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Journal articles on the topic '16S rDNA gene sequencing'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

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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2

Wang, Haiyin, Pengcheng Du, Juan Li, et al. "Comparative analysis of microbiome between accurately identified 16S rDNA and quantified bacteria in simulated samples." Journal of Medical Microbiology 63, no. 3 (2014): 433–40. http://dx.doi.org/10.1099/jmm.0.060616-0.

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Although 16S rRNA gene (rDNA) sequencing is the gold standard for categorizing bacteria or characterizing microbial communities its clinical utility is limited by bias in metagenomic studies, in either the experiments or the data analyses. To evaluate the efficiency of current metagenomic methods, we sequenced seven simulated samples of ten bacterial species mixed at different concentrations. The V3 region of 16S rDNA was targeted and used to determine the distribution of bacterial species. The number of target sequences in individual simulated samples was in the range 1–1000 to provide a bett

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Chatellier, Sonia, Nathalie Mugnier, Françoise Allard, et al. "Comparison of two approaches for the classification of 16S rRNA gene sequences." Journal of Medical Microbiology 63, no. 10 (2014): 1311–15. http://dx.doi.org/10.1099/jmm.0.074377-0.

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The use of 16S rRNA gene sequences for microbial identification in clinical microbiology is accepted widely, and requires databases and algorithms. We compared a new research database containing curated 16S rRNA gene sequences in combination with the lca (lowest common ancestor) algorithm (RDB-LCA) to a commercially available 16S rDNA Centroid approach. We used 1025 bacterial isolates characterized by biochemistry, matrix-assisted laser desorption/ionization time-of-flight MS and 16S rDNA sequencing. Nearly 80 % of isolates were identified unambiguously at the species level by both classificat

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Korczak, Bożena, Henrik Christensen, Stefan Emler, Joachim Frey, and Peter Kuhnert. "Phylogeny of the family Pasteurellaceae based on rpoB sequences." International Journal of Systematic and Evolutionary Microbiology 54, no. 4 (2004): 1393–99. http://dx.doi.org/10.1099/ijs.0.03043-0.

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Sequences of the gene encoding the β-subunit of the RNA polymerase (rpoB) were used to delineate the phylogeny of the family Pasteurellaceae. A total of 72 strains, including the type strains of the major described species as well as selected field isolates, were included in the study. Selection of universal rpoB-derived primers for the family allowed straightforward amplification and sequencing of a 560 bp fragment of the rpoB gene. In parallel, 16S rDNA was sequenced from all strains. The phylogenetic tree obtained with the rpoB sequences reflected the major branches of the tree obtained wit

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Lawton, Samantha J., Allison M. Weis, Barbara A. Byrne, et al. "Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing." Journal of Veterinary Diagnostic Investigation 30, no. 3 (2018): 354–61. http://dx.doi.org/10.1177/1040638718762562.

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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared to conventional biochemical testing methods and nucleic acid analyses (16S rDNA sequencing, hippurate hydrolysis gene testing, whole genome sequencing [WGS]) for species identification of Campylobacter isolates obtained from chickens ( Gallus gallus domesticus, n = 8), American crows ( Corvus brachyrhynchos, n = 17), a mallard duck ( Anas platyrhynchos, n = 1), and a western scrub-jay ( Aphelocoma californica, n = 1). The test results for all 27 isolates were in 100% agreement between MALDI

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Li, Yong Feng, Yi Xuan Wang, Lu Wang, and Zhan Qing Wang. "Sequence Length Variation of Internal Genic Space of 16S rDNA-23S rDNA in Bacterium with High Yield of Hydrogen Production." Advanced Materials Research 183-185 (January 2011): 1413–16. http://dx.doi.org/10.4028/www.scientific.net/amr.183-185.1413.

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To develop the identification of species for fermentative biohydrogen-producing bacterium, scholars have found a method which is based on PCR amplification of the 16S rRNA gene (rDNA)-23S rDNA intergenic regions. In the study, a large fragment of the rDNA operon, including the 16S rDNA, the intergenic spacer region (ISR) and approximately 2000 bases of the 23S rDNA, were polymerasechain reaction (PCR) amplified. The PCR amplification of the genomic DNA of Leptonema ilk strain 3055 using primers directed against conserved regions of the rRNA operon provided evidence that the 16S and 23S rRNA ge

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Carvalho-Netto, Osmar Vaz de, Daniel Dias Rosa, and Luis Eduardo Aranha Camargo. "Identificarion of contaminant bacteria in cachaça yeast by 16s rDNA gene sequencing." Scientia Agricola 65, no. 5 (2008): 508–15. http://dx.doi.org/10.1590/s0103-90162008000500010.

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Cachaça is a typical Brazilian liquor produced from the distillation of fermented sugarcane juice mainly by Saccharomyces cerevisiae. Most of the domestic production is artisanal, and producers usually are not concerned regarding microbiological control of the fermentation. This study aimed to characterize the contaminant bacterial community of the yeast used in the production of cachaça in an artisanal still. Four samples were collected, of which one (NA) was used for comparison purposes and was collected one year earlier. The remaining samples were collected at three different periods: at th

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Agudelo-Pérez, Sergio, A. Melissa Moreno, Juliana Martínez-Garro, et al. "16S rDNA Sequencing for Bacterial Identification in Preterm Infants with Suspected Early-Onset Neonatal Sepsis." Tropical Medicine and Infectious Disease 9, no. 7 (2024): 152. http://dx.doi.org/10.3390/tropicalmed9070152.

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Background: The high prevalence of suspected early-onset neonatal sepsis among preterm infants leads to immediate antibiotic administration upon admission. Notably, most blood cultures for suspected early-onset neonatal sepsis do not yield a causative pathogen. This study aimed to assess polymerase chain reaction (PCR) targeting the variable region V4 of the 16S ribosomal gene (16S rDNA) and Sanger sequencing for bacterial identification in preterm infants with suspected early-onset neonatal sepsis. Methods: Therefore, this prospective study was conducted. Preterm infants with suspected early-

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Hinrikson, Hans Peter, Fabrizio Dutly, and Martin Altwegg. "Evaluation of a Specific Nested PCR Targeting Domain III of the 23S rRNA Gene of “Tropheryma whippelii” and Proposal of a Classification System for Its Molecular Variants." Journal of Clinical Microbiology 38, no. 2 (2000): 595–99. http://dx.doi.org/10.1128/jcm.38.2.595-599.2000.

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“Tropheryma whippelii”-associated infections are usually confirmed histopathologically by using light microscopy. PCR assays targeting the 16S rRNA gene (16S rDNA) of “T. whippelii” are increasingly being applied for this purpose. Compared to microscopic analysis, PCR seems to be more sensitive, as indicated by the fact that several cases of Whipple's disease with negative histopathological findings but positive PCR results have been reported. Considering the lack of pathognomonic clinical features for this disease and the fact that “T. whippelii” DNA has repeatedly been found in patients with

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10

da Silva, Cleiziane Bispo, Hellen Ribeiro Martins dos Santos, Phellippe Arthur Santos Marbach, et al. "First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds." PeerJ 7 (November 20, 2019): e7452. http://dx.doi.org/10.7717/peerj.7452.

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Background Intragenomic variability in 16S rDNA is a limiting factor for taxonomic and diversity characterization of Bacteria, and studies on its occurrence in natural/environmental populations are scarce. In this work, direct DNA amplicon sequencing coupled with frequent-cutter restriction analysis allowed detection of intragenomic 16S rDNA variation in culturable endophytic bacteria from cacao seeds in a fast and attractive manner. Methods Total genomic DNA from 65 bacterial strains was extracted and the 16S rDNA hyper variable V5–V9 regions were amplified for enzyme digestion and direct San

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LI, Xin, Xiao-fei ZHU, Cheng-fei ZHANG, Peter Cathro, Seneviratne CJ, and Song SHEN. "Endodontic bacteria from primary and persistent endodontic lesions in Chinese patients as identified by cloning and 16S ribosomal DNA gene sequencing." Chinese Medical Journal 126, no. 4 (2013): 634–39. http://dx.doi.org/10.3760/cma.j.issn.0366-6999.20122285.

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Background Few literatures pertain to the 16S ribosomal DNA (16S rDNA) analysis of bacteria contributing to primary and persistent endodontic lesions, with no information available for the Chinese population. As such, we investigated endodontic bacteria associated with primary and persistent endodontic lesions in adult Chinese patients living in Beijing, China using 16S rDNA gene sequencing techniques. Methods Endodontic microbial samples were obtained from fourteen adult Chinese patients and subjected to DNA extraction. Pllymerase chain reaction (PCR) products were cloned and 100 clones from

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Stubbs, Simon L. J., Jon S. Brazier, Paul R. Talbot, and Brian I. Duerden. "PCR-Restriction Fragment Length Polymorphism Analysis for Identification of Bacteroides spp. and Characterization of Nitroimidazole Resistance Genes." Journal of Clinical Microbiology 38, no. 9 (2000): 3209–13. http://dx.doi.org/10.1128/jcm.38.9.3209-3213.2000.

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Bacteroides spp. are opportunist pathogens that cause blood and soft tissue infections and are often resistant to antimicrobial agents. We have developed a combined PCR-restriction fragment length polymorphism (RFLP) technique to characterize the 16S rRNA gene for identification purposes and the nitroimidazole resistance (nim) gene for detection of resistance to the major antimicrobial agent used to treat Bacteroidesinfections: metronidazole (MTZ). PCR-RFLP analysis of 16S ribosomal (rDNA) with HpaII and TaqI produced profiles that enabled discrimination of type strains and identification of 7

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Li, Xu-Ming, Qing Lv, Ya-Jun Chen, Lu-Biao Yan, and Xin Xiong. "Association between childhood obesity and gut microbiota: 16S rRNA gene sequencing-based cohort study." World Journal of Gastroenterology 30, no. 16 (2024): 2249–57. http://dx.doi.org/10.3748/wjg.v30.i16.2249.

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BACKGROUND This study aimed to identify characteristic gut genera in obese and normal-weight children (8-12 years old) using 16S rDNA sequencing. The research aimed to provide insights for mechanistic studies and prevention strategies for childhood obesity. Thirty normal-weight and thirty age- and sex-matched obese children were included. Questionnaires and body measurements were collected, and fecal samples underwent 16S rDNA sequencing. Significant differences in body mass index (BMI) and body-fat percentage were observed between the groups. Analysis of gut microbiota diversity revealed lowe

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Satokari, Reetta M., Elaine E. Vaughan, Antoon D. L. Akkermans, Maria Saarela, and Willem M. de Vos. "Bifidobacterial Diversity in Human Feces Detected by Genus-Specific PCR and Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 67, no. 2 (2001): 504–13. http://dx.doi.org/10.1128/aem.67.2.504-513.2001.

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ABSTRACT We describe the development and validation of a method for the qualitative analysis of complex bifidobacterial communities based on PCR and denaturing gradient gel electrophoresis (DGGE).Bifidobacterium genus-specific primers were used to amplify an approximately 520-bp fragment from the 16S ribosomal DNA (rDNA), and the fragments were separated in a sequence-specific manner in DGGE. PCR products of the same length from different bifidobacterial species showed good separation upon DGGE. DGGE of fecal 16S rDNA amplicons from five adult individuals showed host-specific populations of bi

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Guan, Jian Fei, Ji Hua Wang, Xiang Liu, Jia Xin, Shan Shan Zhang, and Dan Zhu. "Biodegradation of 2,2' 4,4-tetrabromodiphenyl Ether in an Aerobic Environment by a Novel Strain of Bacillus sp." Advanced Materials Research 771 (September 2013): 45–49. http://dx.doi.org/10.4028/www.scientific.net/amr.771.45.

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The environmental safety of 2,2,4,4-tetrabromodiphenyl ether (BDE-47), a widely used flame retardant, has been the topic of controversial discussions during the past decade years. In this study, we investigated the BDE-47 degradation by a novel bacteria obtained from electronic waste recycling site soil sample in Taizhou, China. Using biochemical characteristics and 16S rDNA gene sequencing, the strain was closely related to Bacillus sp. with a 99% 16S rDNA gene sequence similarity. It could use BDE-47 as the sole carbon source and energy source for its growth. The optimal growth environment w

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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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Wang, Jiayi, Jianlei Gu, Yizhong Wang, et al. "16S rDNA Gene Sequencing Analysis in Functional Dyspepsia Treated With Fecal Microbiota Transplantation." Journal of Pediatric Gastroenterology and Nutrition 64, no. 3 (2017): e80-e82. http://dx.doi.org/10.1097/mpg.0000000000001476.

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Chishty, Nadim, Srinivasan R, Dinesh K. Kumawat, Yogesh Franklin, and Anil Tripathi. "Diversity of Lactic Acid Bacteria in dairy products of Southern Rajasthan." South Asian Journal of Experimental Biology 3, no. 2 (2013): 92–96. http://dx.doi.org/10.38150/sajeb.3(2).p92-96.

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Lactic acid bacteria (LAB) are a group of gram positive, non spore forming, cocci or rod shaped, catalase negative and fastidious organisms. They are considered as “GRAS” (Generally Recognized As Safe) organisms. A total of 86 bacterial isolates were isolated from different samples of raw milk, buttermilk and curd by using MRS agar and M17 agar. Lactic Acid Bacteria have similar nutritional and growth requirements, it becomes difficult and laborious to identify them by classical methods. Hence, molecular typing was attempted to find the diversity, 16S rDNA gene amplification was done using spe

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Coombs, Justin T., and Christopher M. M. Franco. "Isolation and Identification of Actinobacteria from Surface-Sterilized Wheat Roots." Applied and Environmental Microbiology 69, no. 9 (2003): 5603–8. http://dx.doi.org/10.1128/aem.69.9.5603-5608.2003.

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ABSTRACT This is the first report of filamentous actinobacteria isolated from surface-sterilized root tissues of healthy wheat plants (Triticum aestivum L.). Wheat roots from a range of sites across South Australia were used as the source material for the isolation of the endophytic actinobacteria. Roots were surface-sterilized by using ethanol and sodium hypochlorite prior to the isolation of the actinobacteria. Forty-nine of these isolates were identified by using 16S ribosomal DNA (rDNA) sequencing and found to belong to a small group of actinobacterial genera including Streptomyces, Microb

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Girdhar, Anurag, Jagdish Chinnappa, Feroze Ganaie, Vandana Govindan, Kadahalli Ravikumar, and Geetha Nagaraj. "Bacterial Profile of Middle Ear Fluid with Recurrent Acute Otitis Media Infection Using Culture Independent 16S rDNA Gene Sequencing." Journal of Pediatric Infectious Diseases 14, no. 03 (2018): 108–15. http://dx.doi.org/10.1055/s-0038-1675786.

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Background Recurrent otitis media is one of the common infections of childhood. The causative bacterial pathogen is one of the major risk factors of recurrent infection. With limited availability of Indian data, we performed this study to identify the bacterial pathogens. Materials and Methods Otitis media cases were diagnosed based on clinical criteria. Thirty-six middle ear fluid (MEF) samples were collected by tympanocentesis and cultured for pathogens. Seventy-eight per cent of the cases had three previous episodes of otitis media in the past 6 months; the remaining 22% had four episodes i

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Tajbakhsh, Mercedeh, Babak Noory Nayer, Kamyar Motavaze, et al. "Phylogenetic relationship of Salmonella enterica strains in Tehran, Iran, using 16S rRNA and gyrB gene sequences." Journal of Infection in Developing Countries 5, no. 06 (2011): 465–72. http://dx.doi.org/10.3855/jidc.1504.

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Introduction: We assessed whether 16S rDNA and gyrB gene sequences, alone or combined, were suitable for determining the phylogenetic relationship among Salmonella enterica strains isolated from Tehran, Iran. Patients over five years of age enrolled in an acute diarrheal surveillance project in Tehran province between May 2004 and October 2006 were selected as our study group. Methodology: 16S ribosomal DNA (rDNA) and gyrB genes from 40 Salmonella isolates obtained from patients with acute diarrhea were sequenced and the data was used to generate phylogenetic trees that facilitated isolate com

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Gunaedi, Tri, Sebastian Margino, Langkah Sembiring, and Rarastoeti Pratiwi. "IDENTIFIKASI DAN KLASIFIKASI BAKTERI AMILOLITIK ISOLAT TG12, TG19, DAN TG31 PENYEBAB KEMASAMAN PADA TEPUNG SAGU BASAH BERDASARKAN ANALISIS GEN 16SrDNA." Berkala Penelitian Hayati 15, no. 1 (2009): 25–30. http://dx.doi.org/10.23869/bphjbr.15.1.20096.

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16SrDNA gene were known essentialy for procaryotic life involved bacteria. The gene very concerved such as usefull for bacterial identification and classification in phylogeny tree constructed. The object of this research were identified and cllassified amylolitic bacteria TG12, TG19 and TG31 isolates, causers sourness on raw starch sago by 16SrDNA gene sequences analysis approach. The native isolates from raw starch sago under traditionality processing arround Jayapura and selected depend on activity amylolitic and organic acid productivity. Before DNA genom extraction, isolates were throught

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Schlunck, Günther, Philip Maier, Barbara Maier, et al. "Next-Generation Sequencing of the Human Aqueous Humour Microbiome." International Journal of Molecular Sciences 25, no. 11 (2024): 6128. http://dx.doi.org/10.3390/ijms25116128.

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The microbiome of the ocular surface has been characterised, but only limited information is available on a possible silent intraocular microbial colonisation in normal eyes. Therefore, we performed next-generation sequencing (NGS) of 16S rDNA genes in the aqueous humour. The aqueous humour was sampled from three patients during cataract surgery. Air swabs, conjunctival swabs from patients as well as from healthy donors served as controls. Following DNA extraction, the V3 and V4 hypervariable regions of the 16S rDNA gene were amplified and sequenced followed by denoising. The resulting Amplico

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Benítez-Páez, Alfonso, Kevin J. Portune, and Yolanda Sanz. "Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer." GigaScience 5, no. 1 (2016): 4. https://doi.org/10.1186/s13742-016-0111-z.

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<strong>Background: </strong>The miniaturised and portable DNA sequencer MinION™ has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide variety of genetic approaches. This technology has demonstrated great potential, especially in genome-wide analyses. In this study, we tested the ability of the MinION™ system to perform amplicon sequencing in order to design new approaches to study microbial diversity using nearly full-length 16S rDNA sequences.<strong>Results: </strong>Using R7.3 chemistry, we generated more than

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Rajan, Sancho, Anwesha Pattanaik, Venkatesh Kumaresan, et al. "Characterization of some naphthalene using bacteria isolated from contaminated Cooum Riverine sediment of the Bay of Bengal (India)." Journal of the Serbian Chemical Society 84, no. 2 (2019): 225–36. http://dx.doi.org/10.2298/jsc180724088r.

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Microorganisms capable of using naphthalene as the sole carbon source were isolated from the contaminated sediment of Cooum River. Twenty one isolates were recovered and nine were selected for enrichment due to differences in their morphological characteristics. Out of nine isolates, only four (NS3-SRMND14B, NS14-SRMND14A, NS15-SRMND14D and NS19- -SRMND14E) were capable of completely utilizing naphthalene as the sole source of carbon in carbon free minimal medium (CFMM) supplemented with naphthalene. 16S rDNA sequencing showed that all the four isolates were distantly related to each other and

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Yang, Chan Jin, Ju Sun Song, Jeong-Ju Yoo, et al. "16S rRNA Next-Generation Sequencing May Not Be Useful for Examining Suspected Cases of Spontaneous Bacterial Peritonitis." Medicina 60, no. 2 (2024): 289. http://dx.doi.org/10.3390/medicina60020289.

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Background and Objectives: Ascites, often associated with liver cirrhosis, poses diagnostic challenges, particularly in detecting bacterial infections. Traditional methods have limitations, prompting the exploration of advanced techniques such as 16S rDNA next-generation sequencing (NGS) for improved diagnostics in such low-biomass fluids. The aim of this study was to investigate whether the NGS method enhances detection sensitivity compared to a conventional ascites culture. Additionally, we aimed to explore the presence of a microbiome in the abdominal cavity and determine whether it has a s

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Ningrum, Siti Gusti, Antonia Kreitlow, Christoph Lämmler, et al. "Molecular Characterisation of an Arcanobacterium sp. Isolate from a Buffalo (Bubalus bubalis)." Journal of Buffalo Science 13 (December 3, 2024): 150–57. https://doi.org/10.6000/1927-520x.2024.13.17.

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The objective of the current investigation was to provide a comprehensive characterisation of an Arcanobacterium isolate derived from Bubalus bubalis. The confirmation of the species identity of Arcanobacterium sp. 15/M226/2/9 in this study was achieved by examining phenotypic characteristics and phylogenetic analysis. These analyses involved determining hemolysis on Columbia sheep blood agar and biochemical parameters using the Api-Coryne test kit, MALDI-TOF MS, and partial sequencing of the universal gene encompassing the 16S ribosomal RNA (rRNA) gene, the 16S-23S rDNA intergenic spacer regi

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Iliyasu, M. Y., R. A. Bamanga, A. F. Umar, E. B. Agbo, and A. Uba. "16S rDNA Sequencing analysis in identification of some multidrug resistant (MDR) bacterial isolates from clinical specimens." Nigerian Journal of Biotechnology 36, no. 2 (2020): 158–66. http://dx.doi.org/10.4314/njb.v36i2.16.

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Accurate identification of bacterial pathogens from clinical specimens and Multidrug Resistant (MDR) characterization is a key to empirical therapy. Twelve (12) bacteria isolates from blood, urine and faecal samples were selected based on the ability to grow on Luria Bertani (LB) agar medium containing 100μg/ml ampicillin, identified by 16S rDNA PCR and sequencing. Identified isolates tagged; U01, U02, U03, U04, S08, U10 and U11 were from urine specimens, S05, S06, S07 and S12 from stool, while B09 was from blood. The isolates were screened for MDR pattern according to Kirby-Bauer disc diffusi

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Barbieri, Elena, Lucia Potenza, Ismaela Rossi, et al. "Phylogenetic Characterization and In Situ Detection of a Cytophaga-Flexibacter-Bacteroides Phylogroup Bacterium in Tuber borchii Vittad. Ectomycorrhizal Mycelium." Applied and Environmental Microbiology 66, no. 11 (2000): 5035–42. http://dx.doi.org/10.1128/aem.66.11.5035-5042.2000.

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ABSTRACT Mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. In this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus Tuber borchii Vittad. Universal eubacterial primers specific for the 5′ and 3′ ends of the 16S rRNA gene (16S rDNA) were used for PCR amplification, direct sequencing, and phylogenetic analyses. The 16S rDNA was amplified directly

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Roth, Andreas, Marga Fischer, Mohamed E. Hamid, Sabine Michalke, Wolfgang Ludwig, and Harald Mauch. "Differentiation of Phylogenetically Related Slowly Growing Mycobacteria Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences." Journal of Clinical Microbiology 36, no. 1 (1998): 139–47. http://dx.doi.org/10.1128/jcm.36.1.139-147.1998.

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Interspecific polymorphisms of the 16S rRNA gene (rDNA) are widely used for species identification of mycobacteria. 16S rDNA sequences, however, do not vary greatly within a species, and they are either indistinguishable in some species, for example, in Mycobacterium kansasii and M. gastri, or highly similar, for example, in M. malmoense and M. szulgai. We determined 16S-23S rDNA internal transcribed spacer (ITS) sequences of 60 strains in the genus Mycobacterium representing 13 species (M. avium, M. conspicuum, M. gastri, M. genavense, M. kansasii,M. malmoense, M. marinum, M. shimoidei, M. si

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Khbaya, Bouchaib, Marc Neyra, Philippe Normand, Karim Zerhari, and Abdelkarim Filali-Maltouf. "Genetic Diversity and Phylogeny of Rhizobia That Nodulate Acacia spp. in Morocco Assessed by Analysis of rRNA Genes." Applied and Environmental Microbiology 64, no. 12 (1998): 4912–17. http://dx.doi.org/10.1128/aem.64.12.4912-4917.1998.

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ABSTRACT Forty rhizobia nodulating four Acacia species (A. gummifera, A. raddiana, A. cyanophylla, and A. horrida) were isolated from different sites in Morocco. These rhizobia were compared by analyzing both the 16S rRNA gene (rDNA) and the 16S-23S rRNA spacer by PCR with restriction fragment length polymorphism (RFLP) analysis. Analysis of the length of 16S-23S spacer showed a considerable diversity within these microsymbionts, but RFLP analysis of the amplified spacer revealed no additional heterogeneity. Three clusters were identified when 16S rDNA analysis was carried out. Two of these cl

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Metsä-Ketelä, Mikko, Laura Halo, Eveliina Munukka, Juha Hakala, Pekka Mäntsälä, and Kristiina Ylihonko. "Molecular Evolution of Aromatic Polyketides and Comparative Sequence Analysis of Polyketide Ketosynthase and 16S Ribosomal DNA Genes from Various Streptomyces Species." Applied and Environmental Microbiology 68, no. 9 (2002): 4472–79. http://dx.doi.org/10.1128/aem.68.9.4472-4479.2002.

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ABSTRACT A 613-bp fragment of an essential ketosynthase gene from the biosynthetic pathway of aromatic polyketide antibiotics was sequenced from 99 actinomycetes isolated from soil. Phylogenetic analysis showed that the isolates clustered into clades that correspond to the various classes of aromatic polyketides. Additionally, sequencing of a 120-bp fragment from the γ-variable region of 16S ribosomal DNA (rDNA) and subsequent comparative sequence analysis revealed incongruity between the ketosynthase and 16S rDNA phylogenetic trees, which strongly suggests that there has been horizontal trans

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Laramée, Louise, John R. Lawrence, and Charles W. Greer. "Molecular analysis and development of 16S rRNA oligonucleotide probes to characterize a diclofop-methyl-degrading biofilm consortium." Canadian Journal of Microbiology 46, no. 2 (2000): 133–42. http://dx.doi.org/10.1139/w99-129.

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Genomic DNA from nine individual bacteria, isolated from a diclofop-methyl-degrading biofilm consortium, was extracted for genetic characterization. The degradation of diclofop-methyl produces metabolites that are known intermediates or substrates for bacteria that degrade a variety of chlorinated aromatic compounds. Accordingly, oligonucleotide primers were designed from specific catabolic genes for chlorinated organic degradation pathways, and tested by PCR to determine if these genes are involved in diclofop-methyl degradation. DNA homology between the PCR products and the known catabolic g

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Ninane, Véronique, Radegonde Mukandayambaje, and Gilbert Berben. "Identification of Lactic Acid Bacteria within the Consortium of a Kefir Grain by Sequencing 16S rDNA Variable Regions." Journal of AOAC INTERNATIONAL 90, no. 4 (2007): 1111–17. http://dx.doi.org/10.1093/jaoac/90.4.1111.

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Abstract The microflora of a kefir grain was identified using a polymerase chain reaction-based strategy combined with 16S rRNA gene sequencing. DNA was extracted from the kefir grain and amplified in its 16S rDNA V1 and V2 regions. To guarantee a good representation of the overall lactic acid bacteria populations, DNA amplification was performed separately with primers specific either to the dominant or to the less abundant bacterial groups. The amplified fragments were cloned in Escherichia coli and then sequenced. Sequences of the V1 region were gathered into 5 groups of similarity and iden

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Tomimura, Kenta, Shin-ichi Miyata, Noriko Furuya, et al. "Evaluation of Genetic Diversity Among ‘Candidatus Liberibacter asiaticus’ Isolates Collected in Southeast Asia." Phytopathology® 99, no. 9 (2009): 1062–69. http://dx.doi.org/10.1094/phyto-99-9-1062.

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The aim of this study was to investigate the genetic diversity and relationships among ‘Candidatus Liberibacter asiaticus’ isolates from different hosts and distinct geographical areas in Southeast Asia. Genetic diversity among ‘Ca. Liberibacter asiaticus’ was estimated by sequencing four well-characterized DNA fragments: the 16S ribosomal DNA (rDNA) and 16S/23S intergenic spacer regions; the outer membrane protein (omp) gene region; the trmU-tufB-secE-nusG-rplKAJL-rpoB region (gene cluster region); and the bacteriophage-type DNA polymerase region. The sequences of the 16S rDNA and 16S/23S int

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Mau, Margit, and Kenneth N. Timmis. "Use of Subtractive Hybridization To Design Habitat-Based Oligonucleotide Probes for Investigation of Natural Bacterial Communities." Applied and Environmental Microbiology 64, no. 1 (1998): 185–91. http://dx.doi.org/10.1128/aem.64.1.185-191.1998.

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ABSTRACT We describe a rapid oligonucleotide probe design strategy based on subtractive hybridization which yields probes for 16S rRNA or rRNA genes of individual members of microbial communities that are specific within the context of those communities. This strategy circumvents the need to sequence many similar or identical clones of dominant members of a community. Radioactively labeled subfragments of a cloned 16S rRNA gene sequence for which a probe is required (target) were hybridized with biotinylated total 16S ribosomal DNA (rDNA) amplified from the microbial community, and the hybrids

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Tan, Wenhui, Ruiyan Chen, Jie Song, et al. "Microbiota analysis with next-generation 16S rDNA gene sequencing in recurrent common bile duct stones." Annals of Translational Medicine 10, no. 10 (2022): 576. http://dx.doi.org/10.21037/atm-22-2247.

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Xu, J., T. Stanley, B. C. Millar, et al. "Difficult-to-identify bacteria: how use of 16S rDNA PCR and gene sequencing can help." British Journal of Biomedical Science 65, no. 1 (2008): 33–36. http://dx.doi.org/10.1080/09674845.2008.11978106.

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Maesha, Afra Nawer, Lolo Wal Marzan, and Yasmin Akter. "Identification and Antibiogram Studies of Pathogenic Bacteria Isolated From Drinking Water (Unpackaged) In Chittagong City, Bangladesh." Journal of Bangladesh Academy of Sciences 42, no. 2 (2018): 137–53. http://dx.doi.org/10.3329/jbas.v42i2.40041.

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Drinking water (unpackaged) samples were collected from twenty roadside shops of different locations in Chittagong metropolitan area, where physicochemical parameters (pH, TDS, temperature) were not exceeded WHO prescribed range in most cases. TVC, TCC, TFCC, TSC, Salmonella spp. and Vibrio spp. were found contaminated as 85%, 70%, 50%, 20%, 30% and 75%, respectively. All the bacterial isolates (n=43) were found positive for 16S rDNA gene, while 12 isolates were coliform positive identified by lacZ gene amplification. Nine bacterial genera were finally identified depending on biochemical chara

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Zhang, Wu Xian, Jin Hua Wang, You He Sun, Biao Li, and Zhi Xiong. "ARDRA and Identification of Intestinal Aerobic Bacteria from 4^th Instar Larvae of Dendrolimu. kikuchii." Advanced Materials Research 518-523 (May 2012): 5523–27. http://dx.doi.org/10.4028/www.scientific.net/amr.518-523.5523.

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Genetic diversity of 11 intestinal aerobic bacteria isolated from Dendrolimu. kikuchii was analysed, using PCR and ARDRA which used enzyme digestion of cloned 16S rRNA gene sequences. The results showed that 11 strains could be divided into 6 groups on 84% similarity level, it indicated that the intestinal aerobic bacteria genetic diversity was abundant. Sequencing the 6 representative strains’ 16S rDNA and submitting to GenBank, the accession number being JQ308104 to JQ308109 respectively. The 6 strains belonged to Klebsiella sp., Lysinibacillus sp., Brevibacillus sp., Bacillus subtilis, Gamm

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Abraham, Wolf-Rainer, Carsten Strömpl, Marc Vancanneyt, et al. "Woodsholea maritima gen. nov., sp. nov., a marine bacterium with a low diversity of polar lipids." International Journal of Systematic and Evolutionary Microbiology 54, no. 4 (2004): 1227–34. http://dx.doi.org/10.1099/ijs.0.02943-0.

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Two cauliform bacteria (CM243T and CM251) isolated by J. Poindexter from the Atlantic Ocean were characterized by 16S rRNA gene sequencing, TaqI restriction fragment length polymorphism and single-strand conformation polymorphism analyses of the internally transcribed 16S–23S rDNA spacer (ITS1) region, analysis of fatty acids from cellular lipids, mass spectrometry of polar lipids and physiological properties. The two strains showed very low diversity of polar lipids with diacyl-sulfoquinovosyl glycerols as the predominant lipids. The two bacterial strains were observed to have nearly identica

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Marchandin, Hélène, Corinne Teyssier, Michèle Siméon de Buochberg, Hélène Jean-Pierre, Christian Carriere, and Estelle Jumas-Bilak. "Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella: implications for phylogeny and taxonomy." Microbiology 149, no. 6 (2003): 1493–501. http://dx.doi.org/10.1099/mic.0.26132-0.

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Among the seven species characterized within the genus Veillonella, three (Veillonella dispar, Veillonella parvula and Veillonella atypica) have so far been isolated from human flora and during infectious processes. Sequencing and analysis of 16S rDNA (rrs) has been described as the best method for identification of Veillonella strains at the species level since phenotypic characteristics are unable to differentiate between species. rrs sequencing for the three species isolated from humans showed more than 98 % identity between them. Four rrs copies were found in the reference strains and in a

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Randazzo, Cinzia L., Sandra Torriani, Antoon D. L. Akkermans, Willem M. de Vos, and Elaine E. Vaughan. "Diversity, Dynamics, and Activity of Bacterial Communities during Production of an Artisanal Sicilian Cheese as Evaluated by 16S rRNA Analysis." Applied and Environmental Microbiology 68, no. 4 (2002): 1882–92. http://dx.doi.org/10.1128/aem.68.4.1882-1892.2002.

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ABSTRACT The diversity and dynamics of the microbial communities during the manufacturing of Ragusano cheese, an artisanal cheese produced in Sicily (Italy), were investigated by a combination of classical and culture-independent approaches. The latter included PCR, reverse transcriptase-PCR (RT-PCR), and denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes (rDNA). Bacterial and Lactobacillus group-specific primers were used to amplify the V6 to V8 and V1 to V3 regions of the 16S rRNA gene, respectively. DGGE profiles from samples taken during cheese production indicated dramatic s

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Pinho-Gomes, A.-C., A. Nasir, R. Mosca, S. Mirza, and I. Kadir. "Intraoperative diagnosis of mitral valve endocarditis secondary to Paenibacillus provencensis." Annals of The Royal College of Surgeons of England 99, no. 2 (2017): e54-e55. http://dx.doi.org/10.1308/rcsann.2016.0312.

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We report the first case of infective endocarditis caused by Paenibacillus provencensis. A mitral valve vegetation was incidentally discovered by intraoperative transoesophageal echocardiography in a 70-year-old woman undergoing aortic valve replacement. The precise identification of the causative agent was by means of genotypic characterisation with 16S rDNA gene sequencing. The patient was successfully treated with a 6-week course of antibiotics postoperatively, following debridement of the valve vegetation.

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Cappello, Simone, Ilaria Corsi, Sabrina Patania, et al. "Characterization of Five Psychrotolerant Alcanivorax spp. Strains Isolated from Antarctica." Microorganisms 11, no. 1 (2022): 58. http://dx.doi.org/10.3390/microorganisms11010058.

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Five psychrotolerant Alcanivorax spp. strains were isolated from Antarctic coastal waters. Strains were screened for molecular and physiological properties and analyzed regarding their growth capacity. Partial 16S rDNA, alk-B1, and P450 gene sequencing was performed. Biolog EcoPlates and the API 20E test were used to evaluate metabolic and biochemical profiles. Bacterial growth in sodium acetate was determined at 4, 15, 20, and 25 °C to evaluate the optimal temperature. Furthermore, the ability of each strain to grow in a hydrocarbon mixture at 4 and 25 °C was assayed. Biosurfactant production

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Yadav, A. K., S. Vardhan, S. Kashyap, M. Yandigeri, and D. K. Arora. "Actinomycetes Diversity among rRNA Gene Clones and Cellular Isolates from Sambhar Salt Lake, India." Scientific World Journal 2013 (2013): 1–11. http://dx.doi.org/10.1155/2013/781301.

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The vertical stratification of actinomycetes diversity in Sambhar salt lake (India’s largest salt lake) was investigated by using cultivable and uncultivable approaches. The isolates from cultured approaches were clustered on the basis of cultural, morphological, biochemical, and cell wall characteristics, and results were further strengthened by 16S rDNA-RFLP into five major groups. 16S rDNA sequencing of the representative isolates from each clusters was identified as belonging toStreptomyces, Actinopolyspora, Microbispora, Saccharopolyspora, andActinoplanesgenera, while culture independent

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Ribič, Alja, and Janja Trček. "Customized 16S-23S rDNA ITS Amplicon Metagenomics for Acetic Acid Bacteria Species Identification in Vinegars and Kombuchas." Microorganisms 12, no. 5 (2024): 1023. http://dx.doi.org/10.3390/microorganisms12051023.

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Acetic acid bacteria (AAB) are involved in food and beverage production bioprocesses, like those in vinegar and kombucha. They oxidize sugars and alcohols into various metabolites, resulting in the final products’ pleasant taste and aroma. The 16S rDNA amplicon metagenomics using Illumina technology is usually used to follow the microbiological development of these processes. However, the 16S rRNA gene sequences among different species of AAB are very similar, thus not enabling a reliable identification down to the species level but only to the genus. In this study, we have constructed primers

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Dionisi, Hebe M., Alice C. Layton, Gerda Harms, Igrid R. Gregory, Kevin G. Robinson, and Gary S. Sayler. "Quantification of Nitrosomonas oligotropha-Like Ammonia-Oxidizing Bacteria and Nitrospira spp. from Full-Scale Wastewater Treatment Plants by Competitive PCR." Applied and Environmental Microbiology 68, no. 1 (2002): 245–53. http://dx.doi.org/10.1128/aem.68.1.245-253.2002.

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ABSTRACT Utilizing the principle of competitive PCR, we developed two assays to enumerate Nitrosomonas oligotropha-like ammonia-oxidizing bacteria and nitrite-oxidizing bacteria belonging to the genus Nitrospira. The specificities of two primer sets, which were designed for two target regions, the amoA gene and Nitrospira 16S ribosomal DNA (rDNA), were verified by DNA sequencing. Both assays were optimized and applied to full-scale, activated sludge wastewater treatment plant (WWTP) samples. If it was assumed that there was an average of 3.6 copies of 16S rDNA per cell in the total population

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Girsova, Natalya, Denis Erokhin, Dmitriy Vorobyov, Damir Bogoutdinov, and Tatyana Kastalyeva. "Identification of 16SrXII-A and 16SrXII-H Phytoplasma Subgroup in Russia, Using 16S rDNA NGS Analysis." Ratarstvo i povrtarstvo, no. 00 (2025): 8. https://doi.org/10.5937/ratpov61-51638.

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The RFLP analysis of the 16S rDNA revealed two distinct phytoplasma groups, 16SrXII-A and 16SrXII-H, suggesting the presence of diverse phytoplasma strains within the analyzed isolates from the Russian State Collection of Pathogenic Microorganisms. Partial 16S rDNA sequences of four phytoplasma, 'Candidatus Phytoplasma', isolates belonging to the 16SrXII group from the three plant species: common hop (Humulus lupulus L.), Indian datura (Datura metel L.) and grapevine (Vitis vinifera L.) are presented. DNA of gene coding 16S rRNA was amplified, using nested PCR with primers P1/16Sr-SR and R16F2

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Simpson, Paul J., R. Paul Ross, Gerald F. Fitzgerald, and Catherine Stanton. "Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum." International Journal of Systematic and Evolutionary Microbiology 54, no. 2 (2004): 401–6. http://dx.doi.org/10.1099/ijs.0.02667-0.

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In a previous study that was based primarily on 16S rDNA sequencing, two groups of bifidobacteria that had been recovered from a pig caecum were proposed to belong to two novel species, termed ‘Bifidobacterium pyschroaerophilum’ and ‘Bifidobacterium aerophilum’. In this study, based on DNA G+C content and partial heat-shock protein 60 (HSP60) gene sequences, the assignment of ‘B. pyschroaerophilum’, corrected to Bifidobacterium pyschraerophilum, to the genus Bifidobacterium was confirmed. The DNA G+C content of ‘B. aerophilum’ was relatively low, which was consistent with its segregation into

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