Samples from the kidney of 100 diseased fish with signs of haemorrhagic septicemia and 50 samples from outlet water of fish farms were taken aseptically and cultured. In the laboratory, 75 colonies of gram-negative bacteria were biochemically diagnosed as motile aeromonads in our Bacteriology Laboratory Unit using API 20E rapid identification system. The genotype identification using specific p...

samples from the kidney of 100 diseased fish with signs of haemorrhagic septicemia and 50 samples from outlet water of fish farms were taken aseptically and cultured. in the laboratory, 75 colonies of gram-negative bacteria were biochemically diagnosed as motile aeromonads in our bacteriology laboratory unit using api 20e rapid identification system. the genotype identification using specific p...

Sequencing of 16S rDNA, and of sodAint and rpoBint in some cases, was applied to DNA from heart valves of 46 patients (36 with definite and 10 with possible endocarditis). Sequence-based identifications were compared with those obtained with conventional methods. Among the 36 definite cases, 30 had positive blood cultures and 6 had negative cultures. Among the 30 positive cases, sequencing of 1...

This study is the first study that provides useful guidelines to clinical microbiologists and technicians on the usefulness of full 16S rRNA sequencing, 5'-end 527-bp 16S rRNA sequencing and the existing MicroSeq full and 500 16S rDNA bacterial identification system (MicroSeq, Perkin-Elmer Applied Biosystems Division, Foster City, California, USA) databases for the identification of all existin...

Avian intestinal spirochetosis (AIS) is a disease of birdscharacterized by a marked colonization of the cecum and/or rectumwith anaerobic intestinal bacteria of the genus Brachyspira. Thepurpose of the study was to determine the occurrence of Brachyspiraspp from avian sources in Iran and to characterize selected isolates bybiochemical and molecular methods. Out of 165 fecal samples obtained fro...

BACKGROUND 16S ribosomal DNA (rDNA) amplicon sequencing is frequently used to analyse the structure of bacterial communities from oceans to the human microbiota. However, computational power is still a major bottleneck in the analysis of continuously enlarging metagenomic data sets. Analysis is further complicated by the technical complexity of current bioinformatics tools. RESULTS Here we pr...

avian intestinal spirochetosis (ais) is a disease of birdscharacterized by a marked colonization of the cecum and/or rectumwith anaerobic intestinal bacteria of the genus brachyspira. thepurpose of the study was to determine the occurrence of brachyspiraspp from avian sources in iran and to characterize selected isolates bybiochemical and molecular methods. out of 165 fecal samples obtained fro...

High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly s...

Massively parallel pyrosequencing of the small subunit (16S) ribosomal RNA gene has revealed that the extent of rare microbial populations in several environments, the 'rare biosphere', is orders of magnitude higher than previously thought. One important caveat with this method is that sequencing error could artificially inflate diversity estimates. Although the per-base error of 16S rDNA ampli...

The main bacteria in peaty, acid grassland soils in the Netherlands were investigated by ribosome isolation, temperature gradient gel electrophoresis, hybridization, cloning, and sequencing. Instead of using only 16S rDNA to determine the sequences present, we focused on rRNA to classify and quantify the most active bacteria. After direct ribosome isolation from soil, a partial amplicon of bact...