Bacterial taxonomy has progressed from reliance on highly artificial culture-dependent techniques involving the study of phenotype (including morphological, biochemical and physiological data) to the modern applications of molecular biology, most recently 16S rRNA gene sequencing, which gives an insight into evolutionary pathways (= phylogenetics). The latter is applicable to culture-independen...

The objective of this study was to investigate the bacterial composition present in root canals of teeth associated with acute apical abscess by molecular identification (16S rRNA) of cultivable bacteria. Two hundred and twenty strains isolated by culture from 20 root canals were subjected to DNA extraction and amplification of the 16S rRNA gene (PCR), followed by sequencing. The resulting nucl...

Phylogenetic composition of bacterial community in soil of a karst forest was analyzed by culture-independent molecular approach. The bacterial 16S rRNA gene was amplified directly from soil DNA and cloned to generate a library. After screening the clone library by RFLP, 16S rRNA genes of representative clones were sequenced and the bacterial community was analyzed phylogenetically. The 16S rRN...

• Three reference query options classify individual reads via alignment to either the premium curated MicroSEQ® ID or curated Greengenes databases as well as an optimal two-step alignment that utilizes both databases Introduction Understanding the diversity of bacterial communities, in almost any environment, has been greatly facilitated by rapid advances in nextgeneration sequencing (NGS) tech...

Introduction: Helicobacter pylori (H. pylori), is a bacterium responsible for upper gastrointestinal tract diseases. The 16s rRNA is a common H. pylori gene which are usually preferred for diagnosis purpose. The aim of this study was to determine the prevalence and abundance of 16s rRNA in fecal samples and also evaluate correlation between the level of 16s rRNA and activities of the cytokine...

Proteus mirabilis ARS68, which demonstrated a very high level of resistance to various aminoglycosides, was isolated in 2003 from an inpatient in Japan. The aminoglycoside resistance of this strain could not be transferred to recipient strains Escherichia coli CSH-2 and E. coli HB101 by a general conjugation experiment, but E. coli DH5alpha was successfully transformed by electroporation with t...

Four Gram-positive cocci were isolated from the cerebrospinal fluid or blood of four different patients, but they could not be identified by an automated conventional identification system, so they were identified using cellular fatty acid (CFA) composition analysis and 16S rRNA gene sequencing analysis. Of these, two strains (SMC-A2662 and SMCA5889), which were previously supposed to be Rothia...

Process surveillance within agricultural biogas plants (BGPs) was concurrently studied by high-throughput 16S rRNA gene amplicon sequencing and an optimized quantitative microscopic fingerprinting (QMF) technique. In contrast to 16S rRNA gene amplicons, digitalized microscopy is a rapid and cost-effective method that facilitates enumeration and morphological differentiation of the most signific...

BACKGROUND West Virginia has the worst oral health in the United States, but the reasons for this are unclear. This pilot study explored the etiology of this disparity using culture-independent analyses to identify bacterial species associated with oral disease. METHODS Bacteria in subgingival plaque samples from twelve participants in two independent West Virginia dental-related studies were...

The bacterial diversity associated with citrus leaf midribs was characterized for citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rRNA gene microarrays and 16S rRNA gene clone library sequencing to determine the microbial community composition for symptomatic and asymptomatic citru...