Journal of Microbiology

Volume 52(8); August 2014

Research Support, Non-U.S. Gov't

Species Delimitation of Three Species within the Russula Subgenus Compacta in Korea: R. eccentrica, R. nigricans, and R. subnigricans: Myung Soo Park , Hyun Lee , Seung-Yoon Oh , Paul Eunil Jung , Soon Ja Seok , Jonathan J. Fong , Young Woon Lim; J. Microbiol. 2014;52(8):631-638. Published online July 4, 2014; DOI: https://doi.org/10.1007/s12275-014-4168-z

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23 Citations

Abstract: Distinguishing individual Russula species can be very difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. In this study, we use the internal transcribed spacer (ITS) and 28S nuclear ribosomal large subunit (LSU) markers to identify and study the genetic diversity of species in the Russula subgenus Compacta in Korea. We focus on two morphologically similar species that are often misidentified for each other: R. nigricans and R. subnigricans. Based on molecular phylogenetic analyses, we identify three subgroups of R. nigricans, with two from Asia and one from Europe/North America. Surprisingly, we find Korean R. subnigricans are more closely related to R. eccentrica from North America than the type specimen of R. subnigricans from Japan. These molecular data, along with habitat data, reveal that Korean R. subnigricans had previously been misclassified and should now be recognized as R. eccentrica. Both ITS and LSU exhibit high interspecific and low intraspecific variation for R. eccentrica, R. nigricans, and R. subnigricans. These markers provide enough resolutional power to differentiate these species and uncover phylogeographic structure, and will be powerful tools for future ecological studies of Russula.

Journal Article

Acinetobacter apis sp. nov., Isolated from the Intestinal Tract of a Honey Bee, Apis mellifera: Pil Soo Kim , Na-Ri Shin , Joon Yong Kim , Ji-Hyun Yun , Dong-Wook Hyun , Jin-Woo Bae; J. Microbiol. 2014;52(8):639-645. Published online August 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4078-0

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35 Citations

Abstract: A novel Gram-negative, obligate aerobic, non-motile, and both coccobacillus- and bacillus-shaped bacterium, designated strain HYN18T, was isolated from the intestinal tract of a honey bee (Apis mellifera). The isolate was oxidasenegative and catalase-positive. Strain HYN18T showed optimum growth at 25°C, pH 6–7, and in the presence of 1% (w/v) NaCl in trypticase soy broth medium. The isolate was negative for hydrolyses of starch, casein, gelatin and urea, indole production from tryptone and hemolysis on sheep blood agar. A phylogenetic analysis based on the 16S rRNA gene and rpoB gene sequence showed that strain HYN18T was most closely related to Acinetobacter nectaris SAP 763.2T and A. boissieri SAP 284.1T with 98.3% and 98.1% similarity (16S rRNA gene), respectively, and 84.4% similarity with Acinetobacter nectaris SAP 763.2T (rpoB gene). The major cellular fatty acids were summed features 3 (comprising C16:1ω7c/C16:1ω6c), C12:0 and C16:0. The main isoprenoid quinone was ubiquinone-9 (Q-9). The polar lipids of strain HYN18T were phosphatidylethanolamine, three unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The DNA G+C content was 40.6 mol%. DNADNA hybridization experiments indicated less than 33 ± 10% relatedness to the closest phylogenetic species, Acinetobacter nectaris SAP 763.2T. Thus, the phenotypic, phylogenetic and genotypic analyses indicate that strain HYN18T is a novel species within the genus Acinetobacter, for which the name Acinetobacter apis is proposed. The type strain is HYN18T (=KACC 16906T =JCM 18575T).

Research Support, Non-U.S. Gov'ts

Pyrosequencing-based Analysis of Fecal Microbial Communities in Three Purebred Pig Lines: Edward Alain B. Pajarillo , Jong Pyo Chae , Marilen P. Balolong , Hyeun Bum Kim , Kang-Seok Seo , Dae-Kyung Kang; J. Microbiol. 2014;52(8):646-651. Published online July 18, 2014; DOI: https://doi.org/10.1007/s12275-014-4270-2

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95 Citations

Abstract: This study examined the fecal bacterial diversity of 15-week-old pigs from three purebred lines: Duroc, Landrace, and Yorkshire. Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. Among the breeds evaluated, Landrace had the most diverse bacterial community composition. Prevotella, Blautia, Oscillibacter, and Clostridium were detected in all samples regardless of breed. On the other hand, Catenibacterium, Blautia, Dialister, and Sphaerochaeta were differentially detected among breeds, as demonstrated by the canonical loading plot. The discriminant analysis of principal components plot also showed clear separation of the three purebred pig lines, with a certain degree of similarity between Landrace and Yorkshire pigs and a distinct separation between Duroc pigs and the other two breeds. Other factors not related to breed, such as season or time of sampling and pen effects, may contribute to shaping the gut microbiota of pigs.

Growth Phase-dependent Roles of Sir2 in Oxidative Stress Resistance and Chronological Lifespan in Yeast: Woo Kyu Kang , Yeong Hyeock Kim , Byoung-Soo Kim , Jeong-Yoon Kim; J. Microbiol. 2014;52(8):652-658. Published online July 5, 2014; DOI: https://doi.org/10.1007/s12275-014-4173-2

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9 Citations

Abstract: Silent Information Regulator 2 (Sir2), a conserved NAD+- dependent histone deacetylase, has been implicated as one of the key factors in regulating stress response and longevity. Here, we report that the role of Sir2 in oxidative stress resistance and chronological lifespan is dependent on growth phase in yeast. In exponential phase, sir2Δ cells were more resistant to H2O2 stress and had a longer chronological lifespan than wild type. By contrast, in post-diauxic phase, sir2Δ cells were less resistant to H2O2 stress and had a shorter chronological lifespan than wild type cells. Similarly, the expression of antioxidant genes, which are essential to cope with oxidative stress, was regulated by Sir2 in a growth phasedependent manner. Collectively, our findings highlight the importance of the metabolic state of the cell in determining whether Sir2 can protect against or accelerate cellular aging of yeast.

Variations of SSU rDNA Group I Introns in Different Isolates of Cordyceps militaris and the Loss of an Intron during Cross-Mating: Tiantian Lian , Tao Yang , Junde Sun , Suping Guo , Huaijun Yang , Caihong Dong; J. Microbiol. 2014;52(8):659-666. Published online July 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3681-4

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7 Citations

Abstract: Cordyceps militaris, the type species of genus Cordyceps, is one of the most popular mushrooms and a nutraceutical in eastern Asia. It is considered a model organism for the study of Cordyceps species because it can complete its life cycle when cultured in vitro. In the present study, the occurrence and sequence variation of SSU rDNA group I introns, Cmi.S943 and Cmi.S1199, among different isolates of C. militaris were analyzed. Based on the secondary structure predictions, the Cmi.S943 intron has been placed in subgroup IC1, and the Cmi.S1199 intron has been placed in subgroup IE. No significant similarity between Cmi.S943 and Cmi.S1199 suggested different origins. Three genotypes, based on the frequency and distribution of introns, were described to discriminate the 57 surveyed C. militaris strains. It was found that the genotype was related to the stroma characteristics. The stromata of all of the genotype II strains, which possessed only Cmi.S943, could produce perithecium. In contrast, the stromata of all genotype III strains, which had both Cmi.S943 and Cmi.S1199, could not produce perithecium. Cmi.S1199 showed the lowest level of intra-specific variation among the tested strains. Group I introns can be lost during strain cross-mating. Therefore, we presumed that during cross-mating and recombination, intron loss could be driven by positive Darwinian selection due to the energetic cost of transcribing long introns.

Evaluation of the Antimicrobial Potency of Silver Nanoparticles Biosynthesized by Using an Endophytic Fungus, Cryptosporiopsis ericae PS4: Lamabam Sophiya Devi , Santa Ram Joshi; J. Microbiol. 2014;52(8):667-674. Published online July 4, 2014; DOI: https://doi.org/10.1007/s12275-014-4113-1

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54 Citations

Abstract: In the present study, silver nanoparticles (AgNPs) with an average particle size of 5.5 ± 3.1 nm were biosynthesized using an endophytic fungus Cryptosporiopsis ericae PS4 isolated from the ethno-medicinal plant Potentilla fulgens L. The nanoparticles were characterized using UV-visible spectrophotometer, transmission electron microscopy (TEM), scanning electron microscopy (SEM), selective area electron diffraction (SAED), and energy dispersive X-ray (EDX) spectroscopy analysis. Antimicrobial efficacy of the AgNPs was analyzed singly and in combination with the antibiotic/antifungal agent chloramphenicol/fluconazole, against five pathogenic microorganisms-Staphylococcus aureus MTCC96, Salmonella enteric MTCC735, Escherichia coli MTCC730, Enterococcus faecalis MTCC2729, and Candida albicans MTCC 183. The activity of AgNPs on the growth and morphology of the microorganisms was studied in solid and liquid growth media employing various susceptibility assays. These studies demonstrated that concentrations of AgNPs alone between 10 and 25 μM reduced the growth rates of the tested bacteria and fungus and revealed bactericidal/fungicidal activity of the AgNPs by delaying the exponential and stationary phases. Examination using SEM showed pits and ruptures in bacterial cells indicating fragmented cell membrane and severe cell damage in those cultures treated with AgNPs. These experimental findings suggest that the biosynthesized AgNPs may be a potential antimicrobial agent.

Effects of Fengycin from Bacillus subtilis fmbJ on Apoptosis and Necrosis in Rhizopus stolonifer: Qunyong Tang , Xiaomei Bie , Zhaoxin Lu , Fengxia Lv , Yang Tao , Xiaoxu Qu; J. Microbiol. 2014;52(8):675-680. Published online August 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3605-3

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75 Citations

Abstract: The lipopeptide antibiotic fengycin, produced by Bacillus subtilis, strongly inhibits growth of filamentous fungi. In this study, we evaluated the effects of fengycin treatment on apoptosis and necrosis in Rhizopus stolonifer by means of cell staining and epifluorescence microscopy. At fengycin concentrations less than 50 μg/ml, treated fungal cells demonstrated a dose-dependent increase in apoptosis-associated markers compared with the untreated control. These markers included chromatin condensation, reactive oxygen species accumulation, mitochondrial membrane potential depolarization, phosphatidylserine externalization, and the occurrence of DNA strand breaks. These results showed that fungal cells were impaired in a number of important functions and entered apoptosis upon treatment with low concentrations of fengycin. In contrast, high concentrations (>50 μg/ml) induced necrosis, indicating that the fungicidal action of fengycin operates via two modes: apoptosis at low concentrations and necrosis at high concentrations. Additionally, the apoptotic effect that we have shown suggests that lower concentrations of fengycin than previously thought may be effective for food preservation.

A Potent Brucella abortus 2308 Δery Live Vaccine Allows for the Differentiation between Natural and Vaccinated Infection: Junbo Zhang , Shuanghong Yin , Fei Guo , Ren Meng , Chuangfu Chen , Hui Zhang , Zhiqiang Li , Qiang Fu , Huijun Shi , Shengwei Hu , Wei Ni , Tiansen Li , Ke Zhang; J. Microbiol. 2014;52(8):681-688. Published online July 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3689-9

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16 Citations

Abstract: Brucellosis is a globally distributed zoonotic disease that causes animal and human diseases. However, the current Brucella abortus vaccines (S19 and RB51) are deficient; they can cause abortion in pregnant animals. Moreover, when the vaccine S19 is used, tests cannot differentiate natural from vaccinated infection. Therefore, a safer and more potent vaccine is needed. A Brucella abortus 2308 ery promoter mutant (Δery) was constructed to overcome these drawbacks. The growth of the Δery mutant was significantly attenuated in macrophages and mice and induced high protective immunity in mice. Moreover, Δery induced an anti-Brucellaspecific IgG (immunoglobulin G) response and stimulated the expression of interferon-gamma (INF-γ) and interleukin-4 (IL-4). Furthermore, the expression of EryA antigen allowed for the serological differentiation between natural and vaccinated infection in mice. These results indicate that the Δery mutant is a potential attenuated live vaccine candidate against virulent Brucella abortus 2308 (S2308) infection.

Bacterial Endophyte Sphingomonas sp. LK11 Produces Gibberellins and IAA and Promotes Tomato Plant Growth: Abdul Latif Khan , Muhammad Waqas , Sang-Mo Kang , Ahmed Al-Harrasi , Javid Hussain , Ahmed Al-Rawahi , Salima Al-Khiziri , Ihsan Ullah , Liaqat Ali , Hee-Young Jung , In-Jung Lee; J. Microbiol. 2014;52(8):689-695. Published online July 4, 2014; DOI: https://doi.org/10.1007/s12275-014-4002-7

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369 Citations

Abstract: Plant growth promoting endophytic bacteria have been identified as potential growth regulators of crops. Endophytic bacterium, Sphingomonas sp. LK11, was isolated from the leaves of Tephrosia apollinea. The pure culture of Sphingomonas sp. LK11 was subjected to advance chromatographic and spectroscopic techniques to extract and isolate gibberellins (GAs). Deuterated standards of [17, 17-2H2]-GA4, [17, 17-2H2]-GA9 and [17, 17-2H2]-GA20 were used to quantify the bacterial GAs. The analysis of the culture broth of Sphingomonas sp. LK11 revealed the existence of physiologically active gibberellins (GA4: 2.97 ± 0.11 ng/ml) and inactive GA9 (0.98 ± 0.15 ng/ml) and GA20 (2.41 ± 0.23). The endophyte also produced indole acetic acid (11.23 ± 0.93 μM/ml). Tomato plants inoculated with endophytic Sphingomonas sp. LK11 showed significantly increased growth attributes (shoot length, chlorophyll contents, shoot, and root dry weights) compared to the control. This indicated that such phyto-hormones-producing strains could help in increasing crop growth.

Anti-influenza Effect of Cordyceps militaris through Immunomodulation in a DBA/2 Mouse Model: Hwan Hee Lee , Heejin Park , Gi-Ho Sung , Kanghyo Lee , Taeho Lee , Ilseob Lee , Man-seong Park , Yong Woo Jung , Yu Su Shin , Hyojeung Kang , Hyosun Cho; J. Microbiol. 2014;52(8):696-701. Published online July 18, 2014; DOI: https://doi.org/10.1007/s12275-014-4300-0

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32 Citations

Abstract: The immune-modulatory as well as anti-influenza effects of Cordyceps extract were investigated using a DBA/2 mouse model. Three different concentrations of Cordyceps extract, red ginseng extract, or drinking water were orally administered to mice for seven days, and then the mice were intranasally infected with 2009 pandemic influenza H1N1 virus. Body weight changes and survival rate were measured daily post-infection. Plasma IL-12, TNF-α, and the frequency of natural killer (NK) cells were measured on day 4 post-infection. The DBA/2 strain was highly susceptible to H1N1 virus infection. We also found that Cordyceps extract had an antiinfluenza effect that was associated with stable body weight and reduced mortality. The anti-viral effect of Cordyceps extract on influenza infection was mediated presumably by increased IL-12 expression and greater number of NK cells. However, high TNF-α expression after infection of H1N1 virus in mice not receiving treatment with Cordyceps extract suggested a two-sided effect of the extract on host immune regulation.

Journal Article

Reducing the Bioactivity of Tannerella forsythia Lipopolysaccharide by Porphyromonas gingivalis: Young-Jae Kim , Sung-Hoon Lee; J. Microbiol. 2014;52(8):702-708. Published online August 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4324-5

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11 Citations

Abstract: Tannerella forsythia is considered a pathogen of periodontitis and forms a biofilm with multi-species bacteria in oral cavity. Lipopolysaccharide is a powerful immunostimulator and induces inflammation and shock. The purpose of this study was to investigate the characteristics of T. forsythia LPS in its co-cultivation with Fusobacterium nucleatum or Porphyromonas gingivalis. T. forsythia was co-cultured in the presence and absence of F. nucleatum and P. gingivalis and then T. forsythia LPS was extracted. The extracts were analyzed by SDS-PAGE and NF-κB reporter CHO cell lines. THP-1 cells were treated with the LPS and evaluated induction of cytokine expression by real-time RT-PCR and ELISA. For analysis of the bioactivity of T. forsythia LPS, the binding assay on LPS-binding protein (LBP) and CD14 was processed. The extracts did not contaminate other molecules except LPS and showed TLR4 agonists. Co-cultured T. forsythia LPS with P. gingivalis exhibited a lower level of induction of TNF-α, IL-1β, and IL-6 expression than singleor co-cultured T. forsythia LPS with F. nucleatum in the conditions of human serum. However, the three T. forsythia LPS did not show difference of cytokine induction in the serum free conditions. Co-cultured T. forsythia LPS with P. gingivalis exhibited a lower affinity to LBP and CD14 as binding site of O-antigen and attached at a lower level to THP-1 cells compared to single- or co-cultured T. forsythia LPS with F. nucleatum. The virulence of T. forsythia LPS was decreased by co-culturing with P. gingivalis and their affinity to LBP and CD14 was reduced, which may due to modification of O-antigen chain by P. gingivalis.

Research Support, Non-U.S. Gov'ts

A Functional and Phylogenetic Comparison of Quorum Sensing Related Genes in Brucella melitensis 16M: Aniel Jessica Leticia Brambila-Tapia , Ernesto Pérez-Rueda; J. Microbiol. 2014;52(8):709-715. Published online July 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3570-x

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4 Citations

Abstract: A quorum-sensing (QS) system is involved in Brucella melitensis survival inside the host cell. Two transcriptional regulators identified in B. melitensis, BlxR and VjbR, regulate the expression of virB, an operon required for bacterial intracellular persistence. In this work, 628 genes affected by VjbR and 124 by BlxR were analyzed to gain insights into their functional and taxonomical distributions among the Bacteria and Archaea cellular domains. In this regard, the Cluster of Orthologous Groups (COG) genes and orthologous genes in 789 nonredundant bacterial and archaeal genomes were obtained and compared against a group of randomly selected genes. From these analyses, we found 71 coaffected genes between VjbR and BlxR. In the COG comparison, VjbR activated genes associated with intracellular trafficking, secretion and vesicular transport and defense mechanisms, while BlxR affected genes related to energy production and conversion (with an equal effect) and translation, ribosomal structure and biogenesis, posttranslational modifications and carbohydrate and amino acid metabolism (with a negative effect). When the taxonomical distribution of orthologous genes was evaluated, the VjbR- and BlxRrelated genes presented more orthologous genes in Crenarchaeota (Archaea), Firmicutes, and Tenericutes and fewer genes in Proteobacteria than expected by chance. These findings suggest that QS system exert a fine-tuning modulation of gene expression, by which VjbR activates genes related to infection persistence and defense, while BlxR represses general bacterial metabolism for intracellular adaptations. Finally, these affected genes present a degree of presence among Bacteria and Archaea genomes that is different from that expected by chance.

NOTE] Assessment of Conjugal Transfer of Antibiotic Resistance Genes in Salmonella Typhimurium Exposed to Bile Salts: Xinlong He , Juhee Ahn; J. Microbiol. 2014;52(8):716-719. Published online April 11, 2014; DOI: https://doi.org/10.1007/s12275-014-3340-9

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6 Citations

Abstract: This study was designed to evaluate the transfer potential of antibiotic resistance genes in antibiotic-resistant Salmonella Typhimurium (S. TyphimuriumR) in the presence of bile salts. The resistance of S. TyphimuriumR to ampicillin, kanamycin, and tetracycline was increased by 64-, 64-, and 512-fold, respectively. The highest transfer frequency from S. TyphimuriumR to Escherichia coli was observed at the bile salt concentration of 160 μg/ml (3.8 × 10-3 transferrants/cells). The expression of traJ and traY was suppressed in S. TyphimuriumR by bile salt. This study provides useful information for understanding the conjugative transfer of antibiotic resistance genes in S. Typhimurium under intestinal conditions.

Publisher’s Erratum to : Bacillus cheonanensis sp. nov. Isolated from Near Poultry Farm Soil: Hyun-Ju Kim , Cheol-Su Park , Siwon Lee , Tae-Young Ahn; J. Microbiol. 2014;52(8):720-720.; DOI: https://doi.org/10.1007/s12275-014-0702-2

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Abstract: Despite the correct article title in the article PDF, due to Publisher’s error during the process of online publication, the title of the article appears incorrectly in the article webpage. The correct title is shown here and a well as in the article PDF. The Publisher deeply apologizes for this mistake.

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