Relevant bibliographies by topics / Bacterial taxonomy / Journal articles
To see the other types of publications on this topic, follow the link: Bacterial taxonomy.

Journal articles on the topic 'Bacterial taxonomy'

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

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 50 journal articles for your research on the topic 'Bacterial taxonomy.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

1

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.

Full text
Abstract:
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.
APA, Harvard, Vancouver, ISO, and other styles
2

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.

Full text
Abstract:
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.
APA, Harvard, Vancouver, ISO, and other styles
3

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.

Full text
Abstract:
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.
APA, Harvard, Vancouver, ISO, and other styles
4

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

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.

Full text
Abstract:
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.
APA, Harvard, Vancouver, ISO, and other styles
6

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.

Full text
Abstract:
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.
APA, Harvard, Vancouver, ISO, and other styles
7

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.

Full text
Abstract:
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.
APA, Harvard, Vancouver, ISO, and other styles
8

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

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.

Full text
APA, Harvard, Vancouver, ISO, and other styles
11

Gyllenberg, M., and T. Koski. "Probabilistic Models for Bacterial Taxonomy." International Statistical Review 69, no. 2 (August 2001): 249–76. http://dx.doi.org/10.1111/j.1751-5823.2001.tb00458.x.

Full text
APA, Harvard, Vancouver, ISO, and other styles
12

Brenner, D. J. "Future trends in bacterial taxonomy." World Journal of Microbiology & Biotechnology 8, S1 (December 1992): 16–17. http://dx.doi.org/10.1007/bf02421479.

Full text
APA, Harvard, Vancouver, ISO, and other styles
13

Austin, Brian. "Taxonomy of bacterial fish pathogens." Veterinary Research 42, no. 1 (2011): 20. http://dx.doi.org/10.1186/1297-9716-42-20.

Full text
APA, Harvard, Vancouver, ISO, and other styles
14

Zheng, Xiang, Qidi Zhu, Zhijun Zhou, Fangtong Wu, Lixuan Chen, Qianrong Cao, and Fuming Shi. "Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits." PLOS ONE 16, no. 4 (April 26, 2021): e0250675. http://dx.doi.org/10.1371/journal.pone.0250675.

Full text
Abstract:
Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.
APA, Harvard, Vancouver, ISO, and other styles
15

Gladka, G. V., N. V. Borzova, O. V. Gudzenko, V. M. Hovorukha, О. А. Havryliuk, and О. B. Tashyrev. "Polyphase Taxonomy of Antarctic Bacteria." Mikrobiolohichnyi Zhurnal 83, no. 3 (June 17, 2021): 3–13. http://dx.doi.org/10.15407/microbiolj83.03.003.

Full text
Abstract:
The phylogenetic structure of bacteria is not always consistent with the traditional classification scheme based on the phenotypic properties of bacteria. That is one of the problems of modern bacterial taxonomy. In addition, traditional methods to identify bacteria using phenotypic properties have a number of disadvantages. In recent decades, significant progress was achieved in the investigation of microbial world using molecular methods for fast identification. The aim of the study was to clarify the species status of four strains of bacteria isolated from black lichens of the cliffs of Galindez Island in the Antarctic on the basis of phenotypic and genetic analysis. Methods. Morphological and cultural properties of bacteria were studied according to generally accepted microbiological methods. Physiological and biochemical ones were investigated using test systems API Coryne and API 20E (bioMerieux SA, France), according to the manufacturer’s instructions. Phylogenetic analysis was performed based on the nucleotide sequences of the 16S rRNA gene. To identify closely related species, a comparative analysis of the nucleotide sequences of 16S rRNA genes was performed using the BLAST software package. The phylogenetic position was determined by constructing trees (dendrograms) to show the position of the studied strains among closely related and typical species (programs ClustalX 2.1, Mega 6.06). The tree was constructed applying ClustalX 2.1 by comparing the nearest neighbors with bootstrap analysis (bootstrap NJ tree) using 1000 bootstrap tests (1000 alternative trees). Then the phylogenetic tree was edited by the program Mega v. 6.00. Results. Based on the results of comparative, phylogenetic and phenotypic analysis, the studied Antarctic strains 180n1, 181n2, 188n2, 190n2 were identified as Pseudomonas fluorescens, Microbacterium foliorum, Sporosarcina aquimarina and Rothia sp., respectively. The coefficient of similarity of 16S rRNA genes of strain 180n1 with such a closely related species from the database P. fluorescens NBRC 14160 was 99.5%; 181n2 with M. foliorum P 333/02 – 99.4%; 188n2 with S. aquimarina SW28 – 99.7%. These strains form common clusters with closely related species on phylogenetic dendrograms. The strain 190n2 can be considered as Rothia sp., since has the remote position from closely related strains in the cluster Rothia and a low percentage of similarity (97.3%) with the species Rothia endophytica YIM 67072. These strains belong to the phyla: Firmicutes, Actinobacteria, Proteobacteria. Conclusions. Phylogenetic and phenotypic analyzes allowed determining the taxonomic position of isolated aerobic chemoorganotrophic microbial strains of the Antarctic. Nucleotide sequences of 16S rRNA genes are deposited in the International GenBank database under numbers HG518622, HG518623, HG518625, HG518626.
APA, Harvard, Vancouver, ISO, and other styles
16

Ackermann, Hans W. "Bacteriophage taxonomy." Microbiology Australia 32, no. 2 (2011): 90. http://dx.doi.org/10.1071/ma11090.

Full text
Abstract:
Bacteriophages or ?phages? are viruses of prokaryotes. At least 5,360 tailed and 179 cubic, filamentous, and pleomorphic bacterial viruses have been examined in the electron microscope since the introduction of negative staining in 1959. Since at least 100 novel bacterial viruses are described every year1, the approximate number of viruses under consideration is over 6,000. Numerically, this makes bacteriophages the largest virus group known. Phages are presently classified in a hierarchical and holistic system with one order and 10 families. Over 96% of phages are tailed and contain dsDNA. The seven families of cubic, filamentous and pleomorphic phages are small and well defined. They contain ds or ss DNA or RNA. The most important developments are reclassifications of the Podoviridae and Myoviridae families of tailed phages.
APA, Harvard, Vancouver, ISO, and other styles
17

Vinatzer, Boris A., Alexandra J. Weisberg, Caroline L. Monteil, Haitham A. Elmarakeby, Samuel K. Sheppard, and Lenwood S. Heath. "A Proposal for a Genome Similarity-Based Taxonomy for Plant-Pathogenic Bacteria that Is Sufficiently Precise to Reflect Phylogeny, Host Range, and Outbreak Affiliation Applied to Pseudomonas syringae sensu lato as a Proof of Concept." Phytopathology® 107, no. 1 (January 2017): 18–28. http://dx.doi.org/10.1094/phyto-07-16-0252-r.

Full text
Abstract:
Taxonomy of plant pathogenic bacteria is challenging because pathogens of different crops often belong to the same named species but current taxonomy does not provide names for bacteria below the subspecies level. The introduction of the host range-based pathovar system in the 1980s provided a temporary solution to this problem but has many limitations. The affordability of genome sequencing now provides the opportunity for developing a new genome-based taxonomic framework. We already proposed to name individual bacterial isolates based on pairwise genome similarity. Here, we expand on this idea and propose to use genome similarity-based codes, which we now call life identification numbers (LINs), to describe and name bacterial taxa. Using 93 genomes of Pseudomonas syringae sensu lato, LINs were compared with a P. syringae genome tree whereby the assigned LINs were found to be informative of a majority of phylogenetic relationships. LINs also reflected host range and outbreak association for strains of P. syringae pathovar actinidiae, a pathovar for which many genome sequences are available. We conclude that LINs could provide the basis for a new taxonomic framework to address the shortcomings of the current pathovar system and to complement the current taxonomic system of bacteria in general.
APA, Harvard, Vancouver, ISO, and other styles
18

HÖFLING, José F., Edvaldo A. R. ROSA, Mirian J. BAPTISTA, and Denise M. P. SPOLIDÓRIO. "New Strategies on Molecular Biology Applied to Microbial Systematics." Revista do Instituto de Medicina Tropical de São Paulo 39, no. 6 (November 1997): 345–52. http://dx.doi.org/10.1590/s0036-46651997000600007.

Full text
Abstract:
Systematics is the study of diversity of the organisms and their relationships comprising classification, nomenclature and identification. The term classification or taxonomy means the arrangement of the organisms in groups (rate) and the nomenclature is the attribution of correct international scientific names to organisms and identification is the inclusion of unknown strains in groups derived from classification. Therefore, classification for a stable nomenclature and a perfect identification are required previously. The beginning of the new bacterial systematics era can be remembered by the introduction and application of new taxonomic concepts and techniques, from the 50’s and 60’s. Important progress were achieved using numerical taxonomy and molecular taxonomy. Molecular taxonomy, brought into effect after the emergence of the Molecular Biology resources, provided knowledge that comprises systematics of bacteria, in which occurs great evolutionary interest, or where is observed the necessity of eliminating any environmental interference. When you study the composition and disposition of nucleotides in certain portions of the genetic material, you study searching their genome, much less susceptible to environmental alterations than proteins, codified based on it. In the molecular taxonomy, you can research both DNA and RNA, and the main techniques that have been used in the systematics comprise the build of restriction maps, DNA-DNA hybridization, DNA-RNA hybridization, sequencing of DNA sequencing of sub-units 16S and 23S of rRNA, RAPD, RFLP, PFGE etc. Techniques such as base sequencing, though they are extremely sensible and greatly precise, are relatively onerous and impracticable to the great majority of the bacterial taxonomy laboratories. Several specialized techniques have been applied to taxonomic studies of microorganisms. In the last years, these have included preliminary electrophoretic analysis of soluble proteins and isoenzymes, and subsequently determination of deoxyribonucleic acid base composition and assessment of base sequence homology by means of DNA-RNA hybrid experiments beside others. These various techniques, as expected, have generally indicated a lack of taxonomic information in microbial systematics. There are numberless techniques and methodologies that make bacteria identification and classification study possible, part of them described here, allowing establish different degrees of subspecific and interspecific similarity through phenetic-genetic polymorphism analysis. However, was pointed out the necessity of using more than one technique for better establish similarity degrees within microorganisms. Obtaining data resulting from application of a sole technique isolatedly may not provide significant information from Bacterial Systematics viewpoint
APA, Harvard, Vancouver, ISO, and other styles
19

Barka, Essaid Ait, Parul Vatsa, Lisa Sanchez, Nathalie Gaveau-Vaillant, Cedric Jacquard, Hans-Peter Klenk, Christophe Clément, Yder Ouhdouch, and Gilles P. van Wezel. "Taxonomy, Physiology, and Natural Products of Actinobacteria." Microbiology and Molecular Biology Reviews 80, no. 1 (November 25, 2015): 1–43. http://dx.doi.org/10.1128/mmbr.00019-15.

Full text
Abstract:
SUMMARYActinobacteriaare Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. ManyActinobacteriahave a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture.Actinobacteriaplay diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species ofCorynebacterium,Mycobacterium,Nocardia,Propionibacterium, andTropheryma), soil inhabitants (e.g.,MicromonosporaandStreptomycesspecies), plant commensals (e.g.,Frankiaspp.), and gastrointestinal commensals (Bifidobacteriumspp.).Actinobacteriaalso play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.
APA, Harvard, Vancouver, ISO, and other styles
20

Lalucat, Jorge, Magdalena Mulet, Margarita Gomila, and Elena García-Valdés. "Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas." Genes 11, no. 2 (January 29, 2020): 139. http://dx.doi.org/10.3390/genes11020139.

Full text
Abstract:
The introduction of genomics is profoundly changing current bacterial taxonomy. Phylogenomics provides accurate methods for delineating species and allows us to infer the phylogeny of higher taxonomic ranks as well as those at the subspecies level. We present as a model the currently accepted taxonomy of the genus Pseudomonas and how it can be modified when new taxonomic methodologies are applied. A phylogeny of the species in the genus deduced from analyses of gene sequences or by whole genome comparison with different algorithms allows three main conclusions: (i) several named species are synonymous and have to be reorganized in a single genomic species; (ii) many strains assigned to known species have to be proposed as new genomic species within the genus; and (iii) the main phylogenetic groups defined by 4-, 100- and 120-gene multilocus sequence analyses are concordant with the groupings in the whole genome analyses. Moreover, the boundaries of the genus Pseudomonas are also discussed based on phylogenomic analyses in relation to other genera in the family Pseudomonadaceae. The new technologies will result in a substantial increase in the number of species and probably split the current genus into several genera or subgenera, although these classifications have to be supported by a polyphasic taxonomic approach.
APA, Harvard, Vancouver, ISO, and other styles
21

van Berkum, Peter, Zewdu Terefework, Lars Paulin, Sini Suomalainen, Kristina Lindström, and Bertrand D. Eardly. "Discordant Phylogenies within the rrn Loci of Rhizobia." Journal of Bacteriology 185, no. 10 (May 15, 2003): 2988–98. http://dx.doi.org/10.1128/jb.185.10.2988-2998.2003.

Full text
Abstract:
ABSTRACT It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of α-Proteobacteria by sequencing analysis of three loci within their rrn operons. Tree topologies generated with 16S rRNA gene sequences were significantly different from corresponding trees assembled with 23S rRNA gene and internally transcribed space region sequences. Besides the incongruence in tree topologies, evidence that distinct segments along the 16S rRNA gene sequences of bacteria currently classified within the genera Bradyrhizobium, Mesorhizobium and Sinorhizobium have a reticulate evolutionary history was also obtained. Our data have important implications for bacterial taxonomy, because currently most taxonomic decisions are based on comparative 16S rRNA gene sequence analysis. Since phylogenetic placement based on 16S rRNA gene sequence divergence perhaps is questionable, we suggest that the proposals of bacterial nomenclature or changes in their taxonomy that have been made may not necessarily be warranted. Accordingly, a more conservative approach should be taken in the future, in which taxonomic decisions are based on the analysis of a wider variety of loci and comparative analytical methods are used to estimate phylogenetic relationships among the genomes under consideration.
APA, Harvard, Vancouver, ISO, and other styles
22

Lay, J. O. "MALDI-TOF mass spectrometry and bacterial taxonomy." TrAC Trends in Analytical Chemistry 19, no. 8 (August 2000): 507–16. http://dx.doi.org/10.1016/s0165-9936(00)00027-3.

Full text
APA, Harvard, Vancouver, ISO, and other styles
23

SOHIER, D., F. BERTHIER, and J. REITZ. "Safety assessment of dairy microorganisms: Bacterial taxonomy☆." International Journal of Food Microbiology 126, no. 3 (September 1, 2008): 267–70. http://dx.doi.org/10.1016/j.ijfoodmicro.2007.08.026.

Full text
APA, Harvard, Vancouver, ISO, and other styles
24

Nadkarni, Mangala, Roy Byun, and Kim-Ly Chhour. "Molecular taxonomy of polymicrobial diseases ? finding novel bacteria not previously considered to be associated with oral diseases." Microbiology Australia 26, no. 3 (2005): 117. http://dx.doi.org/10.1071/ma05117.

Full text
Abstract:
Recombinant DNA technology and molecular biology have brought a revolution to the limitations imposed by traditional taxonomic methods of bacterial identification based solely on cultivation. Following on from the novel research of Carl Woese, molecular taxonomy is generally based on variations in the sequence of the 16S rRNA gene and has brought a new perspective to our understanding of the diversity of uncultured bacteria in a multitude of microbial habitats. Analysis of the polymicrobial oral diseases is no exception.
APA, Harvard, Vancouver, ISO, and other styles
25

Sant’Anna, Fernando Hayashi, Keli Cristine Reiter, Patrícia de Fátima Almeida, and Luciane Maria Pereira Passaglia. "Systematic review of descriptions of novel bacterial species: evaluation of the twenty-first century taxonomy through text mining." International Journal of Systematic and Evolutionary Microbiology 70, no. 4 (April 1, 2020): 2925–36. http://dx.doi.org/10.1099/ijsem.0.004070.

Full text
Abstract:
Although described bacterial species increased in the twenty-first century, they correspond to a tiny fraction of the actual number of species living on our planet. The volume of textual data of these descriptions constitutes valuable information for revealing trends that in turn could support strategies for improvement of bacterial taxonomy. In this study, a text mining approach was used to generate bibliometric data to verify the state-of-art of bacterial taxonomy. Around 9700 abstracts of bacterial classification containing the expression ‘sp. nov.’ and published between 2001 and 2018 were downloaded from PubMed and analysed. Most articles were from PR China and the Republic of Korea, and published in the International Journal of Systematic and Evolutionary Microbiology. From about 10 800 species names detected, 93.33 % were considered valid according to the rules of the Bacterial Code, and they corresponded to 82.98 % of the total number of species validated between 2001 and 2018. Streptomyces , Bacillus and Paenibacillus each had more than 200 species described in the period. However, almost 40 % of all species were from the phylum Proteobacteria . Most bacteria were Gram-stain-negative, bacilli and isolated from soil. Thirteen species and one genus homonyms were found. With respect to methodologies of bacterial characterization, the use of terms related to 16S rRNA and polar lipids increased along these years, and terms related to genome metrics only began to appear from 2009 onward, although at a relatively lower frequency. Bacterial taxonomy is known as a conservative discipline, but it gradually changed in terms of players and practices. With the advent of the mandatory use of genomic analyses for species description, we are probably witnessing a turning point in the evolution of bacterial taxonomy.
APA, Harvard, Vancouver, ISO, and other styles
26

Waymouth, Vicky, Rebecca E. Miller, Sabine Kasel, Fiona Ede, Andrew Bissett, and Cristina Aponte. "Soil Bacterial Community Responds to Land-Use Change in Riparian Ecosystems." Forests 12, no. 2 (January 28, 2021): 157. http://dx.doi.org/10.3390/f12020157.

Full text
Abstract:
Riparian forests were frequently cleared and converted to agricultural pastures, but in recent times these pastures are often revegetated in an effort to return riparian forest structure and function. We tested if there is a change in the soil bacterial taxonomy and function in areas of riparian forest cleared for agricultural pasture then revegetated, and if soil bacterial taxonomy and function is related to vegetation and soil physicochemical properties. The study was conducted in six riparian areas in south-eastern Australia, each comprising of three land-use types: remnant riparian forest, cleared forest converted to pasture, and revegetated pastures. We surveyed three strata of vegetation and sampled surface soil and subsoil to characterize physicochemical properties. Taxonomic and functional composition of soil bacterial communities were assessed using 16S rRNA gene sequences and community level physiological profiles, respectively. Few soil physiochemical properties differed with land use despite distinct vegetation in pasture relative to remnant and revegetated areas. Overall bacterial taxonomic and functional composition of remnant forest and revegetated soils were distinct from pasture soil. Land-use differences were not consistent for all bacterial phyla, as Acidobacteria were more abundant in remnant soils; conversely, Actinobacteria were more abundant in pasture soils. Overall, bacterial metabolic activity and soil carbon and nitrogen content decreased with soil depth, while bacterial metabolic diversity and evenness increased with soil depth. Soil bacterial taxonomic composition was related to soil texture and soil fertility, but functional composition was only related to soil texture. Our results suggest that the conversion of riparian forests to pasture is associated with significant changes in the soil bacterial community, and that revegetation contributes to reversing such changes. Nevertheless, the observed changes in bacterial community composition (taxonomic and functional) were not directly related to changes in vegetation but were more closely related to soil attributes.
APA, Harvard, Vancouver, ISO, and other styles
27

Bell, Terrence H., Franck O. P. Stefani, Katrina Abram, Julie Champagne, Etienne Yergeau, Mohamed Hijri, and Marc St-Arnaud. "A Diverse Soil Microbiome Degrades More Crude Oil than Specialized Bacterial Assemblages Obtained in Culture." Applied and Environmental Microbiology 82, no. 18 (July 1, 2016): 5530–41. http://dx.doi.org/10.1128/aem.01327-16.

Full text
Abstract:
ABSTRACTSoil microbiome modification may alter system function, which may enhance processes like bioremediation. In this study, we filled microcosms with gamma-irradiated soil that was reinoculated with the initial soil or cultivated bacterial subsets obtained on regular media (REG-M) or media containing crude oil (CO-M). We allowed 8 weeks for microbiome stabilization, added crude oil and monoammonium phosphate, incubated the microcosms for another 6 weeks, and then measured the biodegradation of crude oil components, bacterial taxonomy, and functional gene composition. We hypothesized that the biodegradation of targeted crude oil components would be enhanced by limiting the microbial taxa competing for resources and by specifically selecting bacteria involved in crude oil biodegradation (i.e., CO-M). Postincubation, large differences in taxonomy and functional gene composition between the three microbiome types remained, indicating that purposeful soil microbiome structuring is feasible. Although phylum-level bacterial taxonomy was constrained, operational taxonomic unit composition varied between microbiome types. Contrary to our hypothesis, the biodegradation of C10to C50hydrocarbons was highest when the original microbiome was reinoculated, despite a higher relative abundance of alkane hydroxylase genes in the CO-M microbiomes and of carbon-processing genes in the REG-M microbiomes. Despite increases in the relative abundances of genes potentially linked to hydrocarbon processing in cultivated subsets of the microbiome, reinoculation of the initial microbiome led to maximum biodegradation.IMPORTANCEIn this study, we show that it is possible to sustainably modify microbial assemblages in soil. This has implications for biotechnology, as modification of gut microbial assemblages has led to improved treatments for diseases likeClostridium difficileinfection. Although the soil environment determined which major phylogenetic groups of bacteria would dominate the assemblage, we saw differences at lower levels of taxonomy and in functional gene composition (e.g., genes related to hydrocarbon degradation). Further studies are needed to determine the success of such an approach in nonsterile environments. Although the biodegradation of certain crude oil fractions was still the highest when we inoculated with the diverse initial microbiome, the possibility of discovering and establishing microbiomes that are more efficient in crude oil degradation is not precluded.
APA, Harvard, Vancouver, ISO, and other styles
28

Montero, Angel, M. Elias Dueker, and Gregory D. O’Mullan. "Culturable bioaerosols along an urban waterfront are primarily associated with coarse particles." PeerJ 4 (December 22, 2016): e2827. http://dx.doi.org/10.7717/peerj.2827.

Full text
Abstract:
The source, characteristics and transport of viable microbial aerosols in urban centers are topics of significant environmental and public health concern. Recent studies have identified adjacent waterways, and especially polluted waterways, as an important source of microbial aerosols to urban air. The size of these aerosols influences how far they travel, their resistance to environmental stress, and their inhalation potential. In this study, we utilize a cascade impactor and aerosol particle monitor to characterize the size distribution of particles and culturable bacterial and fungal aerosols along the waterfront of a New York City embayment. We seek to address the potential contribution of bacterial aerosols from local sources and to determine how their number, size distribution, and taxonomic identity are affected by wind speed and wind direction (onshore vs. offshore). Total culturable microbial counts were higher under offshore winds (average of 778 CFU/m3± 67), with bacteria comprising the majority of colonies (58.5%), as compared to onshore winds (580 CFU/m3± 110) where fungi were dominant (87.7%). The majority of cultured bacteria and fungi sampled during both offshore winds (88%) and onshore winds (72%) were associated with coarse aerosols (>2.1 µm), indicative of production from local sources. There was a significant correlation (p < 0.05) of wind speed with both total and coarse culturable microbial aerosol concentrations. Taxonomic analysis, based on DNA sequencing, showed that Actinobacteria was the dominant phylum among aerosol isolates. In particular,StreptomycesandBacillus, both spore forming genera that are often soil-associated, were abundant under both offshore and onshore wind conditions. Comparisons of bacterial communities present in the bioaerosol sequence libraries revealed that particle size played an important role in microbial aerosol taxonomy. Onshore and offshore coarse libraries were found to be most similar. This study demonstrates that the majority of culturable bacterial aerosols along a New York City waterfront were associated with coarse aerosol particles, highlighting the importance of local sources, and that the taxonomy of culturable aerosol bacteria differed by size fraction and wind direction.
APA, Harvard, Vancouver, ISO, and other styles
29

Gyllenberg, Mats, and Timo Koski. "Bayesian predictiveness, exchangeability and sufficientness in bacterial taxonomy." Mathematical Biosciences 177-178 (May 2002): 161–84. http://dx.doi.org/10.1016/s0025-5564(01)00096-7.

Full text
APA, Harvard, Vancouver, ISO, and other styles
30

Vandamme, P., B. Pot, M. Gillis, P. de Vos, K. Kersters, and J. Swings. "Polyphasic taxonomy, a consensus approach to bacterial systematics." Microbiological reviews 60, no. 2 (1996): 407–38. http://dx.doi.org/10.1128/mmbr.60.2.407-438.1996.

Full text
APA, Harvard, Vancouver, ISO, and other styles
31

Vandamme, P., B. Pot, M. Gillis, P. de Vos, K. Kersters, and J. Swings. "Polyphasic taxonomy, a consensus approach to bacterial systematics." Microbiological reviews 60, no. 2 (1996): 407–38. http://dx.doi.org/10.1128/mr.60.2.407-438.1996.

Full text
APA, Harvard, Vancouver, ISO, and other styles
32

Bolduc, Benjamin, Ho Bin Jang, Guilhem Doulcier, Zhi-Qiang You, Simon Roux, and Matthew B. Sullivan. "vConTACT: an iVirus tool to classify double-stranded DNA viruses that infectArchaeaandBacteria." PeerJ 5 (May 3, 2017): e3243. http://dx.doi.org/10.7717/peerj.3243.

Full text
Abstract:
Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.
APA, Harvard, Vancouver, ISO, and other styles
33

Soutar, Craig D., and John Stavrinides. "Phylogenetic analysis supporting the taxonomic revision of eight genera within the bacterial order Enterobacterales." International Journal of Systematic and Evolutionary Microbiology 70, no. 12 (December 1, 2020): 6524–30. http://dx.doi.org/10.1099/ijsem.0.004542.

Full text
Abstract:
The diverse members of the Enterobacterales are agriculturally and medically relevant species that have continued to undergo taxonomic revision. To assess the current taxonomy of 64 genera of the Enterobacterales , we carried out a phylogenetic analysis using 32 single-copy core proteins. The resulting phylogeny was robust, and shows that eight genera – Biostraticola , Enterobacillus , Gibbsiella , Limnobaculum , Izhakiella , ‘Nissabacter’, Rosenbergiella and Samsonia – are currently assigned to incorrect families. Taxonomic reassignment of these genera was also supported by average amino acid identity comparisons. We propose taxonomic revision of these genera to reflect their phylogenetic position within the Enterobacterales .
APA, Harvard, Vancouver, ISO, and other styles
34

Chun, Jongsik, and Fred A. Rainey. "Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea." International Journal of Systematic and Evolutionary Microbiology 64, Pt_2 (February 1, 2014): 316–24. http://dx.doi.org/10.1099/ijs.0.054171-0.

Full text
Abstract:
The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.
APA, Harvard, Vancouver, ISO, and other styles
35

Colman, D. R., E. C. Toolson, and C. D. Takacs-Vesbach. "Do diet and taxonomy influence insect gut bacterial communities?" Molecular Ecology 21, no. 20 (September 14, 2012): 5124–37. http://dx.doi.org/10.1111/j.1365-294x.2012.05752.x.

Full text
APA, Harvard, Vancouver, ISO, and other styles
36

SIMIDU, U., K. KITA-TSUKAMOTO, T. YASUMOTO, and M. YOTSU. "Taxonomy of Four Marine Bacterial Strains That Produce Tetrodotoxin." International Journal of Systematic Bacteriology 40, no. 4 (October 1, 1990): 331–36. http://dx.doi.org/10.1099/00207713-40-4-331.

Full text
APA, Harvard, Vancouver, ISO, and other styles
37

Vilas-Bôas, G. T., A. P. S. Peruca, and O. M. N. Arantes. "Biology and taxonomy ofBacillus cereus,Bacillus anthracis, andBacillus thuringiensis." Canadian Journal of Microbiology 53, no. 6 (June 2007): 673–87. http://dx.doi.org/10.1139/w07-029.

Full text
Abstract:
Three species of the Bacillus cereus group (Bacillus cereus, Bacillus anthracis , and Bacillus thuringiensis ) have a marked impact on human activity. Bacillus cereus and B. anthracis are important pathogens of mammals, including humans, and B. thuringiensis is extensively used in the biological control of insects. The microbiological, biochemical, and genetic characteristics of these three species are reviewed, together with a discussion of several genomic studies conducted on strains of B. cereus group. Using bacterial systematic concepts, we speculate that to understand the taxonomic relationship within this group of bacteria, special attention should be devoted also to the ecology and the population genetics of these species.
APA, Harvard, Vancouver, ISO, and other styles
38

Sajnaga, Ewa, and Waldemar Kazimierczak. "Evolution and taxonomy of nematode-associated entomopathogenic bacteria of the genera Xenorhabdus and Photorhabdus: an overview." Symbiosis 80, no. 1 (January 2020): 1–13. http://dx.doi.org/10.1007/s13199-019-00660-0.

Full text
Abstract:
AbstractEntomopathogenic bacteria from the genera Photorhabdus and Xenorhabdus are closely related Gram-negative bacilli from the family Enterobacteriaceae (γ-Proteobacteria). They establish obligate mutualistic associations with soil nematodes from the genera Steinernema and Heterorhabditis to facilitate insect pathogenesis. The research of these two bacterial genera is focused mainly on their unique interactions with two different animal hosts, i.e. nematodes and insects. So far, studies of the mutualistic bacteria of nematodes collected from around the world have contributed to an increase in the number of the described Xenorhabdus and Photorhabdus species. Recently, the classification system of entomopatogenic nematode microsymbionts has undergone profound revision and now 26 species of the genus Xenorhabdus and 19 species of the genus Photorhabdus have been identified. Despite their similar life style and close phylogenetic origin, Photorhabdus and Xenorhabdus bacterial species differ significantly in e.g. the nematode host range, symbiotic strategies for parasite success, and arrays of released antibiotics and insecticidal toxins. As the knowledge of the diversity of entomopathogenic nematode microsymbionts helps to enable the use thereof, assessment of the phylogenetic relationships of these astounding bacterial genera is now a major challenge for researchers. The present article summarizes the main information on the taxonomy and evolutionary history of Xenorhabdus and Photorhabdus, entomopathogenic nematode symbionts.
APA, Harvard, Vancouver, ISO, and other styles
39

Belov, Andrey A., Vladimir S. Cheptsov, Elena A. Vorobyova, Natalia A. Manucharova, and Zakhar S. Ezhelev. "Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample." Geosciences 9, no. 4 (April 10, 2019): 166. http://dx.doi.org/10.3390/geosciences9040166.

Full text
Abstract:
The arid Mojave Desert is one of the most significant terrestrial analogue objects for astrobiological research due to its genesis, mineralogy, and climate. However, the knowledge of culturable bacterial communities found in this extreme ecotope’s soil is yet insufficient. Therefore, our research has been aimed to fulfil this lack of knowledge and improve the understanding of functioning of edaphic bacterial communities of the Central Mojave Desert soil. We characterized aerobic heterotrophic soil bacterial communities of the central region of the Mojave Desert. A high total number of prokaryotic cells and a high proportion of culturable forms in the soil studied were observed. Prevalence of Actinobacteria, Proteobacteria, and Firmicutes was discovered. The dominance of pigmented strains in culturable communities and high proportion of thermotolerant and pH-tolerant bacteria were detected. Resistance to a number of salts, including the ones found in Martian regolith, as well as antibiotic resistance, were also estimated.
APA, Harvard, Vancouver, ISO, and other styles
40

de Macario, Everly Conway, and Alberto J. L. Macario. "Monoclonal Antibodies for Bacterial Identification and Taxonomy: 1985 and Beyond." Clinics in Laboratory Medicine 5, no. 3 (September 1985): 531–44. http://dx.doi.org/10.1016/s0272-2712(18)30858-8.

Full text
APA, Harvard, Vancouver, ISO, and other styles
41

Margos, Gabriele, Volker Fingerle, Sally Cutler, Alexander Gofton, Brian Stevenson, and Agustín Estrada-Peña. "Controversies in bacterial taxonomy: The example of the genus Borrelia." Ticks and Tick-borne Diseases 11, no. 2 (March 2020): 101335. http://dx.doi.org/10.1016/j.ttbdis.2019.101335.

Full text
APA, Harvard, Vancouver, ISO, and other styles
42

Haggerty, John Matthew, and Elizabeth Ann Dinsdale. "Distinct biogeographical patterns of marine bacterial taxonomy and functional genes." Global Ecology and Biogeography 26, no. 2 (October 10, 2016): 177–90. http://dx.doi.org/10.1111/geb.12528.

Full text
APA, Harvard, Vancouver, ISO, and other styles
43

Gürtler, V., and B. C. Mayall. "Genomic approaches to typing, taxonomy and evolution of bacterial isolates." International Journal of Systematic and Evolutionary Microbiology 51, no. 1 (January 1, 2001): 3–16. http://dx.doi.org/10.1099/00207713-51-1-3.

Full text
APA, Harvard, Vancouver, ISO, and other styles
44

Wang, Qiong, George M. Garrity, James M. Tiedje, and James R. Cole. "Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy." Applied and Environmental Microbiology 73, no. 16 (June 22, 2007): 5261–67. http://dx.doi.org/10.1128/aem.00062-07.

Full text
Abstract:
ABSTRACT The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (≥95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/ .
APA, Harvard, Vancouver, ISO, and other styles
45

Fritze, Dagmar. "Taxonomy of the Genus Bacillus and Related Genera: The Aerobic Endospore-Forming Bacteria." Phytopathology® 94, no. 11 (November 2004): 1245–48. http://dx.doi.org/10.1094/phyto.2004.94.11.1245.

Full text
Abstract:
The conspicuous morphological feature of endospore formation has lent itself from early on as an easily recognized property for taxonomic differentiation. Prior to 1980, the year of the compilation of the Approved Lists of Bacterial Names, four genera of aerobic endospore-forming bacteria had been established, with the genus Bacillus being the largest and most prominent. However, modern developments in taxonomic methodology have helped to reveal an enormous breadth in physiological and genetical diversity within the groups of aerobic bacteria that have endospore formation as a common trait. To better reflect this existing diversity and to provide more appropriate taxonomic arrangements, numerous valid descriptions of new genera and new species have been realized as well as many reclassifications that became necessary. Today, the group of aerobic endospore-forming bacteria embraces more than 25 genera and over 200 species.
APA, Harvard, Vancouver, ISO, and other styles
46

Huval, J. Hansel, Roger Latta, Rebecca Wallace, Donn J. Kushner, and Russell H. Vreeland. "Description of two new species ofHalomonas:Halomonas israelensissp.nov. andHalomonas canadensissp.nov." Canadian Journal of Microbiology 41, no. 12 (December 1, 1995): 1124–31. http://dx.doi.org/10.1139/m95-156.

Full text
Abstract:
Six well-known strains of halotolerant bacteria, including two strains previously identified only as NRCC 41227 and Ba1have been compared using 125 phenotypic characters and DNA–DNA hybridization. Although these strains represent some of the most heavily studied salt-tolerant bacteria, they have never been taxonomically compared. The data presented show that these bacteria form a relatively homogeneous group related at the genus level. The taxonomic comparison showed that these six organisms represented four distinct species all related above the 65% Jaccard coefficient level. In addition to two previously identified bacterial species, Halomonas elongata (ATCC 33173T) and Halomonas halodurans (ATCC 29686T), the strains included in this study represent two previously unnamed Halomonas species. These two new taxa have been assigned the names Halomonas israelensis (ATCC 43985T) and Halomonas canadensis (NRCC 41227T = ATCC 43984). DNA–DNA hybridizations show that these two species are related to the type species H. elongata at 54.9 and 48.9%, respectively.Key words: Halomonas, taxonomy, israelensis, canadensis, halotolerant.
APA, Harvard, Vancouver, ISO, and other styles
47

Jousselin, Emmanuelle, Yves Desdevises, and Armelle Coeur d'acier. "Fine-scale cospeciation between Brachycaudus and Buchnera aphidicola : bacterial genome helps define species and evolutionary relationships in aphids." Proceedings of the Royal Society B: Biological Sciences 276, no. 1654 (September 9, 2008): 187–96. http://dx.doi.org/10.1098/rspb.2008.0679.

Full text
Abstract:
Aphids harbour an obligatory symbiont, Buchnera aphidicola , providing essential amino acids not supplied by their diet. These bacteria are transmitted vertically and phylogenic analyses suggest that they have ‘cospeciated’ with their hosts. We investigated this cospeciation phenomenon at a fine taxonomic level, within the aphid genus Brachycaudus . We used DNA-based methods of species delimitation in both organisms, to avoid biases in the definition of aphid and Buchnera species and to infer association patterns without the presumption of a specific interaction. Our results call into question certain ‘taxonomic’ species of Brachycaudus and suggest that B. aphidicola has diversified into independently evolving entities, each specific to a ‘phylogenetic’ Brachycaudus species. We also found that Buchnera and their hosts simultaneously diversified, in parallel. These results validate the use of Buchnera DNA data for inferring the evolutionary history of their host. The Buchnera genome evolves rapidly, making it the perfect tool for resolving ambiguities in aphid taxonomy. This study also highlights the usefulness of species delimitation methods in cospeciation studies involving species difficult to conceptualize—as is the case for bacteria—and in cases in which the taxonomy of the interacting organisms has not been determined independently and species definition depends on host association.
APA, Harvard, Vancouver, ISO, and other styles
48

Mäntynen, Sari, Elina Laanto, Lotta-Riina Sundberg, Minna M. Poranen, Hanna M. Oksanen, and ICTV Report Consortium. "ICTV Virus Taxonomy Profile: Finnlakeviridae." Journal of General Virology 101, no. 9 (September 1, 2020): 894–95. http://dx.doi.org/10.1099/jgv.0.001488.

Full text
Abstract:
Finnlakeviridae is a family of icosahedral, internal membrane-containing bacterial viruses with circular, single-stranded DNA genomes. The family includes the genus, Finnlakevirus, with the species, Flavobacterium virus FLiP. Flavobacterium phage FLiP was isolated with its Gram-negative host bacterium from a boreal freshwater habitat in Central Finland in 2010. It is the first described single-stranded DNA virus with an internal membrane and shares minimal sequence similarity with other known viruses. The virion organization (pseudo T=21 dextro) and major capsid protein fold (double-β-barrel) resemble those of Pseudoalteromonas phage PM2 (family Corticoviridae), which has a double-stranded DNA genome. A similar major capsid protein fold is also found in other double-stranded DNA viruses in the kingdom Bamfordvirae. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Finnlakeviridae, which is available at ictv.global/report/finnlakeviridae.
APA, Harvard, Vancouver, ISO, and other styles
49

Wachsmuth, Kaye. "Genotypic Approaches to the Diagnosis of Bacterial Infections: Plasmid Analyses and Gene Probes." Infection Control 6, no. 3 (March 1985): 100–109. http://dx.doi.org/10.1017/s0195941700062767.

Full text
Abstract:
AbstractPractical genetic approaches have been helpful in the diagnosis, epidemiology, and taxonomy of bacterial pathogens encountered in our laboratory at the Centers for Disease Control. There are many examples in which plasmid profiles have been used to define epidemic strains of enteric bacteria, staphylococci, pseudomonads, vibrios, and other pathogenic bacteria. Current methodologies should allow the microbiology laboratory to use plasmid profiles routinely and to identify plasmids associated with bacterial pathogenesis.Simplified DNA-DNA hybridization procedures have been used in our laboratory to survey or “probe” thousands of Escherichia coli colonies for the presence of enterotoxin genes, eliminating traditional tissue culture or animal assays. Research scientists continue to develop gene probes for a number of bacterial toxins and hemolysins and for the identification of pathogens such as legionellae and salmonellae. These and other probes as well as hybridization “kits” may be commercially available to diagnostic laboratories within the next few years.
APA, Harvard, Vancouver, ISO, and other styles
50

Oro, Violeta, Magdalena Knezevic, Zoran Dinic, and Dusica Delic. "Bacterial Microbiota Isolated from Cysts of Globodera rostochiensis (Nematoda: Heteroderidae)." Plants 9, no. 9 (September 4, 2020): 1146. http://dx.doi.org/10.3390/plants9091146.

Full text
Abstract:
The potato cyst nematode (PCN) Globodera rostochiensis is a plant parasite of potato classified into a group of quarantine organisms causing high economic losses worldwide. Due to the long persistence of the parasite in soil, cysts harbor numerous bacteria whose presence can lead to cyst death and population decline. The cysts of G. rostochiensis found in two potato fields were used as a source of bacteria. The universal procedure was applied to extract DNA from bacteria which was then sequenced with 16S primers. The aims of the study were to identify bacterial microbiota associated with the PCN populations and to infer their phylogenetic relationships based on the maximum likelihood and Bayesian phylogeny of the 16S sequences. In addition, the impact of the most significant climate and edaphic factors on bacterial diversity were evaluated. Regarding the higher taxonomy, our results indicate that the prevalent bacterial classes were Bacilli, Actinobacteria and Alphaproteobacteria. Phylogenetic analyses clustered Brevibacterium frigoritolerans within the family Bacillaceae, confirming its recent reclassification. Long-term climate factors, such as air temperature, insolation hours, humidity and precipitation, as well as the content of soil organic matter, affected the bacterial diversity. The ability of cyst nematodes to persist in soil for a long time qualifies them as a significant natural source to explore the soil bacterial microbiota.
APA, Harvard, Vancouver, ISO, and other styles
You might also be interested in the bibliographies on the topic 'Bacterial taxonomy' for other source types:
Dissertations / Theses Books
We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!

To the bibliography