Taxonomic status of the zoanthid genera Palythoa and Protopalythoa has been in question for almost a century. Separation of the two genera has been based on traditional morphological methods (colony and polyp form, nematocyst size and form, and number of septa), with Palythoa polyps embedded in a well developed coenenchyme and Protopalythoa polyps standing free and clear of the coenenchyme. Her...

MOTIVATION Many current studies of complex microbial communities rely on the isolation of community genomic DNA, amplification of 16S ribosomal RNA genes (rDNA) and subsequent examination of community structure through interrogation of the amplified 16S rDNA pool by high-throughput sequencing, phylogenetic microarrays or quantitative PCR. RESULTS Here we describe the development of a mathemat...

Although 16S rRNA gene (rDNA) sequencing is the gold standard for categorizing bacteria or characterizing microbial communities its clinical utility is limited by bias in metagenomic studies, in either the experiments or the data analyses. To evaluate the efficiency of current metagenomic methods, we sequenced seven simulated samples of ten bacterial species mixed at different concentrations. T...

Phylogenetic analysis of a 500 bp fragment of the secA gene has been performed on 35 phytoplasma isolates representing 10 of the 16S rDNA groups. The lineages obtained coincide with those delineated by 16S rDNA phylogenetic analysis but much greater genetic variability was evident. In addition, phylogenetic analysis based on part of the 23S rDNA gene combined with T-RFLP (terminal restriction f...

Using full 16S ribosomal RNA (rRNA) gene sequencing as the gold standard, 20 non-duplicating anaerobic Gram positive bacilli isolated from blood cultures were analysed by the MicroSeq 500 16S rDNA bacterial identification system. The MicroSeq system successfully identified 13 of the 20 isolates. Four and three isolates were misidentified at the genus and species level, respectively. Although th...

Candidatus Liberibacter asiaticus’ is the most widespread of the three species of ‘Ca. Liberibacter’ that cause citrus greening disease (huanglongbing). To ascertain the phylogenetic relationships among Indian isolates that have higher diversity in the 16S rDNA than Asian isolates of this species, we collected symptomatic leaves from Northeast India, Papua New Guinea and Timor-Leste (East Timor...

Fourteen strains of nitrogen-fixing bacteria were isolated from different agricultural plant species, including cassava, maize and sugarcane, using nitrogen-deprived selective isolation conditions. Ability to fix nitrogen was verified by the acetylene reduction assay. All potentially nitrogen-fixing strains tested showed positive hybridization signals with a nifH probe derived from Azospirillum...

Products containing probiotic bacteria are gaining popularity, increasing the importance of their accurate speciation. Unfortunately, studies have suggested that improper labeling of probiotic species is common in commercial products. Species identification of a bank of commercial probiotic strains was attempted using partial 16S rDNA sequencing, carbohydrate fermentation analysis, and cellular...

UNLABELLED Identity of causative agent of rhinosporidiosis (Rhinosporidium seeberi) has been controversial since the disease was described in 1900. Extensive sequence alignments and phylogenetic analyses of 16S rRNA gene detected recently by us in R. seeberi , revealed 99% similarity with 16S rDNA in chloroplasts of flowering plants. Study demonstrates R. seeberi is a pigmented prokaryote displ...