Abstract：
:Sequences in public databases may contain a number of sequencing errors. A double binomial model describing the distribution of indel-excluded similarity coefficients (S) among repeatedly sequenced 16S rRNA was previously developed and it produced a confidence interval of S useful for testing sequence identity among sequences of 400-bp length. We characterized patterns in sequencing errors found in nearly complete 16S rRNA sequences of Vibrionaceae as highly variable in reported sequence length and containing a small number of indels. To accommodate these characteristics, a simple binomial model for distribution of the similarity coefficient (H) that included indels was derived from the double binomial model for S. The model showed good fit to empirical data. By using either a pre-determined or bootstrapping estimated standard probability of base matching, we were able to use the exact binomial test to determine the relative level of sequencing error for a given pair of duplicated sequences. A limitation of the method is the requirement that duplicated sequences for the same template sequence be paired, but this can be overcome by using only conserved regions of 16S rRNA sequences and pairing a given sequence with its highest scoring BLAST search hit from the nr database of GenBank.
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
Zo YG,Colwell RRdoi
10.1016/j.mimet.2007.11.013subject
Has Abstractpub_date
2008-02-01 00:00:00pages
166-79issue
2eissn
0167-7012issn
1872-8359pii
S0167-7012(07)00391-0journal_volume
72pub_type
杂志文章abstract：:Analysis of microbial community structure in complex environmental samples using nucleic acid techniques requires efficient unbiased DNA extraction procedures; however, humic acids and other contaminants complicate the isolation of PCR-amplifiable DNA from compost and other organic-rich samples. In this study, combina...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(01)00377-3
更新日期：2002-05-01 00:00:00
abstract：:A novel method for the measurement of dissolved adenosine-5'-triphosphate and guanosine-5'-triphosphate (D-ATP and D-GTP, respectively) in marine and freshwater habitats was developed and applied to samples collected from the oligotrophic North Pacific Ocean. Both D-ATP and D-GTP are co-precipitated by authigenically ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(01)00301-3
更新日期：2001-11-01 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：:Chlamydophila pneumoniae (C. pneumoniae) has been detected in macrophages (Mø) and dendritic cells (DC) in vascular diseases. To understand the importance of these cell types in C. pneumoniae infection and transmission, we infected DC and cultivated them with Mø in a coculture model system which precludes cell-to-cell...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2007.12.010
更新日期：2008-03-01 00:00:00
abstract：:Direct extraction of Cryptosporidium DNA from 46 stools by bead-beating, guanidine thiocyanate and silica purification provided slightly lower PCR positivity (93.5% vs. 100%) and higher threshold cycle values (mean 34.93 vs. 28.03; P=0.00) than spin-column extraction from boiled, semi-purified oocyst suspensions. Howe...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.02.006
更新日期：2012-04-01 00:00:00
abstract：:One of the known limitations for biosensor assays is the high limit of detection for target cells within complex samples (e.g., Escherichia coli at 10(4) to 10(5) CFU/mL) due to poor capture efficiencies. Currently, researchers can only estimate the cell capture efficiency necessary to produce a positive signal for an...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2007.11.004
更新日期：2008-01-01 00:00:00
abstract：:This paper reports a novel electrochemical immunosensor for the sensitive detection of staphylococcal enterotoxin A (SEA) based on self-assembly monolayer (SAM) and protein A immobilization on gold electrode. Three different methods of protein A immobilization were tested: physical adsorption, cross-linking using glut...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.05.016
更新日期：2012-10-01 00:00:00
abstract：:MTS or {3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl}-2H-tetrazolium, inner salt) is converted into soluble formazan by mitochondrial dehydrogenase of viable cells, thus serving as an indicator of cell viability. Accordingly, a MTS-based assay was developed to evaluate anti-leishmanial acti...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.10.011
更新日期：2006-07-01 00:00:00
abstract：:For routine mass screening, the use of microarrays is hampered because one chip can only analyze one sample. 16S rRNA gene PCR products of several bacterial strains or mixtures thereof were consecutively loaded on a single electronic microarray and successfully analyzed using probes specific for the bacterial strains....
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(03)00168-4
更新日期：2003-11-01 00:00:00
abstract：:Xylella fastidiosa is a member of the gamma proteobacteria. It is fastidious, insect-vectored and xylem-limited and causes a variety of diseases, some severe, on a wide range of economically important perennial crops, including grape and citrus. Antibody based detection assays are commercially available for X. fastidi...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.07.020
更新日期：2015-10-01 00:00:00
abstract：:Bacterial endosymbionts such as Rickettsia and Wolbachia play prominent roles in the development and behaviour of their insect hosts, such as whiteflies, aphids, psyllids and mealybugs. Accumulating studies have emphasized the importance of establishing experimental insect populations that are either lacking or bearin...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2019.105797
更新日期：2020-01-01 00:00:00
abstract：:We modified Wayne's pyrazinamidase test against Mycobacterium tuberculosis to indirectly measure pyrazinamidase activity via pyrazinoic acid in liquid medium. The modified pyrazinamidase test was easy to perform and its results were in complete agreement with those of the conventional Wayne's method, highlighting its ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2018.09.018
更新日期：2018-11-01 00:00:00
abstract：:A discontinuous lactate dehydrogenase coupled assay is described for the evaluation of the pyruvate carboxylase activity (Pc, EC 6.4.1.1) in a glutamate overproducing strain of Corynebacterium glutamicum. After an initial permeabilisation period of the cells, the method consisted of the fluorometric determination of t...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(99)00104-9
更新日期：1999-12-01 00:00:00
abstract：:MALDI-ToF MS can be used to identify microorganisms directly from blood cultures. This study compared two methods of sample preparation. Similar levels of genus- (91% vs 90%) and species-level identifications (79% vs 74%) were obtained with differential centrifugation and SDS methods. The SDS method is faster and requ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2016.05.026
更新日期：2016-08-01 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：:Aggregatibacter (A.) actinomycetemcomitans is a periodontopathogenic bacterium causing aggressive periodontitis. Here we describe a single-step transconjugation system as novel and easily applicable protocol for site-specific genetic manipulation of A. actinomycetemcomitans. Deletion of PgaC, which is involved in the ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2018.04.002
更新日期：2018-05-01 00:00:00
abstract：:To date, no single reported DNA extraction method is suitable for the efficient extraction of DNA from all fungal species. The efficiency of extraction is of particular importance in PCR-based medical diagnostic applications where the quantity of fungus in a tissue biopsy may be limited. We subjected 16 medically rele...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.06.008
更新日期：2006-04-01 00:00:00
abstract：:Multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) has been shown to be very promising for the typing of Burkholderia pseudomallei and mallei. The currently available set of loci requires high resolution allele size measurement due to short repeat units. The present work was aimed at expanding the ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2009.03.005
更新日期：2009-06-01 00:00:00
abstract：BACKGROUND:Mycoplasma genitalium resistance to antibiotic treatments is increasing, with very limited treatment alternatives on the horizon. Surveillance via sequencing of multiple M. genitalium loci would allow: monitoring of known antibiotic resistance mutations, associations between resistance/treatment failure and ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2020.106089
更新日期：2020-12-01 00:00:00
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journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(02)00185-9
更新日期：2003-03-01 00:00:00
abstract：:Bacillus anthracis, the causative agent of the human disease anthrax, Bacillus cereus, a food-borne pathogen capable of causing human illness, and Bacillus thuringiensis, a well-characterized insecticidal toxin producer, all cluster together within a very tight clade (B. cereus group) phylogenetically and are indistin...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2003.11.004
更新日期：2004-03-01 00:00:00
abstract：:A fused protein composed of a carbohydrate-binding module and green fluorescence protein (GFP) was developed to measure the exopolysaccharides (EPShs) present in Escherichia coli microcolonies. The cleavage of the GFP part of this protein using a site-specific protease allowed for the non-invasive and quantitative eva...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.05.013
更新日期：2015-07-01 00:00:00
abstract：:Pseudomonas aeruginosa is an opportunistic pathogen responsible for numerous infections acquired in hospital especially in persons whose immune systems are weakened, such as with patient suffering from AIDS or cystic fibrosis. This bacterium produces a great diversity of virulence factors among them hydrogen cyanide (...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.04.005
更新日期：2012-07-01 00:00:00
abstract：:Quantification of the biosurfactants produced by a variety of microorganisms is a time taking and difficult task due to the lack of rapid, efficient and accurate methods. This work presents a simple turbidometric method for quantification of crude biosurfactants based on their property to become insoluble at low pH va...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2008.09.010
更新日期：2009-01-01 00:00:00
abstract：:In this research work, the synthesis of Ag doped hydroxyapatite coatings for dental or orthopedic implants was performed. The main goal was to determine the influence of Ag content on the roughness and antimicrobial performance of the prepared thin films. The films were deposited on Ti6Al4V alloy by means of RF magnet...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2016.03.016
更新日期：2016-06-01 00:00:00
abstract：:Rapid identification of bacterial pathogens facilitates earlier optimization of antibiotic treatment and reduces morbidity and mortality in sepsis patients. The aim of this research was to design an in-house chemical-free method for direct bacterial identification in positive blood culture (BC) broths and to compare t...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2020.106065
更新日期：2021-01-01 00:00:00
abstract：:The susceptibility protocol established in this study takes into account that complex media are capable to buffer H2O2 which otherwise may adulterate test results. Furthermore, we demonstrate that clinical isolates of Staphylococcus aureus showed a higher resistance against H2O2 than Streptococcus pyogenes after 30 mi...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2018.11.001
更新日期：2018-12-01 00:00:00
abstract：:Bacterial metabolic activity is associated with the onset and progression mechanisms of oral biofilm-mediated disease; however, at present no method to monitor bacterial metabolism exists, especially for periodontopathic bacteria. Therefore, we aimed to establish a novel method for monitoring the metabolic activity of...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.05.015
更新日期：2015-08-01 00:00:00
abstract：:This paper describes a simple method for the isolation of salt-tolerant myxobacteria from marine conditions. As the results show in this paper, salt-tolerant myxobacteria are found to be able to grow, but unable to form fruiting bodies at high salt concentrations. The fruiting body structures of the salt-tolerant stra...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(02)00029-5
更新日期：2002-07-01 00:00:00
abstract：:The reproducibility and reliability of quantitative microbiological assessments using the DNA-DNA hybridization "checkerboard method" (CKB) were assessed. The data originated from 180 chronic periodontitis patients, who were enrolled in a clinical trial and sampled at baseline, and 3 and 12m post-therapy. The samples ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.01.010
更新日期：2015-03-01 00:00:00
