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Bacterial Identification (bacterial + identification)
Selected AbstractsActive bacterial community structure along vertical redox gradients in Baltic Sea sedimentENVIRONMENTAL MICROBIOLOGY, Issue 8 2008Anna Edlund Summary Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179, ,64 and ,337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labelled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labelled DNA and DNA from reverse transcription polymerase chain reaction showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences, indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths. [source] Significance of bacterial identification by molecular biology methodsENDODONTIC TOPICS, Issue 1 2004David A. Spratt Rapid advances in molecular biology over the last 20 years have provided a bewildering array of techniques aimed at helping us to tease apart all aspects of biology. The discipline of microbiology has gained greatly from these advances especially with respect to detection and identification of micro-organisms. Indeed these molecular biology techniques have changed the way we classy all life on Earth. An important part of endodontic microbiology is detection and identification of the micro-organisms associated with initiation and progression of this polymicrobial infection. A range of appropriate molecular techniques are reviewed in the present article and include aspects of comparative 16S rRNA gene sequencing, polymerase chain reaction detection, strategies for identification of unculturable bacteria, and whole community analysis. Some of these techniques are widely used in endodontic microbiology while others are used by only a few workers. The advantages and disadvantages of all the techniques are discussed and put into perspective. [source] Standards for bacterial identification by fluorescence in situ hybridization within eukaryotic tissue using ribosomal rRNA-based probesINFLAMMATORY BOWEL DISEASES, Issue 8 2006Alexander Swidsinski MD [source] Phenotypic and genotypic characterization of competitive exclusion products for use in poultryJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2003R.D. Wagner Abstract Aims: Phenotypic and genotypic bacteria identification methods were compared for their efficacy in determining the composition of competitive exclusion (CE) products. Methods and Results: Phenotypic methods used for bacterial identification were fatty acid methyl ester profiles, biochemical assays and carbohydrate utilization profiles. Genotypic methods were MicroSeq16S rRNA sequence analysis and BLAST searches of the GenBank sequence database. Agreement between phenotypic and genotypic methods for identification of bacteria isolated from the Preempt CE product was 20%. A defined test mixture of bacteria was identified to the species level 100% by BLAST analysis, 64% by MicroSeq and 36% by phenotypic techniques. Conclusions: The wide range of facultative and obligate anaerobic bacteria present in a CE product are more accurately identified with 16S rRNA sequence analyses than with phenotypic identification techniques. Significance and Impact of the Study: These results will provide guidelines for manufacturers of CE products to submit more reliable product information for market approval by regulatory agencies. [source] Comparison between two PCR-based bacterial identification methods through artificial neural network data analysisJOURNAL OF CLINICAL LABORATORY ANALYSIS, Issue 1 2008Jie Wen Abstract The 16S ribosomal ribonucleic acid (rRNA) and 16S-23S rRNA spacer region genes are commonly used as taxonomic and phylogenetic tools. In this study, two pairs of fluorescent-labeled primers for 16S rRNA genes and one pair of primers for 16S-23S rRNA spacer region genes were selected to amplify target sequences of 317 isolates from positive blood cultures. The polymerase chain reaction (PCR) products of both were then subjected to restriction fragment length polymorphism (RFLP) analysis by capillary electrophoresis after incomplete digestion by Hae III. For products of 16S rRNA genes, single-strand conformation polymorphism (SSCP) analysis was also performed directly. When the data were processed by artificial neural network (ANN), the accuracy of prediction based on 16S-23S rRNA spacer region gene RFLP data was much higher than that of prediction based on 16S rRNA gene SSCP analysis data(98.0% vs. 79.6%). This study proved that the utilization of ANN as a pattern recognition method was a valuable strategy to simplify bacterial identification when relatively complex data were encountered. J. Clin. Lab. Anal. 22:14,20, 2008. © 2008 Wiley-Liss, Inc. [source] PCR identification of Rhizobium radiobacter in post-operative endophthalmitisACTA OPHTHALMOLOGICA, Issue 2007V VINH Purpose: To present 2 cases of PCR identification of Rhizobium radiobacter in post-operative endophthalmitis. Methods: Microbiological identification was carried out using samples from aqueous humor and/or vitreous. Conventional cultures were performed using a Brain Heart Infusion broth. We used broad-range eubacterial PCR amplification followed by direct sequencing. Results: In both cases, Rhizobium radiobacter was identified using eubacterial PCR and cultures of vitreous from vitreous tap. An 81-year-old female presented an endophthalmitis 4 weeks after an cataract surgery. Inflammation and infection were controlled after 2 intravitreal antibiotic injections and the final visual acuity was of 20/24 at the one-year follow-up exam. A 75-year-old male who underwent a cataract surgery presented an endophthalmitis 9 days after. This patient was treated by 3 intravitreal antibiotic injections and a vitrectomy. The 6-month follow-up exam showed an optic nerve atrophy with a poor visual outcome (20/120). Both patients had an initial marked anterior chamber inflammation with a hypopyon and a severe retinal vasculitis was observed in the second case. Conclusions: Rhizobium radiobacter is a rare pathogen involved in postoperative endophthalmitis. As it is an environmental soil organism, we may assume that the patient's exposure to outdoor environnement and moist soil remains the source of this organism. This gram negative rod is resistant to vancomycin and have an intermediate resistance to most antibiotics used to treat post-operative endophthalmitis. PCR allows a swifter bacterial identification than do cultures and may help choose the most efficient antibiotics. [source] | |||||||||||||