Showing papers in "Journal of Microbiological Methods in 2017"

TL;DR: In conclusion, the revision of the literature available up to date demonstrated that MALDI-TOF MS represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates in clinical settings.

TL;DR: This review provides an overview and a critical discussion of techniques used to visualize different matrix compounds, to determine the concentration of solutes and the diffusive properties of the biofilm matrix.

TL;DR: The goal of this review is to give an overview of the process, from sample to analysis, and discuss how to optimize your resources to achieve the most from your NGS-based research.

TL;DR: A genome editing tool using a two-plasmid strategy is developed and used to generate a marker-free mutant of ATCC 824 that produced an isopropanol-butanol-ethanol mixture and Whole-genome sequencing confirmed that no off-target modifications were present in the mutants.

TL;DR: Safranin staining provided similar results as crystal violet, but with higher reproducibility, and is recommended for biofilm biomass quantification.

TL;DR: Rapid Salmonella detection using Recombinase Aided Amplification was established and should be a great choice for monitoring contamination, such as foodborneSalmonella or for similar purposes.

TL;DR: It is observed that uptake of propidium ions across intact cell membranes for Dinoroseobacter shibae and Bacillus subtilis and apparently a high membrane potential facilitates breakthrough of the double-charged propidium ion and can mark viable cells as dead.

TL;DR: 3DμFMP could selectively preconcentrate enterohemorrhagic Escherichia coli O157:H7 in 100mL by a factor of 700 within 1h using antibody-conjugated magnetic nanoparticles (Ab-MNPs) and the development of 3D microfluidic magnetic preconcentrator made of plastic via 3D printing without the need for any assembly is reported.

TL;DR: The assay was 100% sensitive and specific for detecting the expected species and offers a quick and accurate strategy for identifying E. coli, E. albertii, and E. fergusonii in either a single reaction or by in silico PCR with sequence assemblies.

TL;DR: This review proposes an overview of all newly available methods available to identify known and/or unknown nematodes with a specific focus on emerging high-throughput molecular techniques.

TL;DR: Results show that 50mM of NaN3 strongly inhibits bacterial growth under natural and enriched resource conditions.

TL;DR: The results present the first molecular-phylogenetic characterization and predictive functional profiles of the microbial mat communities in Lake Obersee, while demonstrating the efficacy of combining both the taxonomic assignment information and functional IDs using the R script created in this study for a more streamlined evaluation of predictivefunctional profiles of microbial communities.

TL;DR: The most efficient method for gene targeting was AMT, but further it was shown to be dependent on the choice of Agrobacterium strain, and there are different advantages and disadvantages of all three gene targeting methods which are discussed, in order to facilitate future approaches for fungal strain improvements.

TL;DR: Results demonstrate the effective use of a PMA-qPCR method for the quantification of the E. coli uidA gene and indicate there are high numbers (2.01×103CCE/100mL) of VBNC E.coli cells leaving the wastewater treatment plant in the final effluent after chlorine treatment.

TL;DR: An overview on advantages and limitations of routinely used phenotypic tests for S. pneumoniae identification is deliberated and the roles and current challenges faced by various molecular identification and serogroup/serotype identification methods are discussed.

TL;DR: It was indicated that among oral Rothia species, R. mucilaginosa is most predominant in the oral cavity of humans, and a novel selective medium, ORSM, was useful for isolating each oral RothIA species.

TL;DR: An improved ASF species-specific and sensitive real-time quantitative polymerase chain reaction (qPCR) for use with SYBR Green chemistry to accurately assess individual ASF member abundance and a nested PCR assay for the detection of lowly abundant ASF members is described.

TL;DR: D. rerio is concluded to be a suitable alternative animal model for the use of a targeted metagenomics approach along with bioinformatics tools to further investigate the relationship between the gluten diet and microbiome profile in the gut ecosystem leading to gastrointestinal diseases and other undesired adverse health effects.

TL;DR: The method showed that at least 5,528,079 sequences were required to reliably characterize microbial communities inhabiting the mesocosms, and provided a criterion to ensure sequencing sufficiency when analyzing the structure of natural microbial communities.

TL;DR: This review confine the analysis to relatively current advancements in biosensors for the detection of whole bacterial cells and the variety of biosensor types and their actual and potential uses are described.

TL;DR: In this article, the use of skimmed milk flocculation (SMF) to simultaneously concentrate viruses, bacteria and protozoa was evaluated, and the mean recoveries with q(RT)PCR were 66%, 24% (MS2), 28% (RoV SA-11), 15% (BVDV), 60% (E. coli), 30% (H. pylori) and 21% (Acanthamoeba castellanii).

TL;DR: The overall categorical agreement was 61.2% (r=0.024), which means that resazurin can not substitute XTT.

TL;DR: It is shown that CsCl density purification of the P. aeruginosa phages, at an initial concentration of 1012-1013pfu/ml, led to the strongest reduction of endotoxins, with an endotoxin removal efficacy of up to 99%, whereas additional purification methods did not result in a complete removal of endot oxins from the phage preparations and only yielded an additional endotoxin removal efficacy.

TL;DR: A two-step real-time PCR-based rapid method for the identification and detection of five Salmonella serotypes that are either overrepresented in human disease or frequently associated with multi-drug resistance, including serotypes Enteritidis, Typhimurium, Newport, Hadar, and Heidelberg.

TL;DR: Detailed NGS beta diversity comparisons indicated that the Mini Kit and PowerSoil Kit are best suited for studies that extract DNA from a variety of water and wastewater samples, and application of Mini Kit or Power soil Kit is recommended as an improvement to NGS protocols for these sampling environments.

TL;DR: A highly efficient Agrobacterium-mediated genetic transformation system for Malassezia furfur and M. pachydermatis is described, combining the transformation protocols of Agaricus bisporus and Cryptococcus neoformans to reveal mechanisms underlying the switch from the non-pathogenic to pathogenic life style.

TL;DR: DNA metabarcoding analysis applied to EDC seems promising, but it must be used along with qPCR, to obtain a more global view of microbial ecology and relative quantification of species of interest within communities.

TL;DR: The serodiagnostic potential of I-PCR assays for an early diagnosis of TB based on the detection of potential mycobacterial antigens and circulating antibodies in body fluids of TB patients is described.

TL;DR: The results suggest this simple and cost-effective serotype specific PCR assay can be used as an alternative to agglutination based techniques to serotype the majority of M. haemolytica collected from bovines, thus averting the need to use animals and invest in expensive sera development for aggLutination assays.

TL;DR: The most probable number approach integrated to loop mediated isothermal technique (MPN-LAMP) focusing on Gram-negative Escherichia coli and Gram-positive Enterococcus faecalis bacterial cells without nucleic acids extraction has the potential to replace conventional MPN method for waterborne pathogens.