Relevant bibliographies by topics / 16S rRNA gene amplification

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Academic literature on the topic '16S rRNA gene amplification'

Author: Grafiati
Published: 4 June 2021
Last updated: 16 February 2022

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Journal articles on the topic "16S rRNA gene amplification"

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Suryani, Laksmi Ambarsari, and Efi Sanfitri Harahap. "AMPLIFIKASI GEN 16S-rRNA BAKTERI TERMOFILIK DARI SUMBER AIR PANAS, GUNUNG PANCAR BOGOR." Jurnal Riset Kimia 3, no. 1 (February 12, 2015): 83. http://dx.doi.org/10.25077/jrk.v3i1.97.

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ABSTRACT Exploration of thermophilic bacteria that produce thermostable enzyme is most useful in application for enzyme base industrial. The aim of of this research is to isolate and amplificate the 16S-rRNA gene from thermophilic bacteria isolate at hotspring, Mount of Pancar, Bogor. The research steps consist of bacteria isolation, chromosomal DNA extraction, and amplification of 16S-rRNA gene. The water sample as source for bacteria was collected from four cauldrons. Temperature and pH for each cauldron are red cauldron 75-80°C, pH 7; black cauldron 55°C, pH 7; white cauldron 57°C, pH 7; and saline cauldron 25°C, pH 6, respectively. The bacteria were cultivated at Luria Bertani (LB) and Thermus media. The chromosomal DNA have been extracted. Gene amplification of 16 S-rRNA have been carried out by using universal primer (Bac F1 and Uni B1). The size of amplicon is ± 1.5kb. Keywords : thermophilic bacteria, chromosomal DNA extraction, amplification of 16S-rRNA gene
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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 (March 29, 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 Alignment Search Tool) analyses in the NCBI (National Centre for Biotechnology Information). Amplification result of 16S rRNA gene bacteria s NCBI site as a reference for identification and phylogeny of bacterial species. BRLI-01 was successfully cultured on rotifer rearing media. The results of the 16S rRNA gene amplification of the isolate bacteria showed a DNA band with a length of 1400 bp. The BLAST result on the NCBI showed that the isolate bacteria BRLI-01 had a percent identity (98.46%) and is in the same phylogony branching position with Vibrio rotiferianus Keywords: Rotifers, Bacteria, Fish waste, 16S rRNA Genes, Phylogeny identification
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Marchesi, Julian R., Takuichi Sato, Andrew J. Weightman, Tracey A. Martin, John C. Fry, Sarah J. Hiom, and William G. Wade. "Design and Evaluation of Useful Bacterium-Specific PCR Primers That Amplify Genes Coding for Bacterial 16S rRNA." Applied and Environmental Microbiology 64, no. 2 (February 1, 1998): 795–99. http://dx.doi.org/10.1128/aem.64.2.795-799.1998.

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ABSTRACT We report the design and evaluation of PCR primers 63f and 1387r for amplification of 16S rRNA genes from bacteria. Their specificity and efficacy were tested systematically with a variety of bacterial species and environmental samples. They were found to be more useful for 16S rRNA gene amplification in ecological and systematic studies than PCR amplimers that are currently more generally used.
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O’Farrell, Katrina A., and Peter H. Janssen. "Detection of Verrucomicrobia in a Pasture Soil by PCR-Mediated Amplification of 16S rRNA Genes." Applied and Environmental Microbiology 65, no. 9 (September 1, 1999): 4280–84. http://dx.doi.org/10.1128/aem.65.9.4280-4284.1999.

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ABSTRACT Oligonucleotide primers were designed and used to amplify, by PCR, partial 16S rRNA genes of members of the bacterial divisionVerrucomicrobia in DNA extracted from a pasture soil. By applying most-probable-number theory to the assay, verrucomicrobia appeared to contribute some 0.2% of the soil DNA. Amplified ribosomal DNA restriction analysis of 53 cloned PCR-amplified partial 16S rRNA gene fragments and comparative sequence analysis of 21 nonchimeric partial 16S rRNA genes showed that these primers amplified only 16S rRNA genes of members of the Verrucomicrobia in DNA extracted from the soil.
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Frank, Jeremy A., Claudia I. Reich, Shobha Sharma, Jon S. Weisbaum, Brenda A. Wilson, and Gary J. Olsen. "Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes." Applied and Environmental Microbiology 74, no. 8 (February 22, 2008): 2461–70. http://dx.doi.org/10.1128/aem.02272-07.

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ABSTRACT rRNA-based studies, which have become the most common method for assessing microbial communities, rely upon faithful amplification of the corresponding genes from the original DNA sample. We report here an analysis and reevaluation of commonly used primers for amplifying the DNA between positions 27 and 1492 of bacterial 16S rRNA genes (numbered according to the Escherichia coli rRNA). We propose a formulation for a forward primer (27f) that includes three sequences not usually present. We compare our proposed formulation to two common alternatives by using linear amplification—providing an assessment that is independent of a reverse primer—and in combination with the 1492 reverse primer (1492r) under the PCR conditions appropriate for making community rRNA gene clone libraries. For analyses of DNA from human vaginal samples, our formulation was better at maintaining the original rRNA gene ratio of Lactobacillus spp. to Gardnerella spp., particularly under stringent amplification conditions. Because our 27f formulation remains relatively simple, having seven distinct primer sequences, there is minimal loss of overall amplification efficiency and specificity.
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Kimura, Hiroyuki, Maki Sugihara, Kenji Kato, and Satoshi Hanada. "Selective Phylogenetic Analysis Targeted at 16S rRNA Genes of Thermophiles and Hyperthermophiles in Deep-Subsurface Geothermal Environments." Applied and Environmental Microbiology 72, no. 1 (January 2006): 21–27. http://dx.doi.org/10.1128/aem.72.1.21-27.2006.

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ABSTRACT Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the G+C content of the 16S rRNA gene and the optimum growth temperatures of most known prokaryotic cultures, was used prior to clone library construction. To validate this technique, hot spring fluid (76°C) and river water (14°C) were used to mimic a deep-subsurface sample contaminated with drilling fluid. After DNA extraction and PCR amplification of the 16S rRNA genes from individual samples separately, the amplified products from river water were observed to be denatured at 82°C and completely digested by exonuclease I (Exo I), while the amplified products from hot spring fluid remained intact after denaturation at 84°C and enzyme digestion with Exo I. DNAs extracted from the two samples were mixed and used as a template for amplification of the 16S rRNA genes. The amplified rRNA genes were denatured at 84°C and digested with Exo I before clone library construction. The results indicated that the 16S rRNA gene sequences from the river water were almost completely eliminated, whereas those from the hot spring fluid remained.
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Conville, Patricia S., Steven H. Fischer, Charles P. Cartwright, and Frank G. Witebsky. "Identification of Nocardia Species by Restriction Endonuclease Analysis of an Amplified Portion of the 16S rRNA Gene." Journal of Clinical Microbiology 38, no. 1 (January 2000): 158–64. http://dx.doi.org/10.1128/jcm.38.1.158-164.2000.

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ABSTRACT Identification of clinical isolates of Nocardia to the species level is important for defining the spectrum of disease produced by each species and for predicting antimicrobial susceptibility. We evaluated the usefulness of PCR amplification of a portion of the Nocardia 16S rRNA gene and subsequent restriction endonuclease analysis (REA) for species identification. Unique restriction fragment length polymorphism (RFLP) patterns were found for Nocardia sp. type strains (except for the N. asteroides type strain) and representative isolates of the drug pattern types of Nocardia asteroides (except for N. asteroides drug pattern type IV, which gave inconsistent amplification). A variant RFLP pattern for Nocardia nova was also observed. Twenty-eight clinical isolates were evaluated both by traditional biochemical identification and by amplification and REA of portions of the 16S rRNA gene and the 65-kDa heat shock protein (HSP) gene. There was complete agreement among the three methods on identification of 24 of these isolates. One isolate gave a 16S rRNA RFLP pattern consistent with the biochemical identification but was not identifiable by its HSP gene RFLP patterns. Three isolates gave 16S rRNA RFLP patterns which were inconsistent with the identification obtained by both biochemical tests and HSP gene RFLP; sequence analysis suggested that two of these isolates may belong to undefined species. The PCR and REA technique described appears useful both for the identification of clinical isolates of Nocardia and for the detection of new or unusual species.
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Korczak, Bożena M., Regina Stieber, Stefan Emler, André P. Burnens, Joachim Frey, and Peter Kuhnert. "Genetic relatedness within the genus Campylobacter inferred from rpoB sequences." International Journal of Systematic and Evolutionary Microbiology 56, no. 5 (May 1, 2006): 937–45. http://dx.doi.org/10.1099/ijs.0.64109-0.

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The genus Campylobacter comprises 17 species, some of which are important animal and human pathogens. To gain more insight into the genetic relatedness of this genus and to improve the molecular tools available for diagnosis, a universal sequencing approach was established for the gene encoding the beta-subunit of RNA polymerase (rpoB) for the genus Campylobacter. A total of 59 strains, including the type strains of currently recognized species as well as field isolates, were investigated in the study. A primer set specific for Campylobacter species enabled straightforward amplification and sequencing of a 530 bp fragment of the rpoB gene. The 16S rRNA gene sequences of all of the strains were determined in parallel. A good congruence was obtained between 16S rRNA and rpoB gene sequence-based trees within the genus Campylobacter. The branching of the rpoB tree was similar to that of the 16S rRNA gene tree, even though a few discrepancies were observed for certain species. The resolution of the rpoB gene within the genus Campylobacter was generally much higher than that of the 16S rRNA gene sequence, resulting in a clear separation of most species and even some subspecies. The universally applicable amplification and sequencing approach for partial rpoB gene sequence determination provides a powerful tool for DNA sequence-based discrimination of Campylobacter species.
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Takeshi, Kouichi, Souichi Makino, Tetsuya Ikeda, Noriko Takada, Atsushi Nakashiro, Kazunori Nakanishi, Keiji Oguma, Yoshinobu Katoh, Hiroyuki Sunagawa, and Tohru Ohyama. "Direct and Rapid Detection by PCR ofErysipelothrix sp. DNAs Prepared from Bacterial Strains and Animal Tissues." Journal of Clinical Microbiology 37, no. 12 (1999): 4093–98. http://dx.doi.org/10.1128/jcm.37.12.4093-4098.1999.

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A PCR method for rapid screening of Erysipelothrix spp. in the slaughterhouse was carried out by using four species-specific sets of oligonucleotide primers after initial amplification with the primer set MO101-MO102, which amplifies the 16S rRNA sequences of all four Erysipelothrix species. The DNA sequences coding for the rRNA gene cluster, including 16S rRNA, 23S rRNA, and the noncoding region downstream of 5S rRNA, were determined in order to design primers for the species-specific PCR detection system. The homology among the 4.5-kb DNA sequences of the rRNA genes ofErysipelothrix rhusiopathiae serovar 2 (DNA Data Bank of Japan accession no. AB019247), E. tonsillarum serovar 7 (accession no. AB019248), E. rhusiopathiae serovar 13 (accession no. AB019249), and E. rhusiopathiae serovar 18 (accession no. AB019250) ranged from 96.0 to 98.4%. The PCR amplifications were specific and were able to distinguish the DNAs from each of the four Erysipelothrix species. The results of PCR tests performed directly with tissue specimens from diseased animals were compared with the results of cultivation tests, and the PCR tests were completed within 5 h. The test with this species-specific system based on PCR amplification with the DNA sequences coding for the rRNA gene cluster was an accurate, easy-to-read screening method for rapid diagnosis of Erysipelothrix sp. infection in the slaughterhouse.
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Jensen, J. S., M. B. Borre, and B. Dohn. "Detection of Mycoplasma genitalium by PCR Amplification of the 16S rRNA Gene." Journal of Clinical Microbiology 41, no. 1 (January 1, 2003): 261–66. http://dx.doi.org/10.1128/jcm.41.1.261-266.2003.

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Dissertations / Theses on the topic "16S rRNA gene amplification"

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Mulheron, Rebecca. "Microbial Community Assembly found with Sponge Orange Band Disease in Xestospongia muta (Giant Barrel Sponge)." NSUWorks, 2014. http://nsuworks.nova.edu/occ_stuetd/18.

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The giant barrel sponge, Xestospongia muta is an iconic and essential species of the coral reefs in South Florida. The sponge has primary roles providing ecosystem services and creating unique habitats for diverse microbial communities. On April 27, 2012 an outbreak of Sponge Orange Band Disease (SOB) was detected off the coast of South Florida. The disease begins with sponge bleaching, followed by mesohyl or “mesohyl” necrosis and often total mesohyl disintegration. Sampling from two diseased populations at Boynton Beach and Fort Lauderdale, FL took place on May 11th and May 29th, 2012. Each of the nine diseased sponges from Boynton Beach and the five diseased sponges from Fort Lauderdale had three separate mesophyl samples collected to examine the effects of disease progression on the microbial community. These included healthy mesohyl from a diseased sponge (HoD), the boundary layer which captured the advancing line of diseased mesohyl (BL) and diseased mesohyl from a diseased sponge (D). Mesohyl from three sponges with no visible signs of SOB disease were also collected from each sampling location to use for healthy controls (HC). Sequencing of the V4 region of the 16S rRNA gene was performed on all of these samples via the “454” pyrosequencing on a Titanium GS FLX platform. The microbial communities associated with the diseased samples revealed a microbiome shift that followed the progression of Sponge Orange Band Disease (SOB) and was dominated by Bacteroidetes, Protebacteria and Chloroflexi. No singular or group of microbes were solely found within the infected mesohyl of Xestospongia muta from both sampling site populations; therefore there is no unequivocal candidate as a definite microbial causative SOB agent. But there were bacteria associated with disease progression that included Armatimonadetes, Caldithrix, Chlorobi, Fibrobacteres, Fusobacteria, GN02, KSB3, OP1, OP2, OP8, Planctomycetes, SR1, TM6, Tenericutes, Verrucomicrobia, WPS-2 and ZB3. Verrucomicrobia and Plantomycetes increased significantly within the D and the BL populations, which was consistent within all the diseased sponges. This study provides a deep sequencing profile of microbial communities within Xestospongia muta affected with SOB Disease and provides a new insight into the sponge healthy microbiome.
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Silveira, Érico Leandro da [UNESP]. "Identificação de comunidades bacterianas de solo por seqüenciamento do gene 16S rRNA." Universidade Estadual Paulista (UNESP), 2004. http://hdl.handle.net/11449/94868.

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Métodos tradicionais de isolamento e cultivo limitam análises da diversidade microbiana no meio ambiente, pois acredita - se que aproximadamente 10% desses microrganismos possam ser cultivados. A ecologia microbiana molecular teve recentes progressos através da construção de bibliotecas metagenômicas, o que constitui uma poderosa abordagem para explorar a diversidade microbiana de solo fornecendo inclusive dados sobre os microrganismos não cultiváveis desse habitat. Este trabalho teve por objetivo comparar e estimar a diversidade de comunidades bacterianas, em solos de duas áreas, sendo solo de Floresta Nativa (SFN) e a outra sob arboreto com eucaliptos (SAE) de uma mesma região. Utilizando oligonucleotídeos iniciadores específicos, o gene 16S rRNA foi amplificado por PCR, os amplicons foram clonados em pGEMR-T e os clones obtidos seqüenciados parcialmente. No solo SFN foram analisados 231 clones e no solo SRE 248 clones. As seqüências obtidas foram submetidas à análise de similaridade de nucleotídeos com o banco de dados GenBank. Os filos bacterianos que mais se destacaram nos dois tipos de solo foram Acidobacteria e Proteobacteria. No solo SFN destacaram-se também as bactérias pertencentes ao filo Bacteroidetes e no solo SAE observou-se alta freqüência das bactérias Actinobacteria. Análises filogenéticas revelaram diferenças em ambos os solos, verificando através de índice de diversidade bacteriana observou-se que o solo sob eucalipto apresentou maior diversidade quando comparado ao solo sob de Floresta Nativa.
Traditional methods of isolation and culture limits the analyses of the microbian diversity in the environment, because it is believed - that approximately 10% of these microrganisms can be cultivated. The molecular microbian ecology have had recent progress through the construction of metagenomics Iibraries, what constitutes a powerful boarding to explore the microbian diversity of soil, also supplying information on the microrganisms that cannot be cultivated on this habitat. This work had the objective of stimate the diversity of bacterial communities, in two areas, an area of Native Forest (SFN) and the another one under eucalypts (SAE) of the same region. Using specific oligonucleotides starters, the gene 16S rRNA was amplified by PCR, amplicons had been cloned in pGEMR-T and the obtained clones were partial/y sequenced. In the soil SFN, 231 clones had been analyzed and 248 clones in the soil SAE. The sequences obtained were submitted to the nucleotides similarity analysis with the GenBank database. The bacterial phylum that was more evident in the two types de soil were Acidobacteria and Proteobacteria. In the soi! SFN the bacteria of the phylum Bacteroidetes were evident and in the soil SRE high frequency of the Actinobacteria bacteria was observed. Phylogenetic analyses reveled an extensive diversity in both soils, verified through diversity index differences in the bacterial communities in both areas, and that the area under eucalypt presented more diversity in relation to the area of Native Forest.
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Silveira, Érico Leandro da. "Identificação de comunidades bacterianas de solo por seqüenciamento do gene 16S rRNA /." Jaboticabal : [s.n.], 2004. http://hdl.handle.net/11449/94868.

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Resumo: Métodos tradicionais de isolamento e cultivo limitam análises da diversidade microbiana no meio ambiente, pois acredita - se que aproximadamente 10% desses microrganismos possam ser cultivados. A ecologia microbiana molecular teve recentes progressos através da construção de bibliotecas metagenômicas, o que constitui uma poderosa abordagem para explorar a diversidade microbiana de solo fornecendo inclusive dados sobre os microrganismos não cultiváveis desse habitat. Este trabalho teve por objetivo comparar e estimar a diversidade de comunidades bacterianas, em solos de duas áreas, sendo solo de Floresta Nativa (SFN) e a outra sob arboreto com eucaliptos (SAE) de uma mesma região. Utilizando oligonucleotídeos iniciadores específicos, o gene 16S rRNA foi amplificado por PCR, os amplicons foram clonados em pGEMR-T e os clones obtidos seqüenciados parcialmente. No solo SFN foram analisados 231 clones e no solo SRE 248 clones. As seqüências obtidas foram submetidas à análise de similaridade de nucleotídeos com o banco de dados GenBank. Os filos bacterianos que mais se destacaram nos dois tipos de solo foram Acidobacteria e Proteobacteria. No solo SFN destacaram-se também as bactérias pertencentes ao filo Bacteroidetes e no solo SAE observou-se alta freqüência das bactérias Actinobacteria. Análises filogenéticas revelaram diferenças em ambos os solos, verificando através de índice de diversidade bacteriana observou-se que o solo sob eucalipto apresentou maior diversidade quando comparado ao solo sob de Floresta Nativa.
Abstract: Traditional methods of isolation and culture limits the analyses of the microbian diversity in the environment, because it is believed - that approximately 10% of these microrganisms can be cultivated. The molecular microbian ecology have had recent progress through the construction of metagenomics Iibraries, what constitutes a powerful boarding to explore the microbian diversity of soil, also supplying information on the microrganisms that cannot be cultivated on this habitat. This work had the objective of stimate the diversity of bacterial communities, in two areas, an area of Native Forest (SFN) and the another one under eucalypts (SAE) of the same region. Using specific oligonucleotides starters, the gene 16S rRNA was amplified by PCR, amplicons had been cloned in pGEMR-T and the obtained clones were partial/y sequenced. In the soil SFN, 231 clones had been analyzed and 248 clones in the soil SAE. The sequences obtained were submitted to the nucleotides similarity analysis with the GenBank database. The bacterial phylum that was more evident in the two types de soil were Acidobacteria and Proteobacteria. In the soi! SFN the bacteria of the phylum Bacteroidetes were evident and in the soil SRE high frequency of the Actinobacteria bacteria was observed. Phylogenetic analyses reveled an extensive diversity in both soils, verified through diversity index differences in the bacterial communities in both areas, and that the area under eucalypt presented more diversity in relation to the area of Native Forest.
Orientadora: Lúcia Maria Carareto Alves
Coorientadora: Eliana Gertrudes Macedo Lemos
Banca: Janete Apparecida Desiderio Sena
Banca: Uderlei Doniseti Silveira Covissi
Mestre
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Grešová, Katarína. "Klasifikace bakterií do taxonomických kategorií na základě vlastností 16s rRNA." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2020. http://www.nusl.cz/ntk/nusl-417246.

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The main goal of this thesis was to design and implement a tool that would be able to classify the sequences of the 16S rRNA gene into taxonomic categories using the properties of the 16S rRNA gene. The created tool analyzes all input sequences simultaneously, which differs from common classification approaches, which classify input sequences individually. This tool relies on the fact that bacteria contain several copies of the 16S rRNA gene, which may differ in sequence. The main contribution of this work is design, implementation and evaluation of the capabilities of this tool. Experiments have shown that the proposed tool is able to identify the corresponding bacteria for smaller datasets and determine the correct ratios of their abundances. However, with larger datasets, the state space becomes very large and fragmented, which requires further improvements in order for it to search the state space in an efficient way.
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Pereira, Juliana Vianna. "Comparação por análise molecular da diversidade bacteriana da saliva de pacientes com diferentes índices de higiene bucal." Universidade Federal do Amazonas, 2009. http://tede.ufam.edu.br/handle/tede/3064.

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The complex microbiota of the oral cavity has been intensively studied and saliva is characterized by microorganisms which colonize different regions of mouth, such as tongue, supragengival and subgingival biofilm. Considering this, the purpose of this study was to evaluate the bacterial diversity of the saliva of patients with different levels of oral hygiene according to the Silness, Löe index. In this research, two genomic libraries of saliva source from 15 patients each were constructed. The pooled samples differ in the average index of Silness, Löe being considered as high or low index within the rate 1.0 to 3.0 and 0 to 0.5, respectively. The DNA saliva was extracted by phenol / chloroform method and 16S rRNA gene for the microorganisms of each sample were amplified and cloned. The sequences obtained were compared to those from sequences of the GenBank NCBI and RDP. The library resultant from saliva of patients with high level of dental biofilm showed 23 OTUs grouped as five known genus: Streptococcus, Granulicaella, Gemella, Peptostreptococcus and Veillonella besides 33.3% of uncultured bacteria. The Library made from saliva of patients with low level of dental biofilm, was significantly different from its counterpart (p = 0.000) and was composed by 42 OTUs, distributed among 11 known genus: Streptococcus, Granulicaella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces, and 24.87% of uncultured bacteria. The genus Streptococcus was the more prevalent in the two libraries, constituting 79.08% of the first and 73.64% the second. In conclusion, patients with low dental biofilm index have saliva with higher bacterial diversity than patients with high dental biofilm index, and despite most uncultivated species aggregate with Steptococcus, they still are new and unknown microorganisms
A complexa microbiota da cavidade bucal tem sido intensivamente estudada e a saliva destaca-se por apresentar microrganismos de diferentes regiões, como a língua, biofilme subgengival e supragengival. Diante disto, o objetivo do presente estudo foi avaliar a diversidade bacteriana da saliva de pacientes com diferentes índices de higiene bucal e para isto, foram construídas duas bibliotecas genômicas da saliva, que foram constituídas por amostras de 15 pacientes cada uma, com a média de índice de biofilme de Silness; Löe diferenciado, sendo a primeira com índice de 1,0 a 3,0 (denominada alto índice) e a segunda, entre 0 a 0,5 (denominada baixo índice). O DNA da saliva foi extraído pelo método fenol/clorofórmio e o gene 16S rRNA para cada biblioteca foi amplificado e clonado. As sequências obtidas foram comparadas com aquelas armazenadas no GenBank do NCBI e RDP. A biblioteca composta pela saliva de pacientes com Alto índice de biofilme dental apresentou cinco Gêneros conhecidos: Streptococcus, Granulicaella, Gemella, Veillonella e Peptostreptococcus e 33,3% de bactérias não-cultivadas, agrupados em 23 OTUs. A Biblioteca, composta pela saliva de pacientes com Baixo índice de biofilme dental, foi diferente siguinificativamente da primeira (p=0,000) e foi composta de 42 OTUs, distribuídas em 11 Gêneros conhecidos: Streptococcus, Granulicaella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces, alem de 24,87% de bactérias não-cultivadas. O Gênero Streptococcus foi o mais prevalente nas duas bibliotecas, constituindo 79,08% da primeira e 73,63% da segunda. Conclui-se que existe maior diversidade bacteriana na saliva de pacientes com Baixo índice de biofilme dental em relação à pacientes com Alto índice de biofilme dental e que apesar da maioria das espécies não-cultivadas agruparem-se com os Streptococcus, ainda contituem-se de microrganismos novos e desconhecidos
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Kim, Min Seok. "AN INTEGRATED INVESTIGATION OF RUMINAL MICROBIAL COMMUNITIES USING 16S rRNA GENE-BASED TECHNIQUES." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1316383870.

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Oliveira, Rosangela Claret de. "Isolamento de ureaplasma e micoplasma do trato reprodutivo de ovinos e caprinos e tipificação genotípica por meio da PFGE e seqüenciamento do gene 16S rRNA." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/10/10134/tde-12012009-105144/.

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Micoplasmas e ureaplasmas têm sido isolados de pequenos ruminantes, mas existem poucos estudos. O Mycoplasma ovine/caprine sorotipo 11, conhecido como cepa 2D, ainda não classificado como espécie, vem sendo relacionado a casos de vulvovaginite e problemas reprodutivos em ovinos e caprinos. Os ureaplasmas apresentam a habilidade em induzirem doenças no trato genital, confirmada por inoculações experimentais de isolados obtidos de animais doentes em animais saudáveis, resultando em moderada granularidade e hiperemia na vulva. Estes ureaplasmas não receberam ainda a designação de espécie, sendo apenas conhecidas suas características sorológicas, nas quais é fundamentada a classificação em nove sorotipos, sendo o IX relacionado a infertilidade e aborto em ovelhas. Este trabalho teve como objetivo o isolamento de micoplasmas e ureaplasmas do trato reprodutivo de fêmeas e machos das espécies caprina e ovina e tipificação genotípica dos isolados por meio de PFGE e sequenciamento do gene 16S rRNA. Foram obtidos 20 isolamentos de ureaplasma no trato reprodutivo de fêmeas e machos da espécie ovina, um isolamento de micoplasma e sete com crescimento misto de micoplasma e ureaplasma. Nas fêmeas da espécie caprina foram obtidos cinco isolamentos, sendo quatro de ureaplasma e um de micoplasma. Dos isolados submetidos a PFGE , 11 de origem ovina resultaram em oito diferentes perfis confirmando a capacidade da técnica em tipificar ureaplasma de origem ovina. O sequenciamento do gene 16S rRNA, analisado pelo UPGMA, permitiu agrupar seis isolados ao Ureaplasma diversum ATCC 49782, e quatro não foram agrupados com nenhuma outra espécies de ureaplasma, quando utilizado o ponto de corte 97%. Em nosso estudo, os isolados de ovino e caprino agrupados às referências de U. diversum não permite concluir que sejam da mesma espécie. A utilização do gene 16S rRNA gera grande quantidade de informações úteis para inferências filogenéticas e pode ser a primeira escolha na investigação de novas espécies. Técnicas filogenéticas como sequenciamento do espaço intergênico 16S-23S rRNA, e gene da urease podem auxiliaram futuramente na classificação dos isolados obtidos de ovino e caprino.
Mycoplasmas and or ureaplasmas have been isolated from small ruminants but are few studied. Mycoplasma ovine/caprine serotype 11, known as 2D strain, has not been classified yet as specie. However, it has been associated to vulvovaginitis and reproductive disorder in caprine and ovine. Ureaplasmas may cause genital tract diseases. Experimental infections with isolates recovered from sick animals resulted in granularity and hyperemia of the vulva. These have not been designated as specie but are divide in nine serological characteristics types. The serotype IX is associated to infertility and abortion in sheep. The present study aims the isolation of mycoplasmas and ureaplasmas from reproductive tract of ovine and caprine, genotyping of isolates by PFGE, and sequencing of their 16S rRNA. Ureaplasma isolates were recovered from the reproductive tract of 20 ovine, being them, male and female. Mycoplasma was isolated alone in one sample. A mixture of mycoplasma and ureaplasma was obtained in seven samples. On the material obtained from female caprine, five isolations were performed. Four of them were ureaplasma and one was a mycoplasma. Eleven isolates from ovine showed eight distinct profiles at PFGE, confirm that the method can typify ovine origin ureaplasmas. Six isolates were grouped to the Ureaplasma diversum ATCC 49782, through the sequencing of their 16S rRNA using the UPGMA. However, when using a 97% cutoff, four isolates could not be grouped to none of the ureaplasma specie. The isolates from ovine and caprine grouped to U. diversum, do not allow conclude that they are all the same specie. The use of 16S rRNA sequencing showed many useful information to phylogenetic inference, and can be the first choice for when investigating new species. Phylogenetic techniques, as sequencing of the intergenic space 16S-23S rRNA and urease gene, can be used to help the classification of new ureaplasma isolates from ovine and caprine.
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De, Moors Anick. "Comparison of gene organization in the region that surrounds the 16S rRNA gene in seven different Sulfolobales." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ32533.pdf.

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Kam, Sin-yee. "Application of 16S rRNA gene sequencing in laboratory diagnosis of mycobacteria other than tuberculosis." Click to view the E-thesis via HKUTO, 2003. http://sunzi.lib.hku.hk/hkuto/record/B31971052.

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Aiemsum-ang, Porntipa. "Isolation, Systematics and Screening of Members of the Streptomyces violaceusniger 16S rRNA Gene Clade." Thesis, University of Newcastle Upon Tyne, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.506611.

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Books on the topic "16S rRNA gene amplification"

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Kirchman, David L. Community structure of microbes in natural environments. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0004.

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Community structure refers to the taxonomic types of microbes and their relative abundance in an environment. This chapter focuses on bacteria with a few words about fungi; protists and viruses are discussed in Chapters 9 and 10. Traditional methods for identifying microbes rely on biochemical testing of phenotype observable in the laboratory. Even for cultivated microbes and larger organisms, the traditional, phenotype approach has been replaced by comparing sequences of specific genes, those for 16S rRNA (archaea and bacteria) or 18S rRNA (microbial eukaryotes). Cultivation-independent approaches based on 16S rRNA gene sequencing have revealed that natural microbial communities have a few abundant types and many rare ones. These organisms differ substantially from those that can be grown in the laboratory using cultivation-dependent approaches. The abundant types of microbes found in soils, freshwater lakes, and oceans all differ. Once thought to be confined to extreme habitats, Archaea are now known to occur everywhere, but are particularly abundant in the deep ocean, where they make up as much as 50% of the total microbial abundance. Dispersal of bacteria and other small microbes is thought to be easy, leading to the Bass Becking hypothesis that “everything is everywhere, but the environment selects.” Among several factors known to affect community structure, salinity and temperature are very important, as is pH especially in soils. In addition to bottom-up factors, both top-down factors, grazing and viral lysis, also shape community structure. According to the Kill the Winner hypothesis, viruses select for fast-growing types, allowing slower growing defensive specialists to survive. Cultivation-independent approaches indicate that fungi are more diverse than previously appreciated, but they are less diverse than bacteria, especially in aquatic habitats. The community structure of fungi is affected by many of the same factors shaping bacterial community structure, but the dispersal of fungi is more limited than that of bacteria. The chapter ends with a discussion about the relationship between community structure and biogeochemical processes. The value of community structure information varies with the process and the degree of metabolic redundancy among the community members for the process.
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Kirchman, David L. Predation and protists. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0009.

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Protists are involved in many ecological roles in natural environments, including primary production, herbivory and carnivory, and parasitism. Microbial ecologists have been interested in these single-cell eukaryotes since Antonie van Leeuwenhoek saw them in his stool and scum from his teeth. This chapter focuses on the role of protozoa (purely heterotrophic protists) and other protists in grazing on other microbes. Heterotrophic nanoflagellates, 3–5 microns long, are the most important grazers of bacteria and small phytoplankton in aquatic environments. In soils, flagellates are also important, followed by naked amoebae, testate amoebae, and ciliates. Many of these protists feed on their prey by phagocytosis, in which the prey particle is engulfed into a food vacuole into which digestive enzymes are released. This mechanism of grazing explains many factors affecting grazing rates, such as prey numbers, size, and composition. Ingestion rates increase with prey numbers before reaching a maximum, similar to the Michaelis–Menten equation describing uptake as a function of substrate concentration. Protists generally eat prey that are about ten-fold smaller than they are. In addition to flagellates, ciliates and dinoflagellates are often important predators in the microbial world and are critical links between microbial food chains and larger organisms Many protists are capable of photosynthesis. In some cases, the predator benefits from photosynthesis carried out by engulfed, but undigested photosynthetic prey or its chloroplasts. Although much can be learnt from the morphology of large protists, small protists (<10 μ‎m) often cannot be distinguished by morphology, and as seen several times in this book, many of the most abundant and presumably important protists are difficult to cultivate, necessitating the use of cultivation-independent methods analogous to those developed for prokaryotes. Instead of the 16S rRNA gene used for bacteria and archaea, the 18S rRNA gene is key for protists. Studies of this gene have uncovered high diversity in natural protist communities and, along with sequences of other genes, have upended models of eukaryote evolution. These studies indicate that the eukaryotic Tree of Life consists almost entirely of protists, with higher plants, fungi, and animals as mere branches.
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Kirchman, David L. Processes in anoxic environments. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0011.

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During organic material degradation in oxic environments, electrons from organic material, the electron donor, are transferred to oxygen, the electron acceptor, during aerobic respiration. Other compounds, such as nitrate, iron, sulfate, and carbon dioxide, take the place of oxygen during anaerobic respiration in anoxic environments. The order in which these compounds are used by bacteria and archaea (only a few eukaryotes are capable of anaerobic respiration) is set by thermodynamics. However, concentrations and chemical state also determine the relative importance of electron acceptors in organic carbon oxidation. Oxygen is most important in the biosphere, while sulfate dominates in marine systems, and carbon dioxide in environments with low sulfate concentrations. Nitrate respiration is important in the nitrogen cycle but not in organic material degradation because of low nitrate concentrations. Organic material is degraded and oxidized by a complex consortium of organisms, the anaerobic food chain, in which the by-products from physiological types of organisms becomes the starting material of another. The consortium consists of biopolymer hydrolysis, fermentation, hydrogen gas production, and the reduction of either sulfate or carbon dioxide. The by-product of sulfate reduction, sulfide and other reduced sulfur compounds, is oxidized back eventually to sulfate by either non-phototrophic, chemolithotrophic organisms or by phototrophic microbes. The by-product of another main form of anaerobic respiration, carbon dioxide reduction, is methane, which is produced only by specific archaea. Methane is degraded aerobically by bacteria and anaerobically by some archaea, sometimes in a consortium with sulfate-reducing bacteria. Cultivation-independent approaches focusing on 16S rRNA genes and a methane-related gene (mcrA) have been instrumental in understanding these consortia because the microbes remain uncultivated to date. The chapter ends with some discussion about the few eukaryotes able to reproduce without oxygen. In addition to their ecological roles, anaerobic protists provide clues about the evolution of primitive eukaryotes.
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Book chapters on the topic "16S rRNA gene amplification"

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Kawasaki, Akitomo, and Peter R. Ryan. "Peptide Nucleic Acid (PNA) Clamps to Reduce Co-amplification of Plant DNA During PCR Amplification of 16S rRNA Genes from Endophytic Bacteria." In The Plant Microbiome, 123–34. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-1040-4_11.

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Rochelle, P. A., J. A. K. Will, J. C. Fry, G. J. S. Jenkins, R. J. Parkes, C. M. Turley, and A. J. Weightman. "Extraction and Amplification of 16S rRNA Genes from Deep Marine Sediments and Seawater to Assess Bacterial Community Diversity." In Nucleic Acids in the Environment, 219–39. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/978-3-642-79050-8_11.

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Benlloch, Susana, Francisco Rodríguez-Valera, Silvia G. Acinas, and Antonio J. Martínez-Murcia. "Heterotrophic bacteria, activity and bacterial diversity in two coastal lagoons as detected by culture and 16S rRNA genes PCR amplification and partial sequencing." In Coastal Lagoon Eutrophication and ANaerobic Processes (C.L.E.AN.), 3–17. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-1744-6_1.

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Hall, Michael, and Robert G. Beiko. "16S rRNA Gene Analysis with QIIME2." In Methods in Molecular Biology, 113–29. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8728-3_8.

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Einarsson, Gisli G., and Sébastien Boutin. "Techniques: culture, identification and 16S rRNA gene sequencing." In The Lung Microbiome, 18–34. Sheffield, United Kingdom: European Respiratory Society, 2019. http://dx.doi.org/10.1183/2312508x.10000819.

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Bally, René, Jacqueline Haurat, and Philippe Normand. "Azospirillum Phylogeny Based on rrs (16S rRNA Gene) Sequences." In Azospirillum VI and Related Microorganisms, 129–35. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/978-3-642-79906-8_12.

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Fantini, Elio, Giulio Gianese, Giovanni Giuliano, and Alessia Fiore. "Bacterial Metabarcoding by 16S rRNA Gene Ion Torrent Amplicon Sequencing." In Methods in Molecular Biology, 77–90. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-1720-4_5.

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Huang, Yu-An, Zhi-An Huang, Zhu-Hong You, Pengwei Hu, Li-Ping Li, Zheng-Wei Li, and Lei Wang. "Precise Prediction of Pathogenic Microorganisms Using 16S rRNA Gene Sequences." In Intelligent Computing Theories and Application, 138–50. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-26969-2_13.

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Singleton, David R., Steven L. Rathbun, Glen E. Dyszynski, and William B. Whitman. "Section 7 update: LIBSHUFF Comparisons of 16S rRNA Gene Clone Libraries." In Molecular Microbial Ecology Manual, 3263–74. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-2177-0_703.

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Duduk, Bojan, Samanta Paltrinieri, Ing-Ming Lee, and Assunta Bertaccini. "Nested PCR and RFLP Analysis Based on the 16S rRNA Gene." In Methods in Molecular Biology, 159–71. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-089-2_14.

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Conference papers on the topic "16S rRNA gene amplification"

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Kazarina, Alisa, Ilva Pole, Viktorija Leonova, Viktorija Igumnova, Janis Kimsis, Valentina Capligina, Renate Ranka, Guntis Gerhards, and Elina Petersone-Gordina. "Insights into archaeological human sample microbiome using 16S rRNA gene sequencing." In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017. http://dx.doi.org/10.1109/bibm.2017.8218018.

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Silva, M. L. R. Bastos, M. C. C. Pereira Lyra, J. Paula Oliveira, H. Almeida Burity, and G. M. Campos-Takaki. "Microbial diversity in Chromobacterium violaceum determined by 16S rRNA gene analysis." In Proceedings of the II International Conference on Environmental, Industrial and Applied Microbiology (BioMicroWorld2007). WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789812837554_0063.

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Chawla, Archit, and Anthony Byrne. "16S rRNA gene sequencing improves microbial diagnosis of culture-negative pleural effusions." In ERS International Congress 2019 abstracts. European Respiratory Society, 2019. http://dx.doi.org/10.1183/13993003.congress-2019.oa5140.

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Brill, Simon, Phillip James, Leah Cuthbertson, Michael Cox, William Cookson, Jadwiga Wedzicha, and Miriam Moffatt. "Profiling the COPD airway microbiome using quantitative culture and 16S rRNA gene sequencing." In ERS International Congress 2016 abstracts. European Respiratory Society, 2016. http://dx.doi.org/10.1183/13993003.congress-2016.oa1787.

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Deljou, A., K. Mousavi, A. Ghasemi, and H. Rahimian. "Identification of Mycobacterium sp. as Alfalfa endophytes using 16s rRNA gene sequence analysis." In Proceedings of the II International Conference on Environmental, Industrial and Applied Microbiology (BioMicroWorld2007). WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789812837554_0013.

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Yamasaki, Kei, Kazuhiro Yatera, Toshinori Kawanami, Kazumasa Fukuda, Shingo Noguchi, Shuya Nagata, Chinatsu Nishida, et al. "The Bacteriological Incidence Of Community-Acquired Pneumonia Using Clone Analysis Of 16S RRNA Gene." In American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California. American Thoracic Society, 2012. http://dx.doi.org/10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a5243.

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Vasileva, E. N., A. M. Afonin, G. A. Akhtemova, V. A. Zhukov, and I. A. Tikhonovich. "Endophytic bacteria isolated from garden pea (Pisum sativum L.)." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.265.

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Endophytic bacteria were isolated from surface-sterilized aerial parts of pea. Taxonomic status of isolated strains was determined by sequencing of 16S rRNA gene. Moreover, genomes of growth-promoting endophytes were sequenced.
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Norashirene, M. J., A. Ahmad Amin, D. Norhidayah, and M. A. Nurul Fithriah. "Identification of cellulolytic thermophiles based on 16S rDNA gene amplification analysis." In 2012 IEEE Colloquium on Humanities, Science and Engineering Research (CHUSER). IEEE, 2012. http://dx.doi.org/10.1109/chuser.2012.6504349.

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Pertiwi, Melati Putri, Patricia Karin Himawan Praseptin, Ika Diana Werdani, Dwi Listyorini, and Sitoresmi Prabaningtyas. "Identification and phylogenetic study of bioluminescent bacteria from squid (Loligo duvaucelii) based on 16S rRNA gene." In INVENTING PROSPEROUS FUTURE THROUGH BIOLOGICAL RESEARCH AND TROPICAL BIODIVERSITY MANAGEMENT: Proceedings of the 5th International Conference on Biological Science. Author(s), 2018. http://dx.doi.org/10.1063/1.5050134.

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Shelton, Jenna L., Elliott Barnhart, Leslie F. Ruppert, Aaron Jubb, Madalyn S. Blondes, and Christina DeVera. "REPETITIVE SAMPLING AND CONTROL THRESHOLD IMPROVE 16S RRNA GENE SEQUENCING RESULTS FROM NIOBRARA SHALE PRODUCED WATER." In GSA 2020 Connects Online. Geological Society of America, 2020. http://dx.doi.org/10.1130/abs/2020am-351340.

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