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rRNA Sequence Analysis (rrna + sequence_analysis)
Selected AbstractsPhenotypic 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] A dual symbiosis shared by two mussel species, Bathymodiolus azoricus and Bathymodiolus puteoserpentis (Bivalvia: Mytilidae), from hydrothermal vents along the northern Mid-Atlantic RidgeENVIRONMENTAL MICROBIOLOGY, Issue 8 2006Sébastien Duperron Summary Bathymodiolus azoricus and Bathymodiolus puteoserpentis are symbiont-bearing mussels that dominate hydrothermal vent sites along the northern Mid-Atlantic Ridge (MAR). Both species live in symbiosis with two physiologically and phylogenetically distinct Gammaproteobacteria: a sulfur-oxidizing chemoautotroph and a methane-oxidizer. A detailed analysis of mussels collected from four MAR vent sites (Menez Gwen, Lucky Strike, Rainbow, and Logatchev) using comparative 16S rRNA sequence analysis and fluorescence in situ hybridization (FISH) showed that the two mussel species share highly similar to identical symbiont phylotypes. FISH observations of symbiont distribution and relative abundances showed no obvious differences between the two host species. In contrast, distinct differences in relative symbiont abundances were observed between mussels from different sites, indicating that vent chemistry may influence the relative abundance of thiotrophs and methanotrophs in these dual symbioses. [source] Influence of long-term land application of Class B biosolids on soil bacterial diversityJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2010H. Zerzghi Abstract Aim:, To evaluate the effect of long-term annual land applications of Class B biosolids on soil bacterial diversity at University of Arizona Marana Agricultural Field Center, Tucson, Arizona. Methods and Results:, Following the final of 20 consecutive years of application of Class B biosolids in March 2005, followed by cotton growth from April to November 2005 surface soil samples (0,30 cm) were collected from control (unamended) and biosolid-amended plots. Total bacterial community DNA was extracted, amplified using 16S rRNA primers, cloned, and sequenced. All 16S rRNA sequences were identified by 16S rRNA sequence analysis and comparison to known sequences in GenBank (NCBI BlastN and Ribosomal Database Project II, RDP). Results showed that the number of known genera (identifiable > 96%) increased in the high rate biosolid plots compared to control plots. Biosolids-amended soils had a broad phylogenetic diversity comprising more than four major phyla: Proteobacteria (32%), Acidobacteria (21%), Actinobacteria (16%), Firmicutes (7%), and Bacteroidetes (6%) which were typical to bacterial diversity found in the unamended arid southwestern soils. Conclusion:, Bacterial diversity was either enhanced or was not negatively impacted following 20 years of land application of Class B biosolids. Significance and Impact of the Study:, This study illustrates that long-term land application of biosolids to arid southwestern desert soils has no deleterious effect on soil microbial diversity. [source] Probiotic characteristics of lactic acid bacteria isolated from kimchiJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2010J.-H. Chang Abstract Aims:, The present work was aimed at identifying strains of lactic acid bacteria (LAB) from kimchi, with properties suitable for use as starter cultures in yogurt fermentation. Methods and Results:, A total of 2344 LAB strains were obtained from two different sources, one group consisted of commercial LAB strains from kimchi, and the second group consisted of those strains isolated from various types of kimchi. The LAB strains from both groups were screened for resistance to biological barriers (acid and bile salts), and the four most promising strains were selected. Further analysis revealed that KFRI342 of the four selected strains displayed the greatest ability to reduce the growth of the cancer cells, SNU-C4. The in vivo efficacy of strains in quinone reductase induction assay was evaluated, and the extent of DNA strand breakage in individual cells was investigated using the comet assay. Strain KFRI342 was identified as Lactobacillus acidophilus by 16S rRNA sequence analysis, showed protection against tumour initiation and imparted immunostimulation as well as protection against DNA damage. Conclusions:, Strain KFRI342, which showed probiotic characteristics reducing cancer cell growth, could be a suitable starter culture for yogurt fermentation because of its strong acid production and high acid tolerance. Significance and Impact of the Study:, This is the first report to describe a bacterium, isolated from kimchi, Lact. acidophilus KFRI342 which has the probiotic characteristics and the acid tolerance needed for its use as a starter culture in yogurt fermentation. [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] 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] Selection of probiotic bacteria for use in shrimp larvicultureAQUACULTURE RESEARCH, Issue 5 2009Jiin-Ju Guo Abstract Three candidate probiotics, Bacillus foraminis, Bacillus cereus biovar toyoi and Bacillus fusiformis, were isolated from hydrogen-producing fermented solution and identified using 16S rRNA sequence analysis. Bacillus foraminis and B. cereus biovar toyoi exhibited strong antagonism against Streptococcus iniae and Photobacterium damselae subsp. piscicida in in vitro co-culture for competitive exclusion assay and then were conducted in the larviculture system of Penaeus monodon reared from zoea 1 to postlarva 1. The daily addition of B. cereus biovar toyoi resulted in significantly deleterious effects on survival (P<0.01) whereas the daily addition of B. fusiformis showed highest survival rate (88.7±0.7%) but no statistically significant difference from control (73.3±12.1%). Bacillus fusiformis was continuously applied in the larviculture system of Litopenaeus vannamei. Administration of B. fusiformis significantly increased survival (P<0.01) in both treatments added daily (87.9±1.7%) and every other day (54.7±1.2%), respectively, at a concentration of 105 CFU mL,1 over control (41.2±1.3%). [source] | ||||||||||