symmetry; however, the ΦEC6098 N-terminus stretched across the inner surface of the capsid shell, reaching nearly to the 5-fold axis of the neighboring pentamer. Thus, this extended N-terminus interconnected pentamers on the inside of the capsid shell, presumably promoting capsid assembly, a function performed by the ΦX174 external scaffolding protein. There were also key differences between the ΦX174-like DNA-binding J proteins and its ΦEC6098 homologue VP8. As seen with the J proteins, C-terminal VP8 residues were bound into a pocket within the major capsid protein; however, its N-terminal residues were disordered, likely due to flexibility. We show that the combined location and interaction of VP8's C-terminus and a portion of VP1's N-terminus are reminiscent of those seen with the ΦX174 and α3 J proteins. IMPORTANCE There is a dramatic structural and morphogenetic divide within the Microviridae. The well-studied ΦX174-like viruses have prominent spikes at their icosahedral vertices, which are absent in gokushoviruses. Instead, gokushovirus major coat proteins form extensive mushroom-like protrusions at the 3-fold axes of symmetry. In addition, gokushoviruses lack an external scaffolding protein, the more critical of the two ΦX174 assembly proteins, but retain an internal scaffolding protein. The ΦEC6098 virion suggests that key external scaffolding functions are likely performed by coat protein domains unique to gokushoviruses. Thus, within one family, different assembly paths have been taken, demonstrating how a two-scaffolding protein system can evolve into a one-scaffolding protein system, or vice versa.
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Affiliation(s)
- Hyunwook Lee
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Alexis J. Baxter
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Carol M. Bator
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Bentley A. Fane
- The BIO5 Institute, Keating Building, University of Arizona, Tucson, Arizona, USA
| | - Susan L. Hafenstein
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
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Van Cauwenberghe J, Santamaría RI, Bustos P, González V. Novel lineages of single-stranded DNA phages that coevolved with the symbiotic bacteria Rhizobium. Front Microbiol 2022; 13:990394. [PMID: 36177468 PMCID: PMC9512667 DOI: 10.3389/fmicb.2022.990394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/19/2022] [Indexed: 11/27/2022] Open
Abstract
This study describes novel single-stranded DNA phages isolated from common bean agriculture soils by infection of the nitrogen-fixing symbiotic bacteria Rhizobium etli and R. phaseoli. A total of 29 phages analyzed have 4.3-6 kb genomes in size and GC 59-60%. They belong to different clades unrelated to other Microviridae subfamilies. Three-dimensional models of the major capsid protein (MCP) showed a conserved β-barrel structural "jelly-roll" fold. A variable-length loop in the MCPs distinguished three Rhizobium microvirus groups. Microviridae subfamilies were consistent with viral clusters determined by the protein-sharing network. All viral clusters, except for Bullavirinae, included mostly microviruses identified in metagenomes from distinct ecosystems. Two Rhizobium microvirus clusters, chaparroviruses, and chicoviruses, were included within large viral unknown clusters with microvirus genomes identified in diverse metagenomes. A third Rhizobium microvirus cluster belonged to the subfamily Amoyvirinae. Phylogenetic analysis of the MCP confirms the divergence of the Rhizobium microviruses into separate clades. The phylogeny of the bacterial hosts matches the microvirus MCP phylogeny, suggesting a coevolutionary history between the phages and their bacterial host. This study provided essential biological information on cultivated microvirus for understanding the evolution and ecological diversification of the Microviridae family in diverse microbial ecosystems.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
- Department of Integrative Biology, University of California, Berkeley, CA, United States
| | - Rosa I. Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
| | - Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
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Genome Sequence of a Microvirus Recovered from Wastewater in Arizona, USA, in October 2020, Encodes a Previously Undescribed DNA-Binding Protein. Microbiol Resour Announc 2022; 11:e0033722. [PMID: 36043869 PMCID: PMC9584320 DOI: 10.1128/mra.00337-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We describe the genome of Microvirus-AZ-2020, which was identified from wastewater in Arizona, USA, in October 2020. Microvirus-AZ-2020 belongs to subfamily Gokushovirinae and contains six (five known and one hypothetical) open reading frames (ORFs), each with >40 codons. HHPred analysis and Colabfold structure prediction suggest that the hypothetical ORF encodes a previously undescribed putative DNA-binding protein.
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