Showing papers in "Journal of Microbiology in 2011"
TL;DR: This review will provide a brief overview of the importance of C. albicans as a public health issue, the experimental tools developed to study its fascinating biology, and some examples of how these have been applied.
Abstract: Candida albicans is the most common human fungal pathogen (Beck-Sague and Jarvis, 1993). It is normally a harmless commensal organism. However, it is a opportunistic pathogen for some immunologically weak and immunocompromised people. It is responsible for painful mucosal infections such as the vaginitis in women and oral-pharangeal thrush in AIDS patients. In certain groups of vulnerable patients it causes severe, life-threatening bloodstream infections and it causes severe, life-threatening bloodstream infections and subsequent infections in the internal organs. There are various fascinating features of the C. albicans life cycle and biology that have made the pathogen the subject of extensive research, including its ability to grow in unicellular yeast, psudohyphal, and hyphal forms (Fig. 1A); its ability to switch between different but stable phenotypic states, and the way that it retains the ability to mate but apparently loses the ability to go through meiosis to complete the sexual cycle. This research has been greatly facilitated by the derivation of the complete C. albicans genome sequence (Braun et al., 2005), the development of a variety of molecular tools for gene manipulation, and a store of underpinning knowledge of cell biology borrowed from the distantly related model yeast Saccharomyces cerevisiae (Berman and Sudbery, 2002; Noble and Johnson, 2007). This review will provide a brief overview of the importance of C. albicans as a public health issue, the experimental tools developed to study its fascinating biology, and some examples of how these have been applied.
420 citations
TL;DR: Regulation of secondary metabolism associated with transcriptional regulatory elements from a broad view as well as the tremendous advances in discovery of cryptic or novel secondary metabolites by genomic mining are summarized.
Abstract: Filamentous fungi produce a variety of secondary metabolites of diverse beneficial and detrimental activities to humankind. The genes required for a given secondary metabolite are typically arranged in a gene cluster. There is considerable evidence that secondary metabolite gene regulation is, in part, by transcriptional control through hierarchical levels of transcriptional regulatory elements involved in secondary metabolite cluster regulation. Identification of elements regulating secondary metabolism could potentially provide a means of increasing production of beneficial metabolites, decreasing production of detrimental metabolites, aid in the identification of ‘silent’ natural products and also contribute to a broader understanding of molecular mechanisms by which secondary metabolites are produced. This review summarizes regulation of secondary metabolism associated with transcriptional regulatory elements from a broad view as well as the tremendous advances in discovery of cryptic or novel secondary metabolites by genomic mining.
152 citations
TL;DR: It is indicated that the bacterial communities in meju were very diverse and a complex microbial consortium containing various microorganisms got involved in me ju fermentation than the authors expected before.
Abstract: Despite the importance of meju as a raw material used to make Korean soy sauce (ganjang) and soybean paste (doenjang), little is known about the bacterial diversity of Korean meju. In this study, the bacterial communities in meju were examined using both culture-dependent and independent methods in order to evaluate the diversity of the bacterial population. Analyses of the 16S rRNA gene sequences of the bacterial strains isolated from meju samples showed that the dominant species were related to members of the genera Bacillus, Enterococcus, and Pediococcus. The community DNAs extracted from nine different meju samples were analyzed by barcoded pyrosequencing method targeting of the V1 to V3 hypervariable regions of the 16S rRNA gene. In total, 132,374 sequences, with an average read length of 468 bp, were assigned to several phyla, with Firmicutes (93.6%) representing the predominant phylum, followed by Proteobacteria (4.5%) and Bacteroidetes (0.8%). Other phyla accounted for less than 1% of the total bacterial sequences. Most of the Firmicutes were Bacillus and lactic acid bacteria, mainly represented by members of the genera Enterococcus, Lactococcus, and Leuconostoc, whose ratio varied among different samples. In conclusion, this study indicated that the bacterial communities in meju were very diverse and a complex microbial consortium containing various microorganisms got involved in meju fermentation than we expected before.
104 citations
TL;DR: Distribution of O. sinensis at the county level is clarified in this work based on both a literature search and fieldwork, which shows that the fungus is confined to the Tibetan Plateau and its surrounding regions.
Abstract: Ophiocordyceps sinensis is one of the best known fungi in Traditional Chinese Medicine. Many efforts have been devoted to locating the production areas of this species resulting in various reports; however, its geographic distribution remains incompletely understood. Distribution of O. sinensis at the county level is clarified in this work based on both a literature search and fieldwork. More than 3600 publications related to O. sinensis were investigated, including scientific papers, books, and online information. Herbarium specimens of O. sinensis and field collections made by this research group during the years 2000-2010 were examined to verify the distribution sites. A total of 203 localities for O. sinensis have been found, of which 106 are considered as confirmed distribution sites, 65 as possible distribution sites, 29 as excluded distribution sites and three as suspicious distribution sites. The results show that O. sinensis is confined to the Tibetan Plateau and its surrounding regions, including Tibet, Gansu, Qinghai, Sichuan, and Yunnan provinces in China and in certain areas of the southern flank of the Himalayas, in the countries of Bhutan, India and Nepal, with 3,000 m as the lowest altitude for the distribution. The fungus is distributed from the southernmost site in Yulong Naxi Autonomous County in northwestern Yunnan Province to the northernmost site in the Qilian Mountains in Qilian County, Qinghai Province, and from the east edge of the Tibetan Plateau in Wudu County, Gansu Province to the westernmost site in Uttarakhand, India. The clarification of the geographic distribution of O. sinensis will lay the foundation for conservation and sustainable use of the species.
91 citations
TL;DR: The results suggest that the fungal cell membrane may be the primary target of fengycin action and commercial surfactin may reduce the antifungal activity of fENgycin.
Abstract: The antifungal activity and mechanism of fengycin in the presence and absence of commercial surfactin against Rhizopus stolonifer were investigated. The MIC (minimal inhibitory concentration) of fengycin without commercial surfactin added was 0.4 mg/ml while the MIC of fengycin with commercial surfactin added was 2.0 mg/ml. Fengycin acted on cell membrane and cellular organs and inhibited DNA synthesis. The antifungal effect of fengycin was reduced after commercial surfactin was added. All these results suggest that the fungal cell membrane may be the primary target of fengycin action and commercial surfactin may reduce the antifungal activity of fengycin.
82 citations
TL;DR: Although the ATCC 19606T type strain and 8 different clinical isolates form biofilms, there are significant variations in the cell density and microscopic structures of these cell aggregates, with 3 of the isolates forming pellicles floating on the surface of stagnant broth cultures.
Abstract: Acinetobacter baumannii is an opportunistic pathogen that causes serious infections in humans by colonizing and persisting on surfaces normally found in hospital settings. The capacity of this pathogen to persist in these settings could be due to its ability to form biofilms on inanimate surfaces. This report shows that although the ATCC 19606T type strain and 8 different clinical isolates form biofilms, there are significant variations in the cell density and microscopic structures of these cell aggregates, with 3 of the isolates forming pellicles floating on the surface of stagnant broth cultures. PCR indicated that, like ATCC 19606T, all 8 clinical isolates harbor all the genetic components of the CsuA/BABCDE chaperone-usher pili assembly system, which is needed for biofilm formation on plastic. Pili detection in cells of all strains examined supports the presence and function of a pilus assembly system. However, only one of them produced the putative ATCC 19606T CsuA/B pilin subunit protein. Hydrophobicity tests and motility assays also showed significant variations among all tested strains and did not result in direct correlations between the biofilm phenotype and cell properties that could affect biofilm formation on abiotic surfaces. This lack of correlation among these 3 phenotypes may reflect some of the variations already reported with this pathogen, which may pose a challenge in the treatment of the infections this pathogen causes in humans using biofilm formation on abiotic surfaces as a target.
79 citations
TL;DR: Results suggest that L. reuteri may be useful as a probiotic agent for improving oral health.
Abstract: The interaction between Lactobacillus reuteri, a probiotic bacterium, and oral pathogenic bacteria have not been studied adequately. This study examined the effects of L. reuteri on the proliferation of periodontopathic bacteria including Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, Porphyromonas gingivalis, and Tannerella forsythia, and on the formation of Streptococcus mutans biofilms. Human-derived L. reuteri strains (KCTC 3594 and KCTC 3678) and rat-derived L. reuteri KCTC 3679 were used. All strains exhibited significant inhibitory effects on the growth of periodontopathic bacteria and the formation of S. mutans biofilms. These antibacterial activities of L. reuteri were attributed to the production of organic acids, hydrogen peroxide, and a bacteriocin-like compound. Reuterin, an antimicrobial factor, was produced only by L. reuteri KCTC 3594. In addition, L. reuteri inhibited the production of methyl mercaptan by F. nucleatum and P. gingivalis. Overall, these results suggest that L. reuteri may be useful as a probiotic agent for improving oral health.
77 citations
TL;DR: The objective of the study was to identify the lipopetides associated with three Bacillus subtilis strains, which are antagonists of Gibberella zeae, and have been shown to be effective in reducing Fusarium head blight in wheat.
Abstract: The objective of the study was to identify the lipopetides associated with three Bacillus subtilis strains. The strains are antagonists of Gibberella zeae, and have been shown to be effective in reducing Fusarium head blight in wheat. The lipopeptide profile of three B. subtilis strains (AS43.3, AS43.4, and OH131.1) was determined using mass spectroscopy. Strains AS43.3 and AS43.4 produced the anti-fungal lipopeptides from the iturin and fengycin family during the stationary growth phase. All three strains produced the lipopeptide surfactin at different growth times. Strain OH131.1 only produced surfactin under these conditions. The antifungal activity of the culture supernatant and individual lipopeptides was determined by the inhibition of G. zeae. Cell-free supernatant from strains AS43.3 and AS43.4 demonstrated strong antibiosis of G. zeae, while strain OH131.1 had no antibiosis activity. These results suggest a different mechanism of antagonism for strain OH131.1, relative to AS43.3 and AS43.4.
71 citations
TL;DR: The physiological and taxonomic characteristics with the DNA-DNA hybridization data supported the identification of strain DR1T in the genus Acinetobacter as a novel species, for which the name AcinetOBacter oleivorans sp.
Abstract: A diesel-oil and n-hexadecane-degrading novel bacterial strain, designated DR1T, was isolated from a rice paddy in Deok-So, South Korea. The strain DR1T cells were Gram-negative, aerobic coccobacilli, and grew at 20–37°C with the optimal temperature of 30°C, and an optimal pH of 6–8. Interestingly, strain DR1T was highly motile (swimming and swarming motility) using its fimbriae, and generated N-acyl homoserine lactones as quorum-sensing signals. The predominant respiratory quinone as identified as ubiquinone-9 (Q-9) and DNA G+C content was 41.4 mol%. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species A. calcoaceticus, A. haemolyticus, A. baumannii, A. baylyi, and A. beijerinckii, with which it evidenced sequence similarities of 98.2%, 97.4%, 97.2%, 97.1%, and 97.0%, respectively. DNA-DNA hybridization values between strain DR1T and other Acinetobacter spp. were all less than 20%. The physiological and taxonomic characteristics with the DNA-DNA hybridization data supported the identification of strain DR1T in the genus Acinetobacter as a novel species, for which the name Acinetobacter oleivorans sp. nov. is proposed. The type strain is DR1T (=KCTC 23045T =JCM 16667T).
70 citations
TL;DR: The purified L-methioninase from solid cultures of A. flavipes displayed unique biochemical and catalytic properties over the currently applied Pseudomonad enzyme.
Abstract: L-Methioninase was purified to electrophoretic homogeneity from cultures of Aspergillus flavipes using anion-exchange and gel filtration chromatography by 12.1 fold compared to the crude enzyme preparation. The purified enzyme had a molecular mass of 47 kDa under denaturing conditions and an isoelectric point of 5.8 with no structural glycosyl residues. The enzyme had optimum activity at pH 7.8 and pH stability from 6.8–8.0 at 35°C. The enzyme appeared to be catalytically stable below 40°C. The enzyme activity was strongly inhibited by DL-propargylglycine, hydroxylamine, PMSF, 2-mercaptoethanol, Hg+, Cu2+, and Fe2+, with slight inhibition by Triton X-100. A flavipes L-methioninase has a higher catalytic affinity towards L-methionine (Km, 6.5 mM and Kcat, 14.1 S−1) followed by a relative demethiolating activity to L-homo-cysteine (Km, 12 mM and Kcat, 9.3 S−1). The enzyme has two absorption maxima at 280 and 420 nm, typical of other PLP-enzymes. Apo-L-methioninase has the ability to reconstitute its structural catalytic state completely upon addition of 0.15 mM PLP. L-Methioninase has neither an appreciable effect on liver function, platelet aggregation, nor hemolysis of human blood. The purified L-methioninase from solid cultures of A. flavipes displayed unique biochemical and catalytic properties over the currently applied Pseudomonad enzyme.
61 citations
TL;DR: It is suggested that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
Abstract: Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×10(6) CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
TL;DR: PA1Ø can be possibly utilized in future phage therapy endeavors since it exhibited strong protective effects against virulent P. aeruginosa infection, suggesting phage-neutrophil co-work is essential for the efficient killing of bacteria in the mouse model.
Abstract: Recently, lytic bacteriophages (phages) have been focused on treating bacterial infectious diseases. We investigated the protective efficacy of a novel Pseudomonas aeruginosa phage, PA1O, in normal and neutropenic mice. A lethal dose of P. aeruginosa PAO1 was administered via the intraperitoneal route and a single dose of PA1O with different multiplicities of infection (MOI) was treated into infected mice. Immunocompetent mice infected with P. aeruginosa PAO1 were successfully protected by PA1O of 1 MOI, 10 MOI or 100 MOI with 80% to 100% survival rate. No viable bacteria were found in organ samples after 48 h of the phage treatment. Phage clearing patterns were different in the presence or absence of host bacteria but PA1O disappeared from all organs after 72 h except spleen in the presence of host bacteria. On the contrary, PA1O treatment could not protect neutropenic mice infected with P. aeruginosa PAO1 even though could extend their lives for a short time. In in vitro phage-neutrophil bactericidal test, a stronger bactericidal effect was observed in phage-neutrophil co-treatment than in phage single treatment without neutrophils, suggesting phage-neutrophil co-work is essential for the efficient killing of bacteria in the mouse model. In conclusion, PA1O can be possibly utilized in future phage therapy endeavors since it exhibited strong protective effects against virulent P. aeruginosa infection.
TL;DR: The high antimicrobial resistance observed in the isolates showed high resistance rates against ampicillin, tetracycline, and sulfamethoxazole-trimethoprim, which raises a broad discussion on the indiscriminate or improper use of antimicrobials, besides the risks of self-medication.
Abstract: Acute diarrhea is a public health problem and an important cause of morbidity and mortality, especially in developing countries The etiology is varied, and the diarrheagenic Escherichia coli pathotypes are among the most important Our objectives were to determine the occurrence of commensal and diarrheagenic E coli strains in fecal samples from children under five years old and their drug susceptibility patterns E coli were isolated from 141 fresh fecal samples; 84 were obtained from clinically injured donors with acute diarrhea (AD) and 57 from clinically healthy donors without diarrhea (WD) Presumptive phenotypic species identification was carried out and confirmed by amplification of specific 16S ribosomal RNA encoding DNA Multiplex PCR was performed to characterize the diarrheagenic E coli strains Drug susceptibility patterns were determined by the disc-diffusion method In total, 220 strains were recovered from the fecal specimens (618% from AD and 382% from WD) Diarrheagenic E coli was identified at a rate of 368% (n=50) in diarrheic feces and 298% (n=25) in non-diarrheic feces Enteroaggregative E coli was the most frequently identified pathotype in the AD group (162%) and the only pathotype identified in the WD group (309%) Enteropathogenic E coli was the second most isolated pathotype (103%), followed by Shiga toxin-producing E coli (74%) and enterotoxigenic E coli (29%) No enteroinvasive E coli strains were recovered The isolates showed high resistance rates against ampicillin, tetracycline, and sulfamethoxazole-trimethoprim The most effective drugs were ceftazidime, ceftriaxone, imipenem and piperacillin-tazobactam, for which no resistance was observed Differentiation between the diarrheagenic E coli pathotypes is of great importance since they are involved in acute diarrheal diseases and may require specific antimicrobial chemotherapy The high antimicrobial resistance observed in our study raises a broad discussion on the indiscriminate or improper use of antimicrobials, besides the risks of self-medication
TL;DR: Resistance rates to the most commonly prescribed antibiotics used in Iran showed that resistance rates were generally higher than previously reported and added to the growing body of evidence that suggests there is increasing antibiotic resistance among H. pylori isolates.
Abstract: The purpose of this study was to evaluate the primary resistance rates of recent clinical Helicobacter pylori isolates to the most commonly used antibiotics in Iran. Two hundreds and ten patients presenting with gastric maladies between January and July of 2009 were enrolled in this study. Endoscopy was performed, and biopsy specimens were collected from each patient for subsequent bacterial culture of H. pylori. Single colony isolates from each patient were then used for antimicrobial susceptibility testing. The disk diffusion method was used to determine susceptibility patterns. One hundred and ninety-seven of the patients were H. pylori positive (93.8%). The rates of resistance to tetracycline, amoxicillin, ciprofloxacin, metronidazole, clarithromycin, and furizoladone were 37.1%, 23.9%, 34.5%, 65.5%, 45.2%, and 61.4%, respectively. A significant association between amoxicillin resistance and disease state (P<0.05) was identified. Furthermore, some double, triple, quadruple, and quintuple combinations of antibiotic resistance were found to be associated with disease state. This study evaluated the prevalence of H. pylori resistance to the most commonly prescribed antibiotics used in Iran and showed that resistance rates were generally higher than previously reported. This data adds to the growing body of evidence that suggests there is increasing antibiotic resistance among H. pylori isolates, which likely is responsible for the decreasing efficacy of anti-H. pylori therapy at the local and global level. Hence, there is a need for continued monitoring of resistance patterns, especially at the local level, and for incorporation of that information into treatment regimens for H. pylori infections.
TL;DR: A small lytic peptide, PTP-7, is very potent to Gram-positive bacteria and is able to kill antibiotic sensitive and resistant Staphylococcus aureus indiscriminately.
Abstract: One of the most important features of bacterial biofilms is their resistance to antibiotics and to the host immune system. In this study, we have found that a small lytic peptide, PTP-7, is very potent to Gram-positive bacteria and is able to kill antibiotic sensitive and resistant Staphylococcus aureus indiscriminately. Further studies have revealed that despite being a cationic peptide, the antibacterial activity of PTP-7 was not affected by the negatively charged extracellular polymeric substance (EPS) of biofilms. PTP-7 could diffuse into the deep layer of S. aureus biofilms to kill bacteria inside biofilms efficiently and effectively. Neither the high concentrations of metal ions nor the acidic pH in biofilms affected the activity of peptide PTP-7. It seems that the unique sequence/structure together with the resistant bacteria killing ability of peptide PTP-7 confers its anti-biofilm activity. This study sheds new light on the treatment of bacterial biofilms, especially various biofilm related infections.
TL;DR: The findings suggested that the red alga Polysiphonia morrowii and isolated two bromophenols may have potential as a therapeutic agent against fish viral diseases, lower than those of ribavirin used as a positive control.
Abstract: Our previous investigation revealed that 80% methanolic extract of the red alga Polysiphonia morrowii has significant antiviral activities against fish pathogenic viruses, infectious hematopoietic necrosis virus (IHNV) and infectious pancreatic necrosis virus (IPNV). The present study was conducted to identify compounds attributed for its antiviral activities and investigate their antiviral activities against IHNV and IPNV. Activity-guided fractionation for 80% methanolic extract of Polysiphonia morrowii using a cell-based assay measuring virus-induced cytopathic effect (CPE) on cells yielded a 90% methanolic fraction, which showed the highest antiviral activity against both viruses among fractions yielded from the extract. From the fraction, two bromophenols were isolated and identified as 3-bromo-4,5-dihydroxybenzyl methyl ether (1) and 3-bromo-4,5-dihydroxybenzaldehyde (2) based on spectroscopic analyses. For both compounds, the concentrations to inhibit 50% of flounder spleen cell (FSP cell) proliferation (CC50) and each viral replication (EC50) were measured. In the pretreatment test, 3-bromo-4,5-dihydroxybenzyl methyl ether (1) and 3-bromo-4,5-dihy-droxybenzaldehyde (2) exhibited significant antiviral activities showing selective index values (SI = CC50/EC50) of 20 to 42 against both IHNV and IPNV. In direct virucidal test, 3-bromo-4,5-dihydroxybenzyl methyl ether (1) showed significant antiviral activites against both viruses while 3-bromo-4,5-dihydroxybenzaldehyde (2) was significantly effective against only IHNV. Although antiviral efficacies of both compounds against IHNV and IPNV were lower than those of ribavirin used as a positive control, our findings suggested that the red alga Polysiphonia morrowii and isolated two bromophenols may have potential as a therapeutic agent against fish viral diseases.
TL;DR: A Gram-positive, endospore-forming, new Bacillus species, strain BL4-6T, was isolated from tidal flat sediment of the Yellow Sea and is proposed to represent the type strain of a novel species, Bacillus manliponensis sp.
Abstract: A Gram-positive, endospore-forming, new Bacillus species, strain BL4-6(T), was isolated from tidal flat sediment of the Yellow Sea. Strain BL4-6(T) is a straight rod, with motility by peritrichate flagella. The cell wall contains meso-diaminopimelic acid, and the major respiratory quinone is menaquinone-7. The major fatty acids are iso-C(15:0) and summed feature 3 (containing C(16:1) ω7c/iso-C(15:0) 2OH, and/or iso-C(15:0) 2OH/C(16:1) ω7c). Cells are catalase-positive and oxidase-negative. The G+C content of the genomic DNA is 38.0 mol%. Based on a comparative 16S rRNA gene sequence analysis, the isolate belongs to the genus Bacillus, forms a clade with the Bacillus cereus group, and is closely related to Bacillus mycoides (98.5%), Bacillus cereus (98.5%), Bacillus anthracis (98.4%), Bacillus thuringiensis (98.4%), Bacillus weihenstephanensis (98.1%), and Bacillus pseudomycoides (97.5%). The isolate showed less than 85% similarity of the gyrA gene sequence and below 95% similarity of the rpoB gene sequence to the members of this group. DNA-DNA relatedness between strain BL4-6(T) and B. cereus group was found to be in a range of 22.8-42.3%, and thus BL4-6(T) represents a unique species. On the basis of these studies, strain BL4-6(T) (=KCTC 13319(T) =JCM 15802(T)) is proposed to represent the type strain of a novel species, Bacillus manliponensis sp. nov.
TL;DR: RNASelector as mentioned in this paper is a computer program for selecting rRNA genes from massive metagenomic and metatranscriptomic sequences using hidden Markov models, which has successfully identified prokaryotic 5S, 26S, and 23S rRNA gene from Roche 454 FLX Titanium-based metagenomics library.
Abstract: Metagenomic and metatranscriptomic shotgun sequencing techniques are gaining popularity as more cost-effective next-generation sequencing technologies become commercially available. The initial stage of bioinfor-matic analysis generally involves the identification of phylogenetic markers such as ribosomal RNA genes. The sequencing reads that do not code for rRNA can then be used for protein-based analysis. Hidden Markov model is a well-known method for pattern recognition. Hidden Markov models that are trained on well-curated rRNA sequence databases have been successfully used to identify DNA sequence coding for rRNAs in pro-karyotes. Here, we introduce rRNASelector, which is a computer program for selecting rRNA genes from massive metagenomic and metatranscriptomic sequences using hidden Markov models. The program successfully identified prokaryotic 5S, 26S, and 23S rRNA genes from Roche 454 FLX Titanium-based metagenomic and metatranscriptomic libraries. The rRNASelector program is available at http://sw.ezbiocloud.net/rrnaselector .
TL;DR: This is among the first studies to report uranium-tolerant aerobic chemoheterotrophs obtained from the pristine uranium ore-bearing site of Domiasiat.
Abstract: Enrichment-based methods targeted at uranium-tolerant populations among the culturable, aerobic, chemo-heterotrophic bacteria from the subsurface soils of Domiasiat (India's largest sandstone-type uranium deposits, containing an average ore grade of 0.1 % U(3)O(8)), indicated a wide occurrence of Serratia marcescens. Five representative S. marcescens isolates were characterized by a polyphasic taxonomic approach. The phylogenetic analyses of 16S rRNA gene sequences showed their relatedness to S. marcescens ATCC 13880 (≥99.4% similarity). Biochemical characteristics and random amplified polymorphic DNA profiles revealed significant differences among the representative isolates and the type strain as well. The minimum inhibitory concentration for uranium U(VI) exhibited by these natural isolates was found to range from 3.5-4.0 mM. On evaluation for their uranyl adsorption properties, it was found that all these isolates were able to remove nearly 90-92% (21-22 mg/L) and 60-70% (285-335 mg/L) of U(VI) on being challenged with 100 μM (23.8 mg/L) and 2 mM (476 mg/L) uranyl nitrate solutions, respectively, at pH 3.5 within 10 min of exposure. his capacity was retained by the isolates even after 24 h of incubation. Viability tests confirmed the tolerance of these isolates to toxic concentrations of soluble uranium U(VI) at pH 3.5. This is among the first studies to report uranium-tolerant aerobic chemoheterotrophs obtained from the pristine uranium ore-bearing site of Domiasiat.
TL;DR: The genomic plasticity, plentiful cell envelope components, inorganic element metabolic abilities and stress response mechanisms found the base for this organism’s survival in the bioleaching niche.
Abstract: Leptospirillum ferriphilum has been identified as the dominant, moderately thermophilic, bioleaching microorganism in bioleaching processes. It is an acidic and chemolithoautrophic bacterium that gains electrons from ferrous iron oxidation for energy production and cell growth. Genetic information about this microorganism has been limited until now, which has hindered its further exploration. In this study, the complete genome of L. ferripilum ML-04 is sequenced and annotated. The bacterium has a single circular chromosome of 2,406,157 bp containing 2,471 coding sequences (CDS), 2 rRNA operons, 48 tRNA genes, a large number of mobile genetic elements and 2 genomic islands. In silico analysis shows L. ferriphilum ML-04 fixes carbon through a reductive citric acid (rTCA) cycle, and obtains nitrogen through ammonium assimilation. The genes related to “cell envelope biogenesis, outer membrane” (6.9%) and “DNA replication, recombination and repair” (5.6%) are abundant, and a large number of genes related to heavy metal detoxification, oxidative and acidic stress defense, and signal transduction pathways were detected. The genomic plasticity, plentiful cell envelope components, inorganic element metabolic abilities and stress response mechanisms found the base for this organism’s survival in the bioleaching niche.
TL;DR: With modifications, the electroporation procedures became a very efficient and reliable tool for F. lipolytica transformation and will be able to yield an efficiency of 2.1 × 104 transformants/ug for integrative linear DNA.
Abstract: Yarrowia lipolytica was usually transformed by heat shock, but linearized integrative vectors always resulted in a low transformation efficiency when electroporation was used. To develop a high efficiency integrative transformation method by electroporation of F. lipolytica, we report here that pretreatment of F. lipolytica with 150 mM LiAc for 1 h before electroporation will approximately 30-fold of increase transformation efficiency. A cell concentration of 10(10)/ml and instrument settings of 1.5 kV will generate the highest transformation efficiencies. We have developed a procedure to transform F. lipolytica that will be able to yield an efficiency of 2.1 × 10(4) transformants/ug for integrative linear DNA. With our modifications, the electroporation procedures became a very efficient and reliable tool for F. lipolytica transformation.
TL;DR: The effect of endophytic bacteria on G. intraradices UT126 and G. clarum BR152B resembled that of a mycorrhiza helper bacteria (MHB) association because the association significantly promoted AMF spore germination and hyphal length.
Abstract: Endophytic bacteria (Pseudomonas aeruginosa UPMP3 and Burkholderia cepacia UMPB3), isolated from within roots of oil palm (Elaeis guineensis Jacq.) were tested for their presymbiotic effects on two arbuscular mcorrhizal fungi, Glomus intraradices UT126 and Glomus clarum BR152B). These endophytic bacteria were also tested for antagonistic effects on Ganoderma boninense PER 71, a white wood rot fungal pathogen that causes a serious disease in oil palm. Spore germination and hyphal length of each arbuscular mycorrhizal fungal (AMF) pairing with endophytic bacteria was found to be significantly higher than spores plated in the absence of bacteria. Scanning electron microscopy (SEM) showed that the endophytic bacteria were scattered, resting or embedded on the surface hyaline layer or on the degraded walls of AMF spores, possibly feeding on the outer hyaline spore wall. The antagonistic effect of the endophytic bacteria was expressed as severe morphological abnormalities in the hyphal structures of G. boninense PER 71. The effects of the endophytic bacteria on G. boninense PER 71 hyphal structures were observed clearly under SEM. Severe inter-twisting, distortion, lysis and shriveling of the hyphal structures were observed. This study found that the effect of endophytic bacteria on G. intraradices UT126 and G. clarum BR152B resembled that of a mycorrhiza helper bacteria (MHB) association because the association significantly promoted AMF spore germination and hyphal length. However, the endophytic bacteria were extremely damaging to G. boninense PER 71.
TL;DR: The results of this study suggest that the oral antibiotic resistome is more diverse and abundant in periodontitis patients than in healthy subjects, suggesting that there is a difference in the diversity and distribution of antibiotic resistance in oral biofilms associated with health and disease.
Abstract: Oral biofilms contain numerous antibiotic resistance determinants that can be transferred within or outside of the oral cavity. The aim of this study was to evaluate the prevalence and the relative level of antibiotic resistance determinants from oral biofilms. Oral biofilm samples that were collected from healthy subjects and periodontitis patients were subjected to qualitative and quantitative analyses for selected antibiotic resistance determinants using PCR. The prevalence of tet(Q), tet(M), cfxA, and bla ( TEM ) was very high both in the patient and the healthy subject group, with a tendency toward higher values in the patient group, with the exception of erm(F), which was more prevalent in the healthy group. The two extended spectrum β-lactam (ESBL) resistance determinants bla ( SHV ) and bla ( TEM ) showed a dramatic difference, as bla ( TEM ) was present in all of the samples and bla ( SHV ) was not found at all. The aacA-aphD, vanA, and mecA genes were rarely detected, suggesting that they are not common in oral bacteria. A quantitative PCR analysis showed that the relative amount of resistance determinants present in oral biofilms of the patient group was much greater than that of the healthy group, exhibiting 17-, 13-, 145-, and 3-fold increases for tet(Q), tet(M), erm(F), and cfxA, respectively. The results of this study suggest that the oral antibiotic resistome is more diverse and abundant in periodontitis patients than in healthy subjects, suggesting that there is a difference in the diversity and distribution of antibiotic resistance in oral biofilms associated with health and disease.
TL;DR: Pelgipeptins are highly potent antibacterial and antifungal agents, particularly against MRSA, and warrant further investigation as possible therapeutic agents for bacteria infections resistant to currently available antibiotics.
Abstract: Two lipopeptide antibiotics, pelgipeptins C and D, were isolated from Paenibacillus elgii B69 strain. The molecular masses of the two compounds were both determined to be 1,086 Da. Mass-spectrometry, amino acid analysis and NMR spectroscopy indicated that pelgipeptin C was the same compound as BMY-28160, while pelgipeptin D was identified as a new antibiotic of the polypeptin family. These two peptides were active against all the tested microorganisms, including antibiotic-resistant pathogenic bacterial strains such as methicillin-resistant Staphylococcus aureus (MRSA). Time-kill assays demonstrated that pelgipeptin D exhibited rapid and effective bactericidal action against MRSA at 4×MIC. Based on acute toxicity test, the intraperitoneal LD50 value of pelgipeptin D was slightly higher than that of the structurally related antimicrobial agent polymyxin B. Pelgipeptins are highly potent antibacterial and antifungal agents, particularly against MRSA, and warrant further investigation as possible therapeutic agents for bacteria infections resistant to currently available antibiotics.
TL;DR: This study investigates the taxonomic affinities, diversity, and host specificities of culturable endophytes in stems of wild rice (Oryza granulata) in China and hypothesizes that wild plants represent a huge reservoir of unknown fungi.
Abstract: Ecological niches in the rhizosphere and phyllosphere of grasses capable of sustaining endophytes have been extensively studied. In contrast, little information regarding the identity and functions of endophytic fungi in stems is available. In this study, we investigated the taxonomic affinities, diversity, and host specificities of culturable endophytes in stems of wild rice (Oryza granulata) in China. Seventy-four isolates were recovered. Low recovery rate (11.7%) indicated that there were relatively few sites for fungal infection. Identification using morphology, morphospecies sorting, and molecular techniques resulted in classification into 50 taxa, 36 of which were recovered only once. Nucleotide sequence similarity analysis indicated that 30% of the total taxa recovered were highly divergent from known species and thus may represent lineages new to science. Most of the taxa were classified as members of the classes Sordariomycetes or Dothideomycetes (mainly in Pleosporales). The presence of Arthrinium and Magnaporthaceae species, most often associated with poaceous plants, suggested a degree of host specificity. A polyphasic approach was employed to identify two Muscodor taxa based on (i) ITS and RPB2 phylogenies, (ii) volatile compounds produced, and (iii) an in vitro bioassay of antifungal activity. This to our knowledge is only the second report regarding the isolation of Muscodor spp. in China. Therefore, we hypothesize that wild plants represent a huge reservoir of unknown fungi. The prevalence, novelty, and species-specificity of unique isolates necessitate a reevaluation of their contribution to ecosystem function and fungal biodiversity.
TL;DR: The aim of this study was to explore the epidemiological features and resistance rates in uropathogens isolated from CBP outpatients in last 10 years, and found a decreasing of activity of ciprofloxacin and a good activity profile of levofloxacins have been reported.
Abstract: Chronic bacterial prostatitis (CBP) is, usually, caused by uropathogens, especially gram-negative bacilli, although infection is sometimes due to Gram-positive and atypical microorganisms. A recent increasing in prevalence of Gram-positive strains has been reported. The aim of this study was to explore the epidemiological features and resistance rates in uropathogens isolated from CBP outpatients in last 10 years. All consecutive outpatients with demonstrated CBP attending a single Sexually Transmitted Disease centre from January 1997 and December 2008, were enrolled and underwent microbiological cultures in first void early morning urine, midstream urine, expressed prostatic secretion, and post prostate massage urine. Prevalence of different bacterial strains was stratified in four different periods: 1997–1999, 2000–2002, 2003–2005, 2006–2008. Any changes observed in epidemiological features and resistance rates in uropathogens over the whole study period have been analyzed. The present study has been planned, thus, as in vitro study. From 6,221 patients, 4,601 Gram-positive and 1,620 Gram-negative bacterial strains have been isolated. Enterococcus faecalis and Escherichia coli strains are the first and second frequent pathogens found, respectively. Significant differences between E. faecalis prevalence in the 1997–1999 and 2006–2008 periods were found. E. coli showed a significant difference between prevalence in 1997–1999 and 2006–2008 periods. Gram-positive organisms showed a decreasing of susceptibility to ciprofloxacin as well as Gram-negative strains, while a good susceptibility to the levofloxacin was evidenced. E. faecalis prevalence seemed to be raised in 2006–2008 periods. Moreover, a decreasing of activity of ciprofloxacin and a good activity profile of levofloxacin have been reported.
TL;DR: Genome-wide transcriptome analyses suggested that some known virulence factors such as CPS are down-regulated in the ΔluxS mutant, which might in part explain virulence attenuation by luxS deletion.
Abstract: Quorum sensing is a widespread chemical communication in response to fluctuation of bacterial population density, and has been implicated into bacterial biofilm formation and regulation of expression of virulence factors. The luxS gene product, S-ribosylhomocysteinase, catalizes the last committed step in biosynthetic pathway of autoinducer 2 (AI-2), a signaling molecule for inter-species quorum sensing. We found a luxS homologue in 05ZYH33, an epidemic strain of Streptococcus suis serotype 2 (SS2) in China. A luxS null mutant (ΔluxS) of 05ZYH33 strain was obtained using an approach of homologous recombination. LuxS was determined to be required for AI-2 production in 05ZYH33 strain of S. suis 2. Inactivation of luxS gene led to a wide range of phenotypic changes including thinner capsular walls, increased tolerance to H2O2, reduced adherence capacity to epithelial cells, etc. In particular, loss of LuxS impaired dramatically its full virulence of SS2 in experimental model of piglets, and functional complementation restored it nearly to the level of parent strain. Genome-wide transcriptome analyses suggested that some known virulence factors such as CPS are down-regulated in the ΔluxS mutant, which might in part explain virulence attenuation by luxS deletion. Similarly, 29 of 71 genes with different expression level were proposed to be targets candidate regulated by LuxS/AI-2-dependent quorum sensing.
TL;DR: A new actinomycete strain, isolated from humus soils in the Western Ghats, was found to be an efficient pigment producer and may have great potential as an industrial resistomycin-producing strain.
Abstract: A new actinomycete strain, isolated from humus soils in the Western Ghats, was found to be an efficient pigment producer. The strain, designated AAA5, was identified as a putative Streptomyces aurantiacus strain based on cultural properties, morphology, carbon source utilization, and analysis of the 16S rRNA gene. The strain produced a reddish-brown pigmented compound during the secondary metabolites phase. A yellow compound was derived from the extracted pigment and was identified as the quinone-related antibiotic resistomycin based on ultraviolet-visible spectrophotometry, fourier transform infrared spectroscopy, liquid chromatography and mass spectroscopy, and nuclear magnetic resonance analyses. The AAA5 strain was found to produce large quantities of resistomycin (52.5 mg/L). It showed potent cytotoxic activity against cell lines viz. HepG2 (hepatic carcinoma) and HeLa (cervical carcinoma) in vitro, with growth inhibition (GI50) of 0.006 and 0.005 μg/ml, respectively. The strain also exhibited broad antimicrobial activities against both Gram-positive and Gram-negative bacteria. Therefore, AAA5 may have great potential as an industrial resistomycin-producing strain.
TL;DR: Most of the tested fungi from the order Polyporales of Basidiomycota exhibited strongAlgicidal activity, suggesting that most fungi that belong to this order have algicidal ability.
Abstract: Approximately 60 fungal isolates from Zijin Mountain (Nanjing, China) were screened to determine their algicidal ability. The results show that 8 fungi belonging to Ascomycota and 5 belonging to Basidiomycota have algicidal ability. Of these fungi, Irpex lacteus T2b, Trametes hirsuta T24, Trametes versicolor F21a, and Bjerkandera adusta T1 showed strong algicidal ability. The order of fungal chlorophyll-a removal efficiency was as follows: T. versicolor F21a > I. lacteus T2b > B. adusta T1 > T. hirsuta T24. In particular, T. versicolor F21a completely removed algal cells within 30 h, showing the strongest algicidal ability. The results also show that all 4 fungal species degraded algal cells through direct attack. In addition, most of the tested fungi from the order Polyporales of Basidiomycota exhibited strong algicidal activity, suggesting that most fungi that belong to this order have algicidal ability. The findings of this work could direct the search for terrestrial fungi for bloom control.
TL;DR: Results indicate that the gabT1, yktc1, and gutB1 genes are involved in the DNJ biosynthetic pathway in B. subtilis MORI, suggesting the possibility of employing these genes to establish a large-scale microbial DNJ overproduction system through genetic engineering and process optimization.
Abstract: 1-Deoxynojirimycin (DNJ), a D-glucose analogue with a nitrogen atom substituting for the ring oxygen, is a strong inhibitor of intestinal α-glucosidase. DNJ has several promising biological activities, including its antidiabetic, antitumor, and antiviral activities. Nevertheless, only limited amounts of DNJ are available because it can only be extracted from some higher plants, including the mulberry tree, or purified from the culture broth of several types of soil bacteria, such as Streptomyces sp. and Bacillus sp. In our previous study, a DNJ-producing bacterium, Bacillus subtilis MORI, was isolated from the traditional Korean fermented food Chungkookjang. In the present study, we report the identification of the DNJ biosynthetic genes in B. subtilis MORI 3K-85 strain, a DNJ-overproducing derivate of the B. subtilis MORI strain generated by γ-irradiation, xhe genomic DNA library of B. subtilis MORI 3K-85 was constructed in Escherichia coli, and clones showing α-glucosidase inhibition activity were selected. After DNA sequencing and a series of subcloning, we were able to identify a putative Operon which consists of gabT1, yktc1, and gutB1 genes predicted to encode putative transaminase, phosphatase, and oxidoreductase, respectively. When a recombinant plasmid containing this Operon sequence was transformed into an E. coli strain, the resulting transformant was able to produce DNJ into the culture medium. Our results indicate that the gabT1, yktc1, and gutB1 genes are involved in the DNJ biosynthetic pathway in B. subtilis MORI, suggesting the possibility of employing these genes to establish a large-scale microbial DNJ overproduction system through genetic engineering and process optimization.