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Journal articles on the topic '16S rDNA sequencing of E. aerogenes'

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Published: 3 June 2025

Last updated: 31 July 2025

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1

Saha, Mihir Lal, Mist Dilara Akter, Tahsin Khan, Aneesa Ansari, and Mohammad Nurul Islam. "Bacterial load and multi‐drug resistance patterns of some ready‐to‐eat street foods of Dhaka city." Dhaka University Journal of Biological Sciences 27, no. 1 (2018): 27–36. http://dx.doi.org/10.3329/dujbs.v27i1.46408.

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Bacterial load and drug resistance pattern associated with some ready-to-eat (RTE) street foods such as Chatpoti, Fuchka, Singara, Panipuri, Ghugni-muri, Chola and water of Dhaka South City Corporation were investigated. Most of the samples were found to be contaminated and the bacterial load ranged from 2.4 × 104 - 9.2 × 106, 1.2 × 103 - 7.3 × 105 and 1.1 × 103 - 1.6 × 106 cfu/g of aerobic heterotrophic, coliform bacteria and Staphylococcus, respectively. The highest coliform load (7.3 × 105 cfu/ml) was found in the water of Gulistan. The highest aerobic heterotrophic bacteria (9.2 × 106 cfu/

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HWANG, CHIU-CHU, PEI-HUI TSENG, YI-CHEN LEE, et al. "Determination of Histamine in Japanese Spanish Mackerel (Scomberomorus niphonius) Meat Implicated in a Foodborne Poisoning." Journal of Food Protection 82, no. 10 (2019): 1643–49. http://dx.doi.org/10.4315/0362-028x.jfp-19-111.

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ABSTRACT An incident of foodborne poisoning causing illness in seven victims due to ingestion of fried Japanese Spanish mackerel (JS mackerel; Scomberomorus niphonius) meat occurred in September 2014 in Hualien County, eastern Taiwan. Of the two suspected fish meats, one raw sample contained 3,318 ppm of histamine and one fried sample contained 1,906 ppm of histamine, levels which are greater than the potential hazard action level (500 ppm) in most illness cases. Given the allergy-like symptoms of the victims and the high histamine content in the suspected fish samples, this foodborne poisonin

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Aldeewan, Ali, Nawres Jaber, Mohanad Abdulhameed, and Basil Abbas. "Microbial risk assessment of dairy products from retail marketplaces in Basrah province, Iraq." Open Veterinary Journal 14, no. 3 (2024): 779. http://dx.doi.org/10.5455/ovj.2024.v14.i3.4.

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Background: Milk-borne bacteria cause degradation of milk products and constitute a significant risk to public health. Aim: The objectives of present study are to determine the microbiological quality of dairy products and to investigate pathogenic microorganisms. Methods: A total of 60 samples of raw milk, homemade cheese and yogurt were randomly selected from different retail marketplaces in Basrah. The bacteriological and biochemical tests were utilised to identify the pathogens in dairy samples, as well as the molecular technique was used as accurate diagnostic test. Results: The prevalenc

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Hashavya, S., I. Gross, A. Michael-Gayego, N. Simanovsky, and R. Lamdan. "The efficacy of 16S ribosomal DNA sequencing in the diagnosis of bacteria from blood, bone and synovial fluid samples of children with musculoskeletal infections." Journal of Children's Orthopaedics 12, no. 2 (2018): 204–8. http://dx.doi.org/10.1302/1863-2548.12.170049.

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Background Musculoskeletal infections are among the most common bacterial infections in children leading to hospitalization, invasive procedures and prolonged antibiotic administration. Blood, synovial and sometimes tissue cultures are essential for the diagnosis and treatment of musculoskeletal infections; 16S ribosomal DNA (rDNA) sequencing is a novel diagnostic tool for the detection of bacteria. While the yield of 16S rDNA sequencing in synovial fluid was previously assessed, data regarding the efficacy of this method from blood samples or partially treated children with suspected musculos

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

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

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Drancourt, Michel, Claude Bollet, Antoine Carlioz, Rolland Martelin, Jean-Pierre Gayral, and Didier Raoult. "16S Ribosomal DNA Sequence Analysis of a Large Collection of Environmental and Clinical Unidentifiable Bacterial Isolates." Journal of Clinical Microbiology 38, no. 10 (2000): 3623–30. http://dx.doi.org/10.1128/jcm.38.10.3623-3630.2000.

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Some bacteria are difficult to identify with phenotypic identification schemes commonly used outside reference laboratories. 16S ribosomal DNA (rDNA)-based identification of bacteria potentially offers a useful alternative when phenotypic characterization methods fail. However, as yet, the usefulness of 16S rDNA sequence analysis in the identification of conventionally unidentifiable isolates has not been evaluated with a large collection of isolates. In this study, we evaluated the utility of 16S rDNA sequencing as a means to identify a collection of 177 such isolates obtained from environmen

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Liao, Feng, Yilan Xia, Wenpeng Gu, Xiaoqing Fu, and Bing Yuan. "Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls." PeerJ 11 (November 3, 2023): e16394. http://dx.doi.org/10.7717/peerj.16394.

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Background Shotgun metagenomic and 16S rDNA sequencing are commonly used methods to identify the taxonomic composition of microbial communities. Previously, we analysed the gut microbiota and intestinal pathogenic bacteria configuration of migratory seagulls by using 16S rDNA sequencing and culture methods. Methods To continue in-depth research on the gut microbiome and reveal the applicability of the two methods, we compared the metagenome and 16S rDNA amplicon results to further demonstrate the features of this animal. Results The number of bacterial species detected by metagenomics graduall

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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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Kim, Daeyoo, Gil Young Park, Dong Yeon Lee, Dong-Oh Lee, and Youngsik Yoon. "Nanopore 16S Amplicon Sequencing Enhances the Understanding of Pathogens in Medically Intractable Diabetic Foot Infections." Foot & Ankle Orthopaedics 7, no. 4 (2022): 2473011421S0072. http://dx.doi.org/10.1177/2473011421s00723.

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Category: Diabetes Introduction/Purpose: Diabetic foot infections (DFIs) cause substantial morbidity and mortality. The mainstay of the treatment is empiric antibiotics and surgical debridement in severe cases. Methods: In this study, we performed nanopore 16S rDNA sequencing from the debridement specimens of DFIs. Fifty-four surgical debridement specimens obtained from 45 patients with medically intractable DFI were included. The 16S rDNA PCR was performed on each specimen, and Nanopore sequencing was performed for up to 3 h. The reads were aligned to the BLAST database, and the results were

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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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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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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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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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Delbès, C., M. Leclerc, E. Zumstein, J. J. Godon, and R. Moletta. "A molecular method to study population and activity dynamics in anaerobic digestors." Water Science and Technology 43, no. 1 (2001): 51–57. http://dx.doi.org/10.2166/wst.2001.0013.

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The applicability of a new molecular fingerprinting method (Single Strand Conformation Polymorphism) to study the microbial populations of anaerobic digestors was investigated. After extraction of total nucleic acids, the 16S rDNA and 16S rRNA molecules were amplified and the amplicons were separated by SSCP electrophoresis. Characteristic and complex peak patterns were obtained, where each peak could be correlated with the 16S rDNA sequence of one micro-organism. The rDNA peak patterns should consist of the most abundant sequences and thus would reflect the diversity of prominent species of d

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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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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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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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Ramírez-Saad, Hugo, Jaap D. Janse, and Antoon DL Akkermans. "Root nodules ofCeanothus caeruleuscontain both the N2-fixingFrankiaendophyte and a phylogetically related Nod-/Fix-actinomycete." Canadian Journal of Microbiology 44, no. 2 (1998): 140–48. http://dx.doi.org/10.1139/w97-138.

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Attempts to isolate the N2-fixing endophyte of Ceanothus caeruleus (Rhamnaceae) root nodules, led to the isolation of nine actinomycetous strains. Owing to their inability to fix nitrogen (Fix-) and nodulate (Nod-), they could not be regarded as the effective endophyte. Characterization was done based on morphological and physiological features and 16S rDNA sequence analysis. The effective Frankia endophyte was characterized without cultivation by amplification, cloning, and sequencing of nearly full length 16S rDNA and partial nifH genes. Phylogenetic analysis based on 16S rDNA revealed that

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HU, JIA-WEI, MIN-JIE CAO, SHUN-CAI GUO, LING-JING ZHANG, WEN-JIN SU, and GUANG-MING LIU. "Identification and Inhibition of Histamine-Forming Bacteria in Blue Scad (Decapterus maruadsi) and Chub Mackerel (Scomber japonicus)." Journal of Food Protection 78, no. 2 (2015): 383–89. http://dx.doi.org/10.4315/0362-028x.jfp-14-296.

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In this study, we investigated the differences in histamine accumulation between blue scad and chub mackerel and methods of inhibiting histamine-forming bacteria and controlling histamine accumulation in fish. The free histidine contents in blue scad and chub mackerel were 1.45 and 2.75 mg/g, respectively. The histamine-forming bacteria isolated from them were identified as Citrobacter freundii, Citrobacter braakii, and Enterobacter aerogenes using 16S rDNA sequence analysis, the VITEK 2 Compact system, and MALDI-TOF MS. The histamine-producing capacities of C. freundii, C. braakii, and E. aer

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Tan, Zhi Lei, Yu Qiao Wei, Shuang Liang, Ran Zhang, Miao Liu, and Shi Ru Jia. "Rapid Identification of Microorganisms Isolated from Pickled Vegetables by MALDI-TOF Mass Spectrometry." Advanced Materials Research 712-715 (June 2013): 494–97. http://dx.doi.org/10.4028/www.scientific.net/amr.712-715.494.

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Matrix-assisted laser desorption/ionization time-off light mass spectrometry (MALDI-TOF MS) is increasingly used as a microbial diagnostic method for species identification of pathogens. However, MALDI-TOF MS identification of food bacteria was seldom reported. Ten strains isolated from different pickled vegetables were rapid identified by MALDI-TOF MS. The results of MALDI-TOF MS were confirmed by 16S rDNA sequencing method. Different score values in MALDI-TOF MS revealed nineLeuconostoc mesenteroides and oneStaphylococcus.Identification success at the species and genus levels was 90% (9/10)

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Song, Wen Feng, De Sheng Ma, You Yi Zhu, Xiao Fang Wei, and Jie Wu. "Diversity and Distribution of Sulfate-Reducing Bacteria in Jilin Oilfield." Advanced Materials Research 937 (May 2014): 297–302. http://dx.doi.org/10.4028/www.scientific.net/amr.937.297.

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To better understand the roles of microorganisms in oil production, diversity and distribution of microbes in Jilin oilfield was studied. Firstly, chromosomal DNA wassuccessfully extracted directly from crude oil samples. Diversity and distribution of microbes was then analyzed based on 16S rDNA libraries. There were totally 21 OTUs were obtained through 16S rDNA sequencing. Of those OTUs, 13 are bacteria in whichProteobacteriais the major family, while 8 are archaea in whichMethanomicrobiais the dominant. Finally, SRB was found in all samples by amplifying theapsAgene using PCR. SRB found in

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Rangel-Castro, J. Ignacio, Jolanta J. Levenfors, and Eric Danell. "Physiological and genetic characterization of fluorescentPseudomonasassociated withCantharellus cibarius." Canadian Journal of Microbiology 48, no. 8 (2002): 739–48. http://dx.doi.org/10.1139/w02-062.

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Fluorescent Pseudomonas spp. isolated from fruiting bodies (FB) of Cantharellus cibarius were characterized physiologically and genetically and were compared with fluorescent Pseudomonas from forest soil and with sequences from the GenBank database. Pseudomonas spp. from FB differed physiologically from isolates from soil lacking FB and had some similarities with the strains obtained from soil underneath the FB. Analyses of the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) patterns and partial sequencing analysis of the 16S-rDNA region indicated that the b

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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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Gu, F., Y. Li, C. Zhou, et al. "Bacterial 16S rRNA/rDNA Profiling in the Liquid Phase of Human Saliva." Open Dentistry Journal 3, no. 1 (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 sal

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Payne, Michael, Robert Azana, and Linda M. N. Hoang. "Review of 16S and ITS Direct Sequencing Results for Clinical Specimens Submitted to a Reference Laboratory." Canadian Journal of Infectious Diseases and Medical Microbiology 2016 (2016): 1–6. http://dx.doi.org/10.1155/2016/4210129.

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We evaluated the performance of 16S and internal transcribed spacer (ITS) region amplification and sequencing of rDNA from clinical specimens, for the respective detection and identification of bacterial and fungal pathogens. Direct rDNA amplification of 16S and ITS targets from clinical samples was performed over a 4-year period and reviewed. All specimens were from sterile sites and submitted to a reference laboratory for evaluation. Results of 16S and ITS were compared to histopathology, Gram and/or calcofluor stain microscopy results. A total of 277 16S tests were performed, with 64 (23%)

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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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Hoogenkamp, Michel A., Bernd W. Brandt, Alexa M. G. A. Laheij, Johannes J. de Soet, and Wim Crielaard. "16S rDNA sequencing and metadata of Dutch dental unit water." Data in Brief 37 (August 2021): 107221. http://dx.doi.org/10.1016/j.dib.2021.107221.

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Hiraishi, Akira, Yong Kook Shin, Yoko Ueda, and Junta Sugiyama. "Automated sequencing of PCR-amplified 16S rDNA on ‘Hydrolink’ gels." Journal of Microbiological Methods 19, no. 2 (1994): 145–54. http://dx.doi.org/10.1016/0167-7012(94)90046-9.

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Boye, Kit, Estrid Høgdall, and Martin Borre. "Identification of bacteria using two degenerate 16S rDNA sequencing primers." Microbiological Research 154, no. 1 (1999): 23–26. http://dx.doi.org/10.1016/s0944-5013(99)80030-5.

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Roux, V., and D. Raoult. "Phylogenetic analysis of the genus Rickettsia by 16S rDNA sequencing." Research in Microbiology 146, no. 5 (1995): 385–96. http://dx.doi.org/10.1016/0923-2508(96)80284-1.

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Roshni, V. "Bacterial Diversity in Fluoride - Contaminated Soils Using 16S rDNA Sequencing." International Journal of Science and Research (IJSR) 12, no. 11 (2023): 337–40. http://dx.doi.org/10.21275/sr231031141716.

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West, Nyree J., and David J. Scanlan. "Niche-Partitioning of ProchlorococcusPopulations in a Stratified Water Column in the Eastern North Atlantic Ocean." Applied and Environmental Microbiology 65, no. 6 (1999): 2585–91. http://dx.doi.org/10.1128/aem.65.6.2585-2591.1999.

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ABSTRACT The in situ community structure of Prochlorococcuspopulations in the eastern North Atlantic Ocean was examined by analysis of Prochlorococcus 16S rDNA sequences with three independent approaches: cloning and sequencing, hybridization to specific oligonucleotide probes, and denaturing gradient gel electrophoresis (DGGE). The hybridization of high-light (HL) and low-light (LL) Prochlorococcus genotype-specific probes to two depth profiles of PCR-amplified 16S rDNA sequences revealed that in these two stratified water columns, an obvious niche-partitioning ofProchlorococcus genotypes occ

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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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Knox, C. Michele, Vickey Cevellos, and Deborah Dean. "16S Ribosomal DNA Typing for Identification of Pathogens in Patients with Bacterial Keratitis." Journal of Clinical Microbiology 36, no. 12 (1998): 3492–96. http://dx.doi.org/10.1128/jcm.36.12.3492-3496.1998.

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The identification of pathogens in patients with bacterial keratitis remains problematic because standard diagnostic tests are negative for 40 to 60% of patients. A cross-sectional study was undertaken to determine if PCR and sequence analysis of 16S ribosomal DNA (rDNA) could be used to detect bacterial pathogens in patients with keratitis. Corneal specimens were collected for culture and rDNA typing. Variable segments of each rDNA specimen were amplified by PCR, sequenced, and aligned with the sequences in GenBank. Eleven patients had microbiologically documented bacterial keratitis, while 1

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Siddiqui, Huma, Karin Lagesen, Alexander J. Nederbragt, Lars M. Eri, Stig L. Jeansson, and Kjetill S. Jakobsen. "Pathogens in Urine from a Female Patient with Overactive Bladder Syndrome Detected by Culture-independent High Throughput Sequencing: A Case Report." Open Microbiology Journal 8, no. 1 (2014): 148–53. http://dx.doi.org/10.2174/1874285801408010148.

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Introduction:Overactive bladder syndrome (OAB) is described as urgency, with or without urgency incontinence. A range of medical conditions shares the symptoms of OAB, however the diagnosis is contingent on the exclusion of urinary tract infection (UTI). Knowing that urine dipstick and routine culture of bacteria can miss UTI diagnosis caused by low-count bacteriuria or “difficult-to-culture” pathogens, we examined a case of OAB with a culture-independent approach.Case presentation:A 61-year-old Norwegian female with a long history of urinary symptoms and a diagnosis of OAB was selected as a s

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Miyajima, M., M. Matsuda, S. Haga, S. Kagawa, B. C. Millar, and J. E. Moore. "Cloning and sequencing of 16S rDNA and 16S-23S rDNA internal spacer region (ISR) from urease-positive thermophilic Campylobacter (UPTC)." Letters in Applied Microbiology 34, no. 4 (2002): 287–89. http://dx.doi.org/10.1046/j.1472-765x.2002.01082.x.

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HAN, TAE MAN, HA SIK SIM, SEUNGHWAN LEE, and HAE CHUL PARK. "A new species Agrypnus (Sabikikorius) uidoensis sp. nov. (Coleoptera: Elateridae) from the Sand Dune Shore of Ui-do Island, Korea." Zootaxa 2134, no. 1 (2009): 60–68. http://dx.doi.org/10.11646/zootaxa.2134.1.5.

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A new species is described belonging to the subgenus Sabikikorius of Agrypnus, Agrypnus (Sabikikorius) uidoensis sp. nov., and isolated from the sand dunes of Ui-do Island, Korea. A key to the species is given with distributional information for each species of this subgenus. Sequencing data of the mitochondrial genes encoding COI (cytochrome c oxidase I) and 16S rDNA (16S ribosomal DNA) are also provided.

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García-García, Natalia, Javier Tamames, and Fernando Puente-Sánchez. "M&Ms: a versatile software for building microbial mock communities." Bioinformatics 38, no. 7 (2022): 2057–59. http://dx.doi.org/10.1093/bioinformatics/btab882.

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Abstract Summary Advances in sequencing technologies have triggered the development of many bioinformatic tools aimed to analyze 16S rDNA sequencing data. As these tools need to be tested, it is important to simulate datasets that resemble samples from different environments. Here, we introduce M&Ms, a user-friendly open-source bioinformatic tool to produce different 16S rDNA datasets from reference sequences, based on pragmatic ecological parameters. It creates sequence libraries for ‘in silico’ microbial communities with user-controlled richness, evenness, microdiversity and source envir

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Alvarez, Elizabeth, Juan F. Mejía, Nicoletta Contaldo, Samanta Paltrinieri, Bojan Duduk, and Assunta Bertaccini. "‘Candidatus Phytoplasma asteris’ Strains Associated with Oil Palm Lethal Wilt in Colombia." Plant Disease 98, no. 3 (2014): 311–18. http://dx.doi.org/10.1094/pdis-12-12-1182-re.

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The distribution of lethal wilt, a severe disease of oil palm, is spreading throughout South America. An incidence of about 30% was recorded in four commercial fields in Colombia. In this study, phytoplasmas were detected in symptomatic oil palm by using specific primers, based on 16S ribosomal DNA (rDNA) sequences, in nested polymerase chain reaction assays. The phytoplasmas were then identified as ‘Candidatus Phytoplasma asteris’, ribosomal subgroup 16SrI-B, through the use of restriction fragment length polymorphism (RFLP) analysis and sequencing. Cloning and sequencing of 16S rDNA from sel

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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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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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Moissenet, Didier, Christophe P. Goujon, Antoine Garbarg-Chenon, and Hoang Vu-Thien. "CDC Group IV c-2: a New RalstoniaSpecies Close to Ralstonia eutropha." Journal of Clinical Microbiology 37, no. 6 (1999): 1777–81. http://dx.doi.org/10.1128/jcm.37.6.1777-1781.1999.

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CDC group IV c-2, an environmental gram-negative bacillus recently proposed for inclusion in the genus Ralstonia, has been isolated in several human infections. Biochemical characterization and 16S ribosomal DNA (rDNA) sequencing with phylogenetic analysis were used to characterize eight clinical isolates and four type strains. Other typing tools, such as pulsed-field gel electrophoresis (PFGE) and randomly amplified polymorphic DNA (RAPD) analysis, were also used. PFGE typing of clinical isolates was unsuccessful because the DNA was degraded, and RAPD analysis was poorly discriminatory. In co

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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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Abhaykumar Dalsaniya, Urvisha Beladiya, and Ramesh K. Kothari. "Predictive modeling of microbial functionality from 16S rDNA sequences using machine learning." World Journal of Biology Pharmacy and Health Sciences 21, no. 2 (2025): 545–54. https://doi.org/10.30574/wjbphs.2025.21.2.0223.

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This study illustrates the possibilities for the use of machine learning algorithms integrating the prediction of microbial functionality regarding functional 16S rDNA sequences and filling the gap in mapping phylogenetic relations of the microbial context to their functionality. Previous 16S rDNA sequencing strategies have proven useful in describing microbial species, but not their functional potential. This study employed several sophisticated forms of supervised and unsupervised machine learning algorithms to interpret 16S rDNA data and predict the functional states of microbes in differen

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Singh, Ruby, O. Colin Stine, David L. Smith, John K. Spitznagel, Mohamed E. Labib, and Henry N. Williams. "Microbial Diversity of Biofilms in Dental Unit Water Systems." Applied and Environmental Microbiology 69, no. 6 (2003): 3412–20. http://dx.doi.org/10.1128/aem.69.6.3412-3420.2003.

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ABSTRACT We investigated the microbial diversity of biofilms found in dental unit water systems (DUWS) by three methods. The first was microscopic examination by scanning electron microscopy (SEM), acridine orange staining, and fluorescent in situ hybridization (FISH). Most bacteria present in the biofilm were viable. FISH detected the β and γ, but not the α, subclasses of Proteobacteria. In the second method, 55 cultivated biofilm isolates were identified with the Biolog system, fatty acid analysis, and 16S ribosomal DNA (rDNA) sequencing. Only 16S identified all 55 isolates, which represente

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Saha, Mihir Lal, Mohammad Nurul Islam, Chaman Binta Aziz, and Mohammad Zabed Hossain. "Molecular identification of bacteria present in the soils of the Madhupur Sal and the Sunderban mangrove forests of Bangladesh." Dhaka University Journal of Biological Sciences 21, no. 2 (2012): 117–23. http://dx.doi.org/10.3329/dujbs.v21i2.11509.

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The present study aimed at identifying the soil bacterial communities in the Madhupur Sal and the Sunderban mangrove forests, the two important forests of Bangladesh. Soil bacteria were identified through sequencing of PCR?amplified fragments of bacterial 16S rDNA. The results showed that the bacterial communities of the Madhupur Sal forest soils and that of the Sunderban mangrove forest soils differed in the morphology of the cells. Data presented here also showed that the bacterial communities of the Sunderban mangrove forest soils were more diverse than that of the Madhupur Sal forest soils

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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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Brim, H., H. Heuer, E. Krögerrecklenfort, M. Mergeay, and K. Smalla. "Characterization of the bacterial community of a zinc-polluted soil." Canadian Journal of Microbiology 45, no. 4 (1999): 326–38. http://dx.doi.org/10.1139/w99-012.

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The bacterial community of a zinc-contaminated soil (Maatheide soil in Lommel, Belgium) was studied using cultivation as well as cultivation-independent techniques. Colony-forming units (CFU) were determined by plating on media with or without metals. Dominant isolates were characterized by fatty acid methyl ester analysis (FAME analysis) and PCR fingerprinting using repetitive extragenic palindromic sequences as primers. DNA was directly extracted from soil samples and used as a template for the PCR amplification of the 16S rDNA (8-1511) or a 16S rDNA fragment (968-1401). Clones resulting fro

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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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Zongo, O., U. Zongo, H. Cisse, et al. "Biochemical and molecular characterization of yeasts and lactic acid bacteria isolated from Borassus aethiopum Mart. sap in Burkina Faso." Food Research 5, no. 2 (2021): 155–63. http://dx.doi.org/10.26656/fr.2017.5(2).471.

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In Burkina Faso, the Palmyra Palm Borassus aethiopum Mart. grows wild and gives natural stands in Central-Eastern and Eastern regions. The sap collected traditionally ferments spontaneously and is a rich medium that allows the growth of different microorganisms. This study aimed to identify yeasts and lactic acid bacteria (LAB) isolated from Borassus aethiopum Mart. fresh and fermented sap in Burkina Faso. A total of ninety strains including thirty LAB and sixty yeasts were isolated in the fresh and fermented sap. The isolates were characterized using standard biochemical method and sequencing

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