Abstract：
:Microsatellites, or short tandem repeats (STR's), are popular tools to discriminate between microbial isolates. Here, we report on the robustness of a microsatellite panel for discrimination of Aspergillus fumigatus isolates. Two major PCR artefacts (stutter peaks and minus-A peaks) can complicate correct interpretation of STR data. We investigated the effect of alterations to the various components of the PCR amplification mixtures on these PCR artefacts and on the reproducibility of this assay. Some extreme conditions led to a loss of signal, but, under all conditions where a signal was obtained, identical typing results were produced. Furthermore, pitfalls with the exchange of results between labs are discussed. These pitfalls are primarily associated with sizing of the obtained PCR fragments.
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
de Valk HA,Meis JF,Klaassen CHdoi
10.1016/j.mimet.2007.01.009subject
Has Abstractpub_date
2007-05-01 00:00:00pages
268-72issue
2eissn
0167-7012issn
1872-8359pii
S0167-7012(07)00028-0journal_volume
69pub_type
杂志文章abstract：:DNA extracts from sediment and water samples are often contaminated with coextracted humic-like impurities. Estuarine humic substances and vascular plant extract were used to evaluate the effect of the presence of such impurities on DNA hybridization and quantification. The presence of humic substances and vascular pl...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/s0167-7012(01)00296-2
更新日期：2001-10-01 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：:RNA based stable isotope probing (SIP) facilitates the detection and identification of active members of microbial populations that are involved in the assimilation of an isotopically labeled compound. (15)N-RNA-SIP is a new method that has been discussed in recent literature but has not yet been tested. Herein, we de...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2009.11.002
更新日期：2010-01-01 00:00:00
abstract：:The food industry requires easy, accurate, and cost-effective techniques for microbial identification to ensure safe products and identify microbial contaminations. In this work, FTIR spectroscopy and MALDI-TOF mass spectrometry were assessed for their suitability and applicability for routine microbial diagnostics of...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2014.05.011
更新日期：2014-08-01 00:00:00
abstract：:The spore is the form released in a bioterrorism attack. There is a real need for definition of new targets for Bacillus anthracis that might be incorporated into emerging biodetection technologies. Particularly of interest are macromolecules found in B. anthracis that are (1) spore-specific, (2) readily accessible on...
journal_title：Journal of microbiological methods
pub_type： 杂志文章,评审
doi：10.1016/s0167-7012(03)00095-2
更新日期：2003-08-01 00:00:00
abstract：:Biofilms possess spatially and temporally varying metabolite concentration profiles at the macroscopic and microscopic scales. This results in varying growth environments that may ultimately drive species diversity, determine biofilm structure and the spatial distribution of the community members. Using non-invasive n...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2008.02.015
更新日期：2008-07-01 00:00:00
abstract：:Rapid identification of non-tuberculous mycobacteria (NTM) species is important in clinical laboratories to stipulate the appropriate therapy and to offer a comprehensive infection control. We applied Fourier-Transform Infrared microspectroscopy to evaluate, whether the most frequent species of NTM can be rapidly and ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2006.08.011
更新日期：2007-02-01 00:00:00
abstract：:Culture-independent studies using next generation sequencing have revolutionized microbial ecology, however, oomycete ecology in soils is severely lagging behind. The aim of this study was to improve and validate standard techniques for using high throughput sequencing as a tool for studying oomycete communities. The ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.01.013
更新日期：2015-03-01 00:00:00
abstract：:Bacteriocin activity can be quantified by a simple parallel line model based on an agar diffusion assay. The quotient between the inhibition zone area and the sensitivity of the indicator bacterium can be used to compare different bacteriocins. Deferred calculations of relative potencies are possible, once purified co...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.01.006
更新日期：2005-07-01 00:00:00
abstract：:An effective microbial preservation technology for the long-term storage of viable prokaryotic cells is described. The method combines an almost instantaneous drying step with minimal stress to the cells during drying to maximize survival on rehydration. This is achieved by contact of a microlitre aliquot of a bacteri...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.02.014
更新日期：2005-10-01 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：:The development of rapid methods for detection of viable Listeria monocytogenes is crucial to prevent listeriosis and product recalls. While immunomagnetic separation has been used for isolating Listeria spp., lack of specificity and pathogenicity determination render this method unsatisfactory. A two-step method usin...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2004.10.006
更新日期：2005-02-01 00:00:00
abstract：:Idiopathic interstitial pneumonias are interstitial lung diseases of unknown etiology which prognosis is usually fatal. Microbiota associated to bronchoalveolar lavage from 20 patients with negative bacterial cultures was explored by 16S-rDNA PCR-DGGE, showing a clearly negative relation among the presence of P. jirov...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2010.03.026
更新日期：2010-07-01 00:00:00
abstract：:Corynebacterium matruchotii is a microbial inhabitant in the oral cavity of humans and is associated with the formation of dental calculi. C. matruchotii forms highly specific morphological units, which are referred to as corn-cobs. Although other Corynebacterium species have frequently been isolated from the oral cav...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2014.06.005
更新日期：2014-09-01 00:00:00
abstract：:The immunoglobulin degrading enzyme of Streptococcus pyogenes, IdeS, is an unusual cysteine protease produced by group A streptococci for which the only known substrate is immunoglobulin G (IgG). To date, IdeS has not been found to cleave any of the known synthetic substrates that other cysteine proteases hydrolyse, t...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2007.04.017
更新日期：2007-08-01 00:00:00
abstract：:Here we demonstrate a cost effective and scalable microbial ecology sequencing platform using the Ion Torrent Personal Genome Machine (PGM). We assessed both PCR amplified 16S rRNA and shotgun metagenomic approaches and generated 100,000+ to 1,000,000+ reads using 'post-light' based sequencing technology within differ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.07.008
更新日期：2012-10-01 00:00:00
abstract：:A new method is described for the rapid real-time screening of antioxidative properties using a recombinant Escherichia coli DPD2511 biosensor. This microplate technique, without time-consuming pre-incubations and handling, has potential for a high-throughput search of bioactive compounds. Special emphasis was given t...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2015.08.018
更新日期：2015-11-01 00:00:00
abstract：:A protein database was constructed and validated with identification rate over 90% for the 4 most common Gram-negative bacteria on agar plates. By protein masses comparison, 120 bacteria of the 4 species from blood culture bottles were identified. The concordance was high (Kappa=0.906) between our method and conventio...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2014.07.021
更新日期：2014-10-01 00:00:00
abstract：:The aim of the present study was to show the efficiency of multi-factorial experimental design to investigate factors affecting the antimicrobial compound production by Brevibacillus brevis EGS9 isolated from mangrove sediment soil. The isolate utilizing different carbon and nitrogen sources showed different growth ch...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2017.09.010
更新日期：2017-11-01 00:00:00
abstract：:Industrial biotechnology aims to compete as a stronger alternative ensuring environmental friendly microbial-based production that seeks to curb the predicament of pollution. However, the high cost of bioprocessing is a severe drawback, and therefore, new approaches must be developed to overcome this challenge. Haloph...
journal_title：Journal of microbiological methods
pub_type： 杂志文章,评审
doi：10.1016/j.mimet.2019.105704
更新日期：2019-11-01 00:00:00
abstract：:The purpose of this study was to develop a detection method for viable E. coli O157:H7 in fresh produce and recreational water. The method was evaluated using eight samples of produce wash and recreational water with or without spiked E. coli O157:H7 at ≤10(2) CFU·ml(-1) and concentrated using dead-end ultrafiltration...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2011.09.010
更新日期：2011-12-01 00:00:00
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：: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：:Characterization of commercial microbial consortia products for human and environmental health risk assessment is a major challenge for regulatory agencies. As a means to develop an approach to assess the potential environmental risk of these products, research was conducted to compare four genomics methods for charac...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2014.11.013
更新日期：2015-01-01 00:00:00
abstract：:Listeria monocytogenes is an important foodborne pathogen responsible for non-invasive and invasive diseases in the elderly, pregnant women, neonates and immunocompromised populations. This bacterium has many similarities with other non-pathogenic Listeria species which makes its detection from food and environmental ...
journal_title：Journal of microbiological methods
pub_type： 杂志文章,评审
doi：10.1016/j.mimet.2012.01.002
更新日期：2012-03-01 00:00:00
abstract：:Quantification of invasive, intracellular bacteria is critical in many areas of cellular microbiology and immunology. We describe a novel and fast approach to determine invasion of bacterial pathogens in adherent cell types such as epithelial cells or fibroblasts based on flow cytometry. Using the CEACAM-mediated upta...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2005.08.013
更新日期：2006-05-01 00:00:00
abstract：:Although epitope tagging has been widely used for analyzing protein function in many organisms, there are few genetic tools for epitope tagging in Tetrahymena. In this study, we describe several C-terminal epitope tagging modules that can be used to express tagged proteins in Tetrahymena cells by both plasmid- and PCR...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2010.07.009
更新日期：2010-09-01 00:00:00
abstract：:An oligonucleotide array based on PCR method containing a combination of probes for taxonomic markers and species-specific virulence genes was developed for the simultaneous identification of 14 Lactic Acid Bacteria (LAB) and food-borne pathogenic bacteria in raw milk. The hypervariable regions V3 and V6 of 16S, toget...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2009.05.015
更新日期：2009-08-01 00:00:00
abstract：:In recent years, the rapid advances of culture-independent methods and new molecular tools have revolutionized our understanding of microbial biodiversity and ecological functions. DNA extraction from microbial communities is a critical step in this process and several methods have been proposed and used, but the infl...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2019.02.005
更新日期：2019-04-01 00:00:00
abstract：:Microbial adhesion is a critical step for infection and colonization of the host. Trichomonas vaginalis, a human urogenital extracellular parasite, relies on host cell adhesion for infection and pathogenesis. Although host cell adhesion of T. vaginalis is strain-dependent and it may be influenced by many environmental...
journal_title：Journal of microbiological methods
pub_type： 杂志文章
doi：10.1016/j.mimet.2012.10.011
更新日期：2013-01-01 00:00:00
