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rRNA Sequencing (rrna + sequencing)
Selected AbstractsHalotaxis of cyanobacteria in an intertidal hypersaline microbial matENVIRONMENTAL MICROBIOLOGY, Issue 3 2010Katharina Kohls Summary An intertidal hypersaline cyanobacterial mat from Abu Dhabi (United Arab Emirates) exhibited a reversible change in its surface colour within several hours upon changes in salinity of the overlying water. The mat surface was orange-reddish at salinities above 15% and turned dark green at lower salinities. We investigated this phenomenon using a polyphasic approach that included denaturing gradient gel electrophoresis, microscopy, high-performance liquid chromatography, hyperspectral imaging, absorption spectroscopy, oxygen microsensor measurements and modelling of salinity dynamics. Filaments of Microcoleus chthonoplastes, identified based on 16S rRNA sequencing and morphology, were found to migrate up and down when salinity was decreased below or increased above 15%, respectively, causing the colour change of the mat uppermost layer. Migration occurred in light and in the dark, and could be induced by different salts, not only NaCl. The influence of salinity-dependent and independent physico-chemical parameters, such as water activity, oxygen solubility, H2S, gravity and light, was excluded, indicating that the observed migration was due to a direct response to salt stress. We propose to term this salinity-driven cyanobacterial migration as ,halotaxis', a process that might play a vital role in the survival of cyanobacteria in environments exposed to continuous salinity fluctuations such as intertidal flats. [source] Folate-producing lactic acid bacteria from cow's milk with probiotic characteristicsINTERNATIONAL JOURNAL OF DAIRY TECHNOLOGY, Issue 3 2010DHANYA GANGADHARAN The probiotic potential of newly isolated lactic acid bacteria from cow's milk was analysed and the efficacy of the selected isolates to produce folic acid was determined by microbiological assay. Two isolates, CM 22 and CM 28 were selected for folate production in skim milk medium and the net folate yield was 12.5 ng and 14.2 ng/mL respectively. The two isolates (CM 22 and CM 28) showed more than 98% similarity to Lactococcus subsp. cremoris and Lactococcus lactis subsp. lactis respectively by 16S rRNA sequencing. [source] The bacterial flora of vacuum-packed cold-smoked salmon stored at 7°C, identified by direct 16S rRNA gene analysis and pure culture techniqueJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2007T.C. Olofsson Abstract Aims:, The indigenous flora of freshly chilled cold-smoked salmon just after the vacuum packaging, and the spoilage flora after storage, in vacuum package at 7°C for 19 days, were to be investigated with two different sampling strategies. Methods and Results:, Identification was performed using 16S rRNA sequencing of both isolated bacteria and bacterial DNA from tissue extract. The indigenous flora of fresh cold-smoked vacuum-packed salmon was dominated by, in order, Brochothrix thermosphacta, Yersinia ruckeri, Photobacterium and Carnobacterium, whereas the spoilage flora of the same product stored at 7°C for 19 days was dominated by Lactobacillus and Photobacterium. The two sampling strategies showed similar results on the fish flora. Several new types of Photobacterium sequences, closely related to Photobacterium iliopiscarium and Photobacterium phosphoreum, were found from both the freshly processed and the stored salmon, indicating that smoked salmon harbours at least three different, as yet unknown, Photobacterium species. Conclusions:, Ten per cent of the bacterial flora multiplying on chilled, vacuum-packed, cold-smoked salmon comprised unknown species. The two sampling strategies complement each other. Significance and Impact of the Study:, As cold-smoked salmon is consumed without heat-treatment, the presence of undefined bacteria in high numbers should be considered in public health assessments. [source] Comparison of 16S rRNA sequencing with conventional and commercial phenotypic techniques for identification of enterococci from the marine environmentJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2006D.F. Moore Abstract Aims:, To compare accuracy of genus and species level identification of presumptive enterococci isolates from the marine environment using conventional biochemical testing, four commercial identification systems and 16S rRNA sequence analysis. Methods and Results:, Ninety-seven environmental bacterial isolates identified as presumptive enterococci on mEI media were tested using conventional and Enterococcus genus screen biochemical tests, four commercial testing systems and 16S rRNA sequencing. Conventional and Enterococcus genus screen biochemical testing, 16S rRNA sequencing and two commercial test systems achieved an accuracy of ,94% for Enterococcus genus confirmation. Conventional biochemical testing and 16S rRNA sequencing achieved an accuracy of ,90% for species level identification. Conclusions:, For confirmation of Enterococcus genus from mEI media, conventional or genus screen biochemical testing, 16S rRNA sequencing and the four commercial systems were correct 79,100% of the time. For speciation to an accuracy of 90% or better, either conventional biochemical testing or 16S rRNA sequencing is required. Significance and Impact of the Study:, Accurate identification of presumptive environmental Enterococcus isolates to genus and species level is an integral part of laboratory quality assurance and further characterization of Enterococcus species from pollution incidents. This investigation determines the ability of six different methods to correctly identify environmental isolates. [source] Soybean meal alters autochthonous microbial populations, microvilli morphology and compromises intestinal enterocyte integrity of rainbow trout, Oncorhynchus mykiss (Walbaum)JOURNAL OF FISH DISEASES, Issue 9 2009D L Merrifield Abstract Rainbow trout were fed either a diet containing fishmeal (FM) as the crude protein source or a diet containing 50% replacement with soybean meal (SBM) for 16 weeks. An enteritis-like effect was observed in the SBM group; villi, enterocytes and microvilli were noticeably damaged compared with the FM group. The posterior intestine microvilli of SBM-fed fish were significantly shorter and the anterior intestine microvilli significantly less dense than the FM-fed fish. Electron microscopy confirmed the presence of autochthonous bacterial populations associated with microvilli of both fish groups. Reduced density of microvilli consequently led to increased exposure of enterocyte tight junctions, which combined with necrotic enterocytes is likely to diminish the protective barrier of the intestinal epithelium. No significant differences in total viable counts of culturable microbial populations were found between the groups in any of the intestinal regions. A total of 1500 isolates were tentatively placed into groups or genera, according to standard methods. Subsequent partial 16S rRNA sequencing revealed species that have not been identified from the rainbow trout intestine previously. Compared with the FM group levels of Psychrobacter spp. and yeast were considerably higher in the SBM group; a reduction of Aeromonas spp. was also observed. [source] New serotype of mutans streptococci isolated from pig oral cavityMICROBIOLOGY AND IMMUNOLOGY, Issue 2 2008Kazuko Takada ABSTRACT Gram-positive streptococcal mutans-like strains, but with clearly different colony formation than S. orisuis on Mitis Salivarius agar, were isolated from the pig oral cavity and identified by 16S rRNA sequencing, G+C content, DNA-DNA homology and extensive biochemical and serological testing. The phenotypic data showed that the strains were similar to S. orisuis except for susceptibility to bacitracin. DNA-DNA homology between the isolates and S. orisuis was 72,81%. However, serological data showed that they have a different sero-specific antigen from S. orisuis and other mutans streptococci. A new serotype, designated p, strains are classified in a serovar of S. orisuis, one of mutans streptococci. [source] Novel Propionibacterium infection in cattleAUSTRALIAN VETERINARY JOURNAL, Issue 3 2000JC FORBES-FAULKNER Objective To describe four cases of infection in cattle, from geographically different places, with a presumptive new species of Propionibacterium, which causes granulomatous lesions in the head, thorax, abdomen, pelvic area and skin. Procedure Gross lesions, ranging from 0.5 to 15 cm and detected during routine carcase inspection at the abattoir, were submitted to the laboratory for routine testing in the National Granuloma Submission Program. The bacterium isolated was identified using morphological characteristics, biochemical reactions, cell wall components, products of fermentation and 16S rRNAgene sequencing. Results Gross lesions submitted for examination consisted of a fibrous outer capsule enclosing thick yellow pus-like material. A Gram-Glynn stain of the histological sections revealed colonies of Gram-positive, filamentous, branching bacteria. Bacteriological culture, cell wall analysis, biochemical reactions and 16S rRNA sequencing identified the organism as a Propionibacterium sp closely related to P cyclohexanicum and the P freudenreichii cluster. Conclusion This is the first report of a Propionibacterium sp closely related to P cyclohexanicum and the P freudenreichii cluster associated with extensive granulomatous lesions in cattle in Queensland. Sequencing data are suggestive of a previously undescribed species of the Propionibacterium genus. [source] | ||||||||||