BACKGROUND Substantial progress in high-throughput metagenomic sequencing methodologies has enabled the characterisation of bacteria from various origins (for example gut and skin). However, the recently-discovered bacterial microbiota present within animal internal tissues has remained unexplored due to technical difficulties associated with these challenging samples. RESULTS We have optimiz...

Bacillus is a diverse bacterial genus characterized by cells growing aerobically and forming dormant endospores. Although Bacillus species were some of the first bacteria ever characterized, their relationships to one another remain enigmatic. The recent deluge of environmental sequencing projects has further complicated our view of Bacillus taxonomy and diversity. In this review we discuss the...

MOTIVATION 16S rDNA hypervariable tag sequencing has become the de facto method for accessing microbial diversity. Illumina paired-end sequencing, which produces two separate reads for each DNA fragment, has become the platform of choice for this application. However, when the two reads do not overlap, existing computational pipelines analyze data from read separately and underutilize the infor...

We evaluated the performance of matrix-assisted laser desorption ionization-time flight mass spectrometry (MALDI-TOF MS) associated with Bruker BioTyper TM V7.0.0 database for identification 713 bacterial strains isolated from seafood products and sea water samples (ANSES B3PA collection) under culture conditions that may have been significantly different those used to create reference spectrum...

Aeromonas spp infections are probably the most common bacterial disease diagnosed in cultured warm water fish. In the present study, six strains of Aeromonas spp bacteria were isolated from the gourami (Colisa lalia) by 16S rDNA sequencing analyses that are pathogenic to freshwater fish. Among them, three were under Aeromonas veronii species, two were Aeromonas sp ATCC and one was Aeromonas hyd...

Exploring the genomic information of a specific uncultured soil bacterium is vital to understand its function in the ecosystem but is still a challenge due to the lack of culture techniques. To examine the genomes of uncultured bacteria, a metagenomic bacterial artificial chromosome library derived from a soil sample was screened for 16S rDNA-containing clones. Five clones (4C6, 5E7, 5G4, 5G12,...

Human saliva can be separated by centrifugation into cell pellet and cell-free supernatant, which are called cellular phase and liquid phase in this study. While it is well documented that the cellular phase of saliva contains hundreds of oral bacteria species, little is known whether the liquid phase of saliva contains any information related to oral microbiota. In this study, we analyzed the ...

BACKGROUND Dental pulp is used for PCR-based detection of DNA derived from host and bacteremic microorganims. Current protocols require odontology expertise for proper recovery of the dental pulp. Dental pulp specimen exposed to laboratory environment yields contaminants detected using universal 16S rDNA-based detection of bacteria. METHODOLOGY/PRINCIPAL FINDINGS We developed a new protocol b...

The human oral microbiome has been known to show strong association with various oral diseases including oral cancer. This study attempts to characterize the community variations between normal, oral potentially malignant disorders (OPMD) and cancer associated microbiota using 16S rDNA sequencing. Swab samples were collected from three groups (normal, OPMD and oral cancer) with nine subjects fr...

In an extensive numerical phenetic survey, a numberof blue, red and gray spored streptomycete strainswere grouped together as Streptomyces cyaneusspecies-group, a taxon which encompasses strainsknown to produce antitumor antibiotics, notably anthracyclines.In the present investigation these and relatedstreptomycetes were the subject of morphological and...