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3. ICTV Virus Taxonomy Profile: Mymonaviridae 2022

Author

Microbiology Society, Ayllón, M.A. [0000-0001-7893-6106], Marzano, Shin-Yi L. [0000-0003-0548-3761], Kondō, Hideki [0000-0001-9220-5350], Turina, Massimo [0000-0002-9659-9470], Jiāng, Dàohóng, Ayllón, María A., Marzano, Shin-Yi L., Kondō, Hideki, Turina, Massimo, Microbiology Society, Ayllón, M.A. [0000-0001-7893-6106], Marzano, Shin-Yi L. [0000-0003-0548-3761], Kondō, Hideki [0000-0001-9220-5350], Turina, Massimo [0000-0002-9659-9470], Jiāng, Dàohóng, Ayllón, María A., Marzano, Shin-Yi L., Kondō, Hideki, and Turina, Massimo

Abstract

Typical members of the family Mymonaviridae produce filamentous, enveloped virions containing a single molecule of linear, negative-sense RNA of about about 10 kb, but some may not produce any virions. The family includes several genera, some with multiple species. Mymonavirids usually infect filamentous fungi, but a few have been identified associated with insects, oomycetes or plants. At least one virus, Sclerotinia sclerotiorum negative-stranded RNA virus 1, induces hypovirulence in its fungal host. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Mymonaviridae, which is available at ictv.global/report/mymonaviridae.

Published
2022

4. Corrigendum: Correction to Validation Lists

Author

The Microbiology Society

Subjects
DNA, Bacterial, Base Composition, RNA, Ribosomal, 16S, Fatty Acids, Sequence Analysis, DNA, Phylogeny, Bacterial Typing Techniques
Published
2022

9. Retraction notice: LaSota fusion (F) cleavage motif-mediated fusion activity is affected by other regions of the F protein from different genotype Newcastle disease virus in a chimeric virus: implication for virulence attenuation

Author

The Microbiology Society

Subjects
Animal
Abstract

The cleavage site sequence of the fusion (F) protein contributes to a wide range of virulence of Newcastle disease virus (NDV). In this study, we identified other important amino acid sequences of the F protein that affect cleavage and modulation of fusion. We generated chimeric Beaudette C (BC) viruses containing the cleavage site sequence of avirulent strain LaSota (Las-Fc) together with various regions of the F protein of another virulent strain AKO. We found that the F1 subunit is important for cleavage inhibition. Further dissection of the F1 subunit showed that replacement of four amino acids in the BC/Las-Fc protein with their AKO counterparts (T341S, M384I, T385A and I386L) resulted in an increase in fusion and replication in vitro. In contrast, the mutation N403D greatly reduced cleavage and viral replication, and affected protein conformation. These findings will be useful in developing improved live NDV vaccines and vaccine vectors.

Published
2020

11. Do specific antimicrobial stewardship interventions have an impact on carbapenem resistance in Gramnegative bacilli? A multicentre quasi-experimental ecological study: time-trend analysis and characterization of carbapenemases

Author

Universidad de Sevilla. Departamento de Microbiología, Universidad de Sevilla. Departamento de Medicina, Universidad de Sevilla. Instituto de Biomedicina de Sevilla (IBIS), Spanish Infectious Diseases and Clinical Microbiology Society (SEIMC), Álvarez-Marín, Rocío, López Cerero, Lorena, Palop-Borras, Begoña, Rojo-Martín, María Dolores, Ruiz-Sancho, Andrés, Herrero-Rodríguez, Carmen, García, María Victoria, Lazo-Torres, Ana María, López, Inmaculada, Martín-Hita, Lina, Nuño-Álvarez, Enrique, Sánchez-Yebra, Waldo, Galán-Sánchez, Fátima, Reguera-Iglesias, José María, Lepe Jiménez, José Antonio, Peñalva, Germán, Pascual Hernández, Álvaro, Cisneros, José Miguel, Universidad de Sevilla. Departamento de Microbiología, Universidad de Sevilla. Departamento de Medicina, Universidad de Sevilla. Instituto de Biomedicina de Sevilla (IBIS), Spanish Infectious Diseases and Clinical Microbiology Society (SEIMC), Álvarez-Marín, Rocío, López Cerero, Lorena, Palop-Borras, Begoña, Rojo-Martín, María Dolores, Ruiz-Sancho, Andrés, Herrero-Rodríguez, Carmen, García, María Victoria, Lazo-Torres, Ana María, López, Inmaculada, Martín-Hita, Lina, Nuño-Álvarez, Enrique, Sánchez-Yebra, Waldo, Galán-Sánchez, Fátima, Reguera-Iglesias, José María, Lepe Jiménez, José Antonio, Peñalva, Germán, Pascual Hernández, Álvaro, and Cisneros, José Miguel

Abstract

Background: Carbapenem-resistant Gram-negative bacilli (CR-GNB) are among the most threatening microorganisms worldwide and carbapenem use facilitates their spread. Antimicrobial stewardship programmes (ASPs) can help to optimize the use of antibiotics. This study evaluates the impact of a multifaceted educational ASP on carbapenem use and on the epidemiology of CR-GNB. Methods: We conducted a quasi-experimental, time-series study in seven hospitals, from January 2014 to September 2018. The key intervention was composed of educational interviews promoting the appropriate use of carbapenems. The primary endpoints were carbapenem consumption and incidence density (ID) of CR-GNB. All non-duplicated CR-GNB clinical isolates were tested using phenotypic assays and PCR for the presence of carbapenemases. Joinpoint regression and interrupted time-series analyses were used to determine trends. Results: A decrease in carbapenem consumption throughout the study period [average quarterly percentage change (AQPC) -1.5%, P < 0.001] and a -8.170 (-16.064 to -0.277) level change following the intervention were observed. The ID of CR-Acinetobacter baumannii decreased (AQPC -3.5%, P = 0.02) and the overall ID of CR-GNB remained stable (AQPC -0.4%, P = 0.52). CR-GNB, CR-Pseudomonas aeruginosa and CR-A. baumannii IDs per hospital correlated with the local consumption of carbapenems. The most prevalent carbapenem resistance mechanisms were OXA-23 for CR-A. baumannii (76.1%), OXA-48 for CR-Klebsiella pneumoniae (66%) and no carbapenemases for CR-P. aeruginosa (91.7%). The epidemiology of carbapenemases was heterogeneous throughout the study, especially for carbapenemase-producing Enterobacteriaceae. Conclusions: In conclusion, a multifaceted, educational interview-based ASP targeting carbapenem prescribing reduced carbapenem use and the ID of CR-A. baumannii.

Published
2021

12. Epidemiology of Pseudomonas aeruginosa in agricultural areas*

Author

Milton N, Schroth, John J, Cho, Sylvia K, Green, Spyros D, Kominos, and Microbiology Society Publishing

Subjects
Crops, Agricultural, 0301 basic medicine, Microbiology (medical), 030106 microbiology, Brassica, Food Contamination, Lactuca, medicine.disease_cause, Microbiology, Lycopersicon, 03 medical and health sciences, Solanum lycopersicum, Vegetables, Ornamental plant, medicine, Soil Microbiology, Apium, Plant Diseases, Solanum tuberosum, biology, Pseudomonas aeruginosa, Brassica napus, fungi, food and beverages, General Medicine, Lettuce, biology.organism_classification, Daucus carota, Horticulture, 030104 developmental biology, Food Microbiology, Cucumis sativus, Water Microbiology, Cucumis, Soil microbiology
Abstract

A prevailing opinion is that the strains of Pseudomonas aeruginosa that infects both plants and humans are two separate species. This study strongly disputes that notion until the modern molecular technology proves otherwise. This paper examines a spectrum of strains occurring in nature, their habitats, dissemination, their relationship to clinical strains, and the environmental conditions that favor their colonization of plants. The isolates were obtained from clinical specimens, plants, soil, and water. The identity of these strains was confirmed using pyocin typing and biochemical assays. The data reveal that agricultural soils, potted ornamental plants, hoses, fountains, and faucets frequently harbored P. aeruginosa. However, it was not commonly found in semi-arid areas, suggesting that moisture and high humidity is necessary for colonization and survival. Though found in soil, P. aeruginosa was seldom isolated on edible plant parts. The pathogenicity of various strains on plants was tested by inoculating vegetables, lettuce slices (Lactuca sativa L. "Great Lakes"), celery stalks (Apium graveolens L. var. Dulce], potato tuber slices (Solanum tuberosum L. "Whiterose"), tomato (Lycopersicon esculentum L. Mill), cucumber (Cucumis sativus L.), rutabaga (Brassica campestris L.), and carrot (Daucus carota L. var sativa). There was considerable variation in the strains' ability to cause rot, but no difference was observed between clinical isolates and others from agricultural fields, water, and soil. Two of the clinical isolates from burn patients, P. aeruginosa PA13 and PA14, exhibited the greatest virulence in causing rot in all the plants that were tested, especially on cucumber, lettuce, potato, and tomato. The study discusses how closely the epidemiology of P. aeruginosa relates to many plant pathogens, and the ability of human isolates to colonize plants and food material under favorable conditions. The biochemical and phenotypic similarity among strains from the clinical and agricultural material is strongly indicative that they are the same species and that plants and soil are natural reservoirs for P. aeruginosa.

Published
2018
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14. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV)

Author

Siddell, Stuart G., Smith, Donald B., Adriaenssens, Evelien, Alfenas-Zerbini, Poliane, Dutilh, Bas E., Garcia, Maria Laura, Junglen, Sandra, Krupovic, Mart, Kuhn, Jens H., Lambert, Amy J., Lefkowitz, Elliot J., Łobocka, Małgorzata, Mushegian, Arcady R., Oksanen, Hanna M., Robertson, David L., Rubino, Luisa, Sabanadzovic, Sead, Simmonds, Peter, Suzuki, Nobuhiro, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Zerbini, F. Murilo, University of Bristol [Bristol], University of Oxford, Quadram Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Utrecht University [Utrecht], Instituto de Biotecnología y Biología Molecular [La Plata] (IBBM), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas [La Plata], Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), Free University of Berlin (FU), Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), University of Alabama at Birmingham [ Birmingham] (UAB), Institute of Biochemistry and Biophysics [Warsaw] (IBB), National Science Foundation [Arlington] (NSF), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, MRC - University of Glasgow Centre for Virus Research, CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Mississippi State University [Mississippi], Okayama University, University of Arizona, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Arizona State University [Tempe] (ASU), D.B.S. is supported by a grant from the Microbiology Society. B.E.D. is supported by the European Research Council (ERC) Consolidator grant 865694: DiversiPHI, the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany ́s Excellence Strategy – EXC 2051 – Project-ID 390713860, the Alexander von Humboldt Foundation in the context of an Alexander von Humboldt-Professorship founded by German Federal Ministry of Education and Research, and the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie Actions Innovative Training Networks grant agreement no. 955 974 (VIROINF). E.J.L. – this publication was supported by the National Institutes of Health (NIH) National Institute of Allergy And Infectious Diseases (NIAID), under Award Number U24AI162625. This work was also supported in part through the Laulima Government Solutions, LLC, prime contract with the NIH NIAID, under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C. A.R.M. is a Program Director at the U.S. National Science Foundation (NSF), the statements and opinions expressed herein are made in a personal capacity and do not constitute endorsement by NSF or the government of the United States. H.M.O. was supported by the University of Helsinki and Academy of Finland funding for FINStruct, part of Biocenter Finland and Instruct-ERIC. D.L.R. is funded by the MRC (MC_UU_12014/12). S.S. acknowledges support from the Mississippi Agricultural and Forestry Experiment Station (MAFES), USDA-ARS project 58-6066-9-033 and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project, under Accession Number 1021 494., European Project: 865694,H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),DiversiPHI(2020), Instituto de Higiene e Medicina Tropical (IHMT), Global Health and Tropical Medicine (GHTM), and TB, HIV and opportunistic diseases and pathogens (THOP)

Subjects
ICTV, Infectious Diseases, Science & Technology, SDG 3 - Good Health and Well-being, Biotechnology & Applied Microbiology, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, virus nomenclature, virus taxonomy, virus classification, QR355 Virology, Life Sciences & Biomedicine, International Committee on Taxonomy of Viruses
Abstract

The taxonomy of viruses is developed and overseen by the International Committee on Taxonomy of Viruses (ICTV), which scrutinizes, approves and ratifies taxonomic proposals, and maintains a list of virus taxa with approved names (https://ictv.global). The ICTV has approximately 180 members who vote by simple majority. Taxon-specific Study Groups established by the ICTV have a combined membership of over 600 scientists from the wider virology community; they provide comprehensive expertise across the range of known viruses and are major contributors to the creation and evaluation of taxonomic proposals. Proposals can be submitted by anyone and will be considered by the ICTV irrespective of Study Group support. Thus, virus taxonomy is developed from within the virology community and realized by a democratic decision-making process. The ICTV upholds the distinction between a virus or replicating genetic element as a physical entity and the taxon category to which it is assigned. This is reflected by the nomenclature of the virus species taxon, which is now mandated by the ICTV to be in a binomial format (genus + species epithet) and is typographically distinct from the names of viruses. Classification of viruses below the rank of species (such as, genotypes or strains) is not within the remit of the ICTV. This article, authored by the ICTV Executive Committee, explains the principles of virus taxonomy and the organization, function, processes and resources of the ICTV, with the aim of encouraging greater understanding and interaction among the wider virology community.

Published
2023
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15. Identification of candidate molecular determinants of the vector competence of Ixodes ricinus for members of the tick-borne encephalitis complex

Author

Lemasson, Manon, Caignard, Grégory, Unterfinger, Yves, Attoui, Houssam, Moutailler, Sara, Bonnet, Sarah, Bell-Sakyi, Lesley, Vitour, Damien, Richardson, Jennifer, Lacour, Sandrine, Virologie UMR1161 (VIRO), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Microbiology Society., ProdInra, Migration, École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

16. Pathological modeling of TBEV infection using human neuronal/glial co-cultures derived from fetal neural progenitor cells and high-throughput screening for anti-viral drugs

Author

Coulpier, Muriel, Virologie UMR1161 (VIRO), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), LabEx IBEID, Microbiology Society., Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and COULPIER, Muriel

Subjects
[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV]Life Sciences [q-bio], [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

17. Mapping protein-protein interactions between tick-borne flaviviruses and their different mammalian hosts

Author

Lacour, Sandrine, Lemasson, Manon, Unterfinger, Yves, Moutailler, Sara, Bonnet, Sarah, Bell-Sakyi, Lesley, Caignard, Grégory, Vitour, Damien, Attoui, Houssam, Richardson, Jennifer, Virologie UMR1161 (VIRO), Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-École nationale vétérinaire d'Alfort (ENVA), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Microbiology Society., ProdInra, Migration, École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), and École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

18. 50 years of the International Committee on Taxonomy of Viruses: progress and prospects

Author

Stuart G. Siddell, Robert L. Harrison, Max L. Nibert, Andrew M. Q. King, Andrew J. Davison, Hélène Sanfaçon, Mart Krupovic, Sead Sabanadzovic, Arvind Varsani, Balázs Harrach, Nick J. Knowles, Andrew M. Kropinski, Francisco Murilo Zerbini, Michael J. Adams, Elliot J. Lefkowitz, B. Douglas Smith, Jens H. Kuhn, Richard J. Orton, Alexander E. Gorbalenya, Arcady Mushegian, Peter Simmonds, University of Hertfordshire [Hatfield] (UH), University of Alabama at Birmingham [ Birmingham] (UAB), The Pirbright Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Hungarian Academy of Sciences (MTA), United States Department of Agriculture (USDA), University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), National Science Foundation [Arlington] (NSF), Harvard Medical School [Boston] (HMS), Mississippi State University [Mississippi], Agriculture and Agri-Food (AAFC), University of Bristol [Bristol], University of Oxford, Arizona State University [Tempe] (ASU), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), University of Glasgow, University of Edinburgh, Leiden University Medical Center (LUMC), Universiteit Leiden, Lomonosov Moscow State University (MSU), The ICTV is supported by Grants from IUMS, the American Society of Virology and the Microbiology Society, and by a Grant from the Wellcome Trust (WT108418AIA) to P.S., A.J.D. and S.G.S. The involvement of J.H.K. was supported in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I. A subcontractor to Battelle Memorial Institute who performed this work is J.H.K., an employee of Tunnell Government Services, Inc. The involvement of A.R.M. was supported in part by the National Science Foundation Individual Research and Development program. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services, US National Science Foundation, or of the institutions and companies affiliated with the authors., The authors are the current ICTV EC Members together with two researchers (R.J.O., D.B.S.) supported by the Wellcome Trust grant detailed below. We gladly acknowledge the dedicated, voluntary efforts of hundreds of virologists based in various parts of the world over the entire period of the existence of the ICTV. The work of the organisation through its EC and Study Groups has always depended upon that contribution and will continue to do so., Institute for Animal Health, the Pirbright Institute, Institut Pasteur [Paris], Agriculture and Agri-Food [Ottawa] (AAFC), University of Oxford [Oxford], and Universidade Federal de Vicosa (UFV)

Subjects
0301 basic medicine, Societies, Scientific, Rabies, [SDV]Life Sciences [q-bio], 030106 microbiology, Library science, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, History, 21st Century, Executive committee, MESH: Viruses, 03 medical and health sciences, Virology, Virus discovery, MESH: Phylogeny, Virus classification, Phylogeny, Virus species, Computational Biology, General Medicine, History, 20th Century, 3. Good health, MESH: Societies, Scientific, 030104 developmental biology, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Online report, MESH: History, 20th Century, Metagenomics, MESH: Metagenomics, MESH: History, 21st Century, MESH: Computational Biology
Abstract

International audience; We mark the 50th anniversary of the International Committee on Taxonomy of Viruses (ICTV) by presenting a brief history of the organization since its foundation, showing how it has adapted to advancements in our knowledge of virus diversity and the methods used to characterize it. We also outline recent developments, supported by a grant from the Wellcome Trust (UK), that are facilitating substantial changes in the operations of the ICTV and promoting dialogue with the virology community. These developments will generate improved online resources, including a freely available and regularly updated ICTV Virus Taxonomy Report. They also include a series of meetings between the ICTV and the broader community focused on some of the major challenges facing virus taxonomy, with the outcomes helping to inform the future policy and practice of the ICTV.

Published
2017
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19. Selection of stress-tolerant indigenous rhizobia nodulating alfalfa (Medicago sativa L.)

Author

Kajić, Sanja, Hajdari, Edita, Komes, Anja, Rajnović, Ivana, Sikora, Sanja, and Croatian Microbiology Society

Subjects
biološka fiksacija dušika, lucerna (Medicago sativa L.), Sinorhizobium meliloti, food and beverages
Abstract

Soil bacterium, Sinorhizobium meliloti is of enormous agricultural value because of its ability to fix atmospheric nitrogen in symbiosis with an important forage crops such as alfalfa. The main aim of this study was to evaluate the stress tolerance of indigenous S. meliloti strains to adverse environmental conditions. Twenty rhizobial strains, isolated from different regions in Croatia, were genotipically characterized to assess diversity amongst natural field population. Stress tolerance assays were performed in order to select indigenous rhizobia with possible higer tolerance to unfavorable soil conditions. The growth of the strains was studied at different pH values, temperatures, carbohydrate sources and different concentrations of NaCl. Biochemical characteristics of rhizobial isolates and the susceptibility to different antibiotics were determined as well. The results showed that most of the strains can grow at temperatures higher than optimal and that strains tolerate both acidic and alkaline environment. It was found that indigenous strains can tolerate extremely high concentrations of NaCl. Lactose agar assay indicates that three isolates probably belong to the genus Agrobacterium. Urease activity was determined in most strains while only a few strains expressed catalase activity. The results showed that all indigenous rhizobial strains belong to the group of fast-growing rhizobia. In comparison to the reference strain, higher resistance of indigenous S. meliloti strains was determined. The results of 16S rDNA genotyping using PCR/RFLP analysis showed that 14 isolates could be assigned to S. meliloti while RAPD and ERIC-PCR fingerprints revealed significant genetic diversity among indigenous rhizobial strains. Better understanding of rhizobial response to adverse environmental conditions is of potential value for improving rhizobial inoculants and efficiency of symbiotic nitrogen fixation.Book

Published
2016

20. Nitrilase enzymes and their role in plant-microbe interactions

Author

Howden, A, Preston, G, and Microbiology, Society for Applied

Subjects
Plant Sciences, fungi, food and beverages
Abstract

Nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. Nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms is relatively underexplored. Current research suggests that nitrilases play important roles in a range of biological processes. In the context of plant-microbe interactions they may have roles in hormone synthesis, nutrient assimilation and detoxification of exogenous and endogenous nitriles. Nitrilases are produced by both plant pathogenic and plant growth-promoting microorganisms, and their activities may have a significant impact on the outcome of plant-microbe interactions. In this paper we review current knowledge of the role of nitriles and nitrilases in plants and plant-associated microorganisms, and discuss how greater understanding of the natural functions of nitrilases could be applied to benefit both industry and agriculture.

Published
2009

21. Building an inclusive culture at scientific meetings: foundations for future progress.

Author

Maringer K, Cunningham-Oakes E, Lane F, Jones KL, Rodrigues de Oliveira BF, Baba-Dikwa A, Mitra A, Perez-Sepulveda B, Chappell CR, Macori G, Donovan-Banfield I, Vohra P, Casey R, Nepal R, and Khan CMA

Subjects
Humans, Information Dissemination, Microbiology, Societies, Scientific organization & administration, Congresses as Topic
Abstract

Scientific meetings and conferences are crucial in knowledge dissemination, fostering collaborations, professional development and inspiring innovative research. However, their traditional structure and organization have remained largely unchanged, perpetuating barriers that continue to exclude scientists from historically marginalized backgrounds. In response, the Microbiology Society has begun its journey to address these longstanding challenges, redesigning its meetings to create a more inclusive culture and a welcoming environment for all participants.

Published
2025
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25. Converting Access Microbiology to an open research platform: community survey results.

Author

Howat AM and Clark J

Abstract

Following the Microbiology Society's successful bid for a Learned Society Curation Award from the Wellcome Trust and Howard Hughes Medical Institute, the Society is converting our sound science, open access journal, Access Microbiology , to an open research platform. As part of this, we conducted a survey of our community to gauge current attitudes towards the platform and here we present some of these results. The majority of respondents (57 %) said they would always or sometimes want to remain anonymous on their peer review report, whilst 75 % of respondents said that as an author they would be happy to make the data underlying their research open. There was a clear desire for a range of research types that are often seen with sound science publications and rigorous research. An encouraging 94 % of respondents stated that the platform is somewhere they would consider publishing, demonstrating the enthusiasm in these respondents for a new publishing platform for their community. Given this data and that from our previous focus group research, the platform will launch as outlined in the original project proposal and adopt a transparent peer review model with an open data policy., Competing Interests: All authors work for the Microbiology Society. The authors declare no other conflicts of interest., (© 2021 The Authors.)

Published
2021
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26. Converting Access Microbiology to an open research platform: focus group and AI review tool research results.

Author

Howat AM, Mulhern A, Logan HF, Redvers-Mutton G, Routledge C, and Clark J

Abstract

The Microbiology Society will be launching an open research platform in October 2021. Developed using funding from the Wellcome Trust and the Howard Hughes Medical Institute (HHMI), the platform will combine our current sound-science journal, Access Microbiology , with artificial intelligence (AI) review tools and many of the elements of a preprint server. In an effort to improve the rigour, reproducibility and transparency of the academic record, the Access Microbiology platform will host both preprints of articles and their Version of Record (VOR) publications, as well as the reviewer reports, Editor's decision, authors' response to reviewers and the AI review reports. To ensure the platform meets the needs of our community, in February 2020 we conducted focus group meetings with various stakeholders. Using articles previously submitted to Access Microbiology , we undertook testing of a range of potential AI review tools and investigated the technical feasibility and utility of including these tools as part of the platform. In keeping with the open and transparent ethos of the platform, we present here a summary of the focus group feedback and AI review tool testing., Competing Interests: All authors work for the Microbiology Society. The authors declare no other conflicts of interest., (© 2021 The Authors.)

Published
2021
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31. In praise of preprints.

Author

Fry NK, Marshall H, and Mellins-Cohen T

Subjects
Bacterial Typing Techniques, Base Composition, DNA, Bacterial, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Fatty Acids
Published
2019
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33. Evaluation of plasma sphingosine 1-phosphate, hepcidin and cardiovascular damage biomarkers (cardiac troponin I and homocysteine) in rats infected with brucellosis and vaccinated (Rev-1, RB-51).

Author

Azimzadeh K, Nasrollahi Nargesabad R, and Vousooghi N

Subjects
Animals, Blood Chemical Analysis, Brucella abortus immunology, Brucella abortus pathogenicity, Brucella melitensis immunology, Brucella melitensis pathogenicity, Brucellosis prevention & control, Copper blood, Disease Models, Animal, Iron blood, Male, Malondialdehyde blood, Rats, Sphingosine blood, Vaccination, Zinc blood, Biomarkers blood, Brucella Vaccine immunology, Brucellosis immunology, Hepcidins blood, Homocysteine blood, Lysophospholipids blood, Plasma chemistry, Sphingosine analogs & derivatives, Troponin I blood
Abstract

Brucellosis is known as one of important zoonosis. Studying the histological and biochemical effects of the disease could help to increase our knowledge about it. The aim of the present study was to evaluate changes of plasma parameters after intraperitoneal injection of two species of Brucella (Brucella melitensis and Brucella abortus) and two vaccines (Rev-1, RB-51) in the rat. Forty male rats were divided into five groups (n = 8 in each group). Two groups received suspensions of Brucella abortus and Brucella melitensis and two other groups were injected intraperitoneally with two mentioned vaccines and the last group received only distilled water. The results showed a significant increase in sphingosine 1-phosphate, Malondialdehyde, hepcidin, homocysteine, cardiac troponin I and copper levels and a considerable decrease in the levels of iron and zinc (P ≤ 0.01) in infected groups compared to the control animals. In vaccinated groups, hepcidin was increased but other parameters were not changed in comparison to the control group. It can be concluded that increase of homocysteine and cardiac troponin I in brucellosis could be a warning for cardiac adverse effects. Besides, increase of sphingosine 1-phosphate probably indicates its stimulant and modulatory effects in anti- Brucellosis biochemical pathways of the host., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Published
2017
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35. Infectivity of Giardia duodenalis Cysts from UV Light-Disinfected Wastewater Effluent Using a Nude BALB/c Mouse Model.

Author

Dos Santos LU, Alves DP, Guaraldo AM, Cantusio Neto R, Durigan M, and Franco RM

Abstract

Giardia duodenalis is a protozoan of public health interest that causes gastroenteritis in humans and other animals. In the city of Campinas in southeast Brazil, giardiasis is endemic, and this pathogen is detected at high concentrations in wastewater effluents, which are potential reservoirs for transmission. The Samambaia wastewater treatment plant (WWTP) in the city of Campinas employs an activated sludge system for sewage treatment and ultraviolet (UV) light for disinfection of effluents. To evaluate this disinfection process with respect to inactivating G. duodenalis cysts, two sample types were investigated: (i) effluent without UV disinfection (EFL) and (ii) effluent with UV disinfection (EFL+UV). Nude immunodeficient BALB/c mice were intragastrically inoculated with a mean dose of 14 cysts of G. duodenalis recovered from effluent from this WWTP, EFL, or EFL+UV. All animals inoculated with G. duodenalis cysts developed the infection, but animals inoculated with UV-exposed cysts released a lower average concentration of cysts in their faeces than animals inoculated with cysts that were not UV disinfected. Trophozoites were also observed in both groups of animals. These findings suggest that G. duodenalis cysts exposed to UV light were damaged but were still able to cause infection.

Published
2013
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36. Cryptosporidium spp. and Giardia spp. in surface water supply of Campinas, southeast Brazil.

Author

Neto RC, dos Santos LU, Sato MI, and Franco RM

Subjects
Brazil, Calcium Carbonate, Filtration, Flocculation, Immunomagnetic Separation, Membranes, Artificial, Cryptosporidium isolation & purification, Giardia isolation & purification, Rivers parasitology, Water parasitology, Water Supply statistics & numerical data
Abstract

Surface water contaminated by domestic sewage discharges is a potential source of pathogens, including protozoa. During 2005-2006, the source water (Atibaia River) of the Surface Water Treatment Plant (WTP) of Campinas city, São Paulo, Brazil was sampled to obtain an assessment of Cryptosporidium oocyst and Giardia cyst concentrations. Calcium carbonate flocculation (CCF) and membrane filtration (MF) concentration techniques, with and without purification by immunomagnetic separation (IMS) were evaluated. The cysts and oocysts were detected by immunofluorescence assay (IFA) and confirmed by differential interference contrast (DIC). Membrane filtration method generally produced higher recovery efficiency. Giardia spp. was detected in 87.5% of the water samples analyzed with densities ranging from 2.5 to 120 cysts per L. Cryptosporidium spp were detected in 62.5% and the concentrations ranged from 15 to 60 oocysts per L. Cryptosporidium oocyst and Giardia cyst concentrations detected in this study were elevated and are associated with discharge of untreated sewage in Atibaia River. Measures should be taken to protect surface water from sources of contamination.

Published
2010
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