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Journal articles on the topic 'Morganii 16s rdna analysis'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Tabassum, Anika, Mihir Lal Saha, and Mohammad Nurul Islam. "Prevalence of multi-drug resistant bacteria in selected street food and water samples." Bangladesh Journal of Botany 44, no. 4 (2018): 621–27. http://dx.doi.org/10.3329/bjb.v44i4.38599.

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Present study was conducted to determine the bacteria and their multi-drug resistance pattern of Velpuri and water of Velpuri shop of different areas of Dhaka city. A total of 74 bacteria were isolated of which 26 isolates were subjected for further study. Eleven and 15 isolates from 26, were found Gram-positive and Gram-negative bacteria, respectively. Three isolates of Gram-positive bacteria were found rod shaped and spore formers which were identified as Bacillus spp. while eight isolates were found round shaped and nonspore formers and identified as Staphylococcus, Streptococcus, Planococc

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Maes, Michael, Asara Vasupanrajit, Ketsupar Jirakran, et al. "Exploration of the Gut Microbiome in Thai Patients with Major Depressive Disorder Shows a Specific Bacterial Profile with Depletion of the Ruminococcus Genus as a Putative Biomarker." Cells 12, no. 9 (2023): 1240. http://dx.doi.org/10.3390/cells12091240.

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Maes et al. (2008) published the first paper demonstrating that major depressive disorder (MDD) is accompanied by abnormalities in the microbiota–gut–brain axis, as evidenced by elevated serum IgM/IgA to lipopolysaccharides (LPS) of Gram-negative bacteria, such as Morganella morganii and Klebsiella Pneumoniae. The latter aberrations, which point to increased gut permeability (leaky gut), are linked to activated neuro-immune and oxidative pathways in MDD. To delineate the profile and composition of the gut microbiome in Thai patients with MDD, we examined fecal samples of 32 MDD patients and 37

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KIM, SHIN-HEE, HAEJUNG AN, KATHARINE G. FIELD, et al. "Detection of Morganella morganii, a Prolific Histamine Former, by the Polymerase Chain Reaction Assay with 16S rDNA–Targeted Primers." Journal of Food Protection 66, no. 8 (2003): 1385–92. http://dx.doi.org/10.4315/0362-028x-66.8.1385.

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A polymerase chain reaction (PCR) assay for the rapid and sensitive detection of the most prolific histamine former, Morganella morganii, was developed.16S rDNA targeted PCR primers were designed, and the primer specificity and sensitivity of the PCR assay were evaluated. The 16S rDNA sequence (1,503 bp) for M. morganii showed 95% identity to those for enteric bacteria, i.e., Enterobacter spp., Klebsiella spp., Citrobacter spp., Hafnia alvei, Proteus spp., and Providencia spp. The unique primers for M. morganii were designed on the basis of the variable regions in the 16S rDNA sequence. The pr

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Dahllöf, Ingela, Harriet Baillie, and Staffan Kjelleberg. "rpoB-Based Microbial Community Analysis Avoids Limitations Inherent in 16S rRNA Gene Intraspecies Heterogeneity." Applied and Environmental Microbiology 66, no. 8 (2000): 3376–80. http://dx.doi.org/10.1128/aem.66.8.3376-3380.2000.

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ABSTRACT Contemporary microbial community analysis frequently involves PCR-amplified sequences of the 16S rRNA gene (rDNA). However, this technology carries the inherent problem of heterogeneity between copies of the 16S rDNA in many species. As an alternative to 16S rDNA sequences in community analysis, we employed the gene for the RNA polymerase beta subunit (rpoB), which appears to exist in one copy only in bacteria. In the present study, the frequency of 16S rDNA heterogeneity in bacteria isolated from the marine environment was assessed using bacterial isolates from the red alga Delisea p

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Lamy, Brigitte, Fréderic Laurent, and Angeli Kodjo. "Validation of a partialrpoBgene sequence as a tool for phylogenetic identification of aeromonads isolated from environmental sources." Canadian Journal of Microbiology 56, no. 3 (2010): 217–28. http://dx.doi.org/10.1139/w10-006.

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A collection of 50 aeromonads isolated from environmental sources were studied, together with all known Aeromonas nomenspecies, by phenotypic, amplified 16S rDNA restriction analysis (16S rDNA RFLP) and by partial sequence alignment of both 16S rDNA and rpoB genes. Although most of the type strain showed a unique phenotypic pattern, a database constructed on type strain phenotype allowed the identification of only 24% of the isolates. Analysis of 16S rDNA RFLP and the rpoB sequence were almost concordant in identifying environmental isolates at the species level, except for strains belonging t

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Emborg, Jette, Paw Dalgaard, and Peter Ahrens. "Morganella psychrotolerans sp. nov., a histamine-producing bacterium isolated from various seafoods." International Journal of Systematic and Evolutionary Microbiology 56, no. 10 (2006): 2473–79. http://dx.doi.org/10.1099/ijs.0.64357-0.

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Mesophilic Morganella morganii (n=6) and psychrotolerant M. morganii-like isolates from various seafoods (n=13), as well as clinical M. morganii isolates (n=3), were characterized by using a polyphasic approach including multi-locus sequencing. Based on the phylogenetic analysis, the 22 strains were divided into two distinct groups comprising mesophilic and psychrotolerant isolates, respectively. This classification was supported by DNA–DNA hybridization studies, whereby a psychrotolerant isolate (strain U2/3T) showed 41.0 and 17.8 % relatedness to the type strains of the mesophilic species Mo

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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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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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9

Grahn, Niclas, Mounira Hmani-Aifa, Karin Fransén, Peter Söderkvist, and Hans-Jürg Monstein. "Molecular identification of Helicobacter DNA present in human colorectal adenocarcinomas by 16S rDNA PCR amplification and pyrosequencing analysis." Journal of Medical Microbiology 54, no. 11 (2005): 1031–35. http://dx.doi.org/10.1099/jmm.0.46122-0.

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Seroepidemiological studies have indicated that Helicobacter pylori infection might be a possible risk factor for colorectal adenocarcinoma (CRC) development. However, limited information is available as to whether or not Helicobacter species are present in CRC tissues. In this study the presence of Helicobacter DNA in 77 CRC biopsies was investigated by means of a Helicobacter species-specific 16S rDNA PCR assay and real-time DNA pyrosequencing of the 16S rDNA variable V3 region. Pyrosequencing revealed the presence of Helicobacter DNA sequences in 21 of 77 biopsy specimens (27 %). 16S rDNA s

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10

BAO, Qiongli, Long-Jun DING, Yizong HUANG, and Keqing XIAO. "Effect of rice straw and/or nitrogen fertiliser inputs on methanogenic archaeal and denitrifying communities in a typical rice paddy soil." Earth and Environmental Science Transactions of the Royal Society of Edinburgh 109, no. 3-4 (2018): 375–86. http://dx.doi.org/10.1017/s1755691018000580.

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ABSTRACTTo understand better the microbial functional populations which are involved in methanogenesis and denitrification in paddy soils with rice straw (RS) and/or nitrogen fertiliser (potassium nitrate, N) application, the dynamics of methanogens and the denitrifying community were monitored simultaneously during the incubation period. The results show that the community structure of methanogens remained relatively stable among treatments based on 16S rDNA analysis, but fluctuated based on 16S rRNA. The Methanocellaceae and Methanosarcinaceae dominated all treatments at 16S rDNA and 16S rRN

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11

Reinoso, Elina, Silvana Dieser, Luis Calvinho, Cristina Bogni, and Liliana Odierno. "Phenotyping and genotyping of streptococci in bovine milk in Argentinean dairy herds." Acta Veterinaria Hungarica 58, no. 3 (2010): 287–95. http://dx.doi.org/10.1556/avet.58.2010.3.2.

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Most veterinary and milk hygiene laboratories identify streptococci and enterococci based on serological and biochemical tests. The analysis of 16S rDNA was suggested to be used for more exact identification; however, its use has not been considered so far in monitoring studies. The objective of the present study was to compare a conventional phenotypic method with restriction fragment length polymorphism analysis of 16S rDNA (16S rDNA RFLP) for identification of streptococci isolated from composite milk samples collected in connection with intramammary infection (IMI) in six Argentinean dairy

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12

Fessehaie, A., S. H. De Boer, and C. A. Lévesque. "Molecular characterization of DNA encoding 16S23S rRNA intergenic spacer regions and 16S rRNA of pectolyticErwiniaspecies." Canadian Journal of Microbiology 48, no. 5 (2002): 387–98. http://dx.doi.org/10.1139/w02-026.

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Sequences of 16S rDNAs and the intergenic spacer (IGS) regions between the 16S and 23S rDNA of bacterial strains from genus Erwinia were determined. Comparison of 16S rDNA sequences from different species and subspecies clearly revealed intraspeciessubspecies homology and interspecies heterogeneity. Phylogenetic analyses of 16S rDNA sequence data revealed that Erwinia spp. formed a discrete monophyletic clade with moderate to high bootstrap values. PCR amplification of the 16S23S rDNA regions using primers complementary to the 3' end of 16S and 5' end of 23S rRNA genes generated two DNA frag

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13

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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Dekowska, Agnieszka, Jolanta Niezgoda, and Barbara Sokołowska. "Genetic Heterogeneity ofAlicyclobacillusStrains Revealed by RFLP Analysis ofvdcRegion andrpoBGene." BioMed Research International 2018 (November 1, 2018): 1–12. http://dx.doi.org/10.1155/2018/9608756.

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PCR-RFLP targeting of the 16S rDNA andrpoBgenes, as well as thevdcregion, was applied to identify and differentiate between the spoilage and non-spoilageAlicyclobacillusspecies. Eight reference strains and 75 strains isolated from spoiled juices, juice concentrates, drinks, its intermediates, and fresh apples were subject to study. Hin6I restriction patterns of the 16S rDNA gene enabled distinguishing between all the species analyzed, while therpoBgene andvdcgene cluster analysis also revealed that there were two major types among theA. acidoterrestrisisolates, one similar to the reference str

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15

Brooks, S. P. J., M. McAllister, M. Sandoz, and M. L. Kalmokoff. "Culture-independent phylogenetic analysis of the faecal flora of the rat." Canadian Journal of Microbiology 49, no. 10 (2003): 589–601. http://dx.doi.org/10.1139/w03-075.

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The dominant faecal flora of the rat was determined using randomly cloned 16S rDNA comparative sequence analysis. A total of 109 near full-length 16S rDNA clones were sequenced, representing 69 unique 16S rRNA phylotypes or operational taxonomic units (OTUs). Estimates of species richness indicated that approximately 338 species were present in the faeces, suggesting that only 20% of species were identified. Only two of 39 Gram-negative clones aligned with previously cultured species, the remainder fell into a separate lineage within the Bacteroides–Cytophaga phylum. Several clones within this

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Grady, Ruth, Michael Anderson, David Drucker, and David Denning. "Partial 16S rDNA analysis of oral Treponema." Reviews in Medical Microbiology 8 (1997): S25. http://dx.doi.org/10.1097/00013542-199712001-00012.

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Zoetendal, Erwin G., Antoon D. L. Akkermans, and Willem M. De Vos. "Temperature Gradient Gel Electrophoresis Analysis of 16S rRNA from Human Fecal Samples Reveals Stable and Host-Specific Communities of Active Bacteria." Applied and Environmental Microbiology 64, no. 10 (1998): 3854–59. http://dx.doi.org/10.1128/aem.64.10.3854-3859.1998.

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ABSTRACT The diversity of the predominant bacteria in the human gastrointestinal tract was studied by using 16S rRNA-based approaches. PCR amplicons of the V6 to V8 regions of fecal 16S rRNA and ribosomal DNA (rDNA) were analyzed by temperature gradient gel electrophoresis (TGGE). TGGE of fecal 16S rDNA amplicons from 16 individuals showed different profiles, with some bands in common. Fecal samples from two individuals were monitored over time and showed remarkably stable profiles over a period of at least 6 months. TGGE profiles derived from 16S rRNA and rDNA amplicons showed similar banding

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18

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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Prüß, Birgit M., Kevin P. Francis, Felix von Stetten, and Siegfried Scherer. "Correlation of 16S Ribosomal DNA Signature Sequences with Temperature-Dependent Growth Rates of Mesophilic and Psychrotolerant Strains of the Bacillus cereusGroup." Journal of Bacteriology 181, no. 8 (1999): 2624–30. http://dx.doi.org/10.1128/jb.181.8.2624-2630.1999.

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ABSTRACT Sequences of the 16S ribosomal DNA (rDNA) from psychrotolerant and mesophilic strains of the Bacillus cereus group revealed signatures which were specific for these two thermal groups of bacteria. Further analysis of the genomic DNA from a wide range of food and soil isolates showed that B. cereus group strains have between 6 and 10 copies of 16S rDNA. Moreover, a number of these environmental strains have both rDNA operons with psychrotolerant signatures and rDNA operons with mesophilic signatures. The ability of these isolates to grow at low temperatures correlates with the prevalen

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Hendrickson, Edwin R., Jo Ann Payne, Roslyn M. Young, et al. "Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe." Applied and Environmental Microbiology 68, no. 2 (2002): 485–95. http://dx.doi.org/10.1128/aem.68.2.485-495.2002.

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ABSTRACT The environmental distribution of Dehalococcoides group organisms and their association with chloroethene-contaminated sites were examined. Samples from 24 chloroethene-dechlorinating sites scattered throughout North America and Europe were tested for the presence of members of the Dehalococcoides group by using a PCR assay developed to detect Dehalococcoides 16S rRNA gene (rDNA) sequences. Sequences identified by sequence analysis as sequences of members of the Dehalococcoides group were detected at 21 sites. Full dechlorination of chloroethenes to ethene occurred at these sites. Deh

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Fukatsu, Takema, and Naruo Nikoh. "Two Intracellular Symbiotic Bacteria from the Mulberry Psyllid Anomoneura mori (Insecta, Homoptera)." Applied and Environmental Microbiology 64, no. 10 (1998): 3599–606. http://dx.doi.org/10.1128/aem.64.10.3599-3606.1998.

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ABSTRACT We characterized the intracellular symbiotic bacteria of the mulberry psyllid Anomoneura mori by performing a molecular phylogenetic analysis combined with in situ hybridization. In its abdomen, the psyllid has a large, yellow, bilobed mycetome (or bacteriome) which consists of many round uninucleated mycetocytes (or bacteriocytes) enclosing syncytial tissue. The mycetocytes and syncytium harbor specific intracellular bacteria, the X-symbionts and Y-symbionts, respectively. Almost the entire length of the bacterial 16S ribosomal DNA (rDNA) was amplified and cloned from the whole DNA o

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Si-Ping, Zheng, Chen Bin, Guan Xiong, and Zheng Wei-Wen. "Diversity analysis of endophytic bacteria withinAzolla microphyllausing PCR-DGGE and electron microscopy." Chinese Journal of Agricultural Biotechnology 5, no. 3 (2008): 269–76. http://dx.doi.org/10.1017/s1479236208002441.

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AbstractUsing 16S rDNA-polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE), electron microscopy and a conventional plating method, the genetic diversity and phenotype polymorphism of the endophytic bacteria withinAzolla microphyllawere explored. The 16S rDNA-PCR-DGGE profile showed a complex and divergent bacterial community, withBacillus cereusas the dominant species, within theAzolla–cyanobacteria association. This result was supported by the fact that endobacterial cells exhibited distinct ultrastructural characteristicsin vivoand,in vitro, bacteria displayed variou

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Moffett, Bruce F., Kerry A. Walsh, Jim A. Harris, and Tom C. J. Hill. "Analysis of Bacterial Community Structure using 16S rDNA Analysis." Anaerobe 6, no. 2 (2000): 129–31. http://dx.doi.org/10.1006/anae.2000.0329.

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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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Buckley, Daniel H., Joseph R. Graber, and Thomas M. Schmidt. "Phylogenetic Analysis of Nonthermophilic Members of the Kingdom Crenarchaeota and Their Diversity and Abundance in Soils." Applied and Environmental Microbiology 64, no. 11 (1998): 4333–39. http://dx.doi.org/10.1128/aem.64.11.4333-4339.1998.

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ABSTRACT Within the last several years, molecular techniques have uncovered numerous 16S rRNA gene (rDNA) sequences which represent a unique and globally distributed lineage of the kingdom Crenarchaeotathat is phylogenetically distinct from currently characterized crenarchaeotal species. rDNA sequences of members of this novel crenarchaeotal group have been recovered from low- to moderate-temperature environments (−1.5 to 32°C), in contrast to the high-temperature environments (temperature, >80°C) required for growth of the currently recognized crenarchaeotal species. We determined the dive

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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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Clawson, Michael L., Jeffrey Gawronski, and David R. Benson. "Dominance ofFrankiastrains in stands ofAlnus incanasubsp.rugosaandMyrica pensylvanica." Canadian Journal of Botany 77, no. 9 (1999): 1203–7. http://dx.doi.org/10.1139/b99-070.

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To address issues of dominance and diversity of Frankia spp. strains, we sequenced 16S rRNA genes from root nodules and strains collected from Alnus incana subsp. rugosa (Du Roi) R.T. Clausen and Myrica pensylvanica Loisel. stands. Of 22 strains isolated previously from A. incana, 16 had the same partial rDNA sequence; the remaining 6 strains composed five additional groups. The groups identified by 16S rDNA analysis corresponded to phenotypic groups established previously by one- and two-dimensional polyacrylamide gel analysis, colony and hyphal morphology, and carbon source utilization patte

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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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Tanner, Michael A., Brett M. Goebel, Michael A. Dojka, and Norman R. Pace. "Specific Ribosomal DNA Sequences from Diverse Environmental Settings Correlate with Experimental Contaminants." Applied and Environmental Microbiology 64, no. 8 (1998): 3110–13. http://dx.doi.org/10.1128/aem.64.8.3110-3113.1998.

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ABSTRACT Phylogenetic analysis of 16S ribosomal DNA (rDNA) clones obtained by PCR from uncultured bacteria inhabiting a wide range of environments has increased our knowledge of bacterial diversity. One possible problem in the assessment of bacterial diversity based on sequence information is that PCR is exquisitely sensitive to contaminating 16S rDNA. This raises the possibility that some putative environmental rRNA sequences in fact correspond to contaminant sequences. To document potential contaminants, we cloned and sequenced PCR-amplified 16S rDNA fragments obtained at low levels in the a

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Chen, J., R. L. Jarret, X. Qin, et al. "16S rDNA Sequence Analysis of Xylella fastidiosa Strains." Systematic and Applied Microbiology 23, no. 3 (2000): 349–54. http://dx.doi.org/10.1016/s0723-2020(00)80064-8.

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Santo Domingo, J. W., M. C. Meckes, J. M. Simpson, B. Sloss, and D. J. Reasoner. "Molecular characterization of bacteria inhabiting a water distribution system simulator." Water Science and Technology 47, no. 5 (2003): 149–54. http://dx.doi.org/10.2166/wst.2003.0305.

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The objective of this study was to monitor the impact of chlorination and chloramination treatments on heterotrophic bacteria (HB) and ammonia-oxidizing bacteria (AOB) inhabiting a water distribution system simulator. HB densities decreased while AOB densities increased when chloramine was added. AOB densities decreased below detection limits after the disinfection treatment was switched back to chlorination. The presence of AOB was confirmed using a group-specific 16S rDNA-PCR method. 16S rDNA sequence analysis showed that most bacterial isolates from feed water, discharge water, and biofilm

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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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Vinuesa, Pablo, Jan L. W. Rademaker, Frans J. de Bruijn, and Dietrich Werner. "Genotypic Characterization ofBradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing." Applied and Environmental Microbiology 64, no. 6 (1998): 2096–104. http://dx.doi.org/10.1128/aem.64.6.2096-2104.1998.

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ABSTRACT We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers

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Dhaouadi, Sabrine, Amira H. Mougou, Chao J. Wu, Mark L. Gleason, and Ali Rhouma. "Sequence analysis of 16S rDNA, gyrB and alkB genes of plant-associated Rhodococcus species from Tunisia." International Journal of Systematic and Evolutionary Microbiology 70, no. 12 (2020): 6491–507. http://dx.doi.org/10.1099/ijsem.0.004521.

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The genus Rhodococcus contains several species with agricultural, biotechnological and ecological importance. Within this genus, many phyllosphere, rhizosphere and endosphere strains are plant growth promoting bacteria, whereas strains designated as R. fascians are plant pathogens. In this study, we isolated 47 Rhodococcus strains from a range of herbaceous and woody plant species. Phylogenetic analysis based on 16S rDNA, gyrB and alkB genes was used to compare our strains with type strains of Rhodococcus . For most of our strains, sequence similarity of the 16S rDNA, gyrB and alkB regions to

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Ahmad, Iftikhar, Shafi Ullah, Abdulaziz Alouffi, et al. "First Molecular-Based Confirmation of Dermacentor marginatus and Associated Rickettsia raoultii and Anaplasma marginale in the Hindu Kush Mountain Range." Animals 13, no. 23 (2023): 3686. http://dx.doi.org/10.3390/ani13233686.

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Ticks of the genus Dermacentor Koch, 1844 (Acari: Ixodidae) are poorly known systematically due to their habitation in harsh topographic environments and high mountains. Dermacentor ticks are diversely distributed in the Palearctic, Nearctic, and Oriental regions. There is no available information on the occurrence of Dermacentor marginatus in Pakistan; thus, the current investigation aimed the first morphological and molecular confirmation of this species and associated Anaplasma marginale and Rickettsia raoultii. Ticks were collected from goats (Capra hircus) and morphologically identified.

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Ivanova, Iliana A., John R. Stephen, Yun-Juan Chang та ін. "A survey of 16S rRNA andamoAgenes related to autotrophic ammonia-oxidizing bacteria of the β-subdivision of the class proteobacteria in contaminated groundwater". Canadian Journal of Microbiology 46, № 11 (2000): 1012–20. http://dx.doi.org/10.1139/w00-099.

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In this study, we investigated the size and structure of autotrophic ammonia oxidizer (AAO) communities in the groundwater of a contamination plume originating from a mill-tailings disposal site. The site has high levels of dissolved N from anthropogenic sources, and exhibited wide variations in the concentrations of NO3-and NH3+ NH4+. Community structures were examined by PCR-DGGE targeting 16S rDNA with band excision and sequence analysis, and by analysis of amoA fragment clone libraries. AAO population sizes were estimated by competitive PCR targeting the gene amoA, and correlated significa

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Xiang, Hui, Gui-Fang Wei, Shihai Jia, et al. "Microbial communities in the larval midgut of laboratory and field populations of cotton bollworm (Helicoverpa armigera)." Canadian Journal of Microbiology 52, no. 11 (2006): 1085–92. http://dx.doi.org/10.1139/w06-064.

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We compared the bacterial communities in the larval midgut of field and laboratory populations of a polyphagous pest, the cotton bollworm (Helicoverpa armigera), using denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA sequences and 16S library sequence analysis. DGGE profiles and 16S rDNA library sequence analysis indicated similar patterns of midgut microbial community structure and diversity: specific bacterial types existed in both populations, and a more diverse microbial community was observed in caterpillars obtained from the field. The laboratory population harbored a

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Ambrožič Dolinšek, Jana, Maja Ravnikar, Jana Žel, et al. "Tissue culture of Pyrethrum (Tanacetum cinerariifolium) and associated microbial contamination." Acta Biologica Slovenica 53, no. 1 (2010): 63–68. http://dx.doi.org/10.14720/abs.53.1.15369.

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   Microbial contamination was observed on several subcultures of Pyrethrum (Tanacetum cinerariifolium) (Trevir.) Schultz-bip. callus lines. The presence of microorganisms- sms was detected by isolation of contaminants in pure culture from 7 out of 34 callus lines and direct ampliication of eubacterial 16S rDNA in the pyrethrum callus and plants and isolated bacteria. Altogether 16 contaminants were further analyzed, observing their morphology on several media and restriction of ampliied 16S rDNA. Analysis revealed presence and persistence of morphologically and genetically d

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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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Layton, A. C., P. N. Karanth, C. A. Lajoie, et al. "Quantification of Hyphomicrobium Populations in Activated Sludge from an Industrial Wastewater Treatment System as Determined by 16S rRNA Analysis." Applied and Environmental Microbiology 66, no. 3 (2000): 1167–74. http://dx.doi.org/10.1128/aem.66.3.1167-1174.2000.

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ABSTRACT The bacterial community structure of the activated sludge from a 25 million-gal-per-day industrial wastewater treatment plant was investigated using rRNA analysis. 16S ribosomal DNA (rDNA) libraries were created from three sludge samples taken on different dates. Partial rRNA gene sequences were obtained for 46 rDNA clones, and nearly complete 16S rRNA sequences were obtained for 18 clones. Seventeen of these clones were members of the beta subdivision, and their sequences showed high homology to sequences of known bacterial species as well as published 16S rDNA sequences from other a

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Li, Yuanping, Yanrong Chen, Yaoning Chen, et al. "Effects of Physico-Chemical Parameters on Actinomycetes Communities during Composting of Agricultural Waste." Sustainability 11, no. 8 (2019): 2229. http://dx.doi.org/10.3390/su11082229.

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The objective of this study was to investigate the influence of physico-chemical parameters on Actinomycetes communities and to prioritize those parameters that contributed to Actinomycetes community composition during the composting of agricultural waste. Denaturing gradient gel electrophoresis of polymerase chain reaction (PCR-DGGE) and redundancy analysis (RDA) were used to determine the relationships between those parameters and Actinomycetes community composition. Quantitative PCR (qPCR) and regression analysis were used to monitor the 16S rDNA copy numbers of Actinomycetes and to analyse

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Breuker, Anja, Anna Blazejak, Klaus Bosecker, and Axel Schippers. "Diversity of Iron Oxidizing Bacteria from Various Sulfidic Mine Waste Dumps." Advanced Materials Research 71-73 (May 2009): 47–50. http://dx.doi.org/10.4028/www.scientific.net/amr.71-73.47.

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More than 100 cultures of acidophilic Fe(II)- and/or sulfur-oxidizing microorganisms from mine waste dumps in 10 different countries all over the world have been maintained in liquid media in the BGR-strain collection for many years. Our 16S rDNA analysis showed that most of the cultivated Fe(II)-oxidizers belong to four genera: Acidithiobacillus, Acidimicrobium, “Ferrimicrobium” and Leptospirillum. All analyzed Acidithiobacillus strains were identified as At. ferrooxidans. The Leptospirillum strains were affiliated with L. ferriphilum or L. ferrooxidans. The Gram-positive strains related to A

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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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Koç İnak, Nafiye. "Molecular Characterization of Dermanyssus gallinae in Türkiye Based on 16S and 18S rDNA." Turkish Journal of Agriculture - Food Science and Technology 11, no. 12 (2023): 2411–16. http://dx.doi.org/10.24925/turjaf.v11i12.2411-2416.6492.

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The poultry red mite, Dermanyssus gallinae (De Geer, 1778), is widely regarded as the significant ectoparasite of egg-laying hens worldwide. Since many molecular studies on poultry red mites have focused on analyzing COI and ITS1-2 genes, the present study aimed to identify 16S rDNA and the relatively understudied nuclear 18S rDNA genes of Turkish D. gallinae populations. Twenty-eight different D. gallinae populations were collected from henhouses throughout Türkiye, and the target genes were amplified using conventional PCR after morphological analysis. Haplotype analyses of the 16S rDNA sequ

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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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Ueda, Kenji, Michiyo Ohno, Kaori Yamamoto, et al. "Distribution and Diversity of Symbiotic Thermophiles, Symbiobacterium thermophilum and Related Bacteria, in Natural Environments." Applied and Environmental Microbiology 67, no. 9 (2001): 3779–84. http://dx.doi.org/10.1128/aem.67.9.3779-3784.2001.

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ABSTRACT Symbiobacterium thermophilum is a tryptophanase-positive thermophile which shows normal growth only in coculture with its supporting bacteria. Analysis of the 16S rRNA gene (rDNA) indicated that the bacterium belongs to a novel phylogenetic branch at the outermost position of the gram-positive bacterial group without clustering to any other known genus. Here we describe the distribution and diversity of S. thermophilum and related bacteria in the environment. Thermostable tryptophanase activity and amplification of the specific 16S rDNA fragment were effectively employed to detect the

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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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Kanagawa, Takahiro, Yoichi Kamagata, Shinobu Aruga, Tetsuro Kohno, Matthias Horn, and Michael Wagner. "Phylogenetic Analysis of and Oligonucleotide Probe Development for Eikelboom Type 021N Filamentous Bacteria Isolated from Bulking Activated Sludge." Applied and Environmental Microbiology 66, no. 11 (2000): 5043–52. http://dx.doi.org/10.1128/aem.66.11.5043-5052.2000.

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ABSTRACT Fifteen filamentous strains, morphologically classified as Eikelboom type 021N bacteria, were isolated from bulking activated sludges. Based on comparative 16S ribosomal DNA (rDNA) sequence analysis, all strains form a monophyletic cluster together with all recognized Thiothrix species (88.3 to 98.7% 16S rDNA sequence similarity) within the gamma-subclass ofProteobacteria. The investigated Eikelboom type 021N isolates were subdivided into three distinct groups (I to III) demonstrating a previously unrecognized genetic diversity hidden behind the uniform morphology of the filaments. Fo

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Navrátilová, Lucie, Magdalena Chromá, Vojtěch Hanulík, and Vladislav Raclavský. "Possibilities in Identification of Genomic Species of Burkholderia cepacia Complex by PCR and RFLP." Polish Journal of Microbiology 62, no. 4 (2013): 373–76. http://dx.doi.org/10.33073/pjm-2013-051.

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The strains belonging to Burkholderia cepacia complex are important opportunistic pathogens in immunocompromised patients and cause serious diseases. It is possible to obtain isolates from soil, water, plants and human samples. Taxonomy of this group is difficult. Burkholderia cepacia complex consists of seventeen genomic species and the genetic scheme is based on recA gene. Commonly, first five genomovars occurre in humans, mostly genomovars II and III, subdivision IIIA. Within this study we tested identification of first five genomovars by PCR with following melting analysis and RFLP. The ex

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Azhar, Minda, Sumaryati Syukur, Dessy Natalia, Vovien, and Jamsari. "SKRINING DAN IDENTIFIKASI BAKTERI PENDEGRADASI INULIN DARI SUMBER AIR PANAS PADANG BALIMBIANG DI SOLOK." Jurnal Riset Kimia 5, no. 1 (2015): 32. http://dx.doi.org/10.25077/jrk.v5i1.175.

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ABSTRACT Thermophilic bacteria and thermotolerant bacteria are potential sources of thermostable of inulin degradating enzyme, an enzyme which converts inulin into fructose and FOS prebiotics. Isolation and identification of 16S rDNA gene inulin degradation bacteria from hot springs of Padang Balimbiang in Solok have been undertaken. Screening of inulin degradation bacteria was done using direct and undirect methods on medium with inulin or inulin-RBB as a sole carbon source. One inulin degradation bacteria have been obtained from 21 isolates. The isolate was designated as UBCT-030. The isolat

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