[Show abstract][Hide abstract] ABSTRACT: Background
Infection by pathogenic viruses results in rapid epithelial damage and significantly impacts on the condition of the upper respiratory tract, thus the effects of viral infection may induce changes in microbiota. Thus, we aimed to define the healthy microbiota and the viral pathogen-affected microbiota in the upper respiratory tract. In addition, any association between the type of viral agent and the resultant microbiota profile was assessed.Methods
We analyzed the upper respiratory tract bacterial content of 57 healthy asymptomatic people (17 health-care workers and 40 community people) and 59 patients acutely infected with influenza, parainfluenza, rhino, respiratory syncytial, corona, adeno, or metapneumo viruses using culture-independent pyrosequencing.ResultsThe healthy subjects harbored primarily Streptococcus, whereas the patients showed an enrichment of Haemophilus or Moraxella. Quantifying the similarities between bacterial populations by using Fast UniFrac analysis indicated that bacterial profiles were apparently divisible into 6 oropharyngeal types in the tested subjects. The oropharyngeal types were not associated with the type of viruses, but were rather linked to the age of the subjects. Moraxella nonliquefaciens exhibited unprecedentedly high abundance in young subjects aged <6 years. The genome of M. nonliquefaciens was found to encode various proteins that may play roles in pathogenesis.Conclusions
This study identified 6 oropharyngeal microbiome types. No virus-specific bacterial profile was discovered, but comparative analysis of healthy adults and patients identified a bacterium specific to young patients, M. nonliquefaciens.
[Show abstract][Hide abstract] ABSTRACT: Leucobacter salsicius M1-8(T) is a member of the Microbacteriaceae family within the class Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium and was previously isolated from a Korean fermented food. Most members of the genus Leucobacter are chromate-resistant and this feature could be exploited in biotechnological applications. However, the genus Leucobacter is poorly characterized at the genome level, despite its potential importance. Thus, the present study determined the features of Leucobacter salsicius M1-8(T), as well as its genome sequence and annotation. The genome comprised 3,185,418 bp with a G+C content of 64.5%, which included 2,865 protein-coding genes and 68 RNA genes. This strain possessed two predicted genes associated with chromate resistance, which might facilitate its growth in heavy metal-rich environments.
Standards in Genomic Sciences 06/2014; 9(3):495-504. · 3.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Kitasatospora cheerisanensis KCTC 2395, which produces antifungal metabolites with bafilomycin derivatives, including bafilomycin C1-amide, was isolated from a soil sample at Mt. Jiri, South Korea. Here, we report its draft genome sequence, which contains 8.04 Mb with 73.6% G+C content and 7,810 protein-coding genes.
[Show abstract][Hide abstract] ABSTRACT: Vanillin is a well-known food and cosmetic additive and has antioxidant and antimutagenic properties. It has also been suggested to have antifungal activity against major human pathogenic fungi, although it is not very effective. In this study, the antifungal activities of vanillin and 33 vanillin derivatives against the human fungal pathogen Cryptococcus neoformans, the main pathogen of cryptococcal meningitis in immunocompromised patients, were investigated. We found a structural correlation between the vanillin derivatives and antifungal activity, showing that the hydroxyl or alkoxy group is more advantageous than the halogenated or nitrated group in benzaldehyde. Among the vanillin derivatives with a hydroxyl or alkoxy group, o-vanillin and o-ethyl vanillin showed the highest antifungal activity against C. neoformans. o-Vanillin was further studied to understand the mechanism of antifungal action. We compared the transcriptome of C. neoformans cells untreated or treated with o-vanillin by using RNA sequencing and found that the compound caused mitochondrial dysfunction and triggered oxidative stress. These antifungal mechanisms of o-vanillin were experimentally confirmed by the significantly reduced growth of the mutants lacking the genes involved in mitochondrial functions and oxidative stress response.
PLoS ONE 02/2014; 9(2):e89122. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Flavobacterium seoulense strain EM1321(T) is the type strain of Flavobacterium seoulense sp. nov., a proposed novel species within the genus Flavobacterium. This strain is a Gram-reaction-negative, aerobic, rod-shaped bacterium isolated from stream water in Bukhansan National Park, Seoul. This organism is motile by gliding. Here, we describe the features of Flavobacterium seoulense EM1321(T), together with its genome sequence and annotation. The genome comprised 3,792,640 bp, with 3,230 protein-coding genes and 52 RNA genes.
Standards in Genomic Sciences 01/2014; 9:34. · 3.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: EzEditor is a Java-based molecular sequence editor allowing manipulation of both DNA and protein sequence alignments for phylogenetic analysis. It has multiple features optimized to connect initial computer-assisted multiple alignment and subsequent phylogenetic analysis by providing manual editing with reference to biological information specific to the genes under consideration. It provides various functionality for editing rRNA alignment using secondary structure information. In addition, it supports simultaneous editing for both DNA and their translated protein sequences for protein-coding genes. EzEditor is the first sequence editing software designed for both RNA and protein coding genes with the visualization of biologically relevant information, and should be useful in molecular phylogenetic studies. EzEditor is based on Java which can be run on all major operating systems, and freely available from http://sw.ezbiocloud.net/ezeditor/.
International Journal of Systematic and Evolutionary Microbiology 12/2013; · 2.79 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, 'M. massiliense', and 'M. bolletii'. In 2011, 'M. massiliense' and 'M. bolletii' were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of 'M. massiliense' within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of 'Mycobacterium massiliense' (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of 'M. bolletii' and 'M. massiliense' at the subspecies level. The genome tree also clearly illustrated that 'M. bolletii' and 'M. massiliense' form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known 'M. massiliense' and 'M. bolletii' strains.
PLoS ONE 11/2013; 8(11):e81560. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Diketopiperazine (DKP) is produced by various organisms, including bacteria, fungi, and animals, and has been suggested as a novel signal molecule involved in the modulation of genes with various biological functions. Vibrio vulnificus, which causes septicemia in humans, produces cyclo(L-phenylalanine-L-proline) (cFP). To understand the biological roles of cFP, the effect of the compound on the expression of the total mRNA in V. vulnificus was assessed by next-generation sequencing (NGS). Based on the transcriptomic analysis, we classified the cFP-regulated genes into functional categories and clustered them according to the expression patterns resulting from treatment with cFP. From a total of 4,673 genes, excepting the genes encoding tRNA in V. vulnificus, 356 genes were up-regulated and 602 genes were down-regulated with an RPKM (reads per kilo-base per million) value above 3. The genes most highly induced by cFP comprised those associated with the transport and metabolism of inorganic molecules, particularly iron. The genes negatively regulated by cFP included those associated with energy production and conversion, as well as carbohydrate metabolism. Noticeably, numerous genes related with biofilm formation were modulated by cFP. We demonstrated that cFP interferes significantly with the biofilm formation of V. vulnificus.
Journal of Microbiology and Biotechnology 10/2013; · 1.32 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A brick-red colored, curved-rod shaped, prostheca-bearing and non-motile bacterial strain, designated JC2236T, was isolated from a seawater sample of Jeju Island, Korea. Result of 16S rRNA gene sequence analysis indicated that the test strain belongs to the family Hyphomonadaceae and represents a distinct phyletic line that reflects a novel genus status within a clade containing genera Litorimonas, Hellea, Robiginitomaculum and Algimonas. The predominant isoprenoid quinone (Q10) and polar lipid profile (PG, GUDG and MGDG) were in line with those of most members of the family. However, the DNA G+C content (49.3 mol%), the abundance of C16:0, the requirement of sea salts for growth, and absence of cell motility differentiated strain JC2236T from other closely related genera. Overall enzymatic traits also demonstrated that the test strain does not closely affiliate with any of the previously described genera. Thus, based on polyphasic taxonomic data, it is proposed that strain JC2236T constitute a novel genus and a novel species belonging to the family Hyphomonadaceae. The name Fretibacter rubidus gen. nov., sp. nov. is therefore proposed for the isolate; type strain is JC2236T (= KACC 16935T = JCM 15585T).
International Journal of Systematic and Evolutionary Microbiology 08/2013; · 2.79 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In previous study, alkaliphilic and thermotolerant bacterium strain, Pseudomonas sp. strain G5, capable of reducing insoluble indigo was isolated from Korean traditional fermentation liquor. Here, we report the draft genome sequence and annotation of strain G5 to provide the genomic information involved in indigo reduction process.
Journal of the Korean Society for Applied Biological Chemistry 06/2013; 56:339-341. · 0.54 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Salinicoccus carnicancri Jung et al. 2010 belongs to the genus Salinicoccus in the family Staphylococcaceae. Members of the Salinicoccus are moderately halophilic and originate from various salty environments. The halophilic features of the Salinicoccus suggest their possible uses in biotechnological applications, such as biodegradation and fermented food production. However, the genus Salinicoccus is poorly characterized at the genome level, despite its potential importance. This study presents the draft genome sequence of S. carnicancri strain Crm(T) and its annotation. The 2,673,309 base pair genome contained 2,700 protein-coding genes and 78 RNA genes with an average G+C content of 47.93 mol%. It was notable that the strain carried 72 predicted genes associated with osmoregulation, which suggests the presence of beneficial functions that facilitate growth in high-salt environments.
Standards in Genomic Sciences 06/2013; 8(2):255-63. · 3.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Escherichia coli AI27 is a putatively commensal strain isolated from feces of a pig. Here we report the draft genome sequence of E. coli AI27. This is the first porcine strain in the phylogenetic group B1 whose genome sequence has been determined.
Journal of bacteriology 12/2012; 194(23):6640-1. · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The high-affinity reductive iron uptake system that includes a ferroxidase (Cfo1) and an iron permease (Cft1) is critical for the pathogenesis of Cryptococcus neoformans. In addition, a mutant lacking CFO1 or CFT1 not only has reduced iron uptake but also displays a markedly increased susceptibility to azole antifungal drugs. Altered antifungal susceptibility of the mutants was of particular interest because the iron uptake system has been proposed as an alternative target for antifungal treatment. In this study, we used transcriptome analysis to begin exploring the molecular mechanisms of altered antifungal susceptibility in a cfo1 mutant. The wild-type strain and the cfo1 mutant were cultured with or without the azole antifungal drug fluconazole and their transcriptomes were compared following sequencing with Illumina Genome Analyzer IIx (GAIIx) technology. As expected, treatment of both strains with fluconazole caused elevated expression of genes in the ergosterol biosynthetic pathway that includes the target enzyme Erg11. Additionally, genes differentially expressed in the cfo1 mutant were involved in iron uptake and homeostasis, mitochondrial functions and respiration. The cfo1 mutant also displayed phenotypes consistent with these changes including a reduced ratio of NAD(+)/NADH and down-regulation of Fe-S cluster synthesis. Moreover, combination treatment of the wild-type strain with fluconazole and the respiration inhibitor diphenyleneiodonium dramatically increased susceptibility to fluconazole. This result supports the hypothesis that down-regulation of genes required for respiration contributed to the altered fluconazole susceptibility of the cfo1 mutant. Overall, our data suggest that iron uptake and homeostasis play a key role in antifungal susceptibility and could be used as novel targets for combination treatment of cryptococcosis. Indeed, we found that iron chelation in combination with fluconazole treatment synergistically inhibited the growth of C. neoformans.
Fungal Genetics and Biology 09/2012; · 3.26 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: An enteric bacterium, Escherichia coli W26 (KACC 16630), was isolated from feces from a healthy cow in South Korea. Here, we report the draft genome sequence of the isolate, which is closely affiliated with commensal strains belonging to E. coli phylogroup B1.
Journal of bacteriology 09/2012; 194(18):5149-50. · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Escherichia coli J53 (F(-) met pro Azi(r)) is a derivative of E. coli K-12 which is resistant to sodium azide. This strain has been widely used as a general recipient strain for various conjugation experiments. Here, we report the genome sequence of E. coli J53 (=KACC 16628).
Journal of bacteriology 07/2012; 194(14):3742-3. · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Mycobacterium abscessus subsp. bolletii is an increasing cause of human pulmonary disease and infections of the skin and soft tissues. Consistent reports of human infections indicate that M. bolletii is a highly pathogenic, emerging species of rapidly growing mycobacteria (RGM). Here we report the first whole-genome sequence of M. abscessus subsp. bolletii BD(T).
Journal of bacteriology 05/2012; 194(10):2756-7. · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A group of bacterial strains formerly known as CDC group M-5 are opportunistic pathogens to humans. In 1993, a name, Neisseria weaveri, was proposed by two independent studies to harbor CDC group M-5 strains, namely N. weaveri Holmes et al. 1993 and N. weaveri Andersen et al. 1993, with two different 'type' strains. However, no study has been conducted on to the relatedness of the two 'type' strains, although the close relationship of the two taxa has long been accepted unofficially. Formally, the status of the name N. weaveri Andersen et al. 1993 is illegitimate because it is a later homonym of N. weaveri Holmes et al., 1993; but the name of the strain is still validly published. In this study, we attempt to resolve the confusion caused by the apparent duplication of the species N. weaveri (with different type strains) using whole genome shotgun sequencing. We also sought to gain insight into the genetic characteristics of N. weaveri by conducting comparative genomics. On the basis of genomic similarities revealed through a comparative genomic study, we propose that N. weaveri Andersen et al. 1993 should be re-classified as a later heterotypic synonym of N. weaveri Holmes et al., 1993.
[Show abstract][Hide abstract] ABSTRACT: Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.
International Journal of Systematic and Evolutionary Microbiology 11/2011; 62(Pt 3):716-21. · 2.79 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Previously, we reported that various oral bacteria regulate interleukin (IL)-8 production differently in gingival epithelial cells. The aim of this study was to characterize the pattern recognition receptor(s) that mediate bacteria-induced IL-8 expression. Among ligands that mimic bacterial components, only a Toll-like receptor (TLR) 9 ligand enhanced IL-8 expression as determined by ELISA. Both normal and immortalized human gingival epithelial (HOK-16B) cells expressed TLR9 intracellularly and showed enhanced IL-8 expression in response to CpG-oligonucleotide. The ability of eight strains of four oral bacterial species to induce IL-8 expression in HOK-16B cells, and their invasion capacity were examined in the absence or presence of 2% human serum. The ability of purified bacterial DNA (bDNA) to induce IL-8 was also examined. Six out of eight strains increased IL-8 production in the absence of serum. Usage of an endosomal acidification blocker or a TLR9 antagonist inhibited the IL-8 induction by two potent strains. In the presence of serum, many strains lost the ability to induce IL-8 and presented substantially reduced invasion capacity. The IL-8-inducing ability of bacteria in the absence or presence of serum showed a strong positive correlation with their invasion index. The IL-8-inducing ability of bacteria in the absence of human serum was also correlated with the immunostimulatory activity of its bDNA. The observed immunostimulatory activity of the bDNA could not be linked to its CpG motif content. In conclusion, oral bacteria induce IL-8 in gingival epithelial cells through TLR9 and the IL-8-inducing ability depends on the invasive capacity and immunostimulating DNA.
Immunology and Cell Biology 10/2011; 90(6):655-63. · 4.21 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The dissimilatory metal reducing bacterium Shewanella sp. strain HN-41 was first reported to produce novel photoactive As-S nanotubes via reduction of As(V) and S(2)O(3)(2-) under anaerobic conditions. Here we report the draft genome sequence and annotation of strain HN-41.
Journal of bacteriology 09/2011; 193(18):5039-40. · 2.69 Impact Factor