DNA stable-isotope probing (DNA-SIP) is a recently developed method with which the incorporation of stable isotope from a labeled substrate is used to identify the function of microorganisms in the environment. The technique has now been used in conjunction with metagenomics to establish links between microbial identity and particular metabolic functions. The combination of DNA-SIP and metagenomics not only permits the detection of rare low-abundance species from metagenomic libraries but also facilitates the detection of novel enzymes and bioactive compounds. We summarize recent progress in SIP-metagenomic techniques and applications and discuss prospects for this combined approach in environmental microbiology and biotechnology.
Animals ; DNA ; genetics ; DNA Probes ; chemistry ; genetics ; metabolism ; DNA, Bacterial ; chemistry ; genetics ; metabolism ; Humans ; Isotope Labeling ; methods ; Metagenomics ; methods ; Molecular Probe Techniques ; Sequence Analysis, DNA ; methods

BACKGROUNDThe catheter related infection caused by Staphylococcus epidermidis biofilm is increasing and difficult to treat by antimicrobial chemotherapy. The properties of biofilms that give rise to antibiotic resistance are only partially understood. This study aimed to elucidate the penetration of erythromycin through Staphylococcus epidermidis biofilm.

METHODSThe penetration ratio of erythromycin through Staphylococcus epidermidis biofilms of 1457, 1457-msrA, and wild isolate S68 was detected by biofilm penetration model at different time points according to the standard regression curve. The RNA/DNA ratio and the cell density within the biofilms were observed by confocal laser microscope and transmission electromicroscope, respectively.

RESULTSThe penetration ratios of erythromycin through the biofilms of 1457, 1457-msrA, and S68 after cultivation for 36 hours were 0.93, 0.55 and 0.4, respectively. The erythromycin penetration ratio through 1457 biofilm (0.58 after 8 hours) was higher than that through the other two (0.499 and 0.31 after 24 hours). Lower growth rate of the cells in biofilm was shown, with reduction of RNA/DNA proportion observed by confocal laser microscope through acridine orange stain. Compared with the control group observed by transmission electrmicroscope, the cell density of biofilm air face was lower than that of agar face, with more cell debris.

CONCLUSIONSErythromycin could penetrate to the Staphylococcus epidermidis biofilm, but could not kill the cells thoroughly. The lower growth rate of the cells within biofilm could help decreasing the erythromycin susceptibility.

Acridine Orange ; Anti-Bacterial Agents ; pharmacokinetics ; Biofilms ; DNA, Bacterial ; analysis ; Erythromycin ; pharmacokinetics ; pharmacology ; Microscopy, Electron, Transmission ; RNA, Bacterial ; analysis ; Staphylococcus epidermidis ; drug effects ; metabolism

OBJECTIVETo determine the frequency of mce gene in Leptospira interrogans, and to investigate the gene transcription levels of L. interrogans before and after infecting cells.

METHODSThe segments of entire mce genes from 13 L.interrogans strains and 1 L.biflexa strain were amplified by PCR and then sequenced after T-A cloning. A prokaryotic expression system of mce gene was constructed; the expression and output of the target recombinant protein rMce were examined by SDS-PAGE and Western Blot assay. Rabbits were intradermally immunized with rMce to prepare the antiserum, the titer of antiserum was measured by immunodiffusion test. The transcription levels of mce gene in L.interrogans serogroup Icterohaemorrhagiae serovar lai strain 56601 before and after infecting J774A.1 cells were monitored by real-time fluorescence quantitative RT-PCR.

RESULTmce gene was carried in all tested L.interrogans strains, but not in L.biflexa serogroup Semaranga serovar patoc strain Patoc I. The similarities of nucleotide and putative amino acid sequences of the cloned mce genes to the reported sequences (GenBank accession No: NP712236) were 99.02%-100% and 97.91%-100%, respectively. The constructed prokaryotic expression system of mce gene expressed rMce and the output of rMce was about 5% of the total bacterial proteins. The antiserum against whole cell of L.interrogans strain 56601 efficiently recognized rMce. After infecting J774A.1 cells, transcription levels of the mce gene in L.interrogans strain 56601 were remarkably up-regulated.

CONCLUSIONThe constructed prokaryotic expression system of mce gene and the prepared antiserum against rMce provide useful tools for further study of the gene function.

Amino Acid Sequence ; Animals ; Bacterial Proteins ; genetics ; metabolism ; DNA, Bacterial ; analysis ; Escherichia coli ; genetics ; metabolism ; Genes, Bacterial ; Leptospira interrogans ; classification ; genetics ; Molecular Sequence Data ; Rabbits ; Recombinant Proteins ; genetics ; metabolism ; Sequence Analysis, Protein ; Serotyping

To investigate the distribution of the genes of two major metallo-beta-lactamases (MBL; i.e., IMP and VIM) and class 1 integrons (intI) in the clinical imipenem-resistant Pseudomonas aeruginosa, a total of 65 isolates, from a university hospital in Sichuan between December 2004 and April 2005 were screened for MBL genes by PCR using primers specific for bla ( IMP-1 ), bla ( VIM ) and bla ( VIM-2 ) genes. The MBL-positive isolates were further assessed for class 1 integrons by PCR using specific primers. The nucleotide sequences of several PCR products were also determined. The results revealed that the bla ( VIM ) gene was found in 81.5% (53/65) of all isolates, bla ( VIM-2 ) gene was found in only 1 isolate and the intI gene was observed in 45.3% (24/53) of bla ( VIM )-positive isolates. One isolate carried simultaneously both bla ( IMP-1 ) and intI genes, and to the best of our knowledge this is the first report of such isolate in southwest China. These observations highlight that the genes for VIM beta-lactamase and class 1 integrons were predominantly present among the imipenem-resistant P. aeruginosa tested, confirming the current widespread threat of imipenem-resistant, integron-borne P. aeruginosa.
Anti-Bacterial Agents/pharmacology ; China ; DNA Primers/chemistry ; Drug Resistance, Bacterial ; Gene Expression Regulation, Bacterial ; Imipenem/*pharmacology ; Integrons ; Microbial Sensitivity Tests ; Models, Genetic ; Pseudomonas Infections/genetics ; Pseudomonas Infections/*microbiology ; Pseudomonas aeruginosa/*metabolism ; Sequence Analysis, DNA ; beta-Lactamases/*metabolism

There are several antigenic variants of Orientia tsutsugamushi. The 56-kDa type-specific antigen (TSA) is responsible for the antigenic variation. Nucleotide sequences of the 56-kDa TSA obtained from 44 eschar samples of Korean scrub typhus patients and from 40 representative strains retrieved from the GenBank database were analyzed phylogenetically. Clinical patient data were assessed based on the genotyping results. Of the 44 nucleotide sequences, 32 (72.7%) clustered with the Boryong genotype, which is the major genotype in Korea. Eleven nucleotide sequences (25%) clustered with the Kawasaki genotype, not identified in Korea until 2010. One nucleotide sequence was consistent with the Karp genotype. The clinical course of the patients infected with each genotype showed no differences. Diagnostic performance of the immunofluorescence assay (IFA) using the 56-kDa TSA from Gilliam, Karp and Boryong as test antigens were not different for the Boryong and Kawasaki genotypes. Although Boryong is still the predominant genotype, the results suggest that Kawasaki genotype is quite prevalent in Chungbuk province of Korea.
Aged ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; DNA, Bacterial/analysis ; Databases, Genetic ; Female ; Genotype ; Humans ; Male ; Middle Aged ; Open Reading Frames ; Orientia tsutsugamushi/*classification/isolation & purification ; Phylogeny ; Republic of Korea ; Scrub Typhus/diagnosis/metabolism/*microbiology ; Sequence Analysis, DNA

There are several antigenic variants of Orientia tsutsugamushi. The 56-kDa type-specific antigen (TSA) is responsible for the antigenic variation. Nucleotide sequences of the 56-kDa TSA obtained from 44 eschar samples of Korean scrub typhus patients and from 40 representative strains retrieved from the GenBank database were analyzed phylogenetically. Clinical patient data were assessed based on the genotyping results. Of the 44 nucleotide sequences, 32 (72.7%) clustered with the Boryong genotype, which is the major genotype in Korea. Eleven nucleotide sequences (25%) clustered with the Kawasaki genotype, not identified in Korea until 2010. One nucleotide sequence was consistent with the Karp genotype. The clinical course of the patients infected with each genotype showed no differences. Diagnostic performance of the immunofluorescence assay (IFA) using the 56-kDa TSA from Gilliam, Karp and Boryong as test antigens were not different for the Boryong and Kawasaki genotypes. Although Boryong is still the predominant genotype, the results suggest that Kawasaki genotype is quite prevalent in Chungbuk province of Korea.
Aged ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; DNA, Bacterial/analysis ; Databases, Genetic ; Female ; Genotype ; Humans ; Male ; Middle Aged ; Open Reading Frames ; Orientia tsutsugamushi/*classification/isolation & purification ; Phylogeny ; Republic of Korea ; Scrub Typhus/diagnosis/metabolism/*microbiology ; Sequence Analysis, DNA

OBJECTIVETo introduce the hairy roots of Phellodendron chinense and determine the content of its active constituents.

METHODTransformed hairy roots of P. chinense were obtained by the transformation of Agrobacterium rhizogenes A4, R1600, ATCC15834 and R1000.

RESULT AND CONCLUSIONIt was clearly demonstrated that T-DNA of A. rhizogenes Ri plasmid was integrated into the cells of hairy roots by PCR. The content of berberine hydrochlodride, which was determined by HPLC, was higher in hairy roots than that in the axenic plantet and callus.

Berberine ; analysis ; metabolism ; Chromatography, High Pressure Liquid ; Culture Techniques ; methods ; DNA, Bacterial ; genetics ; Phellodendron ; genetics ; metabolism ; Plant Roots ; genetics ; metabolism ; Plants, Medicinal ; genetics ; metabolism ; Rhizobium ; genetics ; Transformation, Genetic

To identify the anti-bacterial compound(s) from Streptomyces hygroscopicus 17997, a geldanamycin producer, silica gel thin layer chromatography (TLC) TLC was used to separate the secondary metabolites of S. hygroscopicus 17997. Compound(s) from the silica gel TLC with anti-Gram positive bacteria activity and becoming red upon color reaction by 2.0 mol/L NaOH was analyzed by HPLC. The UV absorption profile and the retention time of a peak of HPLC were identical to those of authentic elaiophylin. A conserved region of dTDP-glucose-4,6-dehydratase (Tgd) gene was amplified by PCR from the genomic DNA of Streptomyces hygroscopicus 17997. DNA sequence analysis of the amplified DNA fragment indicated that it should be the tgd gene of elaiophylin biosynthetic gene cluster. These results implied that the compound in the peak of HPLC was elaiophylin, a macrodiolide antibiotic. The compound was then confirmed to be elaiophylin by LC-(+)-ESI-MS, which revealed that Streptomyces hygroscopicus 17997 was an elaiophylin producer. At the same time, a fast procedure, which consisted of silica gel TLC, color reaction, HPLC, PCR detection and DNA sequence analysis of tgd gene, and LC-(+)-ESI-MS, was established for rapid identification of elaiophylin and its producer.
Benzoquinones ; metabolism ; Chromatography, Liquid ; methods ; DNA, Bacterial ; genetics ; Hydro-Lyases ; genetics ; Lactams, Macrocyclic ; metabolism ; Macrolides ; analysis ; isolation & purification ; metabolism ; Mass Spectrometry ; methods ; Sequence Analysis, DNA ; Streptomyces ; genetics ; isolation & purification ; metabolism

Xanthomonas campestris pv. campestris ( Xcc), causative agent of the black rot disease of cruciferous crops worldwide, produces large amount of extracellular polysaccharide( EPS), which has found wide applications in industry. In order to clone genes involved in EPS biosynthesis, Xcc wild-type strain 8004 was mutagenized with transposon Tn5gus A5, and a number of EPS-defective mutants were isolated. The Tn5gusA5 insertion sites in the mutants were analyzed by using thermal asymmetric interlaced PCR(TAIL-PCR), and the corresponding genes were identified by homology blast to the completely sequenced genome of Xcc 8004 strain. A novel gene, waxE, identified from the EPS-defective mutant 151D09, was found to be disrupted by the insertion of Tn5gusA5 in the open reading frame(ORF) with genome coordinates 4478998bp to 4479819bp.This gene showed 52% similarity to the kdtX gene of Serratia marcescens and 50% to the waaE of Klebsiella pneumoniae at amino acid level, with characteristics of glycostransferase 2 family domain. In order to identify the function of waxE gene, waxE gene deletion mutant of Xcc 8004 was constructed by gene replacement strategy in which waxE gene of genome was replaced by kanamycin resistant gene kan. The waxE gene deletion mutant strain, named Xcc 8570, was confirmed by both PCR and southern analysis. The growth rate of the deletion mutant 8570 in rich medium was not affected, but the EPS yield reduced by 35% as compared with the wildtype strain 8004. The deletion mutant could be completmented in trans with plasmid pLATC8976 harboring an intact waxE gene, and the EPS yield of the mutant was restored. The combined data showed that waxE gene involved in EPS biosynthesis in Xcc.
Amino Acid Sequence ; Bacterial Proteins ; chemistry ; genetics ; metabolism ; Blotting, Southern ; Cloning, Molecular ; DNA Transposable Elements ; genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; Polysaccharides, Bacterial ; genetics ; metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Xanthomonas campestris ; genetics ; metabolism

No abstract available.
Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/chemistry/genetics/metabolism ; Drug Resistance, Bacterial ; Integrons/*genetics ; Microbial Sensitivity Tests ; Pseudomonas aeruginosa/drug effects/*enzymology/isolation & purification ; Sequence Analysis, DNA ; beta-Lactamases/*genetics