Abstract：
:Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, comparisons of closely related bacterial species and individual isolates by whole-genome sequencing approaches remains prohibitively expensive for most laboratories. Here we report the development and testing of a biochemical approach for targeted sequencing of only those chromosomal regions that differ between two DNA preparations. The method, designated GFE (genome fragment enrichment) uses competitive solution hybridization and positive selection to obtain genomic DNA fragments that are present in one pool of fragments but not another. Repeated comparisons of the genomes of Enterococcus faecalis and E. faecium led to the identification of 225 putative genome-specific DNA fragments. Species and strain variations within these fragments were confirmed by both experimental and bioinformatic analyses. The E. faecalis genome-specific sequences identified included both a preponderance of those predicted to encode surface-exposed proteins, as well as several previously described unique marker regions embedded within highly conserved rrn operons. The GFE strategy we describe efficiently identified genomic differences between two enterococcal genomes, and will be widely applicable for studying genetic variation among closely related bacterial species.
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
Shanks OC,Santo Domingo JW,Graham JEdoi
10.1016/j.mimet.2005.12.006subject
Has Abstractpub_date
2006-08-01 00:00:00pages
321-30issue
2eissn
0167-7012issn
1872-8359pii
S0167-7012(05)00389-1journal_volume
66pub_type
杂志文章abstract：:Enterococcus faecalis, a gram-positive opportunistic pathogen, has become one of the leading causes of nosocomial infections. Normally a resident of the gastrointestinal tract, extensive use of antibiotics has resulted in the rise of E. faecalis strains that are resistant to multiple antibiotics. This, compounded with...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.04.011
更新日期：2012-07-01 00:00:00
abstract：:The S. PneumoStrip test is a recently developed reverse hybridization strip-based commercial assay that allows for the identification of 76 pneumococcal serotypes, 42 individually and 34 in pairs, according to their specific gene sequences. The test was validated with reference strains of 92 different pneumococcal ser...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2017.08.010
更新日期：2017-12-01 00:00:00
abstract：:The objective of this study was to evaluate the effects of increased PCR cycle number on sequencing results from samples with low microbial biomass, including bovine milk, and murine pelage and blood. We hypothesized that subjecting DNA from such samples to higher PCR cycle numbers would increase 16S rRNA sequencing c...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2020.106033
更新日期：2020-09-01 00:00:00
abstract：:Using robotics and the MPN technique, a 96-microwell method was developed to compare two procedures for enumeration of viable chlorine-treated B. atrophaeus spores: broth-culture enrichment followed by real-time polymerase chain reaction analysis; and filter plating on agar. Recoveries of chlorine-treated spores were ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2007.07.011
更新日期：2007-10-01 00:00:00
abstract：:This study was conducted to evaluate the efficacy of the mini-VIDAS Listeria monocytogenes (LMO) system (BioMérieux Vitek, Inc., Missouri, USA) for detection of L. monocytogenes in environmental and fish samples from three Portuguese cold-smoking plants and from their fresh fish suppliers. Mini-VIDAS-LMO is a fully au...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(00)00118-4
更新日期：2000-04-01 00:00:00
abstract：:As part of a major European research project, a diagnostic PCR assay, including an internal amplification control, was developed and validated in a collaborative trial for the detection of Escherichia coli O157. The assay is based on amplification of sequences of the rfbE O157 gene. The collaborative trial, including ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章,多中心研究
doi：10.1016/j.mimet.2003.08.012
更新日期：2003-12-01 00:00:00
abstract：:MALDI-TOF MS identified a 6250-Da protein specific to Sequence Type-1 (ST-1) strains and a 7625-Da protein specific to ST-17 strains when used for identification of Group B streptococci. The strains of these STs are major causes of meningitis and late-onset-disease in neonates. This rapid method of identification coul...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2011.05.017
更新日期：2011-08-01 00:00:00
abstract：:The purpose of this study was to determine the interactions between arsenic (As) resistant bacteria and As, using surface-enhanced Raman scattering (SERS) and Fourier transform infrared (FTIR) spectroscopy. According to our 16S rDNA results, eight bacteria isolated from the environment can be identified to four genera...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.03.018
更新日期：2012-06-01 00:00:00
abstract：:In our current study we were identifying 26 bacterial isolates using a SCIEX 5800 TOF/TOF MALDI instrument and an external database. The results were compared with the results of a Vitek® MS system and in case of discrepancies at the species level 16s rRNA sequencing was performed for further verification. ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2019.105685
更新日期：2019-09-01 00:00:00
abstract：:The analysis of soil fungal communities by molecular fingerprinting and subsequent identification of the underlying populations require the amplification of a phylogenetically informative gene fragment. In this study we tested the reliability and suitability of the previously published fungal primer combination (NS1/F...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.06.014
更新日期：2006-04-01 00:00:00
abstract：:Volatile compounds (VCs) are produced by all microorganisms as part of their normal metabolism. The aim of this study was to determine whether bacterial VC profiles could be used to discriminate between selected bacterial species and strains in vitro. Selected Ion Flow Tube Mass Spectrometry (SIFT-MS) was used to quan...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2010.12.001
更新日期：2011-02-01 00:00:00
abstract：:Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bac...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/0167-7012(85)90023-5
更新日期：1985-01-01 00:00:00
abstract：:The global combat against MTB is limited by challenges in accurate affordable detection. In this study, a rapid, affordable, single tube system for detection of unamplified MTB16s rDNA was developed. Utilizing a AuNP based FRET system, this assay achieved a sensitivity and specificity of 98.6% and 90% respectively. ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2017.06.001
更新日期：2017-08-01 00:00:00
abstract：:A novel in vitro onychomycosis model was developed to easily predict the topical activity potential of novel antifungal drugs. The model encompasses drug activity and diffusion through bovine hoof slices in a single experimental set-up. Results correspond well with the antifungal susceptibility assay and Franz cell di...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.03.009
更新日期：2015-05-01 00:00:00
abstract：:Exocellulases play a key role in cleaving the accessible ends of cellulose molecules to release soluble glucose and cellobiose. To date, there have been no screens for exocellulase owing to assay protocol limitations, the high cost of substrates, and low activity of exocellulases compared with endocellulases. This stu...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2013.07.010
更新日期：2013-09-01 00:00:00
abstract：:Limited biological samples of microbial origin often yield insufficient amounts of genomic DNA, making application of standard techniques of genetic analysis, like amplified fragment length polymorphism (AFLP), virtually impossible. The Phi29 DNA polymerase based whole genome amplification (WGA) method has the potenti...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.03.009
更新日期：2005-11-01 00:00:00
abstract：:Expressed sequence tags (ESTs) from fungal-infected plant tissues are composed of a mixture of plant and fungal sequences. Using freely available software and tools, a novel procedure is described for distinguishing plant and fungal DNA sequences. Although the GenBank non-redundant (NR) database is larger and therefor...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(03)00067-8
更新日期：2003-09-01 00:00:00
abstract：:Host DNA may adversely affect metagenomic studies focusing on the prokaryotic microbiota. This study compared the levels of host DNA in subgingival plaque collected by paper points and curette, using quantitative PCR. Lower proportions of host DNA and higher proportions of bacterial DNA were recovered from samples col...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.01.023
更新日期：2015-04-01 00:00:00
abstract：:Gene expression analysis provides significant insight to understand regulatory mechanisms of biology, yet acquisition and reproduction of quality data, as well as data confirmation and verification remain challenging due to a lack of proper quality controls across different assay platforms. We present a set of six uni...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2006.10.014
更新日期：2007-03-01 00:00:00
abstract：:Herein, an open-source method to generate quantitative bacterial growth data from high-throughput microplate assays is described. The bacterial lag time, maximum specific growth rate, doubling time and delta OD are reported. Our method was validated by carbohydrate utilization of lactobacilli, and visual inspection re...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2016.11.015
更新日期：2017-01-01 00:00:00
abstract：:The mesophilic fungus Eupenicillium parvum 4-14 is an important producer of thermotolerant hemicellulolytic and cellulolytic enzymes. The aim of this study was to establish a method for genetic manipulation of the fungus by Agrobacterium tumefaciens. The promotor PgpdA of a glyceraldehyde-3-phosphate dehydrogenase gen...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2018.01.013
更新日期：2018-03-01 00:00:00
abstract：:Activated charcoal is a carbonaceous adsorbent with a high internal porosity, and hence a large internal surface area. Cells of a strain of Escherichia coli O157:H7 seeded into oyster tissue homogenates were completely bound to untreated charcoal after an incubation period of 15 min at room temperature. In contrast, a...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2006.09.012
更新日期：2007-02-01 00:00:00
abstract：:Transposon Integration mediated Mutagenesis (TIM) is a broadly applicable tool for protein engineering. This method combines random integration of modified bacteriophage Mu transposons with their subsequent defined excision employing type IIS restriction endonuclease AarI. TIM enables deletion or insertion of an arbit...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2008.06.017
更新日期：2008-10-01 00:00:00
abstract：:An alternative 16S rRNA-targeted oligonucleotide probe specific for Archaea was developed and used for detection of methanogens in anaerobic reactors. The designed probe was checked for its specificity by computer-aided comparative sequence analysis. For in situ application, optimal stringency conditions were adjusted...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2004.11.017
更新日期：2005-04-01 00:00:00
abstract：:To hydrolyze blood meal (BM) effectively, two mutants were generated using ultra-violet mutagenesis. Single-factor experiments, the Plackett-Burman technique and response surface methodology were used to optimize the fermentation conditions. This study successfully generated a mutant and innovatively provided importan...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2014.03.017
更新日期：2014-06-01 00:00:00
abstract：:To ensure quality management during the production processes of probiotics and for efficacy testing in vivo, accurate tools are needed for the identification and quantification of probiotic strains. In this study, a strain-specific qPCR assay based on Suppression Subtractive Hybridisation (SSH) for identifying unique ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2016.02.011
更新日期：2016-04-01 00:00:00
abstract：:We report here the construction of a plasmid vector designed for the efficient electrotransformation of the periodontal pathogen Porphyromonas gingivalis. The novel Escherichia coli-Bacteroides/P. gingivalis shuttle vector, designated pTIO-1, is based on the 11.0-kb E. coli-Bacteroides conjugative shuttle vector, pVAL...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2014.07.032
更新日期：2014-10-01 00:00:00
abstract：:Bacillus anthracis, the causative agent of anthrax, is a potential source of bioterrorism. The existing assays for its identification lack specificity due to the close genetic relationship it exhibits to other members of the B. cereus group. Our comparative analyses of protein sequences from Bacillus species have iden...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2011.08.015
更新日期：2011-12-01 00:00:00
abstract：:Rapid and sensitive detection of extended-spectrum β-lactamases (ESBLs) is essential for infection control and antimicrobial treatment. Recently, a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based MBT STAR-BL software module has been used for detecting β-lactamase activ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2019.105734
更新日期：2019-12-01 00:00:00
abstract：:A 16S rRNA gene-based fingerprinting method was developed for the identification of Azotobacteraceae and tested onto 48 soil isolates and 28 reference strains belonging to the free-living nitrogen-fixing bacterial group and to the most common species found in soil samples. According to this method, the 16S rRNA gene w...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2004.01.006
更新日期：2004-05-01 00:00:00
