Relevant bibliographies by topics / Bacterial taxonomy

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Academic literature on the topic 'Bacterial taxonomy'

Author: Grafiati
Published: 4 June 2021
Last updated: 5 February 2022

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Journal articles on the topic "Bacterial taxonomy"

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Ramasamy, Dhamodharan, Ajay Kumar Mishra, Jean-Christophe Lagier, Roshan Padhmanabhan, Morgane Rossi, Erwin Sentausa, Didier Raoult, and Pierre-Edouard Fournier. "A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species." International Journal of Systematic and Evolutionary Microbiology 64, Pt_2 (February 1, 2014): 384–91. http://dx.doi.org/10.1099/ijs.0.057091-0.

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Currently, bacterial taxonomy relies on a polyphasic approach based on the combination of phenotypic and genotypic characteristics. However, the current situation is paradoxical in that the genetic criteria that are used, including DNA–DNA hybridization, 16S rRNA gene sequence nucleotide similarity and phylogeny, and DNA G+C content, have significant limitations, but genome sequences that contain the whole genetic information of bacterial strains are not used for taxonomic purposes, despite the decreasing costs of sequencing and the increasing number of available genomes. Recently, we diversified bacterial culture conditions with the aim of isolating uncultivated bacteria. To classify the putative novel species that we cultivated, we used a polyphasic strategy that included phenotypic as well as genomic criteria (genome characteristics as well as genomic sequence similarity). Herein, we review the pros and cons of genome sequencing for taxonomy and propose that the incorporation of genome sequences in taxonomic studies has the advantage of using reliable and reproducible data. This strategy, which we name taxono-genomics, may contribute to the taxonomic classification of bacteria.
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Jones, Dorothy, and William D. Grant. "Peter Henry Andrews Sneath. 17 November 1923 — 9 September 2011." Biographical Memoirs of Fellows of the Royal Society 59 (January 2013): 337–57. http://dx.doi.org/10.1098/rsbm.2013.0008.

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Peter Sneath revolutionized the practice of bacterial taxonomy over a 30-year period. He was the first to apply Adansonian principles to bacterial taxonomy, arguing that a robust system required that bacteria should be subjected to many phenotypic (phenetic) tests, all given equal weight, with analysis of the subsequent binary test scores being used to derive groups that could be given taxonomic rank (taxa). The procedures came to be known collectively as ‘numerical taxonomy’. A further innovation was the realization that the then embryonic discipline of computing could be harnessed to derive taxa from these very large sets of data. Computer-aided numerical taxonomy became the method of choice for classifying bacteria by the early 1960s. Much of Peter’s effort as Director of a Medical Research Council (MRC) Research Unit in Leicester in the 1960s and early 1970s was to reassess the taxonomy of most of the medically important bacteria. This information was then interrogated to determine the minimum number of tests required to identify new isolates reliably. The tests available in commercial identification kits in use today directly reflect these original numerical analyses. Later, after appointment to the Foundation Chair of Medical Microbiology at the University of Leicester, he carried out, together with colleagues, the most important revision of bacterial nomenclature for more than a century, the 1980 ‘Approved lists of bacterial names’. He was also a member, Vice Chairman and then Chairman of Bergey’s Trust, the organization responsible for Bergey’s manual of determinative bacteriology (later Bergey’s manual of systematic bacteriology ), the definitive account of bacterial taxonomy and properties. He continued to edit volumes and contribute sections right up to his death.
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Norris, Vic, Tanneke den Blaauwen, Armelle Cabin-Flaman, Roy H. Doi, Rasika Harshey, Laurent Janniere, Alfonso Jimenez-Sanchez, et al. "Functional Taxonomy of Bacterial Hyperstructures." Microbiology and Molecular Biology Reviews 71, no. 1 (March 2007): 230–53. http://dx.doi.org/10.1128/mmbr.00035-06.

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SUMMARY The levels of organization that exist in bacteria extend from macromolecules to populations. Evidence that there is also a level of organization intermediate between the macromolecule and the bacterial cell is accumulating. This is the level of hyperstructures. Here, we review a variety of spatially extended structures, complexes, and assemblies that might be termed hyperstructures. These include ribosomal or “nucleolar” hyperstructures; transertion hyperstructures; putative phosphotransferase system and glycolytic hyperstructures; chemosignaling and flagellar hyperstructures; DNA repair hyperstructures; cytoskeletal hyperstructures based on EF-Tu, FtsZ, and MreB; and cell cycle hyperstructures responsible for DNA replication, sequestration of newly replicated origins, segregation, compaction, and division. We propose principles for classifying these hyperstructures and finally illustrate how thinking in terms of hyperstructures may lead to a different vision of the bacterial cell.
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York, Ashley. "Next-generation bacterial taxonomy." Nature Reviews Microbiology 16, no. 10 (September 3, 2018): 583. http://dx.doi.org/10.1038/s41579-018-0083-3.

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Staley, James T. "The bacterial species dilemma and the genomic–phylogenetic species concept." Philosophical Transactions of the Royal Society B: Biological Sciences 361, no. 1475 (October 11, 2006): 1899–909. http://dx.doi.org/10.1098/rstb.2006.1914.

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The number of species of Bacteria and Archaea ( ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA–DNA hybridization and phenotypic characterization. Recently, 16S rRNA gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. Although 16S phylogeny is arguably excellent for classification of Bacteria and Archaea from the Domain level down to the family or genus, it lacks resolution below that level. Newer approaches, including multilocus sequence analysis, and genome sequence and microarray analyses, promise to provide necessary information to better understand bacterial speciation. Indeed, recent data using these approaches, while meagre, support the view that speciation processes may occur at the subspecies level within ecological niches (ecovars) and owing to biogeography (geovars). A major dilemma for bacterial taxonomists is how to incorporate this new information into the present hierarchical system for classification of Bacteria and Archaea without causing undesirable confusion and contention. This author proposes the genomic–phylogenetic species concept (GPSC) for the taxonomy of prokaryotes. The aim is twofold. First, the GPSC would provide a conceptual and testable framework for bacterial taxonomy. Second, the GPSC would replace the burdensome requirement for DNA hybridization presently needed to describe new species. Furthermore, the GPSC is consistent with the present treatment at higher taxonomic levels.
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Zakhia, Frédéric, and Philippe de Lajudie. "La taxonomie bactérienne moderne : revue des techniques — application à la caractérisation des bactéries nodulant les légumineuses (BNL)." Canadian Journal of Microbiology 52, no. 3 (March 1, 2006): 169–81. http://dx.doi.org/10.1139/w05-092.

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Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.Key words: polyphasic taxonomy, molecular characterization, bacteria, prokaryotes, legume nodulating bacteria, Rhizobium.
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Gajdács, Márió. "Taxonomy and nomenclature of bacteria with clinical and scientific importance: current concepts for pharmacists and pharmaceutical scientists." Acta Pharmaceutica Hungarica 89, no. 4 (March 7, 2020): 99–108. http://dx.doi.org/10.33892/aph.2019.89.99-108.

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Taxonomy is the science of the classification of various living organisms consisting of three independent, but interrelated disciplines, namely classification, nomenclature and identification. With the advent of molecular biological methods and sequencing, a revolution is currently occurring with regards to the reporting of novel taxa and changes in the taxonomy of already described bacterial species. The applications of taxonomic changes can be broad ranging: they may impact the clinical care of patients, through variations in choosing the appropriate antimicrobial susceptibility testing standards or data interpretation, or even their clinical relevance and epidemiology. The aim of this paper was to aid healthcare professionals and pharmaceutical scientists to navigate through the ‘maze’ of bacterial taxonomy, and to aid in finding authentic information regarding the description of taxonomic changes and to present some examples of changes in bacterial taxonomy which have proven to be clinically significant.
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Gyllenberg, M., and T. Koski. "Probabilistic Models for Bacterial Taxonomy." International Statistical Review / Revue Internationale de Statistique 69, no. 2 (August 2001): 249. http://dx.doi.org/10.2307/1403815.

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SAKAZAKI, Riichi. "Bacterial Taxonomy and Food Microbiology." Japanese Journal of Food Microbiology 11, no. 1 (1994): 1–7. http://dx.doi.org/10.5803/jsfm.11.1.

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Kim, Young Sook, and Sook-Jin Jang. "Basic Concepts of Bacterial Taxonomy." Korean Journal of Clinical Microbiology 15, no. 3 (2012): 79. http://dx.doi.org/10.5145/kjcm.2012.15.3.79.

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Dissertations / Theses on the topic "Bacterial taxonomy"

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Kim, Bongcheol. "Polyphasic taxonomy of thermophilic actinomycetes." Thesis, University of Newcastle Upon Tyne, 1999. http://hdl.handle.net/10443/1757.

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Molecular systematic methods were applied in a series of studies designed to resolve the taxonomic relationships of thermophilic actinomycetes known to be difficult to classify using standard taxonomic procedures. The test strains included representatives of clusters defined in an extensiven umerical phenetic survey of thermophilic streptomycetesa nd twelve marker strains. The resultant genotypic data together with the results of corresponding phenotypic studies were used to highlight novel taxa and to improve the circumscription of validly described species. The most comprehensive study was undertaken to clarify relationships within and between representative alkalitolerant, thermophilic and neutrophilic, thermophilic streptomycetes isolated from soil and appropriate marker strains. The resultant data, notably those from DNA: DNA relatedness studies, supported the taxonomic integrity of the validly described species Streptomyces thermodiastaticus, Streptomyces thermoviolaceus and Streptomyces thermovulgaris. However, the genotypic and phenotypic data clearly show that Streptomyces thermonitrificans Desai and Dhala 1967 and Streptomyces thermovulgaris (Henssen 1957) Goodfellow et al. 1987 represent a single species. On the basis of the priority, Streptomyces thermonitrificans is a later subjective synonym of Streptomyces thermovulgaris. Similarly, eight out of eleven representative alkalitolerant, thermophilic isolates and three out of sixteen representative neutrophilic, thermophilic isolates had a combination of properties consistent with their classification as Streptomyces thermovulgaris. One of the remaining alkalitolerant, thermophilic isolate, Streptomyces strain TA56, merited species status. The name Streptomyces thermoalcalitolerans sp. nov. is proposed for this strain. A neutrophilic, thermophilic isolate, Streptomyces strain NAR85, was identified as Streptomyces thermodiastaticus. Four other neutrophilic thermophilic isolates assigned to a numerical phenetic cluster and a thermophilic isolates from poultry faeces were also considered to warrant species status; the names Streptomyces eurythermophilus sp. nov. and Streptomyces thermocoprophilus sp. nov. are proposed to accommodate these strains. It was also concluded that additional comparative taxonomic studies are required to clarify the relationships between additional thermophilic streptomycete strains included in the present investigation. A corresponding polyphasic approach was used to clarify the taxonomy of six thermophilic isolates provisionally assigned to either the genera Amycolatopsis or Excellospora. Two of the isolates, strain NT202 and NT303, had properties consistent with their classification in the genus Amycolatopsis. However, the genotypic and phenotypic data also showed that these strains formed a new centre of taxonomic variation for which the name Amycolatopsis eurythermus sp. nov. is proposed. Similarly, the four remaining strains formed two new centre of taxonomic variation within the genus Excellospora. It is proposed that isolates TA113 and TA114 be designated Excellospora alcalithermophilus sp. nov. Similarly, the name Excellospora thermoalcalitolerans sp. nov. is proposed for strains TA86 and TA111. An emended description is also given for the genus Excellospora.
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Brady, Carrie Louise. "Taxonomy of Pantoea associated with bacterial blight of Eucalyptus." Pretoria : [s.n.], 2005. http://upetd.up.ac.za/thesis/available/etd-02092006-110117.

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Cosgaya, Castro Clara. "Not the usual suspects: membrane translocation, pathogenic potential and bacterial species of the Acinetobacter baumannii group." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/668097.

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The most clinically relevant species of the Acinetobacter genus are comprised within the Acinetobacter baumannii group (Ab group, i. e. A. baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, Acinetobacter seifertii and A. pittii-like/A. dijskhoorniae). Among these species A. baumannii is the most prevalent and usually shows multidrug resistance. This, and the fact that the Ab group species cannot be distinguished by phenotypic methods, has led to the misidentification of the species of the Ab group as A. baumannii in the clinical settings. Nevertheless, in the last years the incidence of the other species of the Ab group has risen, partly due to the use of molecular techniques and mass spectrometry tools. This thesis has characterised, using both genotypic (rpoB-based and MLSA phylogenetic analyses, and whole genome sequence analysis) and phenotypic (carbon utilisation assays and MALDI-TOF MS) techniques, a group of strains mainly recovered from human samples that represents a new bacterial species within the Ab group for which the name of Acinetobacter dijkshoorniae has been proposed. The genome of the type strain of the novel species has been sequenced and the identification of the species of the Ab group by MALDI-TOF MS has been optimised, since the novel species (A. dijkshoorniae and A. seifertii) could not be identified by this technique prior to this study. MALDI-TOF MS was shown to be rapid and accurate in the discrimination of all the species of the Ab group, indicating its suitability for the implementation of this technique in the clinical settings. In addition, the use of MALDI- TOF MS allowed the identification of members of the Ab group in market meat from Peru, leading to the first identification of A. dijkshoorniae from food and in South America. We also evaluated the differences among the species of the Ab group beyond those at the taxonomic level and found that while A. baumannii still presents the higher rates of antimicrobial resistance, this species and A. nosocomialis, which usually are more prevalent in our hospitals and have worst outcomes, showed a minor pathogenicity in terms of biofilm formation and virulence in the Caenorhabditis elegans infection model. In contrast, A. pittii, A. seifertii and A. dijkshoorniae presented a higher pathogenicity in the phenotypes studied. This data suggests the emergence of the non-baumannii species of the Ab group as well as different degrees of adaptation to the human host and the need of studying them as distinct entities. The rise on the antimicrobial resistance of A. baumannii has drastically reduced the therapeutic options left to treat infections caused by this pathogen. In view of the lack of effective antimicrobial drugs there is an urgent need for novel therapeutic approaches. In order to find novel targets for the development of antimicrobial drugs against A. baumannii, we evaluated the dual role of transport-related proteins in antimicrobial resistance and virulence using a transposon mutant strain collection derived from the A. baumannii AB5075 strain. The antimicrobial susceptibility of the mutant strains was compared against the wild- type strain and led to the identification of novel antimicrobial substrates for known efflux pumps and uncharacterised transport-related proteins which seem to participate in the transport of antibiotics across membranes. The evaluation of the virulence in the Galleria mellonella infection model also identified transport-related proteins putatively involved in the virulence of A. baumannii. This results are still preliminary but show the dual role of transport- related proteins in the antimicrobial resistance and pathogenicity of A. baumannii and open a new line of research that might help to gain further knowledge about the virulence of this pathogen while finding novel targets for the development of new antimicrobial drugs against A. baumannii.
Dentro del género Acinetobacter, las especies del grupo Acinetobacter baumannii (Ab) (i. e. A. baumannii, Acinetobacter nosocomialis, Acinetobacter pittii y Acinetobacter seifertii y A. pittii-like/A. dijskhoorniae) destacan por su gran relevancia clínica, siendo A. baumannii el patógeno del grupo Ab de mayor importancia debido a su frecuente aislamiento y su usual fenotipo de multirresistencia. Esto, sumado a que las especies del grupo Ab son indistinguibles a nivel fenotípico, ha conllevado que habitualmente hayan sido erróneamente identificadas en el ámbito clínico como A. baumannii. Sin embargo, en los últimos años se ha observado un aumento en la incidencia de las otras especies del grupo Ab, en parte gracias a las técnicas moleculares, que han revolucionado la taxonomía de este género, y también al uso de la espectrometría de masas MALDI-ToF (EM MALDI-TOF). Este estudio proporciona las pruebas fenotípicas y genotípicas que respaldan la delineación de una nueva especie dentro del grupo Ab, para la cual se ha propuesto el nombre de Acinetobacter dijkshoorniae. El genoma de la cepa tipo de esta nueva especie ha sido secuenciado, y se ha puesto a punto la identificación mediante EM MALDI-TOF de los nuevos miembros del grupo Ab (A. dijkshoorniae y A. seifertii) así como ha sido optimizado para el resto de especies del grupo. Rasgos como la formación de biofilm o la virulencia en el modelo animal de Caenhorabditis elegans muestran que A. baumannii, junto con A. nosocomialis, presentan menor potencial patogénico que las otras especies del grupo Ab, y que A. dijkshoorniae es especialmente virulenta. Estos datos sugieren diferentes niveles de adaptación al ámbito hospitalario, y remarca la necesidad de identificar y estudiar las especies del grupo Ab individualmente. Además, a nivel de susceptibilidad antimicrobiana, A. baumannii sigue siendo la especie que presenta mayores tasas de resistencia. Finalmente, hemos hallado nuevas proteínas implicadas en el transporte de membrana que, de manera preliminar, parecen participar en la resistencia a antibióticos y virulencia de A. baumannii, y cuya caracterización podría aportar nuevas dianas para el desarrollo de fármacos antimicrobianos para tratar las infecciones causadas por A. baumannii multirresistente.
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Albarral, Ávila Vicenta. "Diversidad intraespecífica y factores de virulencia en el “complejo de especies de Aeromonas hydrophila” (A. Hydrophila, A. Salmonicida, A. Bestiarum)." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/125472.

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The genus Aeromonas comprises 26 currently recognized species, some of them divided in to several subspecies. They are ubiquitous in fresh water, but found in chlorinated, brackish and marine water. Aeromonas strains are obtained from a wide variety of foods, as well as clinical samples. Aeromonas species are the cause of intestinal and extra-intestinal infections although the mechanisms that cause bacterial diarrhoea are not yet clearly established. The “A. hydrophila complex” (A. hydrophila, A. salmonicida, A. bestiarum, A. piscicola and A. popoffii), includes A. salmonicida, an important pathogen of fish, and A. hydrophila, an opportunistic pathogen in humans. The virulence of these species is multifactorial and involves complex pathogenic mechanisms associated with toxins (cytotoxic and cytotonic), proteases, haemolysins, lipases, adhesins, agglutinins, pili, etc. A phylogenetic study was performed from a collection of 128 strains belonging to the “A. hydrophila complex", determining partial sequences of dnaJ, cpn60, gyrB and rpoD genes, this analysis allowed us to clarify the taxonomy of this group of Aeromonas species, showing a polyphyletic origin that challenges the existence of the group as such. The population analysis of the studied strains revealed as strong linkage disequilibrium, typical of a clonal population, and a high genetic diversity. We also studied the prevalence and distribution of different virulence factors in the population to establish its pathogenic potential. For this purpose, we determined several enzymatic activities and the antibiotic sensitivity profile of these strains. We also detected the presence of act (aerolysin), alt (cytotonic toxin) and ast (cytotonic toxin) genes by PCR as well as the adhesion capacity and cytopathic effect of the strains on the Caco-2 cell line. The results obtained revealed a high pathogenic of potential the studied Aeromonas strains, regardless of their origin.
El género Aeromonas está constituido actualmente por 26 especies reconocidas, algunas de las cuales incluyen varias subespecies. Son habitantes ubicuos del agua dulce, pero también de aguas cloradas, salobres y marinas. Se han obtenido cepas de Aeromonas de una amplia variedad de alimentos, y se han aislado de muestras clínicas. Algunas especies de Aeromonas son causantes de infecciones intestinales y extraintestinales aunque los mecanismos por los que causan diarreas bacterianas no están todavía establecidos de manera clara. Dentro del “complejo A. hydrophila” (A. hydrophila, A. salmonicida, A. bestiarum, A. piscicola y A. popoffii), hay que destacar A. salmonicida como patógeno importante de peces y A. hydrophila como patógeno oportunista de humanos. La virulencia de estas especies es multifactorial e implica mecanismos de patogenicidad complejos asociados a toxinas (citotóxicas y citotónicas), proteasas, hemolisinas, lipasas, adhesinas, aglutininas, pili, etc. A partir de una colección de 128 de cepas del “complejo A. hydrophila”, se ha realizado un estudio filogenético, poblacional y de factores de patogenicidad. El estudio filogenético con las secuencias parciales de los genes cpn60, dnaJ, gyrB, y rpoD, ha permitido clarificar la taxonomía de las especies del “complejo A. hydrophila”, demostrándose que posee un origen polifilético que cuestionaría la posible existencia del grupo como tal. El análisis de la población de las cepas estudiadas revela un fuerte desequilibrio de ligamiento, típico de una población clonal, y una elevada diversidad genética. También se ha estudiado la prevalencia y distribución de diversos factores de virulencia en la población estudiada para poder establecer su potencial patogénico. Para ello se han determinado actividades enzimáticas, el perfil de sensibilidad a antibióticos, la detección por PCR de los genes act (aerolisina/hemolisina), alt (toxina citotónica) y ast (toxina citotónica), y la capacidad de adherencia y efecto citopático de las cepas en la línea celular Caco-2. Los resultados obtenidos revelan un elevado potencial patogénico de las cepas de Aeromonas estudiadas, independientemente de su origen.
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Tian, Long. "Tackling the current limitations of bacterial taxonomy with genome-based classification and identification on a crowdsourcing Web service." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/103055.

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Bacterial taxonomy is the science of classifying, naming, and identifying bacteria. The scope and practice of taxonomy has evolved through history with our understanding of life and our growing and changing needs in research, medicine, and industry. As in animal and plant taxonomy, the species is the fundamental unit of taxonomy, but the genetic and phenotypic diversity that exists within a single bacterial species is substantially higher compared to animal or plant species. Therefore, the current "type"-centered classification scheme that describes a species based on a single type strain is not sufficient to classify bacterial diversity, in particular in regard to human, animal, and plant pathogens, for which it is necessary to trace disease outbreaks back to their source. Here we discuss the current needs and limitations of classic bacterial taxonomy and introduce LINbase, a Web service that not only implements current species-based bacterial taxonomy but complements its limitations by providing a new framework for genome sequence-based classification and identification independently of the type-centric species. LINbase uses a sequence similarity-based framework to cluster bacteria into hierarchical taxa, which we call LINgroups, at multiple levels of relatedness and crowdsources users' expertise by encouraging them to circumscribe these groups as taxa from the genus-level to the intraspecies-level. Circumscribing a group of bacteria as a LINgroup, adding a phenotypic description, and giving the LINgroup a name using the LINbase Web interface allows users to instantly share new taxa and complements the lengthy and laborious process of publishing a named species. Furthermore, unknown isolates can be identified immediately as members of a newly described LINgroup with fast and precise algorithms based on their genome sequences, allowing species- and intraspecies-level identification. The employed algorithms are based on a combination of the alignment-based algorithm BLASTN and the alignment-free method Sourmash, which is based on k-mers, and the MinHash algorithm. The potential of LINbase is shown by using examples of plant pathogenic bacteria.
Doctor of Philosophy
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Pradhanang, Prakash Man. "Bacterial wilt of potato caused by Ralstonia solanacearum biovar 2A : a study of the ecology and taxonomy of the pathogen in Nepal." Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.245336.

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Rouli, Laetitia. "Etude systématique des génomes bactériens." Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM5038.

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Débutée en 2005, l'ère du pangénome a connu un important essor ces dernières années, notamment grâce aux progrès des techniques de séquençage haut débit. Le pangénome, qui est divisé en deux grandes parties, le core génome et le génome accessoire, offre un grand éventail d'utilisation. Au cours de ces trois dernières années, nous avons étudié cette gamme de possibilités en nous basant sur des pathogènes humains tel que Coxiella burnetii, Kingella kingae et Bacillus anthracis. Ainsi, outre la découverte d'une nouvelle espèce de Kingella et l'étude de quelques génomes spécifiques, nous nous sommes attardés sur le lien entre pangénome et pathogénicité, sur l'importance des SNPs (Single Nucleotide Polymorphism), ainsi que sur la corrélation entre pangénome et taxonomie et donc, par extension, nous avons étudié la notion d'espèce bactérienne
The pangenome area began in 2005 and had known a huge increase thanks to the improvement of the Next Generation Sequencing methods. The pangenome, which is divided into two parts, the core and the accessory genome, offer a large panel of uses. During the last three years, we have studied all these possibilities. We based our work on human pathogens as Coxiella burnetii, Kingella kingae and Bacillus anthracis. Thus, in addition to the discovery of a new Kingella species and the study of some specific genomes, we studied in details the link between pangenome and pathogenicity, the importance of SNPs (Single Nucleotide Polymorphism) and the correlation between pangenome and taxonomy. Finally, we worked on the bacterial species definition
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Bautista, Guerrero Hector Hugo. "Phylogenomic study and specific diversity depiction of frankia genus : special focus on non-cultivable strains and ecological implications." Phd thesis, Université Claude Bernard - Lyon I, 2010. http://tel.archives-ouvertes.fr/tel-00838567.

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The depiction of the phylogenetic structure of the genus Frankia is still troublesome and the evolutionary forces guiding the speciation, dispersion and diversity are not well documented. The current phylogeny has been defined on the basis of the comparative analysis of the 16S rRNA gene sequence while de genomospecies definition is still subjected to DNA-DNA hybridization trials. Aiming to bring to light the genomic variability of the genus and its translation into the ecological and specific diversity, our studies consisted in, firstly, evaluating the specific diversity within the genus and the ability of the Amplified Fragment Length Polymorphism technique (AFLP) to describe Frankia genomospecies and their phylogenetic liaisons. Moreover this technique was also tested for the study of the non isolated Frankia directly in the actinorhizal nodules. Secondly, we defined a MLSA (Multilocus Sequence analysis) scheme which allowed us to establish a phylogeny of the genus by using a hundred of strains and for the first time to describe the phylogenetic divergence of a group of non culturable strains exhibiting the particular ability (phenotype) of sporulating in planta (Sp+). The Sp+ strains are distributed into two divergent clades whose structure is highly correlated to the host genotype. The importance of genetic markers having impact over ecology of the strains has been revised. In this regard we have studied the phylogenetic analysis and the occurrence of the genetic components for the siderophore production and of the sodF gene in Frankia.
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Souza, Danilo Tosta. "Exploração da diversidade bacteriana de esponjas marinhas por abordagens dependente e independente de cultivo." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/11/11138/tde-06012017-113512/.

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Este estudo descreve a diversidade e composição das comunidades bacterianas associadas a cinco esponjas marinhas, e o potencial destes microrganismos como produtores de substâncias bioativas com propriedades fungicidas. As esponjas vivem em simbiose com microrganismos que apresentam alto interesse ecológico, evolutivo e biotecnológico. Contudo, este sistema microbiano permanece pobremente entendido. Para totalmente compreender a biologia desses animais é necessário descrever os fatores ecológicos e evolutivos influenciando a estrutura e dinâmica de sua microbiota. Nesta tese é defendida a hipótese de que a composição taxonômica e estrutura das comunidades bacterianas se correlaciona com o parentesco filogenético de seus hospedeiros. Neste trabalho, as comunidades bacterianas associadas às esponjas Aplysina fulva, Aiolochroia crassa, Chondrosia collectrix, Didiscus oxeata e Scopalina ruetzleri foram examinadas usando a plataforma Ion torrent para sequenciamento parcial do gene 16S rRNA. A água do mar circundante aos espécimes foram coletadas para comparações com a microbiota de esponjas. As análises detectaram um complexo e específico sistema microbiano vivendo em esponjas, com as unidades taxonômicas operacionais dominantes classificadas nos filos: Acidobacteria, Actinobacteria, Chloroflexi, Proteobacteria e Gemmatimonadetes. Apesar da ocorrência simpátrica dos espécimes, as comunidades bacterianas diferiram significativamente entre as espécies de esponjas e a água do mar. Contudo, foi observado que as comunidades bacterianas habitando esponjas filogeneticamente mais próximas (A. fulva e A. crassa) são mais similares uma para com a outra, do que quando comparado com as comunidades em um táxon mais distante filogenitacamente (C. collectrix). O isolamento de bactérias foi realizado nas esponjas D. oxeata e S. ruetzleri. Cinquenta e seis linhagens foram isoladas e classificadas em três filos: Actinobacteria, Proteobacteria e Firmicutes. As análises filogenéticas indicaram cinco possíveis novas espécies bacterianas. Com base na taxonomia polifásica, um dos isolados, denominado ASPSP 40, foi caracterizado como pertencente a uma nova espécie do gênero Saccharopolyspora, para qual o nome Saccharopolyspora spongiae sp. nov. foi proposto. Dois isolados bacterianos demonstraram forte atividade antagônica contra as seguintes espécies de Pythium: P. aphanidermatum, P. graminicola e P. ultimum. Os metabólitos secundários desses isolados, assim identificados como pertencentes aos gêneros Terrabacter sp. ASPSP 140 e Bacillus sp. ASPSP 434, foram identificados por LC-MS/MS como sendo uma mistura de dipepitídeos cíclicos pertencentes à classe das dicetopiperazinas (DKP). Este é o primeiro relato da atividade fungicida e, consequentemente, a detecção de DKP a partir do gênero Terrabacter.
This study describes the diversity of associated bacterial communities to five marine sponges, and the potential of these microorganisms as producers of bioactive substances with fungicidal properties. Sponges live in symbiosis with microorganisms that have a high ecological interest, evolutionary and biotechnological. However, this microbial system remains poorly understood. To fully understand sponge biology, it is necessary to describe the ecological and evolutionary factors that influence the structure and dynamics of their microbial communities. In this work, it is supported the hypothesis that the taxonomic composition and structure of bacterial communities correlate with phylogenetic relatedness of their corresponding hosts. Bacterial communities associated with the sponges Aplysina fulva, Aiolochroia crassa, Chondrosia collectrix, Didiscus oxeata and Scopalina ruetzleri were examined using the Ion Torrent platform for partial sequencing of the 16S rRNA gene. Seawater surrounding specimens were collected for comparisons. The analysis detected a complex and specific microbial system living in sponges, with the operational taxonomic units dominant classified in the phyla: Acidobacteria, Actinobacteria, Chloroflexi, Proteobacteria and Gemmatimonadetes. Despite sympatric occurrence of the specimens, the studied sponges presented different bacterial compositions that differed from those observed in seawater. However, lower dissimilarities in bacterial communities were clearly observed within sponges from the same phylogenetic group (A. fulva and A. crassa). Isolation of bacteria was done from the sponges D. oxeata and S. ruetzleri. Fifty-six strains were isolated and classified into three phyla: Actinobacteria, Proteobacteria and Firmicutes. Phylogenetic analysis indicated five possible novel bacterial species. Based in a polyphasic taxonomy approach, one of the isolates denominated ASPSP 40 was identified as belonging to a novel species of the genus Saccharopolyspora for which the name, Saccharopolyspora spongiae sp. nov. has been proposed. All bacterial isolates were evaluated by their antagonisms against Pythium species. Two of them, Terrabacter sp. ASPSP 140 and Bacillus sp. ASPSP 434 demonstrated strong potential in inhibiting the following species P. aphanidermatum, P. ultimum and P. graminicola. The bioactive secondary metabolites of both, characterized by LC-MS/MS, were identified as a mixture of cyclic dipepitides belonging to the class of diketopiperazine (DKP). This is the first report of fungicidal activity, and thus the detection of DKP of the genus Terrabacter.
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Diop, Awa. "Analyse des séquences des génomes bactériens en tant que source d'information taxonomique." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0276/document.

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L’Identification rapide et la classification microbienne précise sont cruciales en microbiologie médicale pour la surveillance de la santé humaine et animale, établir un diagnostic clinique approprié et choisir des mesures thérapeutiques et de contrôle optimales. Cependant, les seuils universels utilisés pour la définition des espèces ne sont pas applicables à de nombreux genres bactériens. C'est notamment le cas des espèces du genre Rickettsia, qui expriment peu de caractéristiques phénotypiques distinctives. Compte tenu de la disponibilité des séquences de près de 100 génomes de Rickettsia, nous avons voulu évaluer une gamme de paramètres taxonomiques basés sur l’analyse des séquences génomiques afin de mettre au point des recommandations pour la classification des isolats au niveau de l’espèce et du genre. En comparant le degré de similarité des séquences de 78 génomes de Rickettsia et 61 génomes de 3 genres étroitement apparentés en utilisant 4 paramètres génomiques, nous avons montré que les outils taxonomiques basés sur les séquences génomiques sont simples à utiliser et rapides, et permettent une classification taxonomique fiable et reproductible des isolats de rickettsies avec des seuils spécifiques. Les résultats obtenus nous ont permis d'élaborer des recommandations pour la classification des isolats de rickettsies au niveau du genre et de l'espèce. À l'aide de la taxono-génomique, nous avons également pu décrire 17 nouvelles espèces bactériennes associées à l'homme. L'utilisation des outils génomiques est donc parfaitement adaptée à la classification taxonomique et peut changer radicalement notre vision de la taxonomie et de l'évolution bactérienne à l'avenir
Rapid identification and precise microbial classification are crucial in medical microbiology for human and animal health monitoring, appropriate clinical diagnosis and selection of optimal therapeutic and control measures. Indeed, the universal used for the definition of species are not applicable to many bacterial genera. This is particularly true of species of the genus Rickettsia which are strictly intracellular alpha-proteobacteria that express few phenotypic characteristics. Given the availability of genomic sequences of nearly 100 rickettsial genomes, we wanted to evaluate a range of taxonomic parameters based on genomic sequence analysis, to develop guidelines for the classification of Rickettsia isolates at the genus and species levels. By comparing the degree of similarity of the sequences of 78 genomes from Rickettsia species and 61 genomes from 3 closely related genera using several genomic parameters, we have shown that genome-based taxonomic tools are simple to use and fast, and allow for a reliable and reproducible taxonomic classification of isolates within species of the genus Rickettsia, with specific thresholds. The obtained results enabled us to develop guidelines for classifying rickettsial isolates at the genus and species levels. Using taxono-genomics, we have also been able to describe 17 new human-associated bacterial species on the basis of a combination of genomic analysis and phenotypic properties. The use of genomic tools is therefore perfectly adapted to taxonomic classification and can dramatically change our vision of taxonomy and bacterial evolution in the future
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Books on the topic "Bacterial taxonomy"

1

Brian, Austin. Modern bacterial taxonomy. Wokingham: Van Nostrand Reinhold, 1986.

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1951-, Austin B., ed. Modern bacterial taxonomy. 2nd ed. London: Chapman & Hall, 1993.

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G, Priest F., ed. Modern bacterial taxonomy. Wokingham, Berkshire, England: Van Nostrand Reinhold (UK), 1986.

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Bauman, Robert W. Microbiology: With diseases by taxonomy. 3rd ed. San Francisco: Benjamin Cummings, 2011.

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Bauman, Robert W. Microbiology: With diseases by taxonomy. 2nd ed. San Francisco, Calif: Pearson Education, 2007.

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Elizabeth, Machunis-Masuoka, ed. Microbiology: With diseases by taxonomy. 3rd ed. San Francisco: Benjamin Cummings, 2011.

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Austin, B., and Kazuo Tsubota. Modern Bacterial Taxonomy. Springer, 1993.

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Bauman, Robert. Microbiology with Diseases by Taxonomy. Pearson Education, Limited, 2006.

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contributor, Machunis-Masuoka Elizabeth, ed. Microbiology: With diseases by taxonomy. Pearson, 2014.

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M, Goodfellow, Jones D, Priest F. G, and Society for General Microbiology, eds. Computer-assisted bacterial systematics. London: Published for the Society for General Microbiology by Academic Press, 1985.

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Book chapters on the topic "Bacterial taxonomy"

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Schleifer, Karl-Heinz, and Wolfgang Ludwig. "Molecular Taxonomy: Classification and Identification." In Bacterial Diversity and Systematics, 1–15. Boston, MA: Springer US, 1994. http://dx.doi.org/10.1007/978-1-4615-1869-3_1.

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Rai, Anusha, Indu, N. Smita, G. Deepshikha, K. Gaurav, K. Dhanesh, G. Suresh, Ch Sasikala, and Ch V. Ramana. "Emerging Concepts in Bacterial Taxonomy." In Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications, 3–22. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-8315-1_1.

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Cohan, Frederick M. "Genomes reveal the cohesiveness of bacterial species taxa and provide a path towards describing all of bacterial diversity." In Trends in the systematics of bacteria and fungi, 282–300. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0282.

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Abstract This book chapter argues that bacterial systematists of the mid-20th century fortuitously created a species-level systematics that actually fits an important universal theory of speciation by discussing taxonomy would allow us to infer the important characteristics of any unknown organism once we classify it to species. It turns out, unexpectedly, that bacterial species taxa share a species-like property with the species taxa of zoology and botany. While recombination within species taxa of all these groups fails to prevent diversification within species, recombination nevertheless appears to act universally as a force of cohesion within species taxa. That is, recurrent recombination within species limits neutral sequence divergence within species taxa of plants, animals, and bacteria; recombination also allows a sharing of generally adaptive genes across a species range. The 95% ANI criterion that demarcates the traditionally defined species taxa of bacteria fortuitously also yields groups of bacteria that are subject to the species-like property of cohesion, where recombination prevents neutral sequence divergence among ecotypes within a species. Use of the ANI criterion, then, not only provides an easily used algorithm for demarcating bacterial species; it also places bacterial demarcation on the same theory-based foundation as the species taxonomy of animals and plants.
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Ventosa, Antonio. "Taxonomy and Phylogeny of Moderately Halophilic Bacteria." In Bacterial Diversity and Systematics, 231–42. Boston, MA: Springer US, 1994. http://dx.doi.org/10.1007/978-1-4615-1869-3_13.

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Kale, Varsha, Lorna Richardson, and Robert D. Finn. "Navigating bacterial taxonomy in a world of unchartered microbial organisms." In Trends in the systematics of bacteria and fungi, 179–97. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0179.

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Abstract This book chapter focuses on state-of-the-art informatics techniques that perform bacterial taxonomic assertions on metabarcoding data sets and MAGs, as well as highlighting some of the advantages and disadvantages of the respective approaches and finishes by exploring why they are yet to be perfectly complementary. Currently, the results of these two approaches can be difficult to compare for the various reasons we highlight, and they are compounded by the fact that the data sets typically have different purposes. Despite the current difficulties, the field is heading in a direction that attempts to harmonize bacterial taxonomy generated by both approaches, ultimately making these comparisons less problematic in the future.
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Göker, Markus. "What can genome analysis offer for bacteria?" In Trends in the systematics of bacteria and fungi, 255–81. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0255.

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Abstract This book chapter is organized as follows: (i) the main approaches to the philosophy of taxonomic classification are recapitulated; (ii) the paradigm of polyphasic taxonomy is discussed in this context; (iii) the causes of conflict between previous classifications and genome-scale analyses are investigated, using examples from recent phylum-wide studies, with a discussion of how markers used in polyphasic taxonomy can be replaced by genome-derived ones; and (iv) the challenges in assigning taxonomic ranks using genome-scale or other data are revisited. The conclusion assesses the chances, or lack thereof, of reconciling taxonomic classifications. Phenetic and phylogenetic thinking still compete with each other on the classification of bacteria, with potentially conflicting and confusing results. Some causes of problematic taxonomic classifications are independent of the type and number of characters that can be used and can only be mitigated if, for example, taxon sampling and branch support are more appropriately taken into account. It may be possible to devise objective criteria for separating bacterial species, but the currently dominating approaches for microbial species delineation may be inadequate. It is even harder to delineate higher taxa; in contrast to claims in the literature, it may prove to be impossible to objectively assign taxonomic ranks above species level.
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Rosselló-Móra, Ramon, and Erko Stackebrandt. "Bridging 200 years of bacterial classification." In Trends in the systematics of bacteria and fungi, 1–20. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0001.

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Abstract This book chapter briefly takes a historical view of the major steps in bacterial systematics leading to the first reconciliation workshop in 1987 and a re-evaluation of the species concept in 2002. New challenges and concepts developed since then will be outlined. Never before has the future of the prokaryotic taxonomy been at such a critical point. The uncertain future, and whether Plan A or Plan B will prevail, depends totally on the wisdom of the ICSP. Perhaps by the time this book is published the situation will have been clarified, but the current situation is as full of uncertainty as of excitement, and none of the scenarios can be predicted. In April 2020, a majority of the ICSP members decided to reject the proposals to use DNA as type material. Therefore, this rejection leaves the only path for microbial ecologists to go through Plan B. Only time will reveal whether this was the best decision for the future of the taxonomy for prokaryotes.
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Tindall, B. J. "Chemical Analysis of Archaea and Bacteria: A Critical Evaluation of its Use in Taxonomy and Identification." In Bacterial Diversity and Systematics, 243–58. Boston, MA: Springer US, 1994. http://dx.doi.org/10.1007/978-1-4615-1869-3_14.

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Solorio-Fernández, Saúl, J. A. Carrasco-Ochoa, and José Fco Martínez-Trinidad. "Unsupervised Feature Selection Methodology for Analysis of Bacterial Taxonomy Profiles." In Lecture Notes in Computer Science, 47–56. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-77004-4_5.

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Meyer, Jean-Marie, and Valérie A. Geoffroy. "Environmental Fluorescent Pseudomonas and Pyoverdine Diversity: How Siderophores Could Help Microbiologists in Bacterial Identification and Taxonomy." In Iron Transport in Bacteria, 451–68. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555816544.ch29.

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Conference papers on the topic "Bacterial taxonomy"

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Ibragimova, S. A., and K. A. Malafeeva. "Symbiosis of soil and rhizosphere bacteria." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.105.

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The presence of symbiosis between different taxonomic groups of soil and rhizosphere bacteria is shown. In the mixed population, a high titer of active cells and the preservation of antagonistic activity against the phytopathogen were noted.
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Vasileva, E. N., A. M. Afonin, G. A. Akhtemova, V. A. Zhukov, and I. A. Tikhonovich. "Endophytic bacteria isolated from garden pea (Pisum sativum L.)." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.265.

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Endophytic bacteria were isolated from surface-sterilized aerial parts of pea. Taxonomic status of isolated strains was determined by sequencing of 16S rRNA gene. Moreover, genomes of growth-promoting endophytes were sequenced.
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Moiseeva, E. V., L. P. Bobrikova, E. V. Karaseva, A. A. Khudokormov, A. A. Samkov, and N. N. Volchenko. "Taxonomic diversity of lipolytic bacteria isolated at oil refineries in Krasnodar that is promising for bio-preparation." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.173.

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From the lipid-containing wastes, 20 strains of bacteria were isolated. According to MALDI, their taxonomic identity is established, the 13 most active lipolytic strains are classified as 8 genera, the dominant is the genus Pseudomonas.
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Kameneva, I., T. Melnichuk, S. Abdurashitov, E. Andronov, A. Yakubovskaya, M. Gritchin, and A. Prikhodko. "The taxonomic composition of the microbial community of the southern chernozem when introducing plant substrates and their destructors." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.109.

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The influence of green manure (phacelia), wheat straw, and cellulolytic association on the taxonomic structure of chernozems southern in the steppe zone of the Crimea was studied. Changes in the proportion among representatives of 11 phila, 14 bacteria, and 2 archaea were established.
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Zulaika, Enny, Andry Prio Utomo, Adisya Prima, Nur Hidayatul Alami, Nengah Dwianita Kuswytasari, Maya Shovitri, and Langkah Sembiring. "Diversity of heavy metal resistant bacteria from Kalimas Surabaya: A phylogenetic taxonomy approach." In PROCEEDING OF INTERNATIONAL BIOLOGY CONFERENCE 2016: Biodiversity and Biotechnology for Human Welfare. Author(s), 2017. http://dx.doi.org/10.1063/1.4985433.

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Lyakhovchenko, N. S., V. Yu Senchenkov, D. A. Myagkov, D. A. Pribylov, A. A. Chepurina, I. A. Nikishin, A. A. Avakova, et al. "Determination of the taxonomic affiliation of the native isolate of the pigment-forming bacterium, separated from the Vezelka river of the city of Belgorod." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.157.

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The paper presents the results of a study of an aboriginal isolate of a pigment-forming bacterium isolated from the Vezelka River in the city of Belgorod, which makes it possible to determine its taxonomic affiliation.
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Melnichuk, T., A. Egovtseva, S. Abdurashitov, E. Andronov, E. Abdurashitova, A. Radchenko, T. Ganotskaya, and L. Radchenko. "Changes in the taxonomic structure of the microbiome of chernozem southern of the rhizosphere Triticum aestivum L. under the influence of associative bacteria strains." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.167.

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The influence of strains associated with Triticum aestivum L. has been established on the taxonomic structure of the rhizosphere of the southern сhernozem of Crimean Steppe. Seventeen dominant families and 126 families with a minor share are defined in the prokaryotic biome.
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