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Journal articles on the topic 'Plastidial 16S rRNA gene'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Sarah, Romac, F. Stern Rowena, Mahdi Bendif El, et al. "PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy." Molecular Ecology Resources 15, no. 6 (2015): 1435–45. https://doi.org/10.1111/1755-0998.12401.

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Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework

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2

Decelle, Johan, Sarah Romac, Rowena F. Stern, et al. "PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy." Molecular Ecology Resources 15, no. 6 (2015): 1435–45. http://dx.doi.org/10.1111/1755-0998.12401.

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3

Beumer, Amy, and Jayne B. Robinson. "A Broad-Host-Range, Generalized Transducing Phage (SN-T) Acquires 16S rRNA Genes from Different Genera of Bacteria." Applied and Environmental Microbiology 71, no. 12 (2005): 8301–4. http://dx.doi.org/10.1128/aem.71.12.8301-8304.2005.

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ABSTRACT Genomic analysis has revealed heterogeneity among bacterial 16S rRNA gene sequences within a single species; yet the cause(s) remains uncertain. Generalized transducing bacteriophages have recently gained recognition for their abundance as well as their ability to affect lateral gene transfer and to harbor bacterial 16S rRNA gene sequences. Here, we demonstrate the ability of broad-host-range, generalized transducing phages to acquire 16S rRNA genes and gene sequences. Using PCR and primers specific to conserved regions of the 16S rRNA gene, we have found that generalized transducing

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4

Akihary, Claudia Valleria, and Beivy Jonathan Kolondam. "PEMANFAATAN GEN 16S rRNA SEBAGAI PERANGKAT IDENTIFIKASI BAKTERI UNTUK PENELITIAN-PENELITIAN DI INDONESIA." PHARMACON 9, no. 1 (2020): 16. http://dx.doi.org/10.35799/pha.9.2020.27405.

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ABSTRACTThe 16S rRNA gene has hyper variable region and different for one bacterial species to another. The gene is being used as research tool to help for accurate identification of bacteria in many fields in Indonesia. As a useful tool, the 16S rRNA gene sequence is important as to explore the potencies of a bacterial species. Sequencing of this gene is very useful for research in clinical study, fisheries, marine science, agricultural science, and animal husbandry in Indonesia. Keywords: 16S rRNA gene, research tool, bacteria, Indonesia ABSTRAKGen 16S rRNA memiliki region yang sangat bervar

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Dewhirst, Floyd E., Zeli Shen, Michael S. Scimeca, et al. "Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter: Implications for Phylogenetic Inference and Systematics." Journal of Bacteriology 187, no. 17 (2005): 6106–18. http://dx.doi.org/10.1128/jb.187.17.6106-6118.2005.

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ABSTRACT Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-t

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6

Chalker, Victoria J., and Joe Brownlie. "Taxonomy of the canine Mollicutes by 16S rRNA gene and 16S/23S rRNA intergenic spacer region sequence comparison." International Journal of Systematic and Evolutionary Microbiology 54, no. 2 (2004): 537–42. http://dx.doi.org/10.1099/ijs.0.02869-0.

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The taxonomy of canine Mollicutes is described, based on phylogenetic analysis of 16S rRNA gene and 16S/23S rRNA intergenic spacer (IGS) region sequences. The nucleotide sequences of the 16S rRNA gene of two untyped mycoplasmas and the IGS region of 11 Mycoplasma species were determined and used for phylogenetic analysis. The two untyped Mycoplasma strains, HRC 689 and VJC 358, were found to be distinct from all known canine mycoplasmas and all published mycoplasma 16S rRNA gene sequences.

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7

Dingman, Douglas W. "Characterization ofPaenibacillus popilliaerRNA operons." Canadian Journal of Microbiology 50, no. 10 (2004): 779–91. http://dx.doi.org/10.1139/w04-068.

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The terminal 39 nucleotides on the 3' end of the 16S rRNA gene, along with the complete DNA sequences of the 5S rRNA, 23S rRNA, tRNAIle, and tRNAAlagenes were determined for Paenibacillus popilliae using strains NRRL B-2309 and Dutky 1. Southern hybridization analysis with a 16S rDNA hybridization probe and restriction-digested genomic DNA demonstrated 8 copies of the 16S rRNA gene in P. popilliae strains KLN 3 and Dutky 1. Additionally, the 23S rRNA gene in P. popilliae strains NRRL B-2309, KLN 3, and Dutky 1 was shown by I-CeuI digestion and pulsed-field gel electrophoresis of genomic DNA to

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8

Paul, Bobby. "Concatenated 16S rRNA sequence analysis improves bacterial taxonomy." F1000Research 11 (September 1, 2023): 1530. http://dx.doi.org/10.12688/f1000research.128320.3.

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Background: Microscopic, biochemical, molecular, and computer-based approaches are extensively used to identify and classify bacterial populations. Advances in DNA sequencing and bioinformatics workflows have facilitated sophisticated genome-based methods for microbial taxonomy although sequencing of the 16S rRNA gene is widely employed to identify and classify bacterial communities as a cost-effective and single-gene approach. However, the 16S rRNA sequence-based species identification accuracy is limited because of the occurrence of multiple copies of the 16S rRNA gene and higher sequence id

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9

Paul, Bobby. "Concatenated 16S rRNA sequence analysis improves bacterial taxonomy." F1000Research 11 (April 3, 2023): 1530. http://dx.doi.org/10.12688/f1000research.128320.2.

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Background: Microscopic, biochemical, molecular, and computer-based approaches are extensively used to identify and classify bacterial populations. Advances in DNA sequencing and bioinformatics workflows have facilitated sophisticated genome-based methods for microbial taxonomy although sequencing of the 16S rRNA gene is widely employed to identify and classify bacterial communities as a cost-effective and single-gene approach. However, the 16S rRNA sequence-based species identification accuracy is limited because of the occurrence of multiple copies of the 16S rRNA gene and higher sequence id

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10

Huang, Y., G. W. Stemke, and J. A. Robertson. "An unusual rRNA gene organization in Mycoplasma fermentans (incognitus strain)." Canadian Journal of Microbiology 41, no. 4-5 (1995): 424–27. http://dx.doi.org/10.1139/m95-056.

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The macro-restriction map of Mycoplasma fermentans (incognitus strain) was constructed and its rRNA genes were located on the map. It was found that this organism contains two sets of rRNA genes. The 16S and 23S rRNA genes were closely linked as two clusters. However, both 5S rRNA genes were separated from the 16S and 23S genes. The two 16S–23S rRNA gene clusters were arranged in an unusual tail to tail orientation.Key words: physical map, rRNA, Mycoplasma fermentans, genome, gene organization.

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11

Nørskov-Lauritsen, Niels. "Increased level of intragenomic 16S rRNA gene heterogeneity in commensal strains closely related to Haemophilus influenzae." Microbiology 157, no. 4 (2011): 1050–55. http://dx.doi.org/10.1099/mic.0.047233-0.

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The 16S rRNA gene sequence of strains closely related to, but excluded from, Haemophilus influenzae was investigated and a conspicuously high number of polymorphic nucleotide positions due to intragenomic 16S rRNA gene heterogeneity was observed. The average frequency of 16S rRNA gene polymorphic nucleotide positions in 31 variant strains was 7.0×10−3, which is approximately ten times the level observed in validated strains of H. influenzae. Sixty-seven polymorphic nucleotide positions in seven strains most likely originated from the simultaneous presence of two distinct types of helix 18 as a

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12

Case, Rebecca J., Yan Boucher, Ingela Dahllöf, Carola Holmström, W. Ford Doolittle, and Staffan Kjelleberg. "Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies." Applied and Environmental Microbiology 73, no. 1 (2006): 278–88. http://dx.doi.org/10.1128/aem.01177-06.

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ABSTRACT Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogen

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Clarridge, Jill E. "Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases." Clinical Microbiology Reviews 17, no. 4 (2004): 840–62. http://dx.doi.org/10.1128/cmr.17.4.840-862.2004.

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SUMMARY The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. Problems remain in that the sequences in some databases are not accurate, th

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14

Lin, Jiun-Nong, Chung-Hsu Lai, Chih-Hui Yang, and Yi-Han Huang. "Validation of 16S rRNA and Complete rpoB Gene Sequence Analysis for the Identification of Elizabethkingia Species." International Journal of Molecular Sciences 24, no. 16 (2023): 13007. http://dx.doi.org/10.3390/ijms241613007.

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Bacteria in the genus Elizabethkingia have emerged as a cause of life-threatening infections in humans. However, accurate species identification of these pathogens relies on molecular techniques. We aimed to evaluate the accuracy of 16S rRNA and complete RNA polymerase β-subunit (rpoB) gene sequences in identifying Elizabethkingia species. A total of 173 Elizabethkingia strains with whole-genome sequences in GenBank were included. The 16S rRNA gene and rpoB gene sequences from the same Elizabethkingia strains were examined. Of the 41 E. meningoseptica strains, all exhibited >99.5% 16S rRNA

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15

Melançon, Pierre, Michel Gravel, Guy Boileau, and Léa Brakier-Gingras. "Reassembly of active 30S ribosomal subunits with an unmethylated in vitro transcribed 16S rRNA." Biochemistry and Cell Biology 65, no. 12 (1987): 1022–30. http://dx.doi.org/10.1139/o87-134.

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A plasmid has been constructed, which contains the 16S ribosomal RNA gene of Escherichia coli immediately downstream from a phage T7 promoter. In vitro transcription of this gene by RNA polymerase of the T7 phage yielded an unmethylated 16S rRNA that could be used for the assembly of functional 30S subunits. These subunits, when assayed in a poly(U)-directed translation assay, were as active as 30S subunits reconstructed with native 16S rRNA. This system opens the possibility of investigating the role of the methylations of the rRNA and the functional consequences of site-directed mutagenesis

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Michon, Anne-Laure, Fabien Aujoulat, Laurent Roudière, et al. "Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella." Microbiology 156, no. 7 (2010): 2080–91. http://dx.doi.org/10.1099/mic.0.038224-0.

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As well as intraspecific heterogeneity, intragenomic heterogeneity between 16S rRNA gene copies has been described for a range of bacteria. Due to the wide use of 16S rRNA gene sequence analysis for taxonomy, identification and metagenomics, evaluating the extent of these heterogeneities in natural populations is an essential prerequisite. We investigated inter- and intragenomic 16S rRNA gene heterogeneity of the variable region V3 in a population of 149 clinical isolates of Veillonella spp. of human origin and in 13 type or reference Veillonella strains using PCR-temporal temperature gel elec

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17

Chun, Jongsik, Jae-Hak Lee, Yoonyoung Jung, et al. "EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences." International Journal of Systematic and Evolutionary Microbiology 57, no. 10 (2007): 2259–61. http://dx.doi.org/10.1099/ijs.0.64915-0.

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16S rRNA gene sequences have been widely used for the identification of prokaryotes. However, the flood of sequences of non-type strains and the lack of a peer-reviewed database for 16S rRNA gene sequences of type strains have made routine identification of isolates difficult and labour-intensive. In the present study, we generated a database containing 16S rRNA gene sequences of all prokaryotic type strains. In addition, a web-based tool, named EzTaxon, for analysis of 16S rRNA gene sequences was constructed to achieve identification of isolates based on pairwise nucleotide similarity values

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18

Ree, Heesoo K., Kaiming Cao, David L. Thurlow, and Robert A. Zimmermann. "The structure and organization of the 16S ribosomal RNA gene from the archaebacterium Thermoplasma acidophilum." Canadian Journal of Microbiology 35, no. 1 (1989): 124–33. http://dx.doi.org/10.1139/m89-019.

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The complete nucleotide sequence of the 16S rRNA gene from Thermoplasma acidophilum, as well as its 5′ and 3′ flanking regions, were determined by the dideoxynucleotide chain termination method. The 16S rRNA gene encodes 1471 nucleotides. The primary and secondary structures of T. acidophilum 16S rRNA both exhibit typical archaebacterial features. The sequence appears to be more closely related to 16S rRNAs of the methanogen–halophile group than to those of the thermoacidophile group. Secondary-structure comparisons generally support this relationship, although there are several examples in wh

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Paul, Bobby. "Concatenated 16S rRNA sequence analysis improves bacterial taxonomy." F1000Research 11 (December 19, 2022): 1530. http://dx.doi.org/10.12688/f1000research.128320.1.

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Background: Microscopic, biochemical, molecular, and computer-based approaches are extensively used to identify and classify bacterial populations. Advances in DNA sequencing and bioinformatics workflows have facilitated sophisticated genome-based methods for microbial taxonomy although sequencing of the 16S rRNA gene is widely employed to identify and classify the bacterial community as a cost-effective and single-gene approach. However, the 16S rRNA sequence-based species identification accuracy is limited by multiple copies of the gene and their higher sequence identity between closely rela

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20

Wolde-meskel, Endalkachew, Zewdu Terefework, Åsa Frostegård, and Kristina Lindström. "Genetic diversity and phylogeny of rhizobia isolated from agroforestry legume species in southern Ethiopia." International Journal of Systematic and Evolutionary Microbiology 55, no. 4 (2005): 1439–52. http://dx.doi.org/10.1099/ijs.0.63534-0.

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The genetic diversity within 195 rhizobial strains isolated from root nodules of 18 agroforestry species (15 woody and three herbaceous legumes) growing in diverse ecoclimatic zones in southern Ethiopia was investigated by using PCR–RFLP of the ribosomal operon [16S rRNA gene, 23S rRNA gene and the internal transcribed spacer (ITS) region between the 16S rRNA and 23S rRNA genes] and 16S rRNA gene partial sequence (800 and 1350 bp) analyses. All of the isolates and the 28 reference strains could be differentiated by using these methods. The size of the ITS varied among test strains (500–1300 bp

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Cloud, Joann L., Jay J. Meyer, June I. Pounder, et al. "Mycobacterium arupense sp. nov., a non-chromogenic bacterium isolated from clinical specimens." International Journal of Systematic and Evolutionary Microbiology 56, no. 6 (2006): 1413–18. http://dx.doi.org/10.1099/ijs.0.64194-0.

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Several Mycobacterium-like organisms related to the Mycobacterium terrae complex have been isolated from clinical samples. In the clinical microbiology laboratory, partial 16S rRNA gene sequencing (approximately the first 500 bp) rather than full 16S rRNA gene sequencing is often used to identify Mycobacterium species. Partial 16S rRNA gene sequence analysis revealed 100 % similarity between 65 clinical isolates and Mycobacterium sp. MCRO 6 (GenBank accession no. X93032). Even after sequencing the nearly full-length 16S rRNA gene, closest similarity was only 99.6 % to Mycobacterium nonchromoge

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Il Jun, Kang, Jangsup Moon, Taek Soo Kim, et al. "238. Direct identification of Bacterial Species with MinION Nanopore Sequencer In Clinical Specimens Suspected of Polybacterial Infection." Open Forum Infectious Diseases 6, Supplement_2 (2019): S136. http://dx.doi.org/10.1093/ofid/ofz360.313.

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Abstract Background Conventional culture tests usually identify only a few bacterial species, which can grow well in the culture system, in the cases of polybacterial infection. 16S rRNA gene nanopore sequencing enables semi-quantitative identification of bacterial genetic materials. We aimed to evaluate usefulness of 16s rRNA gene nanopore sequencing in the cases suspected of polybacterial infection. Methods The research was conducted in a single university hospital for one year. Conventional bacterial culture identification and nanopore sequencing of 16s rRNA gene were carried out simultaneo

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Zhou, Zibo, Xiangzhi Li, Xiaojian Chen, et al. "Comparison of P1 and 16S rRNA genes for detection of Mycoplasma pneumoniae by nested PCR in adults in Zhejiang, China." Journal of Infection in Developing Countries 9, no. 03 (2015): 244–53. http://dx.doi.org/10.3855/jidc.5149.

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Introduction: Mycoplasma pneumoniae (M. pneumoniae) is the most common atypical pathogen that causes respiratory infections in humans. Laboratory tests are important in the diagnosis of M. pneumoniae because of the atypical features in clinical signs and symptoms. Nowadays, both the P1 adhesin gene and 16S ribosomal (r) RNA (rRNA) gene of M. pneumoniae have been widely detected by polymerase chain reaction (PCR). The purpose of the present study was to evaluate the most suitable target in the detection of M. pneumonia via nested PCR. Methodology: Both the P1 adhesin gene and 16S rRNA gene for

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Sakamoto, Mitsuo, and Moriya Ohkuma. "Usefulness of the hsp60 gene for the identification and classification of Gram-negative anaerobic rods." Journal of Medical Microbiology 59, no. 11 (2010): 1293–302. http://dx.doi.org/10.1099/jmm.0.020420-0.

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The hsp60 gene sequences were determined for 121 strains of Gram-negative anaerobic rods, including the genera Bacteroides, Barnesiella, Butyricimonas, Odoribacter, Parabacteroides, Paraprevotella, Porphyromonas, Prevotella and Tannerella. The mean pairwise hsp60 gene sequence similarity (73.8–97.1 %) between species in each genus, except for the genus Tannerella that comprises one species, was significantly less than that of the 16S rRNA gene sequence (88.3–96.3 %). Only pairwise hsp60 gene sequence similarity (97.1 %) of the genus Paraprevotella was higher than that of the 16S rRNA gene sequ

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Rissanen, AJ, M. Buck, and S. Peura. "16S rRNA gene sequences of Candidatus Methylumidiphilus (Methylococcales), a putative methanotrophic genus in lakes and ponds." Aquatic Microbial Ecology 88 (January 27, 2022): 25–30. http://dx.doi.org/10.3354/ame01983.

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A putative novel methanotrophic genus, Candidatus Methylumidiphilus (Methylococcales), was recently shown to be ubiquitous and one of the most abundant methanotrophic genera in water columns of oxygen-stratified lakes and ponds in boreal and subarctic areas. However, it has probably escaped detection in many previous studies that used 16S rRNA gene amplicon sequencing due to insufficient database coverage, as previously analysed metagenome-assembled genomes (MAGs) affiliated with Ca. Methylumidiphilus do not contain 16S rRNA genes. Therefore, we screened MAGs affiliated with the genus for thei

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Al-Ahmad, Ali, Thorsten Mathias Auschill, Gabriele Braun, Elmar Hellwig, and Nicole Birgit Arweiler. "Overestimation of Streptococcus mutans prevalence by nested PCR detection of the 16S rRNA gene." Journal of Medical Microbiology 55, no. 1 (2006): 109–13. http://dx.doi.org/10.1099/jmm.0.46280-0.

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This study was carried out in order to compare two PCR-based methods in the detection of Streptococcus mutans. The first PCR method was based on primers for the 16S rRNA gene and the second method was based on specific primers that targeted the glucosyltransferase gene (gtfB). Each PCR was performed with eight different streptococci from the viridans group, five other streptococci and 17 different non-streptococcal bacterial strains. Direct use of the S. mutans 16S rRNA gene-specific primers revealed that Streptococcus gordonii and Streptococcus infantis were also detected. After amplifying th

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Lee, I. M., K. D. Bottner-Parker, Y. Zhao, R. E. Davis, and N. A. Harrison. "Phylogenetic analysis and delineation of phytoplasmas based on secY gene sequences." International Journal of Systematic and Evolutionary Microbiology 60, no. 12 (2010): 2887–97. http://dx.doi.org/10.1099/ijs.0.019695-0.

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The secY gene sequence is more variable than that of the 16S rRNA gene. Comparative phylogenetic analyses with 16S rRNA and secY gene sequences from 80 and 83 phytoplasma strains, respectively, were performed to assess the efficacy of these sequences for delineating phytoplasma strains within each 16Sr group. The phylogenetic interrelatedness among phytoplasma taxa inferred by secY gene-based phylogeny was nearly congruent with that inferred by 16S rRNA gene-based phylogeny. Phylogenetic analysis based on the secY gene permitted finer differentiation of phytoplasma strains, however. The secY g

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Guimaraes-Peres, A., F. Portaels, P. de Rijk, et al. "Comparison of Two PCRs for Detection of Mycobacterium ulcerans." Journal of Clinical Microbiology 37, no. 1 (1999): 206–8. http://dx.doi.org/10.1128/jcm.37.1.206-208.1999.

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Two nested PCRs for the detection of Mycobacterium ulcerans were compared by using a collection of 65 clinical specimens. The first method amplifies the gene coding for 16S rRNA, and the second method amplifies a repetitive DNA sequence. The sensitivities of bacterioscopy, culture, 16S rRNA gene PCR, and repetitive-sequence PCR were 29, 34, 80, and 85%, respectively. Compared to the 16S rRNA gene PCR, the repetitive-sequence PCR was faster, easier to perform, and less expensive.

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Mastropaolo, Matthew D., Mary L. Thorson, and Ann M. Stevens. "Comparison of Bacteroides thetaiotaomicron and Escherichia coli 16S rRNA gene expression signals." Microbiology 155, no. 8 (2009): 2683–93. http://dx.doi.org/10.1099/mic.0.027748-0.

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There are barriers to cross-expression of genes between Bacteroides spp. and Escherichia coli. In this study, a lux-based reporter system was developed for Bacteroides and used to compare the promoter structure and function of a Bacteroides thetaiotaomicron 4001 (BT4001) 16S rRNA promoter with those of E. coli in vivo. Analysis of the BT4001 sequences upstream of the 16S rRNA gene revealed the same overall structure known for E. coli 16S rRNA promoters in that there were two promoters separated by ∼150 bp. However, the BT4001 16S rRNA promoter contains the proposed Bacteroides −7 and −33 conse

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Villemur, Richard, Philippe Constant, Annie Gauthier, Martine Shareck, and Réjean Beaudet. "Heterogeneity between 16S ribosomal RNA gene copies borne by one Desulfitobacterium strain is caused by different 100-200 bp insertions in the 5´ region." Canadian Journal of Microbiology 53, no. 1 (2007): 116–28. http://dx.doi.org/10.1139/w06-111.

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Strains of Desulfitobacterium hafniense, such as strains PCP-1, DP7, TCE1, and TCP-A, have unusual long 16S ribosomal RNA (rRNA) genes due to an insertion of approximately 100 bp in the 5' region. In this report, we analyzed the 16S rRNA genes of different Desulfitobacterium strains to determine if such an insertion is a common feature of desulfitobacteria. We amplified this region by polymerase chain reaction (PCR) from eight Desulfitobacterium strains (D. hafniense strains PCP-1, DP7, TCP-A, TCE1, and DCB-2; D. dehalogenans; D. chlororespirans; and Desulfitobacterium sp. PCE1) and resolved e

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Al-Musawi, Akeel Mohammad. "Genetic Characterization of Hyalomma Anatolicum (Ixodoidea: Ixodidae) in Babylon Province Middle Iraq." SAR Journal of Pathology and Microbiology 4, no. 06 (2023): 73–77. http://dx.doi.org/10.36346/sarjpm.2023.v04i06.003.

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This study was included molecular study of Hyalomma anatolicum (Ixodoidea: Ixodidae) based on 16S rRNA gene collected from three regions' in Babylon province. The results of gel electrophoresis image (1.5 % agarose) shows the amplicons of a partial region within large subunit RNA gene (size= 450 bp). The sequencing data has reported species of H. anatolicum 16S rRNA gene (OQ162293) to OQ162298 these species revealed close matching on the phylogenetic tree to an isolate of H. anatolicum for different countries. This study represents first in Babylon Governorate to diagnose H. anatolicum by targ

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Porob, Seema, Hillary A. Craddock, Yair Motro, et al. "Quantification and Characterization of Antimicrobial Resistance in Greywater Discharged to the Environment." Water 12, no. 5 (2020): 1460. http://dx.doi.org/10.3390/w12051460.

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In disenfranchised communities, untreated greywater (wastewater without sewage) is often environmentally discharged, resulting in potential human exposure to antimicrobial-resistant bacteria (ARB), including extended-spectrum beta-lactamase (ESBL) producers. We sought to examine the abundance of ARB, specifically ESBLs, and antimicrobial resistance genes (ARGs) in greywater from off-grid, pastoral Bedouin villages in Southern Israel. Greywater samples (n = 21) collected from five villages were analyzed to enumerate fecal coliforms and Escherichia coli. ESBL producers were recovered on CHROMaga

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Zhang, Run, Chun Liu, Liang Li, Hui Na Yang, and Jing Liang Yang. "Detection of Methanogens in Anaerobic Granular Sludge by FISH Targeting for Functional Genes." Advanced Materials Research 518-523 (May 2012): 299–304. http://dx.doi.org/10.4028/www.scientific.net/amr.518-523.299.

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Methanogens play an important role in the anaerobic digestion and production of methane, and show significant influence on the performance of anaerobic wastewater treatment process. Then the methanogens in anaerobic granular sludge samples from full-scale UASB bioreactors treating avermectin or starch wastewater were detected by FISH using 16S rRNA gene-based probe and functional gene-based probes. The results showed that the hybridization of methanogens in simultaneous FISH with mcrA gene-based and 16S rRNA gene-based probes was high coincident and the coincidence degree was about 60%-80%, im

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Wu, Xueling, Hong Duan, Hongwei Fan, Zhenzhen Zhang, and Lili Liu. "Comparative Study of PCR-Based Approaches for the Genetic Characterization of Three Strains of Acidithiobacillus caldus Isolated from Different Sites in China." Polish Journal of Microbiology 62, no. 4 (2013): 351–58. http://dx.doi.org/10.33073/pjm-2013-048.

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Comparative study of the genetic characteristics among three Acidithiobacillus caldus strains isolated from different typical environments in China was performed using a combination of molecular methods, namely sequencing analysis of PCR-amplified 16S rRNA genes and 16S-23S rRNA gene intergenic spacers (ITS), repetitive element PCR (rep-PCR), arbitrarily primed PCR (AP-PCR) fingerprinting and random amplified polymorphic DNA (RAPD). Both of the 16S rRNA gene and 16S-23S rRNA gene intergenic spacers sequences of the three strains exhibited small variations, with 99.9-100%, 99.7-100% identity re

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SOMAN, CHITRA, H. N. ANJANEYAPPA, B. T. NAVEEN KUMAR, T. N. DEVANAND, R. P. SATHISH, and MALATHI SHEKAR. "DNA barcoding of Cynoglossus arel using mitochondrial COI and 16S rRNA genes." Indian Journal of Animal Sciences 90, no. 7 (2020): 1074–79. http://dx.doi.org/10.56093/ijans.v90i7.106685.

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DNA barcoding is not a substitute for taxonomy; however, it does provide a powerful tool to aid species identifications and focus on future taxonomic research efforts. In the present study, an attempt is made to identify and validate Cynoglossus arel collected from the Mangalore coast by DNA barcoding using mitochondrial COI and 16S rRNA genes. The primer pairs used in the study could successfully amplify 646 bp segment of COI and 616 bp segment of 16S rRNA gene in C. arel. The K2P average genetic distance calculated among species in the Cynoglossidae family was 0.22 and 0.09 among COI and 16S

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Valiunas, Deividas, Rasa Jomantiene та Robert Edward Davis. "Evaluation of the DNA-dependent RNA polymerase β-subunit gene (rpoB) for phytoplasma classification and phylogeny". International Journal of Systematic and Evolutionary Microbiology 63, Pt_10 (2013): 3904–14. http://dx.doi.org/10.1099/ijs.0.051912-0.

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Phytoplasmas are classified into 16Sr groups and subgroups and ‘Candidatus Phytoplasma ’ species, largely or entirely based on analysis of 16S rRNA gene sequences. Yet, distinctions among closely related ‘Ca. Phytoplasma ’ species and strains based on 16S rRNA genes alone have limitations imposed by the high degree of rRNA nucleotide sequence conservation across diverse phytoplasma lineages and by the presence in a phytoplasma genome of two, sometimes sequence-heterogeneous, copies of the 16S rRNA gene. Since the DNA-dependent RNA polymerase (DpRp) β-subunit gene (rpoB) exists as a single copy

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Schouls, Leo M., Corrie S. Schot, and Jan A. Jacobs. "Horizontal Transfer of Segments of the 16S rRNA Genesbetween Species of the Streptococcus anginosusGroup." Journal of Bacteriology 185, no. 24 (2003): 7241–46. http://dx.doi.org/10.1128/jb.185.24.7241-7246.2003.

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ABSTRACT The nature in variation of the 16S rRNA gene of members of the Streptococcus anginosus group was investigated by hybridization and DNA sequencing. A collection of 708 strains was analyzed by reverse line blot hybridization. This revealed the presence of distinct reaction patterns representing 11 different hybridization groups. The 16S rRNA genes of two strains of each hybridization group were sequenced to near-completion, and the sequence data confirmed the reverse line blot hybridization results. Closer inspection of the sequences revealed mosaic-like structures, strongly suggesting

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Miyashita, Mika, Takeshi Sakane, Ken-ichiro Suzuki, and Yasuyoshi Nakagawa. "16S rRNA gene and 16S-23S rRNA gene internal transcribed spacer sequences analysis of the genus Myxococcus." FEMS Microbiology Letters 282, no. 2 (2008): 241–45. http://dx.doi.org/10.1111/j.1574-6968.2008.01127.x.

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Darmawati, Sri, Langkah Sembiring, Widya Asmara, Wayan T. Artama, and Masashi Kawaichi. "Phylogenetic relationship of Gram Negative Bacteria of Enterobacteriaceae Family in the Positive Widal Blood Cultures based on 16S rRNA Gene Sequences." Indonesian Journal of Biotechnology 19, no. 1 (2015): 64. http://dx.doi.org/10.22146/ijbiotech.8635.

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The purpose of this study was to analyze the phylogenetic relationship of Gram negative bacteria (3strains of Salmonella typhi, 1 strain of Escherichia coli, 1 strain of Serratia marcescens, and 3 strains of Enterobactercloacae) of Enterobacteriaceae family in positive Widal blood cultures based on 16S rRNA gene sequences. Theresults respectively showed that each two 16S rRNA gene clones of Serratia marcescens KD 08.4 had a closerelationship with 16S rRNA gene of Serrratia marcescens ATCC 13880 (similarity: 99.53-99.8%), Eschericia coliBA 30.1 with Eschericia coli ATCC 11775T (similarity: 99.3

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Ogarkov, O. B., S. N. Zhdanova, E. A. Orlova, et al. "16S-ITS-23S rRNA operon segment sequencing provides necessary and sufficient conditions for bacterial species-specific identification." Russian Journal of Infection and Immunity 12, no. 5 (2022): 976–80. http://dx.doi.org/10.15789/2220-7619-ros-1871.

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Introduction. Sequencing of the 16S rRNA gene is the predominant method for assessing microbial communities and strain molecular identification. The short reads (2nd generation sequencing)-based technology does not allow analysis beyond the 16S rRNA gene. The taxonomic verification level of samples usually remains at the genus or even family level. Currently, there have been proposed the latest versions of long-read technologies (Oxford Nanopore MinION, PacBio) for amplicon sequencing of near-complete ribosomal operon, including genes 16S, 23S, 5S, and internal transcribed spacer (ITS). At the

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Kiran Kumar, Mondeddu, Charu Tyagi, Arjun Sahu, et al. "Identification and Characterization of Staphylococcus aureus 16S rRNA gene isolated from different Food Specimens from South Indian Region." Journal of Drug Delivery and Therapeutics 10, no. 5 (2020): 24–32. http://dx.doi.org/10.22270/jddt.v10i5.4340.

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Staphylococcus aureus (S. aureus) associated food-borne diseases have global impact on human health. Genome wide analyses have shown that S. aureus contains specific endotoxin expressing gene and produce toxic proteins which is responsible for food contamination. Appropriate detection of pathogens is one of the major tool to avoid infection rate and reduce the health and socio-economic burden to human being. In addition, inappropriate handing the specimens, misdiagnosis and limited standard medical support could directly influence the infection rate. The objective of this study was to id

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Axelrood, Paige E., Monica L. Chow, Christopher C. Radomski, Joseph M. McDermott, and Julian Davies. "Molecular characterization of bacterial diversity from British Columbia forest soils subjected to disturbance." Canadian Journal of Microbiology 48, no. 7 (2002): 655–74. http://dx.doi.org/10.1139/w02-059.

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Bacteria from forest soils were characterized by DNA sequence analysis of cloned 16S rRNA gene fragments (16S clones). Surface organic matter and mineral soil samples from a British Columbia Ministry of Forests Long-Term Soil Productivity (LTSP) installation were collected during winter and summer from two disturbance treatments: whole-tree harvesting with no soil compaction (plot N) and whole-tree harvesting plus complete surface organic matter removal with heavy soil compaction (plot S). Phylogenetic analyses revealed that 87% of 580 16S clones were classified as Proteobacteria, Actinobacter

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Reischl, U., K. Feldmann, L. Naumann, et al. "16S rRNA Sequence Diversity in Mycobacterium celatum Strains Caused by Presence of Two Different Copies of 16S rRNA Gene." Journal of Clinical Microbiology 36, no. 6 (1998): 1761–64. http://dx.doi.org/10.1128/jcm.36.6.1761-1764.1998.

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Direct sequencing of the 16S rRNA gene (16S rDNA) ofMycobacterium celatum isolates showed ambiguities, suggesting heterogeneity. Cloned 16S rDNA yielded two copies of the gene, which differed by insertion of a thymine at position 214 and by additional mismatches. Restriction fragment length polymorphism analysis confirmed the presence of two copies of 16S rDNA within the bacterial chromosome.

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Win, Nang Kyu Kyu, Seung-Yeol Lee, Assunta Bertaccini, Shigetou Namba, and Hee-Young Jung. "‘Candidatus Phytoplasma balanitae’ associated with witches’ broom disease of Balanites triflora." International Journal of Systematic and Evolutionary Microbiology 63, Pt_2 (2013): 636–40. http://dx.doi.org/10.1099/ijs.0.041566-0.

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A phytoplasma was identified in naturally infected wild Balanites triflora plants exhibiting typical witches’ broom symptoms (Balanites witches’ broom: BltWB) in Myanmar. The 16S rRNA gene sequence revealed that BltWB phytoplasma had the highest similarity to that of ‘Candidatus Phytoplasma ziziphi’ and it was also closely related to that of ‘Candidatus Phytoplasma ulmi ’. Phylogenetic analysis of the 16S rRNA gene sequences indicated that the BltWB phytoplasma clustered as a discrete subclade with Elm yellows phytoplasmas. RFLP analysis of the 16S rRNA gene including the 16S–23S spacer region

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Wang, Li-Ting, Fwu-Ling Lee, Chun-Ju Tai, and Hiroaki Kasai. "Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group." International Journal of Systematic and Evolutionary Microbiology 57, no. 8 (2007): 1846–50. http://dx.doi.org/10.1099/ijs.0.64685-0.

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The Bacillus subtilis group comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the gyrB gene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whether gyrB gene sequence analysis could be used for phylogenetic analysis and species identification of members of the B. subtilis group, the congruence of gyrB grouping with both 16S rRNA gene sequencing and DNA–DNA hybridization data was evaluated. Ranges of gyrB nucleotide and translated amino acid seque

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Metfies, Katja, and Linda K. Medlin. "Feasibility of Transferring Fluorescent In Situ Hybridization Probes to an 18S rRNA Gene Phylochip and Mapping of Signal Intensities." Applied and Environmental Microbiology 74, no. 9 (2008): 2814–21. http://dx.doi.org/10.1128/aem.02122-07.

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ABSTRACT DNA microarray technology offers the possibility to analyze microbial communities without cultivation, thus benefiting biodiversity studies. We developed a DNA phylochip to assess phytoplankton diversity and transferred 18S rRNA probes from dot blot or fluorescent in situ hybridization (FISH) analyses to a microarray format. Similar studies with 16S rRNA probes have been done determined that in order to achieve a signal on the microarray, the 16S rRNA molecule had to be fragmented, or PCR amplicons had to be <150 bp in length to minimize the formation of a secondary structure in th

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Edberg, Andreas, Margaretha Jurstrand, Eva Johansson, et al. "A comparative study of three different PCR assays for detection of Mycoplasma genitalium in urogenital specimens from men and women." Journal of Medical Microbiology 57, no. 3 (2008): 304–9. http://dx.doi.org/10.1099/jmm.0.47498-0.

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The aim of this study was to compare conventional 16S rRNA gene PCR, real-time 16S rRNA gene PCR and real-time Mycoplasma genitalium adhesin protein (MgPa) gene PCR as detection methods for M. genitalium infection. The study also determined the prevalence of M. genitalium in male and female patients attending a sexually transmitted infections clinic in a rural area in the west of Sweden. First void urine (FVU) and/or urethral swabs were collected from 381 men, and FVU and/or cervical swabs and/or urethral swabs were collected from 298 women. A total of 213 specimens were used in the PCR compar

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Kwon, Soon-Wo, Jin-Young Park, Jong-Shik Kim, et al. "Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences." International Journal of Systematic and Evolutionary Microbiology 55, no. 1 (2005): 263–70. http://dx.doi.org/10.1099/ijs.0.63097-0.

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A total of 128 strains was isolated from more than 23 legume hosts in Korea. Phylogenetic relationships between these Korean isolates and reference strains of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium were analysed using their 16S rRNA gene and internally transcribed spacer (ITS) region sequences. Among the Bradyrhizobium strains, dendrograms based on both the 16S rRNA gene and ITS region sequences produced two main groups. The ITS tree yielded at least two new clusters that were discernable from the seven previously delineated genospecies. Large discrepancies were

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Minegishi, Hiroaki, Masahiro Kamekura, Tomomi Kitajima-Ihara, et al. "Gene orders in the upstream of 16S rRNA genes divide genera of the family Halobacteriaceae into two groups." International Journal of Systematic and Evolutionary Microbiology 62, no. 1 (2012): 188–95. http://dx.doi.org/10.1099/ijs.0.031708-0.

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In many prokaryotic species, 16S rRNA genes are present in multiple copies, and their sequences in general do not differ significantly owing to concerted evolution. At the time of writing, the genus Haloarcula of the family Halobacteriaceae comprises nine species with validly published names, all of which possess two to four highly heterogeneous 16S rRNA genes. Existence of multiple heterogeneous 16S rRNA genes makes it difficult to reconstruct a biological phylogenetic tree using their sequence data. If the orthologous gene is able to be discriminated from paralogous genes, a tree reconstruct

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Hubu, Herlin S., Stenly Wullur, Veibe Warouw, Elvy L. Ginting, Robert A. Bara, and Adnan S. Wantasen. "FILOGENI MOLEKULER BAKTERI DARI MEDIA PEMELIHARAAN ROTIFER YANG DIBERI OLAHAN LIMBAH IKAN SEBAGAI SUMBER NUTRISI." JURNAL PESISIR DAN LAUT TROPIS 9, no. 1 (2021): 38. http://dx.doi.org/10.35800/jplt.9.1.2021.33574.

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This study aims to identify and construct molecular phylogeny of an isolate bacteria from culture media of rotifer Brachionus rotudiforis supplied with processed fishery waste feed as nutritional source. The use of fish waste-based food for rotifer showed positive effects on growth and nutrient content of the rotifers. Genomic DNA of the isolate bacteria BRLI- 01 was extracted and the 16S rRNA gene was amplified using primers (8F and 1492F) and further sequenced using Sanger sequence technique. The 16S rRNA gene was analysed using SeqScanner® and MEGA® followed with BLAST (Basic Local Alignmen

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