1
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Higuchi A, Tojo M, Mochizuki T. Sensitivity of Globisporangium ultimum to the fungicide metalaxyl is enhanced by the infection with a toti-like mycovirus. Microbiol Res 2024; 285:127742. [PMID: 38723390 DOI: 10.1016/j.micres.2024.127742] [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: 02/23/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 06/15/2024]
Abstract
In recent years, numerous oomycete mycoviruses have been discovered; however, very few studies have focused on their effects on the host oomycete phenotype. In this study, we investigated the impact of toti-like Pythium ultimum RNA virus 2 (PuRV2) infection on the phytopathogenic soil-borne oomycete Globisporangium ultimum, which serves as a model species for Globisporangium and Pythium, specifically the UOP226 isolate in Japan. We generated a PuRV2-free isogenic line through hyphal tip isolation using high-temperature culture and subsequently compared the phenotypic characteristics and gene expression profiles of UOP226 and the PuRV2-free isogenic line. Our findings revealed that the metalaxyl sensitivity of UOP226 was greater than that of the PuRV2-free isogenic line, whereas the mycelial growth rate and colony morphology remained unchanged in the absence of the fungicide. Furthermore, transcriptome analyses using RNA-seq revealed significant downregulation of ABC-type transporter genes, which are involved in fungicide sensitivity, in UOP226. Our results suggest that PuRV2 infection influences the ecology of G. ultimum in agricultural ecosystems where metalaxyl is applied.
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Affiliation(s)
- Aika Higuchi
- Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Osaka 599-8531, Japan
| | - Motoaki Tojo
- Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Osaka 599-8531, Japan
| | - Tomofumi Mochizuki
- Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Osaka 599-8531, Japan; Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Sakai, Osaka 599-8531, Japan.
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2
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Boorse C. Wakefield's Harm-Based Critique of the Biostatistical Theory. THE JOURNAL OF MEDICINE AND PHILOSOPHY 2024; 49:367-388. [PMID: 38885259 DOI: 10.1093/jmp/jhae017] [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: 06/20/2024] Open
Abstract
Jerome Wakefield criticizes my biostatistical analysis of the pathological-as statistically subnormal biological part-functional ability relative to species, sex, and age-for its lack of a harm clause. He first charges me with ignoring two general distinctions: biological versus medical pathology, and disease of a part versus disease of a whole organism. He then offers 10 counterexamples that, he says, are harmless dysfunctions but not medical disorders. Wakefield ends by arguing that we need a harm clause to explain American psychiatry's 1973 decision to declassify homosexuality. I reply, first, that his two distinctions are philosophic fantasies alien to medical usage, invented only to save his own harmful-dysfunction analysis (HDA) from a host of obvious counterexamples. In any case, they do not coincide with the harmless/harmful distinction. In reality, medicine admits countless chronic diseases that are, contrary to Wakefield, subclinical for most of their course, as well as many kinds of typically harmless skin pathology. As for his 10 counterexamples, no medical source he cites describes them as he does. I argue that none of his examples contradicts the biostatistical analysis: all either are not part-dysfunctions (situs inversus, incompetent sperm, normal-flora infection) or are indeed classified as medical disorders (donated kidney, Typhoid Mary's carrier status, latent tuberculosis or HIV, cherry angiomas). And if Wakefield's HDA fits psychiatry, the fact that it does not fit medicine casts doubt on psychiatry's status as a medical specialty.
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3
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Gontier N. Situating physiology within evolutionary theory. J Physiol 2024; 602:2401-2415. [PMID: 37755322 DOI: 10.1113/jp284410] [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: 07/20/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
Traditionally defined as the science of the living, or as the field that beyond anatomical structure and bodily form studies functional organization and behaviour, physiology has long been excluded from evolutionary research. The main reason for this exclusion is that physiology has a presential and futuristic outlook on life, while evolutionary theory is traditionally defined as the study of natural history. In this paper, I re-evaluate these classic science divisions and situate physiology within the history of the evolutionary sciences, as well as within debates on the Extended Evolutionary Synthesis and the need for a Third Way of Evolution. I then briefly point out how evolutionary physiology in particular contributes to research on function, causation, teleonomy, agency and cognition.
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Affiliation(s)
- Nathalie Gontier
- Applied Evolutionary Epistemology Lab & Centro de Filosofia das Ciências, Departamento de História e Filosofia das Ciências, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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4
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Moubset O, Filloux D, Fontes H, Julian C, Fernandez E, Galzi S, Blondin L, Chehida SB, Lett JM, Mesléard F, Kraberger S, Custer JM, Salywon A, Makings E, Marais A, Chiroleu F, Lefeuvre P, Martin DP, Candresse T, Varsani A, Ravigné V, Roumagnac P. Virome release of an invasive exotic plant species in southern France. Virus Evol 2024; 10:veae025. [PMID: 38566975 PMCID: PMC10986800 DOI: 10.1093/ve/veae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/27/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.
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Affiliation(s)
- Oumaima Moubset
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Denis Filloux
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Hugo Fontes
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles 13200, France
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, Avignon 84911, France
| | - Charlotte Julian
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Emmanuel Fernandez
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Serge Galzi
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Laurence Blondin
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | | | | | - François Mesléard
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles 13200, France
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, Avignon 84911, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, 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, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Salywon
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ 85008, USA
| | - Elizabeth Makings
- Vascular Plant Herbarium, School of Life Sciences, Arizona State University, 734 West Alameda Drive, Tempe Tempe, AZ 85282, USA
| | - Armelle Marais
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon 33140, France
| | | | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Rd, Cape Town 7925, South Africa
| | - Thierry Candresse
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon 33140, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, 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 7700, South Africa
| | - Virginie Ravigné
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Philippe Roumagnac
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
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5
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Shishkova K, Gergova R, Tasheva E, Shishkov S, Sirakov I. Molecular Screening for High-Risk Human Papillomaviruses in Patients with Periodontitis. Viruses 2023; 15:v15030809. [PMID: 36992516 PMCID: PMC10059129 DOI: 10.3390/v15030809] [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: 03/08/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Members of the Papillomaviridae family account for 27.9-30% of all infectious agents associated with human cancer. The aim of our study was to investigate the presence of high-risk HPV (human papilloma virus) genotypes in patients with periodontitis and a pronounced clinical picture. To achieve this goal, after proving the bacterial etiology of periodontitis, the samples positive for bacteria were examined for the presence of HPV. The genotype of HPV is also determined in samples with the presence of the virus proven by PCR (polymerase chain reaction). All positive tests for bacteria associated with the development of periodontitis indicated the presence of HPV. There was a statistically significant difference in HPV positive results between the periodontitis positive target group and the control group. The higher presence of high-risk HPV genotypes in the target group, which was also positive for the presence of periodontitis-causing bacteria, has been proven. A statistically significant relationship was established between the presence of periodontitis-causing bacteria and high-risk strains of HPV. The most common HPV genotype that tests positive for bacteria associated with the development of periodontitis is HPV58.
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Affiliation(s)
- Kalina Shishkova
- Laboratory of Virology, Faculty of Biology, University of Sofia "St. Kl. Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Raina Gergova
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, 2 "Zdrave" Str., 1431 Sofia, Bulgaria
- G-Lab Ltd., 2 "Hristo Belchev", 1000 Sofia, Bulgaria
| | - Elena Tasheva
- Department of Zoology and Anthropology, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Stoyan Shishkov
- Laboratory of Virology, Faculty of Biology, University of Sofia "St. Kl. Ohridski", 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
| | - Ivo Sirakov
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, 2 "Zdrave" Str., 1431 Sofia, Bulgaria
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6
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Li N, Li C, Hu T, Li J, Zhou H, Ji J, Wu J, Kang W, Holmes EC, Shi W, Xu S. Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China. MICROBIOME 2023; 11:6. [PMID: 36631833 PMCID: PMC9832778 DOI: 10.1186/s40168-022-01446-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/08/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The economic and environmental value of honeybees has been severely challenged in recent years by the collapse of their colonies worldwide, often caused by outbreaks of infectious diseases. However, our understanding of the diversity, prevalence, and transmission of honeybee viruses is largely obscure due to a lack of large-scale and longitudinal genomic surveillance on a global scale. RESULTS We report the meta-transcriptomic sequencing of nearly 2000 samples of the two most important economic and widely maintained honeybee species, as well as an associated ectoparasite mite, collected across China during 2016-2019. We document the natural diversity and evolution of honeybee viruses in China, providing evidence that multiple viruses commonly co-circulate within individual bee colonies. We also expanded the genomic data for 12 important honeybee viruses and revealed novel genetic variants and lineages associated with China. We identified more than 23 novel viruses from the honeybee and mite viromes, with some exhibiting ongoing replication in their respective hosts. Together, these data provide additional support to the idea that mites are an important reservoir and spill-over host for honeybee viruses. CONCLUSIONS Our data show that honeybee viruses are more widespread, prevalent, and genetically diverse than previously realized. The information provided is important in mitigating viral infectious diseases in honeybees, in turn helping to maintain sustainable productive agriculture on a global scale. Video Abstract.
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Affiliation(s)
- Nannan Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Cixiu Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Juan Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Hong Zhou
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Jingkai Ji
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Jiangli Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Weipeng Kang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Edward C Holmes
- Sydeny Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
| | - Shufa Xu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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7
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Wirth J, Young M. Viruses in Subsurface Environments. Annu Rev Virol 2022; 9:99-119. [PMID: 36173700 DOI: 10.1146/annurev-virology-093020-015957] [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: 11/09/2022]
Abstract
Over the past 20 years, our knowledge of virus diversity and abundance in subsurface environments has expanded dramatically through application of quantitative metagenomic approaches. In most subsurface environments, viral diversity and abundance rival viral diversity and abundance observed in surface environments. Most of these viruses are uncharacterized in terms of their hosts and replication cycles. Analysis of accessory metabolic genes encoded by subsurface viruses indicates that they evolved to replicate within the unique features of their environments. The key question remains: What role do these viruses play in the ecology and evolution of the environments in which they replicate? Undoubtedly, as more virologists examine the role of viruses in subsurface environments, new insights will emerge.
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Affiliation(s)
- Jennifer Wirth
- Department of Plant Science and Plant Pathology and Thermal Biology Institute, Montana State University, Bozeman, Montana, USA;
| | - Mark Young
- Department of Plant Science and Plant Pathology and Thermal Biology Institute, Montana State University, Bozeman, Montana, USA;
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8
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Rosario K, Van Bogaert N, López-Figueroa NB, Paliogiannis H, Kerr M, Breitbart M. Freshwater macrophytes harbor viruses representing all five major phyla of the RNA viral kingdom Orthornavirae. PeerJ 2022; 10:e13875. [PMID: 35990902 PMCID: PMC9390326 DOI: 10.7717/peerj.13875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/19/2022] [Indexed: 01/18/2023] Open
Abstract
Research on aquatic plant viruses is lagging behind that of their terrestrial counterparts. To address this knowledge gap, here we identified viruses associated with freshwater macrophytes, a taxonomically diverse group of aquatic phototrophs that are visible with the naked eye. We surveyed pooled macrophyte samples collected at four spring sites in Florida, USA through next generation sequencing of RNA extracted from purified viral particles. Sequencing efforts resulted in the detection of 156 freshwater macrophyte associated (FMA) viral contigs, 37 of which approximate complete genomes or segments. FMA viral contigs represent putative members from all five major phyla of the RNA viral kingdom Orthornavirae. Similar to viral types found in land plants, viral sequences identified in macrophytes were dominated by positive-sense RNA viruses. Over half of the FMA viral contigs were most similar to viruses reported from diverse hosts in aquatic environments, including phototrophs, invertebrates, and fungi. The detection of FMA viruses from orders dominated by plant viruses, namely Patatavirales and Tymovirales, indicate that members of these orders may thrive in aquatic hosts. PCR assays confirmed the presence of putative FMA plant viruses in asymptomatic vascular plants, indicating that viruses with persistent lifestyles are widespread in macrophytes. The detection of potato virus Y and oat blue dwarf virus in submerged macrophytes suggests that terrestrial plant viruses infect underwater plants and highlights a potential terrestrial-freshwater plant virus continuum. Defining the virome of unexplored macrophytes will improve our understanding of virus evolution in terrestrial and aquatic primary producers and reveal the potential ecological impacts of viral infection in macrophytes.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
| | - Noémi Van Bogaert
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States,Present Address: FVPHouse, Berlare, Belgium
| | | | - Haris Paliogiannis
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States,Present Address: MIO-ECSDE, Athens, Greece
| | - Mason Kerr
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
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9
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Stenglein MD. The Case for Studying New Viruses of New Hosts. Annu Rev Virol 2022; 9:157-172. [PMID: 35671564 DOI: 10.1146/annurev-virology-100220-112915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virology has largely focused on viruses that are pathogenic to humans or to the other species that we care most about. There is no doubt that this has been a worthwhile investment. But many transformative advances have been made through the in-depth study of relatively obscure viruses that do not appear on lists of prioritized pathogens. In this review, I highlight the benefits that can accrue from the study of viruses and hosts off the beaten track. I take stock of viral sequence diversity across host taxa as an estimate of the bias that exists in our understanding of host-virus interactions. I describe the gains that have been made through the metagenomic discovery of thousands of new viruses in previously unsampled hosts as well as the limitations of metagenomic surveys. I conclude by suggesting that the study of viruses that naturally infect existing and emerging model organisms represents an opportunity to push virology forward in useful and hard to predict ways.Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mark D Stenglein
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA;
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10
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Abstract
The debate over whether viruses are living organisms tends to be paradigmatically determined. The metabolic paradigm denies that they are, while new research evidences the opposite. The purpose of this paper is to deliver a generic model for viral contexts that explains why viruses are alive. It will take a systems biology approach, with a qualitative part (using metacybernetics) to provide deeper explanations of viral contexts, and a quantitative part (using Fisher Information deriving from the variational principle of Extreme Physical Information) which is in principle able to take measurements and predict outcomes. The modelling process provides an extended view of the epigenetic processes of viruses. The generic systems biology model will depict viruses as autonomous entities with metaphysical processes of autopoietic self-organisation and adaptation, enabling them to maintain their physical viability and hence, within their populations, mutate and evolve. The autopoietic epigenetic processes are shown to describe their capability to change, and these are both qualitatively and quantitatively explored, the latter providing an approach to make measurements of physical phenomena under uncertainty. Viruses maintain their fitness when they are able to maintain their stability, and this is indicated by information flow efficacy. A brief case study is presented on the COVID-19 virus from the perspective that it is a living system, and this includes outcome predictions given Fisher Information conditions for known contexts.
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11
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Kieft K, Adams A, Salamzade R, Kalan L, Anantharaman K. vRhyme enables binning of viral genomes from metagenomes. Nucleic Acids Res 2022; 50:e83. [PMID: 35544285 PMCID: PMC9371927 DOI: 10.1093/nar/gkac341] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/17/2022] [Accepted: 04/22/2022] [Indexed: 01/11/2023] Open
Abstract
Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs supervised machine learning to identify nucleotide feature similarities, which are compiled into iterations of weighted networks and refined bins. To refine bins, vRhyme utilizes unique features of viral genomes, namely a protein redundancy scoring mechanism based on the observation that viruses seldom encode redundant genes. Using simulated viromes, we displayed superior performance of vRhyme compared to available binning tools in constructing more complete and uncontaminated vMAGs. When applied to 10,601 viral scaffolds from human skin, vRhyme advanced our understanding of resident viruses, highlighted by identification of a Herelleviridae vMAG comprised of 22 scaffolds, and another vMAG encoding a nitrate reductase metabolic gene, representing near-complete genomes post-binning. vRhyme will enable a convention of binning uncultivated viral genomes and has the potential to transform metagenome-based viral ecology.
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Affiliation(s)
- Kristopher Kieft
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, USA,Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
| | - Alyssa Adams
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, USA,Computation and Informatics in Biology and Medicine, University of Wisconsin–Madison, Madison, WI, USA
| | - Rauf Salamzade
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA,Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, USA
| | - Lindsay Kalan
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, USA,Department of Medicine, University of Wisconsin–Madison, Madison, WI, USA
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12
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Grupstra CGB, Lemoine NP, Cook C, Correa AMS. Thank you for biting: dispersal of beneficial microbiota through 'antagonistic' interactions. Trends Microbiol 2022; 30:930-939. [PMID: 35393166 DOI: 10.1016/j.tim.2022.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/23/2022]
Abstract
Multicellular organisms harbor populations of microbial symbionts; some of these symbionts can be dispersed through the feeding activities of consumers. Studies of consumer-mediated microbiota dispersal generally focus on pathogenic microorganisms; the dispersal of beneficial microorganisms has received less attention, especially in the context of 'antagonistic' trophic interactions (e.g., herbivory, parasitism, predation). Yet, this 'trophic transmission' of beneficial symbionts has significant implications for microbiota assembly and resource species (e.g., prey) health. For example, trophic transmission of microorganisms could assist with environmental acclimatization and help resource species to suppress other consumers or competitors. Here, we highlight model systems and approaches that have revealed these potential 'silver-linings' of antagonism as well as opportunities and challenges for future research.
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Affiliation(s)
- C G B Grupstra
- BioSciences Department, Rice University, Houston, TX 77098, USA.
| | - N P Lemoine
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; Department of Zoology, Milwaukee Public Museum, Milwaukee, WI 53233, USA
| | - C Cook
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - A M S Correa
- BioSciences Department, Rice University, Houston, TX 77098, USA
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13
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Broecker F. Editorial for the Special Issue: The Role of the Virome in Health and Disease. Microorganisms 2021; 10:microorganisms10010020. [PMID: 35056466 PMCID: PMC8778850 DOI: 10.3390/microorganisms10010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/22/2022] Open
Affiliation(s)
- Felix Broecker
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
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14
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Merges D, Dal Grande F, Greve C, Otte J, Schmitt I. Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions. Environ Microbiol 2021; 23:6637-6650. [PMID: 34697892 DOI: 10.1111/1462-2920.15802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/01/2021] [Indexed: 11/28/2022]
Abstract
Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep-sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool-seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%-40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population-specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.
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Affiliation(s)
- Dominik Merges
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany.,Department of Biological Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany
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15
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Abstract
Recent human activity has profoundly transformed Earth biomes on a scale and at rates that are unprecedented. Given the central role of symbioses in ecosystem processes, functions, and services throughout the Earth biosphere, the impacts of human-driven change on symbioses are critical to understand. Symbioses are not merely collections of organisms, but co-evolved partners that arise from the synergistic combination and action of different genetic programs. They function with varying degrees of permanence and selection as emergent units with substantial potential for combinatorial and evolutionary innovation in both structure and function. Following an articulation of operational definitions of symbiosis and related concepts and characteristics of the Anthropocene, we outline a basic typology of anthropogenic change (AC) and a conceptual framework for how AC might mechanistically impact symbioses with select case examples to highlight our perspective. We discuss surprising connections between symbiosis and the Anthropocene, suggesting ways in which new symbioses could arise due to AC, how symbioses could be agents of ecosystem change, and how symbioses, broadly defined, of humans and “farmed” organisms may have launched the Anthropocene. We conclude with reflections on the robustness of symbioses to AC and our perspective on the importance of symbioses as ecosystem keystones and the need to tackle anthropogenic challenges as wise and humble stewards embedded within the system.
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Affiliation(s)
- Erik F Y Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS 38677 USA
| | - Alexandra S Penn
- Department of Sociology and Centre for Evaluation of Complexity Across the Nexus, University of Surrey, Guildford, Surrey, GU2 7XH UK
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16
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Xiao Y, Li W, Yang X, Xu P, Jin M, Yuan H, Zheng W, Soberón M, Bravo A, Wilson K, Wu K. Rapid spread of a densovirus in a major crop pest following wide-scale adoption of Bt-cotton in China. eLife 2021; 10:e66913. [PMID: 34263726 PMCID: PMC8324301 DOI: 10.7554/elife.66913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/13/2021] [Indexed: 12/21/2022] Open
Abstract
Bacillus thuringiensis (Bt) crops have been widely planted and the effects of Bt-crops on populations of the target and non-target insect pests have been well studied. However, the effects of Bt-crops exposure on microorganisms that interact with crop pests have not previously been quantified. Here, we use laboratory and field data to show that infection of Helicoverpa armigera with a densovirus (HaDV2) is associated with its enhanced growth and tolerance to Bt-cotton. Moreover, field monitoring showed a much higher incidence of cotton bollworm infection with HaDV2 in regions cultivated with Bt-cotton than in regions without it, with the rate of densovirus infection increasing with increasing use of Bt-cotton. RNA-seq suggested tolerance to both baculovirus and Cry1Ac were enhanced via the immune-related pathways. These findings suggest that exposure to Bt-crops has selected for beneficial interactions between the target pest and a mutualistic microorganism that enhances its performance on Bt-crops under field conditions.
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Affiliation(s)
- Yutao Xiao
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Wenjing Li
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant Protection and Soil Fertility, Hubei Academy of Agricultural SciencesWuhanChina
| | - Xianming Yang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Pengjun Xu
- Tobacco Research Institute, Chinese Academy of Agricultural SciencesQingdaoChina
- Lancaster Environment Centre, Lancaster UniversityLancasterUnited Kingdom
| | - Minghui Jin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - He Yuan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Weigang Zheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Mario Soberón
- Instituto de Biotecnología, Universidad Nacional Autónoma de MéxicoMorelosUnited States
| | - Alejandra Bravo
- Instituto de Biotecnología, Universidad Nacional Autónoma de MéxicoMorelosUnited States
| | - Kenneth Wilson
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
- Lancaster Environment Centre, Lancaster UniversityLancasterUnited Kingdom
| | - Kongming Wu
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
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17
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Wakefield JC, Conrad JA. Harm as a Necessary Component of the Concept of Medical Disorder: Reply to Muckler and Taylor. THE JOURNAL OF MEDICINE AND PHILOSOPHY 2021; 45:350-370. [PMID: 32437578 DOI: 10.1093/jmp/jhaa008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Wakefield's harmful dysfunction analysis asserts that the concept of medical disorder includes a naturalistic component of dysfunction (failure of biologically designed functioning) and a value (harm) component, both of which are required for disorder attributions. Muckler and Taylor, defending a purely naturalist, value-free understanding of disorder, argue that harm is not necessary for disorder. They provide three examples of dysfunctions that, they claim, are considered disorders but are entirely harmless: mild mononucleosis, cowpox that prevents smallpox, and minor perceptual deficits. They also reject the proposal that dysfunctions need only be typically harmful to qualify as disorders. We argue that the proposed counterexamples are, in fact, considered harmful; thus, they fail to disconfirm the harm requirement: incapacity for exertion is inherently harmful, whether or not exertion occurs, cowpox is directly harmful irrespective of indirect benefits, and colorblindness and anosmia are considered harmful by those who consider them disorders. We also defend the typicality qualifier as viably addressing some apparently harmless disorders and argue that a dysfunction's harmfulness is best understood in dispositional terms.
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Affiliation(s)
| | - Jordan A Conrad
- Katholieke Universiteit Leuven, Leuven, BE, and New York University, New York, USA
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18
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Bolívar A, Tarlak F, Costa JCCP, Cejudo-Gómez M, Bover-Cid S, Zurera G, Pérez-Rodríguez F. A new expanded modelling approach for investigating the bioprotective capacity of Latilactobacillus sakei CTC494 against Listeria monocytogenes in ready-to-eat fish products. Food Res Int 2021; 147:110545. [PMID: 34399522 DOI: 10.1016/j.foodres.2021.110545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 10/21/2022]
Abstract
Understanding the role of food-related factors on the efficacy of protective cultures is essential to attain optimal results for developing biopreservation-based strategies. The aim of this work was to assess and model growth of Latilactobacillus sakei CTC494 and Listeria monocytogenes CTC1034, and their interaction, in two different ready-to-eat fish products (i.e., surimi-based product and tuna pâté) at 2 and 12 °C. The existing expanded Jameson-effect and a new expanded Jameson-effect model proposed in this study were evaluated to quantitatively describe the effect of microbial interaction. The inhibiting effect of the selected lactic acid bacteria strain on the pathogen growth was product dependent. In surimi product, a reduction of lag time of both strains was observed when growing in coculture at 2 °C, followed by the inhibition of the pathogen when the bioprotective L. sakei CTC494 reached the maximum population density, suggesting a mutualism-antagonism continuum phenomenon between populations. In tuna pâté, L. sakei CTC494 exerted a strong inhibition of L. monocytogenes at 2 °C (<0.5 log increase) and limited the growth at 12 °C (<2 log increase). The goodness-of-fit indexes indicated that the new expanded Jameson-effect model performed better and appropriately described the different competition patterns observed in the tested fish products. The proposed expanded competition model allowed for description of not only antagonistic but also mutualism-based interactions based on their influence on lag time.
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Affiliation(s)
- Araceli Bolívar
- Department of Food Science and Technology, Faculty of Veterinary, Agrifood Campus of International Excellence (ceiA3), University of Cordoba, 14014 Córdoba, Spain.
| | - Fatih Tarlak
- Department of Nutrition and Dietetics, Istanbul Gedik University, 34876 Istanbul, Turkey
| | - Jean Carlos Correia Peres Costa
- Department of Food Science and Technology, Faculty of Veterinary, Agrifood Campus of International Excellence (ceiA3), University of Cordoba, 14014 Córdoba, Spain
| | - Manuel Cejudo-Gómez
- Department of Food Science and Technology, Faculty of Veterinary, Agrifood Campus of International Excellence (ceiA3), University of Cordoba, 14014 Córdoba, Spain
| | - Sara Bover-Cid
- Food Safety and Functionality Programme, Institute of Agriculture and Food Research and Technology (IRTA), Finca Camps i Armet s/n, 17121, Monells, Girona, Spain
| | - Gonzalo Zurera
- Department of Food Science and Technology, Faculty of Veterinary, Agrifood Campus of International Excellence (ceiA3), University of Cordoba, 14014 Córdoba, Spain
| | - Fernando Pérez-Rodríguez
- Department of Food Science and Technology, Faculty of Veterinary, Agrifood Campus of International Excellence (ceiA3), University of Cordoba, 14014 Córdoba, Spain
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19
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Zhong J, Yang ZZ, Yang X, Guo ZJ, Xie W, Zhang YJ. Molecular characterization of a novel partitivirus and a fusarivirus coinfecting the fungus Nigrospora sphaerica. Arch Virol 2021; 166:2325-2331. [PMID: 34057607 DOI: 10.1007/s00705-021-05095-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
In this report, we describe the molecular characterization of two novel mycoviruses coinfecting the plant pathogenic fungus Nigrospora sphaerica, which were designated "Nigrospora sphaerica fusarivirus 1" (NsFV1) and "Nigrospora sphaerica partitivirus 1" (NsPV1). NsFV1 has an undivided genome measuring 6,147 nt, excluding the polyA tail, and was predicted to contain two nonoverlapping open reading frames (ORF1 and 2). The larger ORF1 encodes a polyprotein containing a conserved RNA-dependent RNA polymerase (RdRp) and a helicase domain that has functions related to RNA replication, and the smaller ORF2 encodes a putative protein with an unknown function. NsPV1 consists of two genome segments, which measure 1,796 bp and 1,455 bp in length. Each of the two dsRNAs has a single ORF, and they are predicted to encode proteins with homology to viral RdRps and coat proteins of members of the family Partitiviridae. Phylogenetic analysis indicated that NsFV1 is a member of the recently proposed family "Fusariviridae", while NsPV1 was determined to belong to the genus Gammapartitivirus in the family Partitiviridae. To the best of our knowledge, this report is the first to describe mycoviruses infecting N. sphaerica.
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Affiliation(s)
- Jie Zhong
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha City, Hunan Province, 410128, People's Republic of China
| | - Ze Zhong Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xin Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhao Jiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wen Xie
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - You Jun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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20
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de Miranda JR, Granberg F, Low M, Onorati P, Semberg E, Jansson A, Berggren Å. Virus Diversity and Loads in Crickets Reared for Feed: Implications for Husbandry. Front Vet Sci 2021; 8:642085. [PMID: 34095270 PMCID: PMC8173086 DOI: 10.3389/fvets.2021.642085] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/22/2021] [Indexed: 11/17/2022] Open
Abstract
Insects generally have high reproductive rates leading to rapid population growth and high local densities; ideal conditions for disease epidemics. The parasites and diseases that naturally regulate wild insect populations can also impact when these insects are produced commercially, on farms. While insects produced for human or animal consumption are often reared under high density conditions, very little is known about the microbes associated with these insects, particularly those with pathogenic potential. In this study we used both target-free and targeted screening approaches to explore the virome of two cricket species commonly reared for feed and food, Acheta domesticus and Gryllus bimaculatus. The target-free screening of DNA and RNA from a single A. domesticus frass sample revealed that only 1% of the nucleic acid reads belonged to viruses, including known cricket, insect, bacterial and plant pathogens, as well as a diverse selection of novel viruses. The targeted screening revealed relatively high levels of Acheta domesticus densovirus, invertebrate iridovirus 6 and a novel iflavirus, as well as low levels of Acheta domesticus volvovirus, in insect and frass samples from several retailers. Our findings highlight the value of multiple screening approaches for a comprehensive and robust cricket disease monitoring and management strategy. This will become particularly relevant as-and-when cricket rearing facilities scale up and transform from producing insects for animal feed to producing insects for human consumption.
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Affiliation(s)
- Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Fredrik Granberg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Matthew Low
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Piero Onorati
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emilia Semberg
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna Jansson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Åsa Berggren
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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21
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Virus Prospecting in Crickets-Discovery and Strain Divergence of a Novel Iflavirus in Wild and Cultivated Acheta domesticus. Viruses 2021; 13:v13030364. [PMID: 33669085 PMCID: PMC7996529 DOI: 10.3390/v13030364] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/19/2022] Open
Abstract
Orthopteran insects have high reproductive rates leading to boom-bust population dynamics with high local densities that are ideal for short, episodic disease epidemics. Viruses are particularly well suited for such host population dynamics, due to their supreme ability to adapt to changing transmission criteria. However, very little is known about the viruses of Orthopteran insects. Since Orthopterans are increasingly reared commercially, for animal feed and human consumption, there is a risk that viruses naturally associated with these insects can adapt to commercial rearing conditions, and cause disease. We therefore explored the virome of the house cricket Acheta domesticus, which is both part of the natural Swedish landscape and reared commercially for the pet feed market. Only 1% of the faecal RNA and DNA from wild-caught A. domesticus consisted of viruses. These included both known and novel viruses associated with crickets/insects, their bacterial-fungal microbiome, or their plant food. Relatively abundant among these viral Operational Taxonomic Units (OTUs) was a novel Iflavirus, tentatively named Acheta domesticus Iflavirus (AdIV). Quantitative analyses showed that AdIV was also abundant in frass and insect samples from commercially reared crickets. Interestingly, the wild and commercial AdIV strains had short, extremely divergent variation hotspots throughout the genome, which may indicate specific adaptation to their hosts’ distinct rearing environments.
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22
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Housekeeping in the Hydrosphere: Microbial Cooking, Cleaning, and Control under Stress. Life (Basel) 2021; 11:life11020152. [PMID: 33671121 PMCID: PMC7922117 DOI: 10.3390/life11020152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/05/2021] [Accepted: 02/12/2021] [Indexed: 12/02/2022] Open
Abstract
Who’s cooking, who’s cleaning, and who’s got the remote control within the waters blanketing Earth? Anatomically tiny, numerically dominant microbes are the crucial “homemakers” of the watery household. Phytoplankton’s culinary abilities enable them to create food by absorbing sunlight to fix carbon and release oxygen, making microbial autotrophs top-chefs in the aquatic kitchen. However, they are not the only bioengineers that balance this complex household. Ubiquitous heterotrophic microbes including prokaryotic bacteria and archaea (both “bacteria” henceforth), eukaryotic protists, and viruses, recycle organic matter and make inorganic nutrients available to primary producers. Grazing protists compete with viruses for bacterial biomass, whereas mixotrophic protists produce new organic matter as well as consume microbial biomass. When viruses press remote-control buttons, by modifying host genomes or lysing them, the outcome can reverberate throughout the microbial community and beyond. Despite recognition of the vital role of microbes in biosphere housekeeping, impacts of anthropogenic stressors and climate change on their biodiversity, evolution, and ecological function remain poorly understood. How trillions of the smallest organisms in Earth’s largest ecosystem respond will be hugely consequential. By making the study of ecology personal, the “housekeeping” perspective can provide better insights into changing ecosystem structure and function at all scales.
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23
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Nasir A, Romero-Severson E, Claverie JM. Investigating the Concept and Origin of Viruses. Trends Microbiol 2020; 28:959-967. [PMID: 33158732 PMCID: PMC7609044 DOI: 10.1016/j.tim.2020.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/21/2022]
Abstract
The ongoing COVID-19 pandemic has piqued public interest in the properties, evolution, and emergence of viruses. Here, we discuss how these basic questions have surprisingly remained disputed despite being increasingly within the reach of scientific analysis. We review recent data-driven efforts that shed light into the origin and evolution of viruses and explain factors that resist the widespread acceptance of new views and insights. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We note that the philosophical aspects of virus evolution also impact the way we might prepare for future outbreaks.
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Affiliation(s)
- Arshan Nasir
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Ethan Romero-Severson
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Jean-Michel Claverie
- Aix Marseille University, CNRS, IGS, Structural and Genomic Information Laboratory (UMR7256), Mediterranean Institute of Microbiology (FR3479), Marseille, France
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24
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Resnik JL, Smilanich AM. The Effect of Phenoloxidase Activity on Survival Is Host Plant Dependent in Virus-Infected Caterpillars. JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:5934963. [PMID: 33089871 PMCID: PMC7583276 DOI: 10.1093/jisesa/ieaa116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Indexed: 06/11/2023]
Abstract
An important goal of disease ecology is to understand trophic interactions influencing the host-pathogen relationship. This study focused on the effects of diet and immunity on the outcome of viral infection for the polyphagous butterfly, Vanessa cardui Linnaeus (Lepidoptera: Nymphalidae) (painted lady). Specifically, we aimed to understand the role that larval host plants play when fighting a viral pathogen. Larvae were orally inoculated with the entomopathogenic virus, Junonia coenia densovirus (JcDV) (Parvovirididae: Densovirinae, Lepidopteran Potoambidensovirus 1) and reared on two different host plants (Lupinus albifrons Bentham (Fabales: Fabaceae) or Plantago lanceolata Linnaeus (Lamiales: Plantaginaceae)). Following viral infection, the immune response (i.e., phenoloxidase [PO] activity), survival to adulthood, and viral load were measured for individuals on each host plant. We found that the interaction between the immune response and survival of the viral infection was host plant dependent. The likelihood of survival was lowest for infected larvae exhibiting suppressed PO activity and feeding on P. lanceolata, providing some evidence that PO activity may be an important defense against viral infection. However, for individuals reared on L. albifrons, the viral infection had a negligible effect on the immune response, and these individuals also had higher survival and lower viral load when infected with the pathogen compared to the controls. Therefore, we suggest that host plant modifies the effects of JcDV infection and influences caterpillars' response when infected with the virus. Overall, we conclude that the outcome of viral infection is highly dependent upon diet, and that certain host plants can provide protection from pathogens regardless of immunity.
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25
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Naddeo V. Development of environmental biotechnology and control of emerging biological contaminants: the grand challenge for a sustainable future. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2020; 92:1246-1248. [PMID: 32914513 DOI: 10.1002/wer.1439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 05/19/2023]
Abstract
Viruses and bacteria are "Angels" that works in environmental biotechnologies for sustainable development and "Demons" that can compromise the quality of life.
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Affiliation(s)
- Vincenzo Naddeo
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, Fisciano (SA), Italy
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26
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Health Impact and Therapeutic Manipulation of the Gut Microbiome. High Throughput 2020; 9:ht9030017. [PMID: 32751130 PMCID: PMC7564083 DOI: 10.3390/ht9030017] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 12/12/2022] Open
Abstract
Recent advances in microbiome studies have revealed much information about how the gut virome, mycobiome, and gut bacteria influence health and disease. Over the years, many studies have reported associations between the gut microflora under different pathological conditions. However, information about the role of gut metabolites and the mechanisms by which the gut microbiota affect health and disease does not provide enough evidence. Recent advances in next-generation sequencing and metabolomics coupled with large, randomized clinical trials are helping scientists to understand whether gut dysbiosis precedes pathology or gut dysbiosis is secondary to pathology. In this review, we discuss our current knowledge on the impact of gut bacteria, virome, and mycobiome interactions with the host and how they could be manipulated to promote health.
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Sariola S, Gilbert SF. Toward a Symbiotic Perspective on Public Health: Recognizing the Ambivalence of Microbes in the Anthropocene. Microorganisms 2020; 8:E746. [PMID: 32429344 PMCID: PMC7285259 DOI: 10.3390/microorganisms8050746] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023] Open
Abstract
Microbes evolve in complex environments that are often fashioned, in part, by human desires. In a global perspective, public health has played major roles in structuring how microbes are perceived, cultivated, and destroyed. The germ theory of disease cast microbes as enemies of the body and the body politic. Antibiotics have altered microbial development by providing stringent natural selection on bacterial species, and this has led to the formation of antibiotic-resistant bacterial strains. Public health perspectives such as "Precision Public Health" and "One Health" have recently been proposed to further manage microbial populations. However, neither of these take into account the symbiotic relationships that exist between bacterial species and between bacteria, viruses, and their eukaryotic hosts. We propose a perspective on public health that recognizes microbial evolution through symbiotic associations (the hologenome theory) and through lateral gene transfer. This perspective has the advantage of including both the pathogenic and beneficial interactions of humans with bacteria, as well as combining the outlook of the "One Health" model with the genomic methodologies utilized in the "Precision Public Health" model. In the Anthropocene, the conditions for microbial evolution have been altered by human interventions, and public health initiatives must recognize both the beneficial (indeed, necessary) interactions of microbes with their hosts as well as their pathogenic interactions.
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Affiliation(s)
- Salla Sariola
- Faculty of Social Sciences, Sociology, University of Helsinki, 00014 Helsinki, Finland;
| | - Scott F. Gilbert
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
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28
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Beaurepaire A, Piot N, Doublet V, Antunez K, Campbell E, Chantawannakul P, Chejanovsky N, Gajda A, Heerman M, Panziera D, Smagghe G, Yañez O, de Miranda JR, Dalmon A. Diversity and Global Distribution of Viruses of the Western Honey Bee, Apis mellifera. INSECTS 2020; 11:E239. [PMID: 32290327 PMCID: PMC7240362 DOI: 10.3390/insects11040239] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/31/2022]
Abstract
In the past centuries, viruses have benefited from globalization to spread across the globe, infecting new host species and populations. A growing number of viruses have been documented in the western honey bee, Apis mellifera. Several of these contribute significantly to honey bee colony losses. This review synthetizes the knowledge of the diversity and distribution of honey-bee-infecting viruses, including recent data from high-throughput sequencing (HTS). After presenting the diversity of viruses and their corresponding symptoms, we surveyed the scientific literature for the prevalence of these pathogens across the globe. The geographical distribution shows that the most prevalent viruses (deformed wing virus, sacbrood virus, black queen cell virus and acute paralysis complex) are also the most widely distributed. We discuss the ecological drivers that influence the distribution of these pathogens in worldwide honey bee populations. Besides the natural transmission routes and the resulting temporal dynamics, global trade contributes to their dissemination. As recent evidence shows that these viruses are often multihost pathogens, their spread is a risk for both the beekeeping industry and the pollination services provided by managed and wild pollinators.
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Affiliation(s)
- Alexis Beaurepaire
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, 3003 Bern, Switzerland;
- Agroscope, Swiss Bee Research Center, 3003 Bern, Switzerland
- UR Abeilles et Environnement, INRAE, 84914 Avignon, France;
| | - Niels Piot
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (N.P.); (G.S.)
| | - Vincent Doublet
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, 86069 Ulm, Germany;
| | - Karina Antunez
- Department of Microbiology, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay;
| | - Ewan Campbell
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen AB24 3FX, UK;
| | - Panuwan Chantawannakul
- Environmental Science Research Center (ESRC), Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Bee Protection Laboratory (BeeP), Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nor Chejanovsky
- Entomology Department, Institute of Plant Protection, The Volcani Center, Rishon Lezion, Tel Aviv 5025001, Israel;
| | - Anna Gajda
- Laboratory of Bee Diseases, Institute of Veterinary Medicine, Warsaw University of Life Sciences, 02-787 Warsaw, Poland;
| | | | - Delphine Panziera
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany;
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (N.P.); (G.S.)
| | - Orlando Yañez
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, 3003 Bern, Switzerland;
- Agroscope, Swiss Bee Research Center, 3003 Bern, Switzerland
| | - Joachim R. de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07 Uppsala, Sweden;
| | - Anne Dalmon
- UR Abeilles et Environnement, INRAE, 84914 Avignon, France;
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29
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Yañez O, Chávez-Galarza J, Tellgren-Roth C, Pinto MA, Neumann P, de Miranda JR. The honeybee (Apis mellifera) developmental state shapes the genetic composition of the deformed wing virus-A quasispecies during serial transmission. Sci Rep 2020; 10:5956. [PMID: 32249797 PMCID: PMC7136270 DOI: 10.1038/s41598-020-62673-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/17/2020] [Indexed: 11/23/2022] Open
Abstract
The main biological threat to the western honeybee (Apis mellifera) is the parasitic mite Varroa destructor, largely because it vectors lethal epidemics of honeybee viruses that, in the absence of this mite, are relatively innocuous. The severe pathology is a direct consequence of excessive virus titres caused by this novel transmission route. However, little is known about how the virus adapts genetically during transmission and whether this influences the pathology. Here, we show that upon injection into honeybee pupae, the deformed wing virus type-A (DWV-A) quasispecies undergoes a rapid, extensive expansion of its sequence space, followed by strong negative selection towards a uniform, common shape by the time the pupae have completed their development, with no difference between symptomatic and asymptomatic adults in either DWV titre or genetic composition. This suggests that the physiological and molecular environment during pupal development has a strong, conservative influence on shaping the DWV-A quasispecies in emerging adults. There was furthermore no evidence of any progressive adaptation of the DWV-A quasispecies to serial intra-abdominal injection, simulating mite transmission, despite the generation of ample variation immediately following each transmission, suggesting that the virus either had already adapted to transmission by injection, or was unaffected by it.
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Affiliation(s)
- Orlando Yañez
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, CH-3000, Switzerland
| | - Julio Chávez-Galarza
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Instituto Nacional de Innovación Agraria (INIA), Av. La Molina, 1981, Lima, Perú
| | | | - M Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, CH-3000, Switzerland
| | - Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden.
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30
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González R, Butković A, Elena SF. From foes to friends: Viral infections expand the limits of host phenotypic plasticity. Adv Virus Res 2020; 106:85-121. [PMID: 32327149 DOI: 10.1016/bs.aivir.2020.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Phenotypic plasticity enables organisms to survive in the face of unpredictable environmental stress. Intimately related to the notion of phenotypic plasticity is the concept of the reaction norm that places phenotypic plasticity in the context of a genotype-specific response to environmental gradients. Whether reaction norms themselves evolve and which factors might affect their shape has been the object of intense debates among evolutionary biologists along the years. Since their discovery, viruses have been considered as pathogens. However, new viromic techniques and a shift in conceptual paradigms are showing that viruses are mostly non-pathogenic ubiquitous entities. Recent studies have shown how viral infections can even be beneficial for their hosts. This may happen especially in the context of stressed hosts, where the virus infection can induce beneficial changes in the host's physiological homeostasis, hence changing the shape of the reaction norm. Despite the fact that underlying physiological mechanisms and evolutionary dynamics are still not well understood, such beneficial interactions are being discovered in a growing number of plant-virus systems. Here, we aim to review these disperse studies and place them into the context of phenotypic plasticity and the evolution of reaction norms. This is an emerging field that is posing many questions that still need to be properly answered. The answers would clearly interest virologists, plant pathologists and evolutionary biologists and likely they will suggest possible future biotechnological applications, including the development of crops with higher survival rates and yield under adverse environmental situations.
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Affiliation(s)
- Rubén González
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain.
| | - Anamarija Butković
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain; The Santa Fe Institute, Santa Fe, NM, United States.
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31
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Takahashi H, Fukuhara T, Kitazawa H, Kormelink R. Virus Latency and the Impact on Plants. Front Microbiol 2019; 10:2764. [PMID: 31866963 PMCID: PMC6908805 DOI: 10.3389/fmicb.2019.02764] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/12/2019] [Indexed: 11/15/2022] Open
Abstract
Plant viruses are thought to be essentially harmful to the lives of their cultivated crop hosts. In most cases studied, the interaction between viruses and cultivated crop plants negatively affects host morphology and physiology, thereby resulting in disease. Native wild/non-cultivated plants are often latently infected with viruses without any clear symptoms. Although seemingly non-harmful, these viruses pose a threat to cultivated crops because they can be transmitted by vectors and cause disease. Reports are accumulating on infections with latent plant viruses that do not cause disease but rather seem to be beneficial to the lives of wild host plants. In a few cases, viral latency involves the integration of full-length genome copies into the host genome that, in response to environmental stress or during certain developmental stages of host plants, can become activated to generate and replicate episomal copies, a transition from latency to reactivation and causation of disease development. The interaction between viruses and host plants may also lead to the integration of partial-length segments of viral DNA genomes or copy DNA of viral RNA genome sequences into the host genome. Transcripts derived from such integrated viral elements (EVEs) may be beneficial to host plants, for example, by conferring levels of virus resistance and/or causing persistence/latency of viral infections. Studies on viral latency in wild host plants might help us to understand and elucidate the underlying mechanisms of latency and provide insights into the raison d’être for viruses in the lives of plants.
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Affiliation(s)
- Hideki Takahashi
- Laboratory of Plant Pathology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Plant Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences and Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University, Wageningen, Netherlands
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32
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Dupont C, Michiels A, Sochard C, Dardenne N, Meyer S, Brault V, Outreman Y, Sentis A. Virus mediated trophic interactions between aphids and their natural enemies. OIKOS 2019. [DOI: 10.1111/oik.06868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Corentin Dupont
- IGEPP, Agrocampus Ouest, INRA, Univ. de Rennes, Univ. Bretagne‐Loire Rennes France
| | - Alexandra Michiels
- UMR 5174; EDB (Laboratoire Évolution and Diversité Biologique); CNRS, Université Toulouse III, IRD, 118 route de Narbonne, FR‐31062 Toulouse Cedex 9 France
| | - Corentin Sochard
- IGEPP, Agrocampus Ouest, INRA, Univ. de Rennes, Univ. Bretagne‐Loire Rennes France
| | - Nathalie Dardenne
- UMR 5174; EDB (Laboratoire Évolution and Diversité Biologique); CNRS, Université Toulouse III, IRD, 118 route de Narbonne, FR‐31062 Toulouse Cedex 9 France
| | - Sophie Meyer
- UMR SVQV, INRA, Univ. de Strasbourg Colmar France
| | | | - Yannick Outreman
- IGEPP, Agrocampus Ouest, INRA, Univ. de Rennes, Univ. Bretagne‐Loire Rennes France
| | - Arnaud Sentis
- UMR 5174; EDB (Laboratoire Évolution and Diversité Biologique); CNRS, Université Toulouse III, IRD, 118 route de Narbonne, FR‐31062 Toulouse Cedex 9 France
- IRSTEA, Aix Marseille Univ., UMR RECOVER, 3275 route Cézanne, FR‐13182 Aix‐en‐Provence France
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33
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May A, Narayanan S, Alcock J, Varsani A, Maley C, Aktipis A. Kombucha: a novel model system for cooperation and conflict in a complex multi-species microbial ecosystem. PeerJ 2019; 7:e7565. [PMID: 31534844 PMCID: PMC6730531 DOI: 10.7717/peerj.7565] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/29/2019] [Indexed: 01/02/2023] Open
Abstract
Kombucha, a fermented tea beverage with an acidic and effervescent taste, is composed of a multispecies microbial ecosystem with complex interactions that are characterized by both cooperation and conflict. In kombucha, a complex community of bacteria and yeast initiates the fermentation of a starter tea (usually black or green tea with sugar), producing a biofilm that covers the liquid over several weeks. This happens through several fermentative phases that are characterized by cooperation and competition among the microbes within the kombucha solution. Yeast produce invertase as a public good that enables both yeast and bacteria to metabolize sugars. Bacteria produce a surface biofilm which may act as a public good providing protection from invaders, storage for resources, and greater access to oxygen for microbes embedded within it. The ethanol and acid produced during the fermentative process (by yeast and bacteria, respectively) may also help to protect the system from invasion by microbial competitors from the environment. Thus, kombucha can serve as a model system for addressing important questions about the evolution of cooperation and conflict in diverse multispecies systems. Further, it has the potential to be artificially selected to specialize it for particular human uses, including the development of antimicrobial ecosystems and novel materials. Finally, kombucha is easily-propagated, non-toxic, and inexpensive, making it an excellent system for scientific inquiry and citizen science.
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Affiliation(s)
- Alexander May
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Psychology, Arizona State University, Tempe, AZ, USA
| | - Shrinath Narayanan
- The Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Joe Alcock
- University of New Mexico, Albuquerque, NM, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Carlo Maley
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
| | - Athena Aktipis
- Department of Psychology, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Biocomputing, Security and Society, Arizona State University, Tempe, AZ, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
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34
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Roossinck MJ. Viruses in the phytobiome. Curr Opin Virol 2019; 37:72-76. [PMID: 31310864 DOI: 10.1016/j.coviro.2019.06.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 11/18/2022]
Abstract
The phytobiome, defined as plants and all the entities that interact with them, is rich in viruses, but with the exception of plant viruses of crop plants, most of the phytobiome viruses remain very understudied. This review focuses on the neglected portions of the phytobiome, including viruses of other microbes interacting with plants, viruses in the soil, viruses of wild plants, and relationships between viruses and the vectors of plant viruses.
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Affiliation(s)
- Marilyn J Roossinck
- Center for Infectious Disease Dynamics, Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, USA.
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35
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Slingenbergh J. Animal Virus Ecology and Evolution Are Shaped by the Virus Host-Body Infiltration and Colonization Pattern. Pathogens 2019; 8:pathogens8020072. [PMID: 31130619 PMCID: PMC6631033 DOI: 10.3390/pathogens8020072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/19/2019] [Accepted: 05/20/2019] [Indexed: 12/24/2022] Open
Abstract
The current classification of animal viruses is largely based on the virus molecular world. Less attention is given to why and how virus fitness results from the success of virus transmission. Virus transmission reflects the infection-shedding-transmission dynamics, and with it, the organ system involvement and other, macroscopic dimensions of the host environment. This study describes the transmission ecology of the world main livestock viruses, 36 in total, a mix of RNA, DNA and retroviruses. Following an iterative process, the viruses are virtually ranked in an outer- to inner-body fashion, by organ system, on ecological grounds. Also portrayed are the shifts in virus host tropism and virus genome. The synthesis of the findings reveals a predictive virus evolution framework, based on the outer- to inner-body changes in the interplay of host environment-transmission modes-organ system involvement-host cell infection cycle-virus genome. Outer-body viruses opportunistically respond to the variation in the external environment. For example, respiratory and enteric viruses tend to be associated with poultry and pig mass rearing. Ruminant and equine viruses tend to be more deep-rooted and host-specific, and also establish themselves in the vital inner-body systems. It is concluded that the framework may assist the study of new emerging viruses and pandemic risks.
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Affiliation(s)
- Jan Slingenbergh
- Formerly Food and Agriculture Organization of the United Nations, 00153 Rome, Italy.
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36
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Goswami R, Subramanian G, Silayeva L, Newkirk I, Doctor D, Chawla K, Chattopadhyay S, Chandra D, Chilukuri N, Betapudi V. Gene Therapy Leaves a Vicious Cycle. Front Oncol 2019; 9:297. [PMID: 31069169 PMCID: PMC6491712 DOI: 10.3389/fonc.2019.00297] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022] Open
Abstract
The human genetic code encrypted in thousands of genes holds the secret for synthesis of proteins that drive all biological processes necessary for normal life and death. Though the genetic ciphering remains unchanged through generations, some genes get disrupted, deleted and or mutated, manifesting diseases, and or disorders. Current treatment options—chemotherapy, protein therapy, radiotherapy, and surgery available for no more than 500 diseases—neither cure nor prevent genetic errors but often cause many side effects. However, gene therapy, colloquially called “living drug,” provides a one-time treatment option by rewriting or fixing errors in the natural genetic ciphering. Since gene therapy is predominantly a viral vector-based medicine, it has met with a fair bit of skepticism from both the science fraternity and patients. Now, thanks to advancements in gene editing and recombinant viral vector development, the interest of clinicians and pharmaceutical industries has been rekindled. With the advent of more than 12 different gene therapy drugs for curing cancer, blindness, immune, and neuronal disorders, this emerging experimental medicine has yet again come in the limelight. The present review article delves into the popular viral vectors used in gene therapy, advances, challenges, and perspectives.
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Affiliation(s)
- Reena Goswami
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States
| | - Gayatri Subramanian
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Liliya Silayeva
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States
| | - Isabelle Newkirk
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States
| | - Deborah Doctor
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States
| | - Karan Chawla
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Dhyan Chandra
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Nageswararao Chilukuri
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States
| | - Venkaiah Betapudi
- Neuroscience Branch, Research Division, United States Army Medical Research Institute of Chemical Defense, Aberdeen, MD, United States.,Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, United States
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37
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Rowan-Nash AD, Korry BJ, Mylonakis E, Belenky P. Cross-Domain and Viral Interactions in the Microbiome. Microbiol Mol Biol Rev 2019; 83:e00044-18. [PMID: 30626617 PMCID: PMC6383444 DOI: 10.1128/mmbr.00044-18] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The importance of the microbiome to human health is increasingly recognized and has become a major focus of recent research. However, much of the work has focused on a few aspects, particularly the bacterial component of the microbiome, most frequently in the gastrointestinal tract. Yet humans and other animals can be colonized by a wide array of organisms spanning all domains of life, including bacteria and archaea, unicellular eukaryotes such as fungi, multicellular eukaryotes such as helminths, and viruses. As they share the same host niches, they can compete with, synergize with, and antagonize each other, with potential impacts on their host. Here, we discuss these major groups making up the human microbiome, with a focus on how they interact with each other and their multicellular host.
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Affiliation(s)
- Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Eleftherios Mylonakis
- Infectious Diseases Division, Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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38
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Abstract
Bees-including solitary, social, wild, and managed species-are key pollinators of flowering plant species, including nearly three-quarters of global food crops. Their ecological importance, coupled with increased annual losses of managed honey bees and declines in populations of key wild species, has focused attention on the factors that adversely affect bee health, including viral pathogens. Genomic approaches have dramatically expanded understanding of the diversity of viruses that infect bees, the complexity of their transmission routes-including intergenus transmission-and the diversity of strategies bees have evolved to combat virus infections, with RNA-mediated responses playing a prominent role. Moreover, the impacts of viruses on their hosts are exacerbated by the other major stressors bee populations face, including parasites, poor nutrition, and exposure to chemicals. Unraveling the complex relationships between viruses and their bee hosts will lead to improved understanding of viral ecology and management strategies that support better bee health.
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Affiliation(s)
- Christina M Grozinger
- Department of Entomology, Center for Pollinator Research, Center for Infectious Disease Dynamics, and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
| | - Michelle L Flenniken
- Department of Plant Sciences and Plant Pathology and Pollinator Health Center, Montana State University, Bozeman, Montana 59717, USA;
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39
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Chitarra W, Cuozzo D, Ferrandino A, Secchi F, Palmano S, Perrone I, Boccacci P, Pagliarani C, Gribaudo I, Mannini F, Gambino G. Dissecting interplays between Vitis vinifera L. and grapevine virus B (GVB) under field conditions. MOLECULAR PLANT PATHOLOGY 2018; 19:2651-2666. [PMID: 30055094 PMCID: PMC6638183 DOI: 10.1111/mpp.12735] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Plant virus infections are often difficult to characterize as they result from a complex molecular and physiological interplay between a pathogen and its host. In this study, the impact of the phloem-limited grapevine virus B (GVB) on the Vitis vinifera L. wine-red cultivar Albarossa was analysed under field conditions. Trials were carried out over two growing seasons by combining agronomic, molecular, biochemical and ecophysiological approaches. The data showed that GVB did not induce macroscopic symptoms on 'Albarossa', but affected the ecophysiological performances of vines in terms of assimilation rates, particularly at the end of the season, without compromising yield and vigour. In GVB-infected plants, the accumulation of soluble carbohydrates in the leaves and transcriptional changes in sugar- and photosynthetic-related genes seemed to trigger defence responses similar to those observed in plants infected by phytoplasmas, although to a lesser extent. In addition, GVB activated berry secondary metabolism. In particular, total anthocyanins and their acetylated forms accumulated at higher levels in GVB-infected than in GVB-free berries, consistent with the expression profiles of the related biosynthetic genes. These results contribute to improve our understanding of the multifaceted grapevine-virus interaction.
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Affiliation(s)
- Walter Chitarra
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA‐VE)Via XVIII Aprile 26Conegliano31015Italy
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)Strada delle Cacce 73Torino10135Italy
| | - Danila Cuozzo
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)Strada delle Cacce 73Torino10135Italy
- Department of Agricultural, Forest, and Food SciencesUniversity of Turin (DISAFA)Largo Paolo Braccini 2Grugliasco10095Italy
| | - Alessandra Ferrandino
- Department of Agricultural, Forest, and Food SciencesUniversity of Turin (DISAFA)Largo Paolo Braccini 2Grugliasco10095Italy
| | - Francesca Secchi
- Department of Agricultural, Forest, and Food SciencesUniversity of Turin (DISAFA)Largo Paolo Braccini 2Grugliasco10095Italy
| | - Sabrina Palmano
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)Strada delle Cacce 73Torino10135Italy
| | - Irene Perrone
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)Strada delle Cacce 73Torino10135Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)Strada delle Cacce 73Torino10135Italy
| | - Chiara Pagliarani
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)Strada delle Cacce 73Torino10135Italy
| | - Ivana Gribaudo
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)Strada delle Cacce 73Torino10135Italy
| | - Franco Mannini
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)Strada delle Cacce 73Torino10135Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant ProtectionNational Research Council (IPSP‐CNR)Strada delle Cacce 73Torino10135Italy
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Tirosh O, Conlan S, Deming C, Lee-Lin SQ, Huang X, Su HC, Freeman AF, Segre JA, Kong HH. Expanded skin virome in DOCK8-deficient patients. Nat Med 2018; 24:1815-1821. [PMID: 30397357 PMCID: PMC6286253 DOI: 10.1038/s41591-018-0211-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/05/2018] [Indexed: 12/25/2022]
Abstract
Human microbiome studies have revealed the intricate interplay of host immunity and bacterial communities to achieve homeostatic balance. Healthy skin microbial communities are dominated by bacteria with low viral representation1-3, mainly bacteriophage. Specific eukaryotic viruses have been implicated in both common and rare skin diseases, but cataloging skin viral communities has been limited. Alterations in host immunity provide an opportunity to expand our understanding of microbial-host interactions. Primary immunodeficient patients manifest with various viral, bacterial, fungal, and parasitic infections, including skin infections4. Dedicator of cytokinesis 8 (DOCK8) deficiency is a rare primary human immunodeficiency characterized by recurrent cutaneous and systemic infections, as well as atopy and cancer susceptibility5. DOCK8, encoding a guanine nucleotide exchange factor highly expressed in lymphocytes, regulates actin cytoskeleton, which is critical for migration through collagen-dense tissues such as skin6. Analyzing deep metagenomic sequencing data from DOCK8-deficient skin samples demonstrated a notable increase in eukaryotic viral representation and diversity compared with healthy volunteers. De novo assembly approaches identified hundreds of novel human papillomavirus genomes, illuminating microbial dark matter. Expansion of the skin virome in DOCK8-deficient patients underscores the importance of immune surveillance in controlling eukaryotic viral colonization and infection.
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Affiliation(s)
- Osnat Tirosh
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Sean Conlan
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Clay Deming
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Shih-Queen Lee-Lin
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Xin Huang
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Julia A Segre
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - Heidi H Kong
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA.
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Azizul Islam SKM, Chung JW, Lee YS, Cho H, Moon SS. Negative Association of Hepatitis B Virus With Hearing Impairment. Am J Audiol 2018; 27:324-332. [PMID: 30167657 DOI: 10.1044/2018_aja-17-0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 05/07/2018] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Hearing impairment is one of the most common chronic diseases causing deterioration of the quality of life in elderly individuals. Several viral infections have been suggested to cause hearing impairment. We investigated association of hepatitis B virus (HBV) infection with hearing impairment using a representative sample of the Korean population. METHOD Participants included 6,583 men and 8,702 women, who were ≥ 20 years of age from the Korea National Health and Nutritional Examination Surveys of the Korean population (2010-2012). Air-conduction pure-tone thresholds were measured in a soundproof booth using an automatic audiometer for each ear at 6 frequencies (500, 1000, 2000, 3000, 4000, and 6000 Hz). An audiometric test and a laboratory examination, including an HBV surface antigen (HBsAg) test, were performed. RESULTS Subjects who are HBsAg positive had lower average of pure-tone thresholds and lower prevalence of hearing impairment at both low/mid and high frequency compared with those without. Adjusted means of hearing thresholds were also lower among subjects who are HBsAg positive compared with subjects who are HBsAg negative. After the adjustment for age and gender, the odds of high-frequency mild hearing impairment were lower for subjects with HBV infection. In the multiple logistic regression analyses adjusting for confounding variables, the significant negative association between HBV infection and high-frequency mild hearing impairment still remained. CONCLUSIONS Contrary to previous reports, subjects who are HBsAg positive had a lower prevalence of hearing impairment compared with subjects who are HBsAg negative. Further studies are warranted to investigate the underlying mechanism regarding their negative relationship.
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Affiliation(s)
- SKM Azizul Islam
- Medical Institute of Dongguk University, Gyeongju, South Korea
- Department of Internal Medicine, College of Medicine, Dongguk University, Gyeongju, South Korea
| | - Jin Wook Chung
- Department of Internal Medicine, College of Medicine, Dongguk University, Gyeongju, South Korea
| | - Young-Sil Lee
- Department of Internal Medicine, College of Medicine, Dongguk University, Gyeongju, South Korea
| | - HoChan Cho
- Department of Internal Medicine, Keimyung University Dongsan Medical Center, Daegu, South Korea
| | - Seong-Su Moon
- Medical Institute of Dongguk University, Gyeongju, South Korea
- Department of Internal Medicine, College of Medicine, Dongguk University, Gyeongju, South Korea
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Sasai S, Tamura K, Tojo M, Herrero ML, Hoshino T, Ohki ST, Mochizuki T. A novel non-segmented double-stranded RNA virus from an Arctic isolate of Pythium polare. Virology 2018; 522:234-243. [DOI: 10.1016/j.virol.2018.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 10/28/2022]
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Cross ST, Kapuscinski ML, Perino J, Maertens BL, Weger-Lucarelli J, Ebel GD, Stenglein MD. Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms. Viruses 2018; 10:E388. [PMID: 30037148 PMCID: PMC6071216 DOI: 10.3390/v10070388] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 11/18/2022] Open
Abstract
Ixodes scapularis ticks harbor a variety of microorganisms, including eukaryotes, bacteria and viruses. Some of these can be transmitted to and cause disease in humans and other vertebrates. Others are not pathogenic, but may impact the ability of the tick to harbor and transmit pathogens. A growing number of studies have examined the influence of bacteria on tick vector competence but the influence of the tick virome remains less clear, despite a surge in the discovery of tick-associated viruses. In this study, we performed shotgun RNA sequencing on 112 individual adult I. scapularis collected in Wisconsin, USA. We characterized the abundance, prevalence and co-infection rates of viruses, bacteria and eukaryotic microorganisms. We identified pairs of tick-infecting microorganisms whose observed co-infection rates were higher or lower than would be expected, or whose RNA levels were positively correlated in co-infected ticks. Many of these co-occurrence and correlation relationships involved two bunyaviruses, South Bay virus and blacklegged tick phlebovirus-1. These viruses were also the most prevalent microorganisms in the ticks we sampled, and had the highest average RNA levels. Evidence of associations between microbes included a positive correlation between RNA levels of South Bay virus and Borrelia burgdorferi, the Lyme disease agent. These findings contribute to the rationale for experimental studies on the impact of viruses on tick biology and vector competence.
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Affiliation(s)
- Shaun T Cross
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Marylee L Kapuscinski
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Jacquelyn Perino
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Bernadette L Maertens
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - James Weger-Lucarelli
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
| | - Gregory D Ebel
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
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From Spatial Metagenomics to Molecular Characterization of Plant Viruses: A Geminivirus Case Study. Adv Virus Res 2018; 101:55-83. [PMID: 29908594 DOI: 10.1016/bs.aivir.2018.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The number of plant viruses that are known likely remains only a vanishingly small fraction of all extant plant virus species. Consequently, the distribution and population dynamics of plant viruses within even the best-studied ecosystems have only ever been studied for small groups of virus species. Even for the best studied of these groups very little is known about virus diversity at spatial scales ranging from an individual host, through individual local host populations to global host populations. To date, metagenomics studies that have assessed the collective or metagenomes of viruses at the ecosystem scale have revealed many previously unrecognized viral species. More recently, novel georeferenced metagenomics approaches have been devised that can precisely link individual sequence reads to both the plant hosts from which they were obtained, and the spatial arrangements of these hosts. Besides illuminating the diversity and the distribution of plant viruses at the ecosystem scale, application of these "geometagenomics" approaches has enabled the direct testing of hypotheses relating to the impacts of host diversity, host spatial variations, and environmental conditions on plant virus diversity and prevalence. To exemplify how such top-down approaches can provide a far deeper understanding of host-virus associations, we provide a case-study focusing on geminiviruses within two complex ecosystems containing both cultivated and uncultivated areas. Geminiviruses are a highly relevant model for studying the evolutionary and ecological aspects of viral emergence because the family Geminiviridae includes many of the most important crop pathogens that have emerged over the past century. In addition to revealing unprecedented degrees of geminivirus diversity within the analyzed ecosystems, the geometagenomics-based approach enabled the focused in-depth analysis of the complex evolutionary dynamics of some of the highly divergent geminivirus species that were discovered.
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Breitbart M, Malki K, Sawaya NA, Bonnain C, Martin MO. Elementary Student Outreach Activity Demonstrating the Use of Phage Therapy Heroes to Combat Bacterial Infections. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2018; 19:jmbe-19-30. [PMID: 29904530 PMCID: PMC5969416 DOI: 10.1128/jmbe.v19i1.1407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/08/2017] [Indexed: 06/08/2023]
Affiliation(s)
- Mya Breitbart
- University of South Florida, Saint Petersburg, FL 33701
| | - Kema Malki
- University of South Florida, Saint Petersburg, FL 33701
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Moore MD, Jaykus LA. Virus-Bacteria Interactions: Implications and Potential for the Applied and Agricultural Sciences. Viruses 2018; 10:E61. [PMID: 29393885 PMCID: PMC5850368 DOI: 10.3390/v10020061] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/28/2018] [Accepted: 01/31/2018] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic virus-bacteria interactions have recently become an emerging topic of study due to multiple significant examples related to human pathogens of clinical interest. However, such omnipresent and likely important interactions for viruses and bacteria relevant to the applied and agricultural sciences have not been reviewed or compiled. The fundamental basis of this review is that these interactions have importance and deserve more investigation, as numerous potential consequences and applications arising from their discovery are relevant to the applied sciences. The purpose of this review is to highlight and summarize eukaryotic virus-bacteria findings in the food/water, horticultural, and animal sciences. In many cases in the agricultural sciences, mechanistic understandings of the effects of virus-bacteria interactions remain unstudied, and many studies solely focus on co-infections of bacterial and viral pathogens. Given recent findings relative to human viral pathogens, further research related to virus-bacteria interactions would likely result in numerous discoveries and beneficial applications.
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Affiliation(s)
- Matthew D Moore
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA.
| | - Lee-Ann Jaykus
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA.
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Berliner AJ, Mochizuki T, Stedman KM. Astrovirology: Viruses at Large in the Universe. ASTROBIOLOGY 2018; 18:207-223. [PMID: 29319335 DOI: 10.1089/ast.2017.1649] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Viruses are the most abundant biological entities on modern Earth. They are highly diverse both in structure and genomic sequence, play critical roles in evolution, strongly influence terran biogeochemistry, and are believed to have played important roles in the origin and evolution of life. However, there is yet very little focus on viruses in astrobiology. Viruses arguably have coexisted with cellular life-forms since the earliest stages of life, may have been directly involved therein, and have profoundly influenced cellular evolution. Viruses are the only entities on modern Earth to use either RNA or DNA in both single- and double-stranded forms for their genetic material and thus may provide a model for the putative RNA-protein world. With this review, we hope to inspire integration of virus research into astrobiology and also point out pressing unanswered questions in astrovirology, particularly regarding the detection of virus biosignatures and whether viruses could be spread extraterrestrially. We present basic virology principles, an inclusive definition of viruses, review current virology research pertinent to astrobiology, and propose ideas for future astrovirology research foci. Key Words: Astrobiology-Virology-Biosignatures-Origin of life-Roadmap. Astrobiology 18, 207-223.
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Affiliation(s)
| | | | - Kenneth M Stedman
- 3 Center for Life in Extreme Environments and Biology Department, Portland State University , Oregon, USA
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Braga LPP, Soucy SM, Amgarten DE, da Silva AM, Setubal JC. Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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49
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Cruz-Muñoz ME, Fuentes-Pananá EM. Beta and Gamma Human Herpesviruses: Agonistic and Antagonistic Interactions with the Host Immune System. Front Microbiol 2018; 8:2521. [PMID: 29354096 PMCID: PMC5760548 DOI: 10.3389/fmicb.2017.02521] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/04/2017] [Indexed: 12/15/2022] Open
Abstract
Viruses are the most abundant and diverse biological entities in the planet. Historically, our main interest in viruses has focused on their pathogenic role, recognized by pandemics that have decimated the world population. However, viral infections have also played a major role in the evolution of cellular organisms, both through interchanging of genes with novel functions and shaping the immune system. Examples abound of infections that seriously compromise the host integrity, but evidence of plant and insect viruses mutualistic relationships have recently surfaced in which infected hosts are better suited for survival, arguing that virus-host interactions are initially parasitic but become mutualistic over years of co-evolution. A similar mutual help scenario has emerged with commensal gut bacteria. EBV is a herpesvirus that shares more than a hundred million years of co-evolution with humans, today successfully infecting close to 100% of the adult world population. Infection is usually acquired early in childhood persisting for the host lifetime mostly without apparent clinical symptoms. Disturbance of this homeostasis is rare and results in several diseases, of which the best understood are infectious mononucleosis and several EBV-associated cancers. Less understood are recently found inborn errors of the immune system that result in primary immunodeficiencies with an increased predisposition almost exclusive to EBV-associated diseases. Puzzling to these scenarios of broken homeostasis is the co-existence of immunosuppression, inflammation, autoimmunity and cancer. Homologous to EBV, HCMV, HHV-6 and HHV-7 are herpesviruses that also latently infect most individuals. Several lines of evidence support a mutualistic equilibrium between HCMV/EBV and hosts, that when altered trigger diseases in which the immune system plays a critical role. Interestingly, these beta and gamma herpesviruses persistently infect all immune lineages and early precursor cells. In this review, we will discuss the evidence of the benefits that infection of immune cells with these herpesviruses brings to the host. Also, the circumstances in which this positive relationship is broken, predisposing the host to diseases characterized by an abnormal function of the host immune system.
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Affiliation(s)
- Mario E Cruz-Muñoz
- Laboratorio de Inmunología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Ezequiel M Fuentes-Pananá
- Unidad de Investigación en Virología y Cáncer, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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50
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Kubiak K, Sielawa H, Chen W, Dzika E. Endosymbiosis and its significance in dermatology. J Eur Acad Dermatol Venereol 2017; 32:347-354. [PMID: 29194776 DOI: 10.1111/jdv.14721] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/02/2017] [Indexed: 12/30/2022]
Abstract
Proposed at the beginning of the twentieth century to explain the origin of eukaryotic organelles from prokaryotes, endosymbiosis is now medically defined by various interaction patterns between microorganisms and their residing hosts, best exemplified by the bacterial endosymbiont Wolbachia identified in arthropods and filarial nematodes, which can influence normal development, reproduction, survival and transmission of the hosts. Based on the transmission modes, vertical or horizontal, and the function of the endosymbionts, the host-symbiont dependence can be divided into primary or secondary. In dermatology, the role of endosymbionts in skin ectoparasitosis has aroused great interests in the past years. Riesia pediculicola is a primary bacterial endosymbiont in body lice Pediculus humanus, and supplement their hosts with vitamin B, especially pantothenic acid. In cimicosis, the Gram-negative Wolbachia can synthesize biotin and riboflavin, which are crucial for the growth and reproduction of the bedbug Cimex lectularius. In human demodicosis and rosacea, further study is required to prove the pathogenic role of the Gram-negative bacteria Bacillus oleronius or the Gram-positive bacteria Bacillus cereus demonstrated in the Demodex mites. The high infection rate of adult female ticks Ixodes ricinus with the Gram-negative bacteria Midichloria mitochondrii present in the mitochondria in diverse ovarian cells, with the high seroprevalence rate in tick-exposed subjects, raises the possibility that this non-pathogenic endosymbiont may play a role in immune response and successful transmission of the tick-borne pathogen. The anaerobic protozoan Trichomonas vaginalis and bacteria Mycoplasma hominis are two obligate parasites in the urogenital epithelium, with partially overlapping symptoms. Intracellular localization of Mycoplasma hominis can avoid host immune response and penetration of antibiotics, while Trichomonas vaginalis infected with Mycoplasma hominis seems to have a higher cytopathic activity and amoeboid transformation rate. Further study on the biology and pathogenesis of different endosymbionts in dermatological parasitosis will help for the development of new treatment modalities.
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Affiliation(s)
- K Kubiak
- Department of Medical Biology, Faculty of Health Sciences, Warmia and Mazury University, Olsztyn, Poland
| | - H Sielawa
- Department of Medical Biology, Faculty of Health Sciences, Warmia and Mazury University, Olsztyn, Poland
| | - W Chen
- Department of Dermatology and Allergy, Technische Universität München, Munich, Germany
| | - E Dzika
- Department of Medical Biology, Faculty of Health Sciences, Warmia and Mazury University, Olsztyn, Poland
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