OBJECTIVES To identify the gram-negative rods grown from blood cultures and a right-knee fluid aspirate from an 80-year-old caucasian man who had undergone a total right knee arthroplastic procedure 6 years ago, and to assess the genetic similarity between the 2 isolates. METHODS We used 3 different approaches: biochemical testing, matrix-assisted laser desorption ionization time-of-flight (M...

A cloned 16S rRNA gene from the extreme thermophilic eubacterium Thermus thermophilus HB8 was used to characterize the in vivo expression of the 16S rRNA genes in this organism by nuclease S1 mapping. The gene represents an isolated transcription unit encoding solely 16S rRNA. Under exponential growth conditions, transcription was initiated at a single promoter, which represents the structural ...

Here we describe the natural occurrence of bacteria of the class Dehalococcoidia (DEH) and their diversity at different depths in anoxic waters of a remote meromictic lake (Lake Pavin) using 16S rRNA gene amplicon sequencing and quantitative PCR. Detected DEH are phylogenetically diverse and the majority of 16S rRNA sequences have less than 91% similarity to previously isolated DEH 16S rRNA seq...

Real time PCR was used in this study to determine the effect of triticale dried distillers grains with solubles (TDDGS) as a replacement for grain or barley silage in finishing diets on the presence of six classical ruminal bacterial species (Succinivibrio dextrinosolvens, Selenomonas ruminantium, Streptococcus bovis, Megasphaera elsdenii, Prevotella ruminicola and Fibrobacter succinogenes) wit...

Haloarchaea are the dominant microbial flora in hypersaline waters with near-saturating salt levels. The haloarchaeal diversity of an Australian saltern crystallizer pond was examined by use of a library of PCR-amplified 16S rRNA genes and by cultivation. High viable counts (10(6) CFU/ml) were obtained on solid media. Long incubation times (> or =8 weeks) appeared to be more important than the ...

Actinomycetes are inexhaustible producers of commercially valuable metabolites, are continually screened for beneficial compounds. The taxonomic and phylogenetic study of novel actinomycetes strains are mostly based on conventional methods and primary DNA structure of 16s rRNA. Although 16s rRNA sequence is well accepted in phylogeny studies, its secondary structures have not been widely used. ...

We evaluated phylogenetic clustering of bacterial and archaeal communities from redox-dynamic subtropical forest soils that were defined by 16S rRNA and rRNA gene sequences. We observed significant clustering for the RNA-based communities but not the DNA-based communities, as well as increasing clustering over time of the highly active taxa detected by only rRNA.

Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae are the three main pathogens causing bovine mastitis, with great losses to the dairy industry. Rapid and specific loop-mediated isothermal amplification methods (LAMP) for identification and differentiation of these three pathogens are not available. With the 16S rRNA gene and 16S-23S rRNA intergenic spacers as target...

Seventeen bacterial strains were isolated from 9 marine mud samples from the inshore environments of the East Sea. Four bacterial strains showed an inhibition against all tested microorganisms Staphylococcus aureus ATCC10832, Escherichia coli JM109, and Fusarium oxysporum. 16S rRNA sequences of four bacterial strains were obtained by PCR using specific primers. PCR products were cloned into E. ...