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Journal articles on the topic 'Strain nomenclature'

Author: Grafiati

Published: 25 May 2024

Last updated: 25 July 2025

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1

Fauquet, C. M., R. W. Briddon, J. K. Brown, et al. "Geminivirus strain demarcation and nomenclature." Archives of Virology 153, no. 4 (2008): 783–821. http://dx.doi.org/10.1007/s00705-008-0037-6.

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2

Zheng, Du-Ping, Tamie Ando, Rebecca L. Fankhauser, R. Suzanne Beard, Roger I. Glass, and Stephan S. Monroe. "Norovirus classification and proposed strain nomenclature." Virology 346, no. 2 (2006): 312–23. http://dx.doi.org/10.1016/j.virol.2005.11.015.

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3

Festing, Michael F. W., Elizabeth M. Simpson, Muriel T. Davisson, and Larry E. Mobraaten. "Revised nomenclature for strain 129 mice." Mammalian Genome 10, no. 8 (1999): 836. http://dx.doi.org/10.1007/s003359901099.

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4

Rülicke, Th, X. Montagutelli, B. Pintado, R. Thon, and H. J. Hedrich. "FELASA guidelines for the production and nomenclature of transgenic rodents." Laboratory Animals 41, no. 3 (2007): 301–11. http://dx.doi.org/10.1258/002367707781282758.

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The standardized nomenclature of rodent strains, genes and mutations has long been the focus of careful attention. Its aim is to provide proper designation of laboratory animals used in research projects and to convey as much information on each strain as possible. Since the development of different techniques to mutate the genome of laboratory rodents on a large scale, the correct application of current nomenclature systems is of increased significance. It facilitates not only the accurate communication of scientific results but is indispensable in controlling the dramatically increased numbe

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5

Ablashi, D., H. Agut, Z. Berneman, et al. "Human herpesvirus-6 strain groups: a nomenclature." Archives of Virology 129, no. 1-4 (1993): 363–66. http://dx.doi.org/10.1007/bf01316913.

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6

Blake, Judith A., Richard Baldarelli, James A. Kadin, et al. "Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology." Nucleic Acids Research 49, no. D1 (2020): D981—D987. http://dx.doi.org/10.1093/nar/gkaa1083.

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Abstract The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for the laboratory mouse, a widely used animal model for comparative studies of the genetic and genomic basis for human health and disease. MGD is the authoritative source for biological reference data related to mouse genes, gene functions, phenotypes and mouse models of human disease. MGD is the primary source for official gene, allele, and mouse strain nomenclature based on the guidelines set by the International Committee on Standardized Nomenclature for Mice. MGD’s biocur

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7

Young, J. M., D. R. W. Watson, and D. W. Dye. "Reconsideration of Arthrobacter ilicis (Mandel et al. 1961) Collins et al. 1982 as a plant-pathogenic species. Proposal to emend the authority and description of the species. Request for an Opinion." International Journal of Systematic and Evolutionary Microbiology 54, no. 1 (2004): 303–5. http://dx.doi.org/10.1099/ijs.0.02929-0.

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Strains now considered to represent the type strain of Arthrobacter ilicis, described as a pathogen of American holly, are not identical. The designated type strain does not represent this pathogen. However, one of the other strains sourced to the type strain of the pathogen does appear to be authentic, but is not a member of A. ilicis. It is proposed that A. ilicis is an unrelated species, not a pathogen of American holly. The nomenclature of A. ilicis can be rectified by emending the authority and by emending the species description to recognize this species as a novel species that is not a

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8

Tindall, B. J. "Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 has priority over Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942 when the two are treated as members of the same species based on the principle of priority and Rule 23a, Note 1 as applied to the corresponding specific epithets. Opinion 94." International Journal of Systematic and Evolutionary Microbiology 64, Pt_10 (2014): 3590–92. http://dx.doi.org/10.1099/ijs.0.069203-0.

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The Judicial Commission affirms that, according to the Rules of the International Code of Nomenclature of Bacteria (including changes made to the wording), the combination Agrobacterium radiobacter (Beijerinck and van Delden 1902) Conn 1942 has priority over the combination Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942 when the two are treated as members of the same species based on the principle of priority as applied to the corresponding specific epithets. The type species of the genus is Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942, even if treated as a late

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9

Wotjak, Carsten T. "C57BLack/BOX? The importance of exact mouse strain nomenclature." Trends in Genetics 19, no. 4 (2003): 183–84. http://dx.doi.org/10.1016/s0168-9525(02)00049-5.

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10

Lang, Elke, and Hans Reichenbach. "Designation of type strains for seven species of the order Myxococcales and proposal for neotype strains of Cystobacter ferrugineus, Cystobacter minus and Polyangium fumosum." International Journal of Systematic and Evolutionary Microbiology 63, Pt_11 (2013): 4354–60. http://dx.doi.org/10.1099/ijs.0.056440-0.

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Ten species of the order Myxococcales with validly published names are devoid of living type strains. Four species of the genus Chondromyces are represented by dead herbarium samples as the type material. For a species of the genus Melittangium and two species of the genus Polyangium , no physical type material was assigned at the time of validation of the names or later on. In accordance with rule 18f of the International Code of Nomenclature of Bacteria the following type strains are designated for these species: strain Cm a14T ( = DSM 14605T = JCM 12615T) as the type strain of Chondromyces

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11

Mehrotra, Akhil, Ajay Sharma, Swati Singh, and Shubham Kacker. "Situs ambiguous with three chambered heart (single atrium), evaluation by four-dimensional X-strain color echocardiography – A case report." Indian Journal of Child Health 9, no. 7 (2022): 131–36. http://dx.doi.org/10.32677/ijch.v9i7.3534.

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Situs ambiguous accounts for 4% of all congenital heart disease (CHD) and has an incidence of 1:10,000 new born births. To standardize the nomenclature for CHD, the international nomenclature society published a globally accepted nomenclature tree for CHD with the 11th Iteration of international classification of disease. According to this publication common atrium, single atrium and atrium communis are denoted as synonyms. The incidence of common atrium among atrial septal defect (ASD) patients is 3–4% only and thus denoting it to be a rare entity. We are presenting an exceedingly rare case o

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12

McQueen, H. J., and S. Spigarelli. "Nomenclature for strain-induced boundaries in hot and cold working." Materials Science and Engineering: A 462, no. 1-2 (2007): 37–44. http://dx.doi.org/10.1016/j.msea.2006.04.151.

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13

Pitt, Alexandra, Ulrike Koll, Johanna Schmidt, and Martin W. Hahn. "Aquirufa ecclesiirivi sp. nov. and Aquirufa beregesia sp. nov., isolated from a small creek and classification of Allopseudarcicella aquatilis as a later heterotypic synonym of Aquirufa nivalisilvae." International Journal of Systematic and Evolutionary Microbiology 70, no. 8 (2020): 4602–9. http://dx.doi.org/10.1099/ijsem.0.004319.

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Two bacterial strains, 50A-KIRBAT and 50C-KIRBAT, were isolated from the same freshwater creek located near Salzburg, Austria. They showed 16S rRNA gene sequence similarities to Aquirufa nivalisilvae of 100 and 99.9 %, respectively. A genome-based phylogenetic reconstruction with amino acid sequences of 119 single-copy genes suggested that the new strains represent two new species of the genus Aquirufa . Pairwise calculated whole-genome average nucleotide identity (gANI) values ranging from 85.4 to 87.5 % confirmed this conclusion. Phenotypic, chemotaxonomic and genomic traits were investigate

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Valles, Camille, Morgane Mailhe, Davide Ricaboni, et al. "Negativibacillus massiliensis gen. nov., sp. nov., a New Bacterial Genus Isolated from a Human Left Colon Sample." Microbiology Research 12, no. 1 (2021): 29–42. http://dx.doi.org/10.3390/microbiolres12010004.

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A new genus, a member of the Ruminococcaceae family, was isolated from the left colon of a healthy woman. Strain Marseille P3213 was a non-motile, spore-forming, Gram-stain negative, rod-shaped bacterium. This strictly anaerobic species reached optimal growth after an incubation of 72 h at 37 °C. The 16S rRNA gene sequence of this strain shared a 93.52% similarity level with Harryflintia acetispora strain V20-281a, its closest phylogenetic neighbor with standing in the nomenclature. Its genome had a size of 2.87 Mb, with a 45.81% G + C content. We hereby propose the creation of Negativibacillu

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15

Coorevits, An, Anna E. Dinsdale, Jeroen Heyrman, et al. "Lysinibacillus macroides sp. nov., nom. rev." International Journal of Systematic and Evolutionary Microbiology 62, Pt_5 (2012): 1121–27. http://dx.doi.org/10.1099/ijs.0.027995-0.

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‘Bacillus macroides’ ATCC 12905T ( = DSM 54T = LMG 18474T), isolated in 1947 from cow dung, was not included in the Approved Lists of Bacterial Names and so it lost standing in bacteriological nomenclature. Reinvestigation of the strain, including DNA–DNA relatedness experiments, revealed that ‘Bacillus macroides’ is genomically distinct from its closest relatives Lysinibacillus xylanilyticus , Lysinibacillus boronitolerans and Lysinibacillus fusiformis (as determined by 16S rRNA gene sequence analysis, with pairwise similarity values of 99.2, 98.8 and 98.5 %, respectively, with the type strai

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16

Assanov, Nigmetulla, Ryskeldi Bazarbayev, Assilbek Mussoyev, Bauyrzhan Otarbayev, and Kairat Iskhan. "The use of RT-PCR in the diagnosis and differentiation of vaccine strains of chicken infectious bronchitis and Newcastle disease." Open Veterinary Journal 13, no. 6 (2023): 732. http://dx.doi.org/10.5455/ovj.2023.v13.i6.8.

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Background: Infectious diseases of young and adult birds with respiratory syndrome are a significant deterrent to the development of industrial poultry farming due to a decrease in productivity and significant mortality. The only effective method of combating viral diseases is timely and targeted vaccination, which largely depends on laboratory diagnostic results. Aim: The aim of this article is to study the real-time reverse transcription polymerase chain reaction, which has the prospect of more effective diagnosis of vaccine strains of chicken infectious bronchitis and Newcastle disease. Met

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17

Ndongo, Sokhna, Mossaab Maaloum, Magali Richez, et al. "Vitreoscilla massiliensis sp. nov., Isolated From the Stool of an Amazonian Patient." Current Microbiology 78, no. 8 (2021): 3313–20. http://dx.doi.org/10.1007/s00284-021-02577-8.

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AbstractStrain SN6T is a non-motile and non-spore-forming gram-negative bacterium which was isolated from the stool sample of an Amazonian patient. The optimum growth was observed at 37 °C, pH 7, and 0–5 g/l of NaCl. Based on the 16S rRNA gene sequence similarity, the strain SN6T exhibited 97.5% identity with Vitreoscilla stercoraria strain ATCC_15218 (L06174), the phylogenetically closest species with standing in nomenclature. The predominant fatty acid was hexadecenoic acid (31%). The genomic DNA G + C content of the strain SN6T was 49.4 mol %. After analysis of taxonogenomic data, phenotypi

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18

Lázaro, Sara, Francisca Fernández-Piñas, Eduardo Fernández-Valiente, Amaya Blanco-Rivero, and Francisco Leganés. "pbpB, a Gene Coding for a Putative Penicillin-Binding Protein, Is Required for Aerobic Nitrogen Fixation in the Cyanobacterium Anabaena sp. Strain PCC7120." Journal of Bacteriology 183, no. 2 (2001): 628–36. http://dx.doi.org/10.1128/jb.183.2.628-636.2001.

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ABSTRACT Transposon mutagenesis of Anabaena sp. strain PCC7120 led to the isolation of a mutant strain, SNa1, which is unable to fix nitrogen aerobically but is perfectly able to grow with combined nitrogen (i.e., nitrate). Reconstruction of the transposon mutation of SNa1 in the wild-type strain reproduced the phenotype of the original mutant. The transposon had inserted within an open reading frame whose translation product shows significant homology with a family of proteins known as high-molecular-weight penicillin-binding proteins (PBPs), which are involved in the synthesis of the peptido

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19

Neustupa, Jiří, Yvonne Němcová, Jana Veselá, Jana Steinová, and Pavel Škaloud. "Leptochlorella corticola gen. et sp. nov. and Kalinella apyrenoidosa sp. nov.: two novel Chlorella-like green microalgae (Trebouxiophyceae, Chlorophyta) from subaerial habitats." International Journal of Systematic and Evolutionary Microbiology 63, Pt_1 (2013): 377–87. http://dx.doi.org/10.1099/ijs.0.047944-0.

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The diversity of green microalgae in subaerial habitats remains largely unexplored and a number of new genus- and species-level lineages have been discovered recently. The traditional green algal genus, Chlorella, which accommodated coccoid unicellular green algal species with globular to oval cells, reproducing entirely by autospores, has been found to be polyphyletic. In this study, we provide a detailed characterization of two strains of microalgae isolated from tree bark in the Mediterranean. These algae share the general Chlorella-like morphology and their 18S rRNA and rbcL gene sequences

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20

Diop, Awa, Khoudia Diop, Enora Tomei, et al. "Collinsella vaginalis sp. nov. strain Marseille-P2666T, a new member of the Collinsella genus isolated from the genital tract of a patient suffering from bacterial vaginosis." International Journal of Systematic and Evolutionary Microbiology 69, no. 4 (2019): 949–56. http://dx.doi.org/10.1099/ijsem.0.003221.

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A strictly anaerobic, Gram-stain-positive, non motile and non-spore-forming rod-shaped bacterium, strain Marseille-P2666T, was isolated using the culturomics approach from a vaginal sample of a French patient suffering from bacterial vaginosis. Cells were saccharolytic and were negative for catalase, oxidase, urease, nitrate reduction, indole production, hydrolysis of aesculin and gelatin. Strain Marseille-P2666T exhibited 97.04 % 16S rRNA sequence similarity to Collinsella tanakaei type strain YIT 12063T, the phylogenetically closest species with standing in nomenclature. The major fatty acid

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21

Demetriou, Victoria L., Eftychia Kyriakou, and Leondios G. Kostrikis. "Near-Full Genome Characterisation of Two Natural Intergenotypic 2k/1b Recombinant Hepatitis C Virus Isolates." Advances in Virology 2011 (2011): 1–7. http://dx.doi.org/10.1155/2011/710438.

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Few natural intergenotypic hepatitis C virus (HCV) recombinants have been characterised, and only RF1_2k/1b has demonstrated widespread transmission. The near-full length genome sequences for two cases of 2k/1b recombinants (CYHCV037 and CYHCV093) sampled in Cyprus were obtained using strain-specific RT-PCR amplification and sequencing protocols. Sequence analysis confirmed their similarity with the original RF1_2k/1b strain from St. Petersburg, N687. These two isolates significantly contribute to the sequence data available on this recombinant and confirm its increasing spread among individua

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22

Lindeberg, Magdalen, John Stavrinides, Jeffrey H. Chang, et al. "Proposed Guidelines for a Unified Nomenclature and Phylogenetic Analysis of Type III Hop Effector Proteins in the Plant Pathogen Pseudomonas syringae." Molecular Plant-Microbe Interactions® 18, no. 4 (2005): 275–82. http://dx.doi.org/10.1094/mpmi-18-0275.

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Pathovars of Pseudomonas syringae interact with their plant hosts via the action of Hrp outer protein (Hop) effector proteins, injected into plant cells by the type III secretion system (TTSS). Recent availability of complete genome sequences for a number of P. syringae pathovars has led to a significant increase in the rate of effector discovery. However, lack of a systematic nomenclature has resulted in multiple names being assigned to the same Hop, unrelated Hops designated by the same alphabetic character, and failure of name choices to reflect consistent standards of experimental confirma

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Singh, Prashant, Jana Šnokhousová, Aniket Saraf, Archana Suradkar, and Josef Elster. "Phylogenetic evaluation of the genus Nostoc and description of Nostoc neudorfense sp. nov., from the Czech Republic." International Journal of Systematic and Evolutionary Microbiology 70, no. 4 (2020): 2740–49. http://dx.doi.org/10.1099/ijsem.0.004102.

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Cyanobacterial strain ARC8 was isolated from seepage coming into the river Dračice, Františkov, Czech Republic, and was characterized using a polyphasic approach. Strain ARC8 showed a typical Nostoc -like morphology and in-depth morphological characterization indicated that it is a member of the genus Nostoc . Furthermore, in the 16S rRNA gene phylogeny inferred using Bayesian inference, maximum likelihood and neighbour joining methods, strain ARC8 clustered within the Nostoc sensu stricto clade. The phylogenetic distance and the positioning of strain ARC8 also indicated that it is a member of

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Saraf, Aniket, Himanshu G. Dawda, Archana Suradkar, Vaibhav Agre, and Prashant Singh. "Fortiea necridiiformans sp. nov., a soil-dwelling cyanobacterium from Pachmarhi Biosphere Reserve, India." International Journal of Systematic and Evolutionary Microbiology 70, no. 8 (2020): 4714–24. http://dx.doi.org/10.1099/ijsem.0.004337.

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Cyanobacterial strain PS4G was isolated from seepage soil sampled at Pachmarhi, Madhya Pradesh, India, and was characterized using a polyphasic approach. The results of morphological analysis showed that strain PS4G had unique morphological characteristics which were not observed in the other described species of the genus Fortiea. In the 16S rRNA gene phylogenetic analysis inferred using Bayesian inference, maximum-likelihood and neighbour-joining methods, strain PS4G clustered within the clade consisting of the members of the genus Fortiea. Furthermore, in the secondary structure analysis us

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Mulet, Magdalena, David Sánchez, Jorge Lalucat, Kyoung Lee, and Elena García-Valdés. "Pseudomonas alkylphenolica sp. nov., a bacterial species able to form special aerial structures when grown on p-cresol." International Journal of Systematic and Evolutionary Microbiology 65, Pt_11 (2015): 4013–18. http://dx.doi.org/10.1099/ijsem.0.000529.

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Pseudomonas sp. KL28T is an aerobic, rod-shaped bacterium that was isolated from the soil of Changwon, South Korea, based on its ability to grow in the presence of linear alkylphenols (C1–C5). Despite several studies on strain KL28T, it could not be assigned to any known species in the genus Pseudomonas. The name ‘Pseudomonas alkylphenolia’ was proposed for KL28T, but the strain had not until now been characterized taxonomically and the name currently has no standing in the bacterial nomenclature. A 16S rRNA gene sequence based phylogenetic analysis suggested an affiliation of strain KL28T wit

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Matthijnssens, Jelle, Max Ciarlet, Sarah M. McDonald, et al. "Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG)." Archives of Virology 156, no. 8 (2011): 1397–413. http://dx.doi.org/10.1007/s00705-011-1006-z.

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27

Kumar, Naresh, Aniket Saraf, Sagarika Pal, and Prashant Singh. "Description of Cylindrospermum solincola sp. nov. from Jammu and Kashmir, India and Further Insights into the Ecological Distribution and Morphological Attributes of Cylindrospermum badium." Diversity 15, no. 5 (2023): 592. http://dx.doi.org/10.3390/d15050592.

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Two cyanobacterial strains KUT1-PS and 18C-PS were collected from the soil surface and vernal pool, respectively, from the Basantgarh village, Udhampur district of the union territory of Jammu and Kashmir, India and characterized by a polyphasic approach. The morphological characterization indicated that both the strains showed typical Cylindrospermum-like morphology and probably belonged to the genus Cylindrospermum. Further, phylogenetic interpretations at the genus level were made using the 16S rRNA gene while the 16S-23S ITS region phylogenetic analysis and secondary structure analysis wer

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Kläring, Karoline, Sarah Just, Ilias Lagkouvardos, et al. "Murimonas intestini gen. nov., sp. nov., an acetate-producing bacterium of the family Lachnospiraceae isolated from the mouse gut." International Journal of Systematic and Evolutionary Microbiology 65, Pt_3 (2015): 870–78. http://dx.doi.org/10.1099/ijs.0.000030.

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Three strains of an anaerobic, Gram-stain-positive coccobacillus were isolated from the intestines of mice. These strains shared 100 % similarity in their 16S rRNA gene sequences, but were distantly related to any described members of the family Lachnospiraceae (<94 %). The most closely related species with names that have standing in nomenclature were Robinsoniella peoriensis , Ruminococcus gnavus , Blautia producta and Clostridium xylanolyticum . Phylogenetic relationships based on 16S rRNA gene sequence analysis were confirmed by partial sequencing of hsp60 genes. The use of an in-house

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29

Chongtrakool, Piriyaporn, Teruyo Ito, Xiao Xue Ma, et al. "Staphylococcal Cassette Chromosome mec (SCCmec) Typing of Methicillin-Resistant Staphylococcus aureus Strains Isolated in 11 Asian Countries: a Proposal for a New Nomenclature for SCCmec Elements." Antimicrobial Agents and Chemotherapy 50, no. 3 (2006): 1001–12. http://dx.doi.org/10.1128/aac.50.3.1001-1012.2006.

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ABSTRACT A description of staphylococcal cassette chromosome mec (SCCmec) elements carried by 615 methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in 11 Asian countries is reported, and a novel nomenclatural system based on their structures is proposed. The 615 strains were classified as type 3A (370 strains), type 2A (207 strains), type 2B (32 strains), type 1B (1 strain), and nontypeable (5 strains). The previously reported type III SCCmec (DDBJ/EMBL/GenBank accession no. AB037671) carried by the MRSA strain 85/2082 was ascertained to be composed of two SCC elements, type

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da Silva Malone, Camila Francieli, Janaína Rigonato, Haywood Dail Laughinghouse, et al. "Cephalothrix gen. nov. (Cyanobacteria): towards an intraspecific phylogenetic evaluation by multilocus analyses." International Journal of Systematic and Evolutionary Microbiology 65, Pt_9 (2015): 2993–3007. http://dx.doi.org/10.1099/ijs.0.000369.

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For more than a decade, the taxonomy of the Phormidiaceae has been problematic, since morphologically similar organisms represent phylogenetically distinct entities. Based on 16S rRNA gene sequence analyses, the polyphyletic genus Phormidium and other gas-vacuolated oscillatorioids appear scattered throughout the cyanobacterial tree of life. Recently, several studies have focused on understanding the oscillatorioid taxa at the generic level. At the specific level, few studies have characterized cyanobacterial strains using combined datasets (morphology, ultrastructure and molecular multilocus

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Pathak, Jyoti, Gandhi Gracy Ramasamy, Aditi Agrawal, et al. "Comparative Transcriptome Analysis to Reveal Differentially Expressed Cytochrome P450 in Response to Imidacloprid in the Aphid Lion, Chrysoperla zastrowi sillemi (Esben-Petersen)." Insects 13, no. 10 (2022): 900. http://dx.doi.org/10.3390/insects13100900.

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The aphid lion, Chrysoperla zastrowi sillemi (Neuroptera: Chrysopidae) is a highly effective beneficial predator of many agricultural pests and has developed resistance to several insecticides. Understanding the molecular mechanism of insecticide resistance in the predators is crucial for its effective application in IPM programs. Therefore, transcriptomes of imidacloprid-resistant and susceptible strains have been assessed using RNA-seq. Cytochrome P450 is one of the important gene families involved in xenobiotic metabolism. Hence, our study focused on the CYP gene family where mining, nomenc

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32

Kuhnert, Peter, Isabelle Brodard, Maher Alsaaod, Adrian Steiner, Michael H. Stoffel, and Joerg Jores. "Treponema phagedenis (ex Noguchi 1912) Brumpt 1922 sp. nov., nom. rev., isolated from bovine digital dermatitis." International Journal of Systematic and Evolutionary Microbiology 70, no. 3 (2020): 2115–23. http://dx.doi.org/10.1099/ijsem.0.004027.

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‘ Treponema phagedenis ’ was originally described in 1912 by Noguchi but the name was not validly published and no type strain was designated. The taxon was not included in the Approved Lists of Bacterial Names and hence has no standing in nomenclature. Six Treponema strains positive in a ‘ T. phagedenis ’ phylogroup-specific PCR test were isolated from digital dermatitis (DD) lesions of cattle and further characterized and compared with the human strain ‘ T. phagedenis ’ ATCC 27087. Results of phenotypic and genotypic analyses including API ZYM, VITEK2, MALDI-TOF and electron microscopy, as w

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Leonard, Susan R., Mark K. Mammel, David A. Rasko, and David W. Lacher. "Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia sp. Cryptic Lineage 1 Strain 7v Harbors a Hybrid Plasmid." Applied and Environmental Microbiology 82, no. 14 (2016): 4309–19. http://dx.doi.org/10.1128/aem.01129-16.

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ABSTRACTHybrid isolates of Shiga toxin-producingEscherichia coli(STEC) and enterotoxigenicE. coli(ETEC) encoding heat-stable enterotoxin (ST) are being reported with increasing frequency from a variety of sources. However, information regarding the plasmids that these strains harbor is scarce. In this study, we sequence and characterize a plasmid, p7v, from the STEC/ETEC hybrid strain 7v. Whole-genome phylogenetic analyses of STEC/ETEC hybrid strains and prototypeE. coliisolates of other pathotypes placed 7v in theEscherichiasp. cryptic lineage 1 (CL1) clade. The complete plasmid, p7v, was det

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34

Gaysina, Lira A., Jeffrey R. Johansen, Aniket Saraf, Rezeda Z. Allaguvatova, Sagarika Pal, and Prashant Singh. "Roholtiella volcanica sp. nov., a New Species of Cyanobacteria from Kamchatkan Volcanic Soils." Diversity 14, no. 8 (2022): 620. http://dx.doi.org/10.3390/d14080620.

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During a study of biodiversity of cyanobacteria in Gorely volcano soils (Kamchatka Peninsula), a strain of heterocytous, a false branching cyanobacterium with gradually tapered filaments, was isolated. Prominent features of the strain were purplish-grey trichomes and firm, distinct multilayered sheaths. Based on the results obtained from the morphological, ecological, and phylogenetic analysis using the 16S rRNA and 16S–23S ITS region, 16S–23S ITS secondary structure analysis, comparison of flanking regions of BoxB and V3 helices, and the p-distance between the 16S–23S ITS region, we describe

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Boxberger, Manon, Sibylle Magnien, Angeline Antezack, et al. "Leucobacter manosquensis sp. nov.—A Novel Bacterial Species Isolated from Healthy Human Skin." Microorganisms 11, no. 10 (2023): 2535. http://dx.doi.org/10.3390/microorganisms11102535.

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Extending our knowledge on human skin microbiota is a challenge to better decipher its role in health and disease. Using the culturomics method, we isolated strain Marseille-Q4368 from the healthy forehead of a 59-year-old woman. We describe here the main characteristics of this bacterium using a taxonogenomic approach. This new bacterial species is Gram-positive, non-motile, and non-spore-forming. Its 16S rRNA sequence exhibited a similarity of 99.59% with Leucobacter chromiiresistens, the most closely related species in terms of nomenclature. However, a digital DNA–DNA hybridization analysis

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Kretschmann, Juliane, Malte Elbrächter, Carmen Zinssmeister, et al. "Taxonomic clarification of the dinophyte Peridinium acuminatum Ehrenb., ≡ Scrippsiella acuminata, comb. nov. (Thoracosphaeraceae, Peridiniales)." Phytotaxa 220, no. 3 (2015): 239. http://dx.doi.org/10.11646/phytotaxa.220.3.3.

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Peridinium acuminatum (Peridiniales, Dinophyceae) was described in the first half of the 19th century, but the name has been rarely adopted since then. It was used as type of Goniodoma, Heteraulacus and Yesevius, providing various sources of nomenclatural and taxonomic confusion. Particularly, several early authors emphasised that the organisms investigated by C.G. Ehrenberg and S.F.N.R. von Stein were not conspecific, but did not perform the necessary taxonomic conclusions. The holotype of P. acuminatum is an illustration dating back to 1834, which makes the determination of the species ambig

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Holmes, Barry, and J. Jim Farmer III. "Correction of the type strain of Aeromonas punctata (Zimmermann 1890) Snieszko 1957 and of A. punctata subsp. punctata from ATCC 15468T to NCMB 74T (=NCIMB 74T= ATCC 23309T)." International Journal of Systematic and Evolutionary Microbiology 70, no. 3 (2020): 2155–57. http://dx.doi.org/10.1099/ijsem.0.003960.

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Under Rule 23a (Note 4) of the Bacteriological Code we ask the Judicial Commission to issue an opinion that will correct two errors that were made on the original 1980 Approved Lists of Bacterial Names. We request that the type strain designations for Aeromonas punctata and Aeromonas punctata subsp. punctata be corrected from ATCC 15468T to NCMB 74T. We also ask that the opinion state the ‘correct’ or best way to write the author citations for several other Aeromonas names in order to avoid future instability in nomenclature when the citations are given.

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Tibayrenc, Michel. "The Relevance of the Predominant Clonal Evolution (PCE) Model for the Molecular Epidemiology and Subspecific Taxonomy of Trypanosoma cruzi." Pathogens 14, no. 5 (2025): 407. https://doi.org/10.3390/pathogens14050407.

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The predominant clonal evolution (PCE) model is often misunderstood. Contrary to common belief, it is not restricted to strict mitotic clonality. Instead, it encompasses processes such as selfing, strong homogamy, and various forms of parthenogenesis, as widely acknowledged by researchers studying clonality. Moreover, the PCE model does not claim that genetic recombination is entirely absent or devoid of epidemiological and evolutionary significance. In this review, I will explore the reciprocal relationship between PCE and molecular epidemiology (strain typing) and discuss the implications of

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Kalinina, Olga, Helene Norder, Sergey Mukomolov, and Lars O. Magnius. "A Natural Intergenotypic Recombinant of Hepatitis C Virus Identified in St. Petersburg." Journal of Virology 76, no. 8 (2002): 4034–43. http://dx.doi.org/10.1128/jvi.76.8.4034-4043.2002.

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ABSTRACT Hepatitis C virus (HCV) evolution is thought to proceed by mutations within the six genotypes. Here, we report on a viable spontaneous HCV recombinant and we show that recombination may play a role in the evolution of this virus. Previously, 149 HCV strains from St. Petersburg had been subtyped by limited sequencing within the NS5B region. In the present study, the core regions of 41 of these strains were sequenced to investigate the concordance of HCV genotyping for these two genomic regions. Two phylogenetically related HCV strains were found to belong to different subtypes, 2k and

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Oberste, M. Steven, David Schnurr, Kaija Maher, Suleiman al-Busaidy, and Mark A. Pallansch. "Molecular identification of new picornaviruses and characterization of a proposed enterovirus 73 serotype." Journal of General Virology 82, no. 2 (2001): 409–16. http://dx.doi.org/10.1099/0022-1317-82-2-409.

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Enteroviruses (EV) have traditionally been identified by using serotype-specific antisera in a virus-neutralization test. Three EV strains isolated in California, USA, in 1955, 1964 and 1978, and a 1995 Oman isolate, were found to be antigenically related to one another; however, the strains were not neutralized by standard EV typing antisera, suggesting that they may represent a new EV serotype. The isolates were characterized genetically by RT–PCR coupled with amplicon sequencing and comparison to a database of enterovirus nucleotide sequences. The strains were 75·3 to 87·2% identical to one

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Ping, Song, Wang Qin-Ying, Wu Hui-Xian, Lu Xiu-Jun, and Wang Yong. "Identification of thecrygene inBacillus thuringiensisstrain WZ-9 and its toxicity againstHenosepilachna vigintioctomaculata." Chinese Journal of Agricultural Biotechnology 5, no. 3 (2008): 245–50. http://dx.doi.org/10.1017/s1479236208002453.

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AbstractBacillus thuringiensisstrain WZ-9, isolated from soil in Hebei province, China, was effective againstHenosepilachna vigintioctomaculatalarvae. The strain presented bipyramidal crystals with a protein band of 130 kDa in SDS–PAGE. The pH changes of the culture media showed important fluctuations during the 24 h growth cycle. The pH varied less in log and stationary phases than it did in the exponential phase. Bioassay results showed that the WZ-9 strain was only harmful to larvae ofH. vigintioctomaculataand not to either adults ofH. vigintioctomaculataor other several lepidopteran and co

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Papke, R. Thane, Emma White, Prajwal Reddy, et al. "A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales." International Journal of Systematic and Evolutionary Microbiology 61, no. 12 (2011): 2984–95. http://dx.doi.org/10.1099/ijs.0.029298-0.

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Members of the order Halobacteriales are obligate extreme halophiles that belong to the domain Archaea. The classification of the Halobacteriales currently relies on a polyphasic approach, which integrates phenotypic, genotypic and chemotaxonomic characterization. However, the most utilized genetic marker for phylogeny, the 16S rRNA gene, has multiple drawbacks for use with the Halobacteriales: the species of many genera exhibit large intragenic differences between multiple ribosomal RNA operons, the gene is too conserved to discriminate reliably at the species level and it appears to be the m

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Gardner, Jeffrey G., and Jorge C. Escalante-Semerena. "In Bacillus subtilis, the Sirtuin Protein Deacetylase, Encoded by the srtN Gene (Formerly yhdZ), and Functions Encoded by the acuABC Genes Control the Activity of Acetyl Coenzyme A Synthetase." Journal of Bacteriology 191, no. 6 (2009): 1749–55. http://dx.doi.org/10.1128/jb.01674-08.

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ABSTRACT This report provides in vivo evidence for the posttranslational control of the acetyl coenzyme A (Ac-CoA) synthetase (AcsA) enzyme of Bacillus subtilis by the acuA and acuC gene products. In addition, both in vivo and in vitro data presented support the conclusion that the yhdZ gene of B. subtilis encodes a NAD+-dependent protein deacetylase homologous to the yeast Sir2 protein (also known as sirtuin). On the basis of this new information, a change in gene nomenclature, from yhdZ to srtN (for sirtuin), is proposed to reflect the activity associated with the YdhZ protein. In vivo contr

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Skuce, Robin A., Thomas P. McCorry, Julie F. McCarroll, et al. "Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR-PCR targets." Microbiology 148, no. 2 (2002): 519–28. http://dx.doi.org/10.1099/00221287-148-2-519.

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The lack of a convenient high-resolution strain-typing method has hampered the application of molecular epidemiology to the surveillance of bacteria of the Mycobacterium tuberculosis complex, particularly the monitoring of strains of Mycobacterium bovis. With the recent availability of genome sequences for strains of the M. tuberculosis complex, novel PCR-based M. tuberculosis-typing methods have been developed, which target the variable-number tandem repeats (VNTRs) of minisatellite-like mycobacterial interspersed repetitive units (MIRUs), or exact tandem repeats (ETRs). This paper describes

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Sundberg, J. P., J. M. Ward, H. HogenEsch, et al. "Training Pathologists in Mouse Pathology." Veterinary Pathology 49, no. 2 (2010): 393–97. http://dx.doi.org/10.1177/0300985810381244.

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Expertise in the pathology of mice has expanded from traditional regulatory and drug safety screening (toxicologic pathology) primarily performed by veterinary pathologists to the highly specialized area of mouse research pathobiology performed by veterinary and medical pathologists encompassing phenotyping of mutant mice and analysis of research experiments exploiting inbred mouse strains and genetically engineered lines. With increasing use of genetically modified mice in research, mouse pathobiology and, by extension, expert mouse research-oriented pathologists have become integral to the s

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Sozzi, Enrica, Gabriele Leo, Fatbardha Lamcja, et al. "Isolation and Molecular Evidence of Tunisian Sheep-like Pestivirus (Pestivirus N) in Persistently Infected Sheep in Northern Italy, 2023." Viruses 16, no. 6 (2024): 815. http://dx.doi.org/10.3390/v16060815.

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Over the last few decades, several pestiviruses have been discovered in ruminants, pigs, and, more recently, in non-ungulate hosts. Consequently, the nomenclature and taxonomy of pestiviruses have been updated. The Tunisian sheep-like pestivirus (TSV, Pestivirus N) is an additional ovine pestivirus genetically closely related to classical swine fever virus (CSFV). In this study, during a survey of pestivirus infections in ovine farms in the Lombardy region of Northern Italy, we identified and isolated a pestivirus strain from a sheep that was found to belong to Pestivirus N species based on it

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Raeburn, Candice, Shin Kasahara, Toshi Komoda, Catherine Abbott, and Peter M. Smooker. "Draft genome sequence and nomenclature adjustment of Rhodococcus qingshengii CS98, a cesium-accumulating strain isolated in Japan." Biotechnology Reports 25 (March 2020): e00415. http://dx.doi.org/10.1016/j.btre.2019.e00415.

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Roldán, M., M. Ramírez, J. del Campo, M. Hernández-Mariné, and J. Komárek. "Chalicogloea cavernicola gen. nov., sp. nov. (Chroococcales, Cyanobacteria ), from low-light aerophytic environments: combined molecular, phenotypic and ecological criteria." International Journal of Systematic and Evolutionary Microbiology 63, Pt_6 (2013): 2326–33. http://dx.doi.org/10.1099/ijs.0.045468-0.

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This work characterizes a unicellular cyanobacterium with nearly spherical cells and thin-outlined sheaths that divide irregularly, forming small packets immersed in a diffluent mucilaginous layer. It was isolated growing on calcite speleothems and walls in a show cave in Collbató (Barcelona, Spain). Spectral confocal laser and transmission electron microscopy were used to describe the morphology, fine structure and thylakoid arrangement. The pigments identified were phycoerythrin, phycocyanin, allophycocyanin and chlorophyll a. Three-dimensional reconstructions, generated from natural fluores

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Belov, Vyacheslav, and Valery Morozov. "Fire Resistance of Non-Crack Resistant Flexural Reinforced Concrete Elements." Applied Mechanics and Materials 725-726 (January 2015): 15–20. http://dx.doi.org/10.4028/www.scientific.net/amm.725-726.15.

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In developed countries only loss of property because of fire makes annually up to 2% of their national income [9, 15]. The bearing capacity of reinforced concrete structures at high temperature impact is lost within several dozens of minutes [1, 3, 5, 10, 12, 18, 25]. Disappointing statistics of increase of both the number of fires and the scope of damage due to them aggravates the actual problem of determination of reinforced concrete structures fire-endurance. The main problems and methods of evaluation of reinforced concrete structure fire resistance are stated. Within the framework of bloc

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Blanco-Rivero, A., F. Leganés, E. Fernández-Valiente, P. Calle, and F. Fernández-Piñas. "mrpA, a gene with roles in resistance to Na+ and adaptation to alkaline pH in the cyanobacterium Anabaena sp. PCC7120." Microbiology 151, no. 5 (2005): 1671–82. http://dx.doi.org/10.1099/mic.0.27848-0.

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Transposon mutagenesis of Anabaena sp. PCC7120 led to the isolation of a mutant strain, PHB11, which grew poorly at pH values above 10. The mutant strain exhibited pronounced Na+ sensitivity; this sensitivity was higher under basic conditions. Mutant PHB11 also showed an inhibition of photosynthesis that was much more pronounced at alkaline pH. Reconstruction of the transposon mutation of PHB11 in the wild-type strain reproduced the phenotype of the original mutant. The wild-type version of the mutated gene was cloned and the mutation complemented. In mutant strain PHB11, the transposon had in

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