gcType: a high-quality type strain genome database for microbial phylogenetic and functional research.

Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.

Sulfitobacter aestuarii sp. nov., a marine bacterium isolated from a tidal flat of the Yellow Sea.

A novel bacterial strain, designated hydD52T, was isolated from a sample of tidal flat sediment of the Yellow Sea in the Republic of Korea. The cells were motile, rod-shaped and Gram-stain-negative. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain hydD52T was a member of the genus Sulfitobacter and most closely related to Sulfitobacter dubius DSM 16472T (98.0 %), Sulfitobacter indolifex HEL-45T (97.8 %) and Sulfitobacter delicatus DSM 28223T (97.6 %). The major fatty acids (>5 %) of hydD52T were C18 : 1ω7c/C18 : 1ω6c, C16 : 0, C18 : 1ω7c 11-methyl and C19 : 0ω8c. The respiratory quinone of strain hydD52T was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified amino lipid. The G+C content of this strain was 64.0 mol%. The DNA-DNA relatedness values of hydD52T with the type strains of S. dubius, S. indolifex and S. delicatus were 18.8, 13.1 and 15.7 %, respectively. Based on the results of morphological, physiological and chemotaxonomic characterization, DNA-DNA hybridization relatedness, and 16S rRNA genes analysis, we concluded that strain hydD52T represents a novel species, for which the name Sulfitobacter aestuarii sp. nov. is proposed. The type strain is hydD52T (=KCTC 32982T=TISTR 2562T).

Flavobacterium tistrianum sp. nov., a gliding bacterium isolated from soil.

A novel gliding bacterial strain, GB 56.1T, was obtained from soil at the Sakaerat Biosphere Reserve, in Nakhon Ratchasima province, Thailand; the strain was characterized using a polyphasic approach. Cells were Gram-stain-negative, yellow, rod shaped and devoid of flagella, but showed gliding motility. Phylogenetic analysis based on 16S rRNA gene sequences found that GB 56.1T was a member of the genus Flavobacterium and that the strain shared the highest sequence similarities with Flavobacterium nitrogenifigens (98.4 %), Flavobacterium anhuiense(98.3 %) and Flavobacterium ginsenosidimutans (97.9 %). The similarities of the sequences of all other species of the genus Flavobacterium were below 97.4 %. The major respiratory quinone of strain GB 56.1T was MK-6; fatty acids were iso-C15:0, C16:1ω6c/C16:1ω7c, C16:0 and C16:0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylserine, an unidentified amino lipid and four polar lipids. The DNA G+C content of this strain was 34.2 mol%. The DNA-DNA relatedness of GB 56.1T was highest against F.anhuiense, with a value of 37.6 %. On the basis of morphological, physiological and chemotaxonomic characteristics, DNA-DNA hybridization relatedness and 16S rRNA gene sequence analysis, we conclude that strain GB 56.1T represents a novel species, for which the name Flavobacterium tistrianum sp. nov. is proposed. The type strain is GB 56.1T (=TISTR 1612T =KCTC 42679T).

Insights into the structure and assembly of the Bacillus subtilis clamp-loader complex and its interaction with the replicative helicase.

The clamp-loader complex plays a crucial role in DNA replication by loading the ß-clamp onto primed DNA to be used by the replicative polymerase. Relatively little is known about the stoichiometry, structure and assembly pathway of this complex, and how it interacts with the replicative helicase, in Gram-positive organisms. Analysis of full and partial complexes by mass spectrometry revealed that a hetero-pentameric τ3-δ-δ' Bacillus subtilis clamp-loader assembles via multiple pathways, which differ from those exhibited by the Gram-negative model Escherichia coli. Based on this information, a homology model of the B. subtilis τ3-δ-δ' complex was constructed, which revealed the spatial positioning of the full C-terminal τ domain. The structure of the δ subunit was determined by X-ray crystallography and shown to differ from that of E. coli in the nature of the amino acids comprising the τ and δ' binding regions. Most notably, the τ-δ interaction appears to be hydrophilic in nature compared with the hydrophobic interaction in E. coli. Finally, the interaction between τ3 and the replicative helicase DnaB was driven by ATP/Mg(2+) conformational changes in DnaB, and evidence is provided that hydrolysis of one ATP molecule by the DnaB hexamer is sufficient to stabilize its interaction with τ3.

The virulence factor PEB4 (Cj0596) and the periplasmic protein Cj1289 are two structurally related SurA-like chaperones in the human pathogen Campylobacter jejuni.

The PEB4 protein is an antigenic virulence factor implicated in host cell adhesion, invasion, and colonization in the food-borne pathogen Campylobacter jejuni. peb4 mutants have defects in outer membrane protein assembly and PEB4 is thought to act as a periplasmic chaperone. The crystallographic structure of PEB4 at 2.2-Å resolution reveals a dimer with distinct SurA-like chaperone and peptidyl-prolyl cis/trans isomerase (PPIase) domains encasing a large central cavity. Unlike SurA, the chaperone domain is formed by interlocking helices from each monomer, creating a domain-swapped architecture. PEB4 stimulated the rate of proline isomerization limited refolding of denatured RNase T(1) in a juglone-sensitive manner, consistent with parvulin-like PPIase domains. Refolding and aggregation of denatured rhodanese was significantly retarded in the presence of PEB4 or of an engineered variant specifically lacking the PPIase domain, suggesting the chaperone domain possesses a holdase activity. Using bioinformatics approaches, we identified two other SurA-like proteins (Cj1289 and Cj0694) in C. jejuni. The 2.3-Å structure of Cj1289 does not have the domain-swapped architecture of PEB4 and thus more resembles SurA. Purified Cj1289 also enhanced RNase T(1) refolding, although poorly compared with PEB4, but did not retard the refolding of denatured rhodanese. Structurally, Cj1289 is the most similar protein to SurA in C. jejuni, whereas PEB4 has most structural similarity to the Par27 protein of Bordetella pertussis. Our analysis predicts that Cj0694 is equivalent to the membrane-anchored chaperone PpiD. These results provide the first structural insights into the periplasmic assembly of outer membrane proteins in C. jejuni.

Complete Genome Sequence of Spirosoma sp. Strain KCTC 42546, Isolated from a Reservoir in South Korea.

This study reports on the complete genome sequence of Spirosoma sp. strain KCTC 42546, isolated from fresh water in a reservoir in South Korea. The genome contained genes for various glycosyl hydrolases, which are associated with degrading sugars and DNA-repairing enzymes.

Effect of Prebiotics-Enhanced Probiotics on the Growth of Streptococcus mutans.

Streptococcus mutans predominantly creates an acidic environment in an oral cavity. This results in dental demineralization and carious lesions. The probiotics are beneficial microorganisms that modulate the bacterial balance in the digestive system. Prebiotics are defined as nondigestible oligosaccharides that are utilized for the selective stimulation of the beneficial microorganisms. The objective of this study was to evaluate the efficacy of the prebiotics, galactooligosaccharides (GOS) and fructooligosaccharides (FOS), for enhancing the probiotic Lactobacillus acidophilus ATCC 4356, for inhibiting Streptococcus mutans (A32-2) for the prevention of dental caries. The growth rate of the S. mutans significantly decreased when cocultured with L. acidophilus in the GOS-supplemented medium at 3%, 4%, and 5%. In the FOS-supplemented medium, the growth rate of S. mutans significantly decreased in all concentrations when cocultured with L. acidophilus. There was no significant difference in the growth rate of L. acidophilus in all concentrations of either GOS or FOS. It can be concluded that the growth rate of S. mutans was significantly retarded when cocultured with L. acidophilus and the proper concentration of prebiotics. These prebiotics have potential for a clinical application to activate the function of the naturally intraoral L. acidophilus to inhibit S. mutans.

The inhibition of Caco-2 proliferation by astaxanthin from Xanthophyllomyces dendrorhous.

PURPOSE: To investigate the efficiency of natural astaxanthin that has been extracted from Xanthophyllomyces dendrorhous in inhibiting the proliferation and viability of colorectal adenocarcinoma cell line (Caco-2; colon cancer cells). METHODOLOGY: Caco-2 cells and normal human oralkeratinocytes (NOKs) were treated with different concentrations of extracted astaxanthin, ranging from 0.075 to 10 mg ml-1, for 24, 48 and 72 h. The number of cells was determined via MTS assay and the proliferating cells were investigated by bromodeoxyuridine (BrdU) assay.Results/Key findings. Of the Caco-2 cells, 30-50 % remained viable, while the NOKs showed 110-120 % survival when treated with 5 mg ml-1 astaxanthin. The Caco-2 cells showed distinct structural shrinkage when treated with the same concentration of astaxanthin. Fluorescent labelling of the DNA of the proliferative cells with BrdU showed a significant decrease in the number of the proliferative Caco-2 cells when the concentration of astaxanthin was increased to 5 mg ml-1. CONCLUSION: The natural astaxanthin from X. dendrorhous, at an appropriate concentration, is effective in terminating the viability of, or retarding the proliferative activity of, Caco-2 cells, without harmful effects on NOKs.

Aureispira maritima sp. nov., isolated from marine barnacle debris.

A novel gliding marine bacterium (strain 59SA(T)) was isolated from marine barnacle debris. A phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct lineage within the genus Aureispira in the family 'Saprospiraceae'. The DNA G+C content of strain 59SA(T) was 38.7 mol%, the major respiratory quinone was MK-7 and the predominant cellular fatty acids were 20 : 4omega6c and 16 : 0. On the basis of the data from DNA-DNA hybridization, physiological and chemotaxonomic analyses and 16S rRNA gene sequence comparisons, strain 59SA(T) represents a novel species of the genus Aureispira, for which the name Aureispira maritima sp. nov. is proposed. The type strain is 59SA(T) (=IAM 15439(T)=TISTR 1726(T)).

Aureispira marina gen. nov., sp. nov., a gliding, arachidonic acid-containing bacterium isolated from the southern coastline of Thailand.

Three strains of gliding bacteria, 24(T), 62 and 71, isolated from a marine sponge and algae from the southern coastline of Thailand, were studied using a polyphasic approach to clarify their taxonomic positions. A phylogenetic analysis based on 16S rRNA gene sequences showed that the three isolates formed a distinct lineage within the family 'Saprospiraceae' of the phylum Bacteroidetes and were related to members of the genus Saprospira. The G+C contents of the isolates were in the range 38-39 mol%. The major respiratory quinone was MK-7. The predominant cellular fatty acids were 20 : 4omega6c (arachidonic acid), 16 : 0 and iso-17 : 0. On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA-DNA hybridization data and 16S rRNA gene sequences, the isolates represent a novel species of a novel genus, for which the name Aureispira marina gen. nov., sp. nov. is proposed. The type strain of Aureispira marina is 24(T) (=IAM 15389(T)=TISTR 1719(T)).