Relevant bibliographies by topics / 16S rDNA profiling

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Academic literature on the topic '16S rDNA profiling'

Author: Grafiati
Published: 28 June 2021
Last updated: 12 February 2022

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Journal articles on the topic "16S rDNA profiling"

1

Gu, F., Y. Li, C. Zhou, D. T. W. Wong, C. M. Ho, F. Qi, and W. Shi. "Bacterial 16S rRNA/rDNA Profiling in the Liquid Phase of Human Saliva." Open Dentistry Journal 3, no. 1 (April 28, 2009): 80–84. http://dx.doi.org/10.2174/1874210600903010080.

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Human saliva can be separated by centrifugation into cell pellet and cell-free supernatant, which are called cellular phase and liquid phase in this study. While it is well documented that the cellular phase of saliva contains hundreds of oral bacteria species, little is known whether the liquid phase of saliva contains any information related to oral microbiota. In this study, we analyzed the bacterial nucleic acid contents of the liquid phase of saliva. Using primers universal to most eubacterial 16S rDNA, we detected large amounts of bacterial 16S rRNA and rDNA in the cell-free phase of saliva. Random sequencing analysis of forty PCR amplicons from the cell-free phase of saliva led to 15 operational taxonomic unit (OTU) groups. Furthermore, using denaturing gradient gel electrophoresis (DGGE), we compared 16S rRNA/rDNA profiles derived from liquid phases and cellular phases of saliva samples, and found positive correlations (Pearson Correlation=0.822,P<0.001) between these sample groups. These findings indicate that the liquid phase of saliva contains numerous bacterial 16S rRNA/rDNA molecules that have correlations with bacteria existing in the cellular phase.
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Wood, Jacqueline, Karen P. Scott, Gorazd Avguštin, C. James Newbold, and Harry J. Flint. "Estimation of the Relative Abundance of DifferentBacteroides and Prevotella Ribotypes in Gut Samples by Restriction Enzyme Profiling of PCR-Amplified 16S rRNA Gene Sequences." Applied and Environmental Microbiology 64, no. 10 (October 1, 1998): 3683–89. http://dx.doi.org/10.1128/aem.64.10.3683-3689.1998.

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ABSTRACT We describe an approach for determining the genetic composition ofBacteroides and Prevotellapopulations in gut contents based on selective amplification of 16S rRNA gene sequences (rDNA) followed by cleavage of the amplified material with restriction enzymes. The relative contributions of different ribotypes to total Bacteroides andPrevotella 16S rDNA are estimated after end labelling of one of the PCR primers, and the contribution ofBacteroides and Prevotellasequences to total eubacterial 16S rDNA is estimated by measuring the binding of oligonucleotide probes to amplified DNA.Bacteroides and Prevotella 16S rDNA accounted for between 12 and 62% of total eubacterial 16S rDNA in samples of ruminal contents from six sheep and a cow. Ribotypes 4, 5, 6, and 7, which include most cultivated rumen Prevotellastrains, together accounted for between 20 and 86% of the total amplified Bacteroides andPrevotella rDNA in these samples. The most abundantBacteroides or Prevotella ribotype in four animals, however, was ribotype 8, for which there is only one known cultured isolate, while ribotypes 1 and 2, which include many colonic Bacteroides spp., were the most abundant in two animals. This indicates that some abundantBacteroides and Prevotella groups in the rumen are underrepresented among cultured rumenPrevotella isolates. The approach described here provides a rapid, convenient, and widely applicable method for comparing the genotypic composition of bacterial populations in gut samples.
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Galovic, Vladislava, Milan Drekic, Sreten Vasic, Sinisa Andrasev, Sasa Pekec, Dejan Stojanovic, and Verica Vasic. "Mitochondrial 16s rDNA profiling and phylogenetic analysis suggest genetic diversity of ash weevil (Stereonichus fraxini De Geer) in Serbia." Genetika 51, no. 2 (2019): 675–86. http://dx.doi.org/10.2298/gensr1902675g.

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This study contributes to knowledge of ash weevil (Stereonychus fraxini De Geer) molecular taxonomy, phylogeny and genetic diversity. Adult and larvae stages of insect were collected from several locations covering northern and central part of Serbia cojoined with homologous sequences with respect to their different geographic origin and hypothesis of their evolutionary relationships. Due to its slow rates of evolution the gene region that covers mitochondrial 16S rDNA, was choice for sequence profiling and phylogenetic reconstruction of ash weevil in correspondence with sequences of related tribes Cionini. Phylogenetic analyses demonstrating clear separation of the native weevil populations and the Cionini tribes. Even though bioinformatic tools confirm that all native specimens belong to species Stereonychus fraxini, different profile of the mitochondrial 16S rDNA in the clade of Serbian specimens indicate intraspecific genomic rearrangement in one specimen detached it to northern geographic position. Those particular specimens invade also different Fraxinus species. Genetic distinctness of other imagos from this particular individual proved by indels and point mutations found in their sequences. By screening the mitochondrial 16S rDNA, molecular evidence suggests the existence of the specimen with rearranged genome that indicate genetic variability in native populations of ash weevil species.
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Adesetan, Titilayo O., Moses O. Efuntoye, and Olubukola O. Babalola. "Genotypic Profiling of Bacillus cereus Recovered from Some Retail Foods in Ogun State, Nigeria, and Their Phylogenetic Relationship." International Journal of Microbiology 2020 (September 14, 2020): 1–9. http://dx.doi.org/10.1155/2020/3750948.

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Identifying Bacillus cereus with conventional methods is neither specific nor rapid because of the close relatedness of the B. cereus group, hence the need for molecular methods. Genotypic profiling of B. cereus isolates from food was obtained by Random Amplified Polymorphic DNA-polymerase chain reaction (RAPD-PCR) using OPR13 primer. A dendrogram was drawn with the Numerical Taxonomy System of Statistic (NTSYS) software. Thirty of the isolates were subjected to molecular identification by 16S rDNA sequencing. The thirty sequences were deposited in GenBank for accession number. Phylogenetic relationship of the 16S rDNA sequence obtained was carried out with the Multiple Alignment using Fast Fourier Transform (MAFFT) software version 7.0. The evolutionary tree was drawn using the Molecular Evolutionary Genetics Analysis (MEGA 6) software. The dendrogram generated for the RAPD profile showed that all the strains are closely related, with a similarity coefficient of 70%. The isolates were confirmed with 16S rDNA sequencing as B. cereus. The thirty sequences deposited in GenBank were given accession numbers: KX574760–KX574769, KX610811–KX610820, MT757957-MT757963, and MT772282-MT772284. By comparing the phylogenetic relationship, eleven of the strains did not cluster with the reference strains from the GenBank but form distinct clades, which means they are likely to be of different ancestors. Conventional methods rarely differentiate bacteria of the same species into clade, neither can it describe their ancestral lineage. Therefore, it is important to employ molecular methods in identifying bacteria to give detailed information about them.
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Raju, Sajan C., Sonja Lagström, Pekka Ellonen, Willem M. de Vos, Johan G. Eriksson, Elisabete Weiderpass, and Trine B. Rounge. "Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling." Journal of Microbiological Methods 147 (April 2018): 76–86. http://dx.doi.org/10.1016/j.mimet.2018.03.003.

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6

Dickinson, Danielle N., Myron T. La Duc, William E. Haskins, Igor Gornushkin, James D. Winefordner, David H. Powell, and Kasthuri Venkateswaran. "Species Differentiation of a Diverse Suite of Bacillus Spores by Mass Spectrometry-Based Protein Profiling." Applied and Environmental Microbiology 70, no. 1 (January 2004): 475–82. http://dx.doi.org/10.1128/aem.70.1.475-482.2004.

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ABSTRACT In this study, we demonstrate the versatility of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOFMS) protein profiling for the species differentiation of a diverse suite of Bacillus spores. MALDI-TOFMS protein profiles of 11 different strains of Bacillus spores, encompassing nine different species, were evaluated. Bacillus species selected for MALDI-TOFMS analysis represented the spore-forming bacterial diversity of typical class 100K clean room spacecraft assembly facilities. A one-step sample treatment and MALDI-TOFMS preparation were used to minimize the sample preparation time. A library of MALDI-TOFMS spectra was created from these nine Bacillus species, the most diverse protein profiling study of the genus reported to date. Linear correlation analysis was used to successfully differentiate the MALDI-TOFMS protein profiles from all strains evaluated in this study. The MALDI-TOFMS protein profiles were compared with 16S rDNA sequences for their bacterial systematics and molecular phylogenetic affiliations. The MALDI-TOFMS profiles were found to be complementary to the 16S rDNA analysis. Proteomic studies of Bacillus subtilis 168 were pursued to identify proteins represented by the biomarker peaks in the MALDI-TOFMS spectrum. Four small, acid-soluble proteins (A, B, C, and D), one DNA binding protein, hypothetical protein ymf J, and four proteins associated with the spore coat and spore coat formation (coat JB, coat F, coat T, and spoIVA) were identified. The ability to visualize higher-molecular-mass coat proteins (10 to 25 kDa) as well as smaller proteins (<10 kDa) with MALDI-TOFMS profiling is critical for the complete and effective species differentiation of the Bacillus genus.
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Rogers, G. B., C. A. Hart, J. R. Mason, M. Hughes, M. J. Walshaw, and K. D. Bruce. "Bacterial Diversity in Cases of Lung Infection in Cystic Fibrosis Patients: 16S Ribosomal DNA (rDNA) Length Heterogeneity PCR and 16S rDNA Terminal Restriction Fragment Length Polymorphism Profiling." Journal of Clinical Microbiology 41, no. 8 (August 1, 2003): 3548–58. http://dx.doi.org/10.1128/jcm.41.8.3548-3558.2003.

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Apajalahti, Juha H. A., Anu Kettunen, Michael R. Bedford, and William E. Holben. "Percent G+C Profiling Accurately Reveals Diet-Related Differences in the Gastrointestinal Microbial Community of Broiler Chickens." Applied and Environmental Microbiology 67, no. 12 (December 1, 2001): 5656–67. http://dx.doi.org/10.1128/aem.67.12.5656-5667.2001.

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ABSTRACT Broiler chickens from eight commercial farms in Southern Finland were analyzed for the structure of their gastrointestinal microbial community by a nonselective DNA-based method, percent G+C-based profiling. The bacteriological impact of the feed source and in-farm whole-wheat amendment of the diet was assessed by percent G+C profiling. Also, a phylogenetic 16S rRNA gene (rDNA)-based study was carried out to aid in interpretation of the percent G+C profiles. This survey showed that most of the 16S rDNA sequences found could not be assigned to any previously known bacterial genus or they represented an unknown species of one of the taxonomically heterogeneous genera, such as Ruminococcus or Clostridium. The data from bacterial community profiling were analyzed byt-test, multiple linear regression, and principal-component statistical approaches. The percent G+C profiling method with appropriate statistical analyses detected microbial community differences smaller than 10% within each 5% increment of the percent G+C profiles. Diet turned out to be the strongest determinant of the cecal bacterial community structure. Both the source of feed and local feed amendment changed the bacteriological profile significantly, whereas profiles of individual farms with identical feed regimens hardly differed from each other. This suggests that the management of typical Finnish farms is relatively uniform or that hygiene on the farm, in fact, has little impact on the structure of the cecal bacterial community. Therefore, feed compounders should have a significant role in the modulation of gut microflora and consequently in prevention of gastrointestinal disorders in farm animals.
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Wood, J., KP Scott, G. Avguštin, CJ Newbold, F. McIntosh, and HJ Flint. "A 16S rDNA-based molecular profiling approach for studying relative changes in ruminal bacterial populations." Reproduction Nutrition Development 37, Suppl. 1 (1997): 30–31. http://dx.doi.org/10.1051/rnd:19970710.

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Scheldeman, Patsy, Marina Rodríguez-Díaz, Johan Goris, Annelies Pil, Elke De Clerck, Lieve Herman, Paul De Vos, Niall A. Logan, and Marc Heyndrickx. "Bacillus farraginis sp. nov., Bacillus fortis sp. nov. and Bacillus fordii sp. nov., isolated at dairy farms." International Journal of Systematic and Evolutionary Microbiology 54, no. 4 (July 1, 2004): 1355–64. http://dx.doi.org/10.1099/ijs.0.63095-0.

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Forty-eight bacterial strains were isolated at dairy farms from raw milk, the milking apparatus, green fodder or feed concentrate after a heat treatment of 30 min at 100 °C. In this way, spore-forming bacteria with a very high intrinsic heat resistance were selected for. The aerobic spore-forming isolates were subjected to a polyphasic taxonomical study, including repetitive element sequence-based PCR typing, whole-cell protein profiling, 16S rDNA sequence analysis, DNA–DNA hybridizations, DNA base composition, fatty acid analysis, and morphological and biochemical characteristics. A comparison of the REP- and (GTG)5-PCR and whole-cell protein SDS-PAGE profiles resulted in three clusters of similar strains. Analysis of the 16S rDNA sequences and DNA–DNA relatedness data showed that these clusters represented three novel species. The highest 16S rDNA similarity to a recognized species found for the three groups was around 94 % with Bacillus lentus and Bacillus sporothermodurans. Further phenotypic characterization supported the proposal of three novel species in the genus Bacillus, Bacillus farraginis, Bacillus fortis and Bacillus fordii. The respective type strains are R-6540T (=LMG 22081T=DSM 16013T), R-6514T (=LMG 22079T=DSM 16012T) and R-7190T (=LMG 22080T=DSM 16014T); their G+C DNA base contents are 43·7, 44·3 and 41·9 mol%, respectively. Although in variable amounts, a predominance of the branched fatty acids iso-C15 : 0 and anteiso-C15 : 0 was observed in all three novel species.
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Dissertations / Theses on the topic "16S rDNA profiling"

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Chen, Hung-Hsuan, and 陳弘軒. "Studies on Gene Map of 16S rDNA and Protein Profiling of Tetrodotoxin-Producing Bacteria." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/49411481138429021460.

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碩士
亞洲大學
保健營養生技學系
103
Tetrodotoxin (TTX) is a low-molecular weight and non-protein neurotoxin. About the TTX-bearing organisms, according to the results of previous studies, TTX was well known produced by exogenously. Those who support the idea of exogenous origins of TTX, believe that TTX is produced by bacteria and acquired through one of two modes. First, the bacteria produce TTX, which is then transferred up through the food chain. In the main studies on Tetrodotoxin contained with species of TTX-bearing organisms, identification of TTX-producing bacteria, ability in producing TTX and medical use of TTX , but few of discussion on the possibly toxic genes and proteins. There explore a value between the TTX-producing bacteria and Tetrodotoxin. Gene analysis techniques are commonly used for bacteria identification because technological advances in molecular biology. In this study we used primer set 8F and U1492R to amplified 16S rDNA, according to the experimental results, we successfully established 16S rDNA sequences data, contained wih 11 strains of TTX-producing bacteria and 20 strains of non TTX-producing bacteria. All of these 16S rDNA sequences had been submitted to NCBI and provided Accession numbers from GenBank. We have explored the possibly species-specific sensitivity of TTX-producing bacteria by DNAMAN for sequence alignment and MEGA4 for phylogenetic tree based on 16S rDNA. The experimental results show that a high degree of consistency of TTX-producing bacteria and non TTX-producing bacteria, there was no specific fragment in 16S rDNA. Therefore, this method does not suitable for the identification of TTX-producing bacteria. In the second chapter, we identification of TTX-producing and non-producing bacteria, and the specificity TTX-associated protein of the TTX-producing bacteria based on SDS-PAGE. Protein separation by SDS-PAGE can be used to estimate relative molecular mass, to determine the relative abundance of major proteins in a sample, and to determine the distribution of proteins among fractions. According to the experimental results show that, TTX-producing bacteria have different species-specific bands in the molecular weight 120.0 and 41.1 kDa. T-014 and T-015 have these species-specific bands, but does not exist in non TTX-producing bacteria. So we surmise that the species-specific bands of T-014 and 015 are the specificity TTX-associated protein in TTX-producing bacteria. Based on the above, we can classify as a first and rapid identification of TTX-producing and non-producing bacteria.
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Vodolánová, Lucie. "Bakteriom stolice při terapii dětských neinfekčních onemocnění." Master's thesis, 2021. http://www.nusl.cz/ntk/nusl-445767.

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The intestinal microbiota is composed of up to 100 trillion microorganisms of which bacteria are overwhelming majority. The microbiota affects the development of the immune system, defence against pathogens, host nutrition, vitamin synthesis or fat storage and its composition is changing throughout life. Some studies point to an association between microbiota composition and the development of inflammatory bowel disease. One of the treatment options is anti-TNFα antibodies therapy, which uptake or antagonize the TNFα cytokine that otherwise mediates inflammation in the intestinal mucosa. The aim of the thesis was to examine how this treatment affects the composition of the intestinal bacteriome in paediatric patients with Crohn's disease, and to find specific bacterial taxa, whose abundance changes during the treatment. By inclusion of patients with juvenile idiopathic arthritis, also treated with anti-TNFα, the study aims to discern specific effects of therapeutically induced intestinal restitution (observable in patients with Crohn's disease) from general effects of anti-TNFα therapy. Stool samples from healthy children were used to determine "healthy" bacteriome. The composition of the bacteriome was studied by profiling the variable region of the V4 gene of 16S rDNA from patients stool samples...
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Purwandari, Anggraini Ratih, and 朴萬達. "Profiling of Intestinal Microbial Diversity by PCR-DGGE Genes Coding for 16S rDNA and Immunity Status of the Orange Spotted Grouper (Epinephelus coioides) Following Probiotic Bacillus subtilis Administration." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/53475441628459158308.

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碩士
國立中山大學
海洋生物研究所
101
Groupers are an important mariculture fish in Taiwan and Southeast Asian countries. The rapidly growing orange spotted grouper (Epinephelus coioides) has experienced relatively severe bacterial disease problems. The proliferation of pathogens in fish can be suppressed by commensal microbiota. In this context, probiotic seem to offer an attractive alternative. Bacillus subtilisis a probiotic bacteriumthat is administered in diet to suppress proliferation of pathogens. In the present study, E.coioideswere fed for 6 months with diets containing B.subtilis at 0 (control), 0.1 % and 1 %. Percent weight gain and feed efficiency of the 0.1 and 1 % groups were significantlybetter than the control group. The innate cellular response, respiratory burst of the fish fed the 1 % and 0.1 % diet was significantly higher compared to the control group on 10 or 20 days after feeding, and even moresignificanton 30 days.ProbioticBacillus subtilis increased the fish’s intestinal microbial diversity as measured by visible band number and Shannon diversity indexin DGGE analysis. Probiotic Bacillus subtilis also stimulated the population of bacterial species likePaenibacillussp,Lactobacillus oenistrain 59 b, and Methilacidophiluminfernorumstrain V4 that beneficial for Epinephelus coioides. The best dose of probiotic Bacillus subtilis based on growth performances, innate cellular responses and profile of microbiota in fish intestines is 0.1 %, which showed equal efficacy as the 1% diet.
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