Despite recent advances in commercially optimized identification systems, bacterial remains a challenging task many routine microbiological laboratories, especially situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this when coupled with well-curated database, such as EzTaxon, containing sequences of type strains prokaryotic species validly published names. Although the EzTaxon database widely isolates, from uncultured prokaryotes...

Advancement of DNA sequencing technology allows the routine use genome sequences in various fields microbiology. The information held proved to provide objective and reliable means taxonomy prokaryotes. Here, we describe minimal standards for quality how they can be applied taxonomic purposes.

A facultative anaerobic bacterium was isolated from a mediator-less microbial fuel cell fed with artificial wastewater containing acetate and designated as PA3. The isolate identified strain of Aeromonas hydrophila based on its biochemical, physiological morphological characteristics well 16S rDNA sequence analysis DNA-DNA hybridization. PA3 used glucose, glycerol, pyruvate hydrogen to reduce Fe(III), nitrate sulfate. Cyclic voltammetry showed that electrochemically active the culture...

A biofilm of Geobacter sulfurreducens will grow on an anode surface and catalyze the generation electrical current by oxidizing acetate utilizing as its metabolic terminal electron acceptor. Here we report qualitative analysis cyclic voltammetry anodes modified with biofilms G. strains DL1 KN400 to predict possible rate-limiting steps in generation. Strain generates approximately 2 8-fold greater than strain depending upon electrode material, enabling comparative electrochemical study...

The application of transgenic plants to clean up environmental pollution caused by the wastes heavy metal mining is a promising method for removing pollutants from soils. However, effect using genetically modified organisms phytoremediation poorly researched topic in terms microbial community structures, despite important role microorganisms health soil. In this study, comparative analysis bacterial and archaeal communities found rhizosphere (GM) versus wild-type (WT) poplar was conducted on...

Subgingival microorganisms are potentially associated with periodontal diseases. However, changes in the subgingival microbiota during progress of diseases poorly understood. In this study, we analyzed bacterial communities paper point samples from 32 Korean individuals no sign disease, gingivitis, or periodontitis using 454 FLX Titanium pyrosequencing. A total 256,113 reads representing 26 phyla, 433 genera, and 1,016 species were detected. Bacteroidetes, Fusobacteria, Synergistetes,...

Airborne microorganisms have significant effects on human health, and children are more vulnerable to pathogens allergens than adults. However, little is known about the microbial communities in air of childcare facilities. Here, we analyzed bacterial fungal 50 samples collected from five daycare centers elementary schools located Seoul, Korea using culture-independent high-throughput pyrosequencing. The contained a wide variety taxa not previously identified child schools. Moreover,...

Abstract Lactobacillus delbrueckii comprises six subspecies, L. subsp. bulgaricus , lactis jakobsenii sunkii and indicus . We investigated the evolution of subspecies using comparative genomics. While defining feature species was gene number increment driven by mobile elements fragmentation, repertoire subspecies-specific gains losses differed among subspecies. The horizontal transfer analyses indicated that frequent transfers between different had occurred when first diverged from common...

Next-generation sequencing has great potential for application in bacterial transcriptomics. However, unlike eukaryotes, bacteria have no clear mechanism to select mRNAs over rRNAs; therefore, rRNA removal is a critical step sequencing-based Duplex-specific nuclease (DSN) an enzyme that, at high temperatures, degrades duplex DNA preference single-stranded DNA. DSN treatment been successfully used normalize the relative transcript abundance mRNA-enriched cDNA libraries from eukaryotic...

Infection by pathogenic viruses results in rapid epithelial damage and significantly impacts on the condition of upper respiratory tract, thus effects viral infection may induce changes microbiota. Thus, we aimed to define healthy microbiota pathogen-affected tract. In addition, any association between type agent resultant profile was assessed.We analyzed tract bacterial content 57 asymptomatic people (17 health-care workers 40 community people) 59 patients acutely infected with influenza,...

A bacterium (named OT-1 T ) that showed algicidal activity was isolated from sea water of Masan Bay, Korea, during an outbreak red tide. Phylogenetic analysis based on 16S rDNA sequences the isolate formed a distinct phyletic lineage within family Flavobacteriaceae Cytophaga – Flavobacterium Bacteroides group. No species with validly published name ⩾93 % rRNA gene sequence similarity to strain . The had major amounts iso-branched and 3-hydroxy fatty acids menaquinone 6 DNA G+C content 34...

A yellow-pigmented, Gram-negative and aerobic bacterial strain, designated AT1026 T , was isolated from a terrestrial sample the Antarctic. Results of 16S rRNA gene sequence analysis indicated that Antarctic isolate belonged to genus Flavobacterium with highest similarity tegetincola (96·4 %). Cells were non-motile, non-gliding psychrotolerant, optimum maximum temperatures about 20 25 °C. Flexirubins absent. The major isoprenoid quinone (MK-6), predominant cellular fatty acids (iso-C 15 : 1...

An actinobacterial strain containing demethylmenaquinone DMK-9(H(4)) as the diagnostic isoprenoid quinone was isolated from a tidal flat sediment sample, South Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that JC2054(T) represents distinct phyletic line within suborder Micrococcineae of order Actinomycetales. The closest phylogenetic neighbour Cellulomonas fermentans, with 94.7 % sequence similarity. novel isolate strictly aerobic and slightly halophilic, optimum...

Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that emerging as human pathogens. The M. was previously composed three species, namely sensu stricto, 'M. massiliense', and bolletii'. In 2011, massiliense' bolletii' were united reclassified a single subspecies within abscessus: subsp. bolletii. However, placement boundary bolletii remains highly controversial with regard to clinical aspects. this study, we revisited taxonomic status members based on comparative...

A Gram-positive bacterial strain containing l -ornithine as the diagnostic diamino acid was isolated from a sea-water-sample East Sea, Korea. phylogenetic analysis based on 16S rRNA gene sequences showed that JC1078 T represents phyletic line within suborder Micrococcineae of order Actinomycetales , adjacent to genus Ornithinimicrobium . The highest sequence similarity values isolate were observed against humiphilum (94·3 %) and Kytococcus sedentarius (94·1 %). strictly aerobic moderately...

Two yellow-pigmented, Gram-negative and aerobic bacterial strains, designated AT1013T AT1047T, were isolated from terrestrial samples of the Antarctic. On basis 16S rRNA gene sequence analyses, two Antarctic strains shared 97.7 % similarity showed moderate relationships to genera Chryseobacterium (92.5-95.3 %), Riemerella (92.3-93.5 Bergeyella (92.5-92.6 %) Kaistella (92.5-93.3 %). In phylogenetic isolates formed a robust monophyletic clade represented distinct phyletic line that equated...

The taxonomic positions of the genera Ruegeria and Silicibacter were evaluated by a polyphasic investigation. It was evident from 16S rRNA gene sequence analysis that both are closely related as they formed monophyletic clade with high similarities (96.9-98.2 %). Several properties commonly found in these taxa strongly suggest should be classified same genus. Further, comparative study based on DNA-DNA hybridization, phenotypic characterization chemotaxonomic indicated members this clade,...

Escherichia coli J53 (F(-) met pro Azi(r)) is a derivative of E. K-12 which resistant to sodium azide. This strain has been widely used as general recipient for various conjugation experiments. Here, we report the genome sequence (=KACC 16628).