4,390 results match your criteria Journal of Microbiological Methods [Journal]


Construction and validation of the Tn5-P-msfGFP transposon as a tool to probe protein expression and localization.

J Microbiol Methods 2019 Apr 17. Epub 2019 Apr 17.

Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven. Faculty of Bioscience Engineering, Kasteelpark Arenberg 22, 3000 Leuven, Belgium. Electronic address:

In this study we report the design, construction and validation of a novel transposon aimed to systematically screen for protein localization and expression patterns in prokaryotes using fluorescence microscopy. Upon random insertion in an open reading frame in the proper frame and orientation, the transposon creates an N-terminal fluorescent protein fusion to the msfGFP reporter. Moreover, in order to examine the localization of fusion proteins whose native expression might be too low or absent, the transposon was fitted with a P promoter that makes the expression of the generated fluorescent protein fusions controllable by anhydrotetracycline. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.04.012DOI Listing

Influence of swabbing solution and swab type on DNA recovery from rigid environmental surfaces.

J Microbiol Methods 2019 Apr 17. Epub 2019 Apr 17.

Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea; Department of Biomedical Laboratory Science, Eulji University, School of Medicine, 77 Gyeryong-ro, 771 beon-gil, Jung-gu, Deajeon 34824, Republic of Korea. Electronic address:

Determination of the metagenome has become an important component of forensic identification, which requires efficient environmental sampling techniques. Therefore, in this study, we compared the efficiency of sample collection using swabbing with cotton swabs and three types of medical swabs (S7, S22, S24) along with three different solutions: phosphate-buffered saline (PBS), 1% Tween 20 + 1% glycerol in PBS (TG), and GS commercial solution (Noble Bio, Hwaseong, Republic of Korea). Combinations of the three solutions with the three types of swabs were tested at different volumes (cotton swab, S7: 0, 30, 50, 70 μL; S22, S24: 0, 70, 100, 130 μL). Read More

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S01677012193020
Publisher Site
http://dx.doi.org/10.1016/j.mimet.2019.04.011DOI Listing
April 2019
1 Read

Development of isothermal amplification methods for rapid and sensitive detection of heat-labile enterotoxin producing Escherichia coli.

J Microbiol Methods 2019 Apr 16. Epub 2019 Apr 16.

Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, PR China. Electronic address:

The objective of this study was to establish a novel isothermal amplification method for detection of heat-labile enterotoxin (LT-I)-producing Escherichia coli. Loop-mediated isothermal amplification (LAMP), cross-priming amplification (CPA), and isothermal multiple-self-matching-initiated amplification (IMSA) were developed and evaluated. Optimal conditions, specificity, and sensitivity tests were performed and compared to qPCR findings. Read More

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S01677012193001
Publisher Site
http://dx.doi.org/10.1016/j.mimet.2019.04.010DOI Listing
April 2019
1 Read

YTOX: A rapid toxicity test based on the dehydrogenase activity of Saccharomyces cerevisiae for detection of contaminants in water samples.

J Microbiol Methods 2019 Apr 15. Epub 2019 Apr 15.

Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo, P.O. Box 9, 13418-900 Piracicaba, SP, Brazil.

A simple generic toxicity method (test) is proposed using baker's yeast to mediate the reduction of the colourless triphenyltetrazolium chloride (TTC) to red, 1,3,5-triphenyl formazan, which can be extracted by dimethyl sulfoxide (DMSO), enabling the identification of reducible toxic compounds (e.g. cadmium, fipronil) in water for consumption. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.04.008DOI Listing

Induction of EGFP expression in Pichia pastoris during co-culture with human endothelial cell line.

J Microbiol Methods 2019 Apr 14. Epub 2019 Apr 14.

Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, 155 Fifth Street, San Francisco, CA 94103.

While Pichia pastoris has been developed into a versatile recombinant protein expression system, there are only few studies that have investigated the efficacious use of this yeast with human cells. In this study, we demonstrated that P. pastoris can be cultured under mammalian cell culture conditions and co-cultured with human endothelial cells. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.04.006DOI Listing
April 2019
2.026 Impact Factor

Osteoarticular infections: Blood as a determinant factor in the isolation of Kingella kingae.

J Microbiol Methods 2019 Apr 12;161:8-11. Epub 2019 Apr 12.

Servei de Microbiologia, Hospital Sant Joan de Déu, Barcelona, Spain. Electronic address:

We assessed the capacity of Kingella kingae to grow in blood culture bottles (BCB), taking into account the concentrations of the microorganism and blood in the culture medium. An initial suspension (McFarland 0.5) of 32 strains of K. Read More

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S01677012193027
Publisher Site
http://dx.doi.org/10.1016/j.mimet.2019.04.009DOI Listing
April 2019
2 Reads

Evaluation of random amplified polymorphic DNA and multiple-locus variable number tandem repeat analyses for Mycoplasma cynos.

J Microbiol Methods 2019 Apr 11;161:1-7. Epub 2019 Apr 11.

Department of Microbiology, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey. Electronic address:

Mycoplasma spp. can cause diseases of the respiratory system as well as urogenital infections, infertility, and anemia. The members of this genus have a low G + C content compared to other bacteria. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.04.004DOI Listing

Rapid detection of heavy metal-induced toxicity in water using a fed-batch sulfur-oxidizing bacteria (SOB) bioreactor.

J Microbiol Methods 2019 Apr 9. Epub 2019 Apr 9.

Department of Biological Environment, Kangwon National University, 192-1 Hyoja-dong, Gangwon-do, Chuncheon-si 200-701, Republic of Korea. Electronic address:

A fed-batch bioreactor based on sulfur-oxidizing bacteria (SOB) was tested for rapid detection of heavy metal-induced toxicity in water. For this evaluation, SOB were exposed to water contaminated by selenium, mercury, hexavalent chromium, arsenic, cyanide, cadmium, and lead for 2 h and their inhibition rates were analyzed based on changes in electrical conductivity (EC). The results demonstrate that SOB were highly inhibited by selenium, mercury, hexavalent chromium, and arsenic but not by cyanide, cadmium, and lead. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.04.007DOI Listing
April 2019
2 Reads

The use of hollow fiber dialysis filters operated in axial flow mode for recovery of microorganisms in large volume water samples with high loadings of particulate matter.

J Microbiol Methods 2019 Apr 8;160:143-153. Epub 2019 Apr 8.

US EPA, Cincinnati, OH, United States of America.

Ultrafiltration concentration of microorganisms in large volume water samples containing high levels of particulate matter was evaluated in a proof of concept study. The organisms tested were Bacillus atrophaeus subspecies globigii spores and MS2 bacteriophage. To produce the large volume samples, fresh water sediment of a known particle size was added to 51 l of tap water. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.04.005DOI Listing

A comparison of methods for enumerating bacteria in direct fed microbials for animal feed.

J Microbiol Methods 2019 Apr 5;160:124-129. Epub 2019 Apr 5.

Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Ave., San Luis Obispo, CA 93407, USA. Electronic address:

Aerobic plate counts are the standard enumeration method for probiotic-containing products. This counting method is limited by the ability of many cells to enter a viable but non-culturable (VBNC) state upon exposure to stressful conditions like dehydration and heating commonly used in probiotic product preparation. Alternative enumeration methods are available including flow cytometry (FC) which counts total live/dead cells by assessing cellular integrity and/or metabolic activity, and quantitative polymerase chain reaction (qPCR) in which enumeration is correlated with the quantity of a nucleic acid target. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.04.003DOI Listing
April 2019
1 Read

Insufficient sensitivity of laser desorption-time of flight mass spectrometry-based detection of hemozoin for malaria screening.

J Microbiol Methods 2019 Apr 3;160:104-106. Epub 2019 Apr 3.

Swiss Tropical and Public Health Institute, Basel, Switzerland; Faculty of Medicine, University Basel, Basel, Switzerland.

Laser desorption-time of flight (LD-TOF) mass spectrometry-based detection of hemozoin was assessed for its performance characteristics as a rapid screening test for malaria. In spite of good specificity of >95%, poor sensitivity of 80.2% for microscopically positive samples makes the easy-to-apply and rapid approach unsuitable for the routine diagnostic setting. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.04.002DOI Listing
April 2019
1 Read

Flurbiprofen-loaded ethanolic liposome particles for biomedical applications.

J Microbiol Methods 2019 Apr 2. Epub 2019 Apr 2.

School of Physical Sciences, Banasthali Vidyapith, Banasthali, Rajasthan, India. Electronic address:

Present study deals with the preparation, characterization and in-vivo evaluation of flurbiprofen loaded ethanolic liposome which provides predetermined and controlled release of drug through a transdermal drug delivery system. Ethanolic liposomes were prepared by using flurbiprofen, phospholipon 90-G, and ethanol in varied concentration ratio. The prepared ethanolic liposomes were optimized and characterized for particle size, zeta potential, polydispersive index and % entrapment efficiency. Read More

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S01677012193013
Publisher Site
http://dx.doi.org/10.1016/j.mimet.2019.04.001DOI Listing
April 2019
3 Reads

Development of a multiplex-PCR to simultaneously detect acquired linezolid resistance genes cfr, optrA and poxtA in enterococci of clinical origin.

J Microbiol Methods 2019 Mar 30;160:101-103. Epub 2019 Mar 30.

National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Germany.

Linezolid-resistant enterococcus spp. are increasingly recognized by diagnostic laboratories. Resistance can be mediated by the expression of cfr, optrA or poxtA. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.025DOI Listing
March 2019
1 Read

A multiplex real-time PCR assay for the detection and differentiation of five bovine pinkeye pathogens.

J Microbiol Methods 2019 Mar 29;160:87-92. Epub 2019 Mar 29.

Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, United States; Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, United States. Electronic address:

Infectious bovine keratoconjunctivitis (IBK), also known as pinkeye, is one of the most common eye diseases in cattle. Several pathogens have been associated with IBK cases, however, Moraxella bovis, Moraxella bovoculi, Mycoplasma bovis, Mycoplasma bovoculi and bovine herpesvirus type 1 (BHV-1) are most frequently observed. A multiplex real-time PCR assay using two reactions was developed for the detection and differentiation of these five pathogens. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.024DOI Listing
March 2019
1 Read

A method to assess influence of different medical tubing on biofilm formation by Acinetobacter baumannii.

J Microbiol Methods 2019 Mar 28;160:84-86. Epub 2019 Mar 28.

Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsin-Chu City, Taiwan; Department of Life Science, National Tsing Hua University, Hsin-Chu City, Taiwan.

In this study, we developed a method to assess influence of different medical tubing on biofilm formation by A. baumannii. The results of biofilm quantification and scanning electron microscopy showed that the biofilm formation susceptibility of different tubing materials was rubber latex > polyvinyl chloride > silicone. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.023DOI Listing

A flow cytometry method for bacterial quantification and biomass estimates in activated sludge.

J Microbiol Methods 2019 Mar 26;160:73-83. Epub 2019 Mar 26.

School of Engineering, Newcastle University, NE1 7RU, UK.

Absolute bacterial quantification receives little serious attention in the literature compared to sequencing, conceivably because it is considered unimportant and facile, or because existing methods are tedious, laborious and/or biased in nature. This is particularly true in engineered systems, including activated sludge, where such information underpins their design and operation. To overcome these limitations we built upon existing work and optimised and comprehensively validated, through comparison with epifluorescence microscopy (EFM), a rapid and precise flow cytometric protocol to enumerate total bacterial numbers in activated sludge. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.022DOI Listing

Establishment of the molecular beacon-loop-mediated isothermal amplification method for the rapid detection of Porphyromonas gingivalis.

J Microbiol Methods 2019 Mar 25;160:68-72. Epub 2019 Mar 25.

Institute for Disease Prevention and Control of PLA, Beijing, China. Electronic address:

Porphyromonas gingivalis, a clinically important oral pathogen causing periodontal disease, is difficult to culture in routine conditions. Hence, it is necessary to establish a reliable technique to detect this pathogen. Previously, our laboratory developed a new isothermal detection method, called MB-LAMP (molecular beacon-Loop-mediated isothermal amplification), which combines the advantages of LAMP and qPCR through the accurate and quantitative detection of LAMP products. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.01.013DOI Listing
March 2019
1 Read

Optimization of PCR primers to detect phylogenetically diverse nrfA genes associated with nitrite ammonification.

J Microbiol Methods 2019 Mar 21;160:49-59. Epub 2019 Mar 21.

USDA-ARS, Urbana, IL, USA. Electronic address:

Dissimilatory nitrate reduction to ammonium (DNRA) is now known to be a more prevalent process in terrestrial ecosystems than previously thought. The key enzyme, a pentaheme cytochrome c nitrite reductase NrfA associated with respiratory nitrite ammonification, is encoded by the nrfA gene in a broad phylogeny of bacteria. The lack of reliable and comprehensive molecular tools to detect diverse nrfA from environmental samples has hampered efforts to meaningfully characterize the genetic potential for DNRA in environmental systems. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.020DOI Listing

Investigating a non-destructive alternative for a preliminary evaluation of fungal growth in solid state fermentations.

J Microbiol Methods 2019 Mar 21;160:60-67. Epub 2019 Mar 21.

School of Chemical Engineering and Analytical Science, The University of Manchester, Oxford road, Manchester M13 9PL, United Kingdom.

Solid state fermentation (SSF) is an ancient technique which keeps attracting the attention of the food and biotechnology industries; however, a direct quantification of microbial biomass is still a fundamental challenge in this type of processes. Typically, growth is measured using indirect and destructive methods which do not allow a continuous evaluation of the evolution of microbial biomass within a single system. This article presents a non-destructive, quick and simple technique, based on digital imaging analysis (DIA) for the evaluation of growth in SSF laboratory experiments. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.021DOI Listing

Exogenous contaminating DNA in Taq polymerases: A method to avoid false-positive results when detecting the bla gene.

J Microbiol Methods 2019 Mar 20;160:36-41. Epub 2019 Mar 20.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova Str., Moscow 119991, Russia. Electronic address:

In the course of developing an assay to identify genes responsible for antibiotic resistance in gram-negative bacteria, it has been found that standard (not DNA-free) Taq DNA polymerases were contaminated with bla gene fragments that varied in length and quantities. The complete bla gene sequence was either absent or was detected in infinitesimal amounts. We developed an approach to avoid false-positive findings caused by contaminating bla gene sequences in conventional polymerases. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.018DOI Listing

Detection of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae using the MALDI Biotyper Selective Testing of Antibiotic Resistance-β-Lactamase (MBT STAR-BL) assay.

J Microbiol Methods 2019 Mar 20;160:154-156. Epub 2019 Mar 20.

Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, Japan; Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.

The MALDI Biotyper Selective Testing of Antibiotic Resistance-β-Lactamase (MBT STAR-BL) assay, which analyzes bacterial induced hydrolysis of cefotaxime using MALDI-TOF MS, correctly identified 100.0% of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae as positive and 94.7% of non-ESBL producers as negative in 80 strains tested. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.019DOI Listing

Rapid detection of coliform bacteria using a lateral flow test strip assay.

Authors:
Tatsuya Tominaga

J Microbiol Methods 2019 Mar 20;160:29-35. Epub 2019 Mar 20.

Saitama Industrial Technology Center North Institute, 2-133, Suehiro, Kumagayashi, Saitama 360-0031, Japan. Electronic address:

Coliform bacteria in foods are enumerated at food processing plants and are used as sanitary and quality indicators. To detect coliform bacteria rapidly, seven Lateral Flow Test Strips (LFTSs) that can detect the genera Aeromonas, Citrobacter, Enterobacter, Hafnia, Klebsiella/Raoultella, Pantoea and Serratia were developed. For 55 tested food isolates, the detection rate of each individual LFTS assay was only 38% to 76%, but the detection rate of the 7 combined assays was 100%. Read More

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S01677012193008
Publisher Site
http://dx.doi.org/10.1016/j.mimet.2019.03.013DOI Listing
March 2019
2 Reads

Lipid-polymer hybrid nanoparticles: Synthesis strategies and biomedical applications.

J Microbiol Methods 2019 Mar 18;160:130-142. Epub 2019 Mar 18.

School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia. Electronic address:

This review article is an updated overview on lipid-polymer hybrid nanoparticles (LPHNs) including the various types of LPHNs polymers used in their preparation, various methods of preparation, their physiochemical, in-vitro and in-vivo evaluation parameters and their application in various delivery systems. LPHNs show a combined advantage of biodegradable polymeric nanoparticles and liposomes. LPHNs mainly consist of a biodegradable polymeric material core containing drugs or any substances which are to be encapsulated then this core is further enclosed by a phospholipid layer i. Read More

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S01677012193005
Publisher Site
http://dx.doi.org/10.1016/j.mimet.2019.03.017DOI Listing
March 2019
4 Reads

Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping.

J Microbiol Methods 2019 Mar 17;160:11-19. Epub 2019 Mar 17.

Institute for Applied Ecology, University of Canberra, ACT 2601, Australia.

Bacterial identification methods used in routine identification of pathogens in medical microbiology include a combination approach of biochemical tests, mass spectrometry or molecular biology techniques. Extensive publicly-available databases of DNA sequence data from pathogenic bacteria have been amassed in recent years; this provides an opportunity for using bacterial genome sequencing for identification purposes. Whole genome sequencing is increasing in popularity, although at present it remains a relatively expensive approach to bacterial identification and typing. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.016DOI Listing

Optimization of media components for the production of N-acetylchitooligosaccharide from chitin by Streptomyces chilikensis through Taguchi experimental design.

J Microbiol Methods 2019 Apr 16;159:194-199. Epub 2019 Mar 16.

School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India; School of Law, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India. Electronic address:

Optimization of media composition for microbial growth is crucial particularly in industrial processes to obtain the desired end product. The waste from sea food industries includes the non-edible parts of shrimp, crabs and prawns which are rich in chitin as the major cause of pollution in coastal areas. Chitin degradation is carried out chemically. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.014DOI Listing

Multiple promoters driving the expression of astaxanthin biosynthesis genes can enhance free-form astaxanthin production.

J Microbiol Methods 2019 Mar 16;160:20-28. Epub 2019 Mar 16.

Department of Biological Science & Technology, I-Shou University, Kaohsiung 82445, Taiwan; Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan. Electronic address:

Astaxanthin possesses various biological properties and is used in the animal and fish feed, food, and beverage industries. In this study, we derived zeaxanthin biosynthesis genes (crtE, crtB, crtI, crtY, and crtZ) from Erwinia uredovora and crtW from Agrobacterium aurantiacum. We fused inducible and constitutive promoters to astaxanthin biosynthesis genes to construct a novel plasmid (dubbed PTP3-6) that can effectively enhance free-form astaxanthin (FFAX) production. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.012DOI Listing

Integration of biological pre-treatment methods for increased energy recovery from paper and pulp biosludge.

J Microbiol Methods 2019 Mar 16;160:93-100. Epub 2019 Mar 16.

Department of Basic Sciences, CET, School of Engineering & Technology, JAIN Deemed-to-be University, 562112, Karnataka, India; Department of Food Technology, Center for Emerging Technology, School of Engineering & Technology, JAIN Deemed-to-be University, 562112, Karnataka, India. Electronic address:

The paper and pulp industry (PPI) produces high quantities of solid and liquid discharge and is regarded as the most polluting industry in the world causing adverse effects to environments and human beings. Hence changes in the way PPI sludge and waste materials are treated is urgently required. Nearly, 10 million tons of waste is generated per year, however PPI waste is enriched with many organic chemicalscontaining a high percentage of lignin, cellulose, and hemicellulose which can be used as valuable raw materials for the production of bioenergy and value-added chemicals. Read More

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S01677012193006
Publisher Site
http://dx.doi.org/10.1016/j.mimet.2019.03.015DOI Listing
March 2019
4 Reads

A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss).

J Microbiol Methods 2019 Mar 16;160:42-48. Epub 2019 Mar 16.

National History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. Electronic address:

Immediate freezing is perhaps the most preferred method used for preserving gut microbial samples, but research on sample preservation has been principally based around samples from mammalian species, and little is known about the advantages or disadvantages relating to different storage methods for fish guts. Fish gut samples may pose additional challenges due to the different chemical and enzymatic profile, as well as the higher water content, which might affect the yield and purity of DNA recovered. To explore this, we took gut content and mucosal scrape samples from 10 rainbow trout (Oncorhynchus mykiss), and tested whether different preservation methods have any effect on the ability to construct high quality genomic libraries for shotgun and 16S rRNA gene sequencing. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.010DOI Listing
March 2019
1 Read

Novel biocompatible poly(acrylamide)-grafted-dextran hydrogels: Synthesis, characterization and biomedical applications.

J Microbiol Methods 2019 Apr 12;159:200-210. Epub 2019 Mar 12.

Department of Pharmaceutics, BLDEA's SSM College of Pharmacy and Research Centre, Vijayapur 586 103, Karnataka, India. Electronic address:

An electro-responsive PAAm-g-Dxt copolymer was synthesized and characterized by HNMR & FTIR spectroscopy, neutralization equivalent, elemental and thermogravimetric analysis to ascertain the grafting reaction. Further, we developed an electro-responsive transdermal drug delivery system (ETDS) utilizing PAAm-g-Dxt copolymer for rivastigmine tartarate delivery through skin. The ETDS were developed using drug-loaded PAAm-g-Dxt hydrogel as the reservoir, and cross-linked dextran-poly(vinyl alcohol) blend films as rate controlling membranes (RCM). Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.009DOI Listing
April 2019
1 Read

Methods for extracting 'omes from microbialites.

J Microbiol Methods 2019 Mar 12;160:1-10. Epub 2019 Mar 12.

Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx 04510, Mexico; Unidad Académica de Yucatán, UNAM, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Yucatán 97302, México.

Microbialites are organo-sedimentary structures formed by complex microbial communities that interact with abiotic factors to form carbonate rich fabrics. Extraction of DNA or total RNA from microbialites can be difficult because of the high carbonate mineral concentration and exopolymeric substances. The methods employed until now include substances such as cetyltrimethylammonium bromide, sodium dodecyl sulfate, xanthogenate, lysozyme and proteinase K, as well as mechanical disruption. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.02.014DOI Listing
March 2019
2 Reads

Optimisation and validation of a PCR to detect viable Tenacibaculum maritimum in salmon skin tissue samples.

J Microbiol Methods 2019 Apr 12;159:186-193. Epub 2019 Mar 12.

Murdoch University, School of Veterinary and Life Sciences, Perth, WA, Australia.

A PCR protocol was optimised and validated for the detection of viable Tenacibaculum maritimum cells in salmon skin tissue. Viability conventional (vPCR) and quantitative PCR (v-qPCR) assays both had a limit of detection of 10 CFU mL viable cells. The v-qPCR assay showed a linear quantification over 4 log units. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.008DOI Listing
April 2019
6 Reads

Green synthesis and characterization of copper nanoparticles by Tinospora cardifolia to produce nature-friendly copper nano-coated fabric and their antimicrobial evaluation.

J Microbiol Methods 2019 Mar 11;160:107-116. Epub 2019 Mar 11.

School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW 2006, Australia. Electronic address:

Metallic nanoparticles such as gold, zinc, copper possess anti-microbial activity. These nanoparticles have a small size which provides a large surface area for the interaction with microbes and there are various mechanisms through which copper nanoparticles (CuNPs) act. The demand of these nanoparticles are increasing in the textile industry as they decrease the catalytic degradation property of various dyes as well as being helpful in the treatment of various topical infections. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.007DOI Listing

Method for culturing Candidatus Ornithobacterium hominis.

J Microbiol Methods 2019 Apr 11;159:157-160. Epub 2019 Mar 11.

Menzies School of Health Research, Charles Darwin University, Darwin, Australia. Electronic address:

Candidatus Ornithobacterium hominis has been detected in nasopharyngeal microbiota sequence data from around the world. This report provides the first description of culture conditions for isolating this bacterium. The availability of an easily reproducible culture method is expected to facilitate deeper understanding of the clinical significance of this species. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.006DOI Listing

Rapid and reasonable molecular identification of bacteria and fungi in microbiological diagnostics using rapid real-time PCR and Sanger sequencing.

J Microbiol Methods 2019 Apr 9;159:148-156. Epub 2019 Mar 9.

Chemical and Veterinary Investigations Office Stuttgart (CVUAS), Schaflandstr. 3/3, 70736 Fellbach, Germany.

Analyses of short subunit gene sequences have been established for taxonomic classification and identification of bacteria and fungi. To produce partial bacterial ribosomal 16S rRNA and rpoB and fungal ribosomal ITS/LSU gene sequences for DNA sequencing, real-time PCR assays supplemented with the nucleic acid stain SYBR Green were created. Generation of PCR products was monitored based on amplification and melting curves. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.005DOI Listing
April 2019
1 Read

Development and evaluation of rapid and specific sdaA LAMP-LFD assay with Xpert MTB/RIF assay for diagnosis of tuberculosis.

J Microbiol Methods 2019 Apr 8;159:161-166. Epub 2019 Mar 8.

Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India. Electronic address:

There is need for rapid and cost-effective diagnostic test for tuberculosis. The present study was carried out to design a Loop-mediated isothermal amplification (LAMP) assay combined with lateral flow dipstick (LFD) as a point-of-care method for diagnosis of TB. LAMP assay targeting sdaA gene combined with LFD for sequence specific detection was standardized in user friendly and rapid format. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.002DOI Listing
April 2019
2 Reads

Assessment of two selective agar media to isolate colistin-resistant bovine Escherichia coli: Correlation with minimal inhibitory concentration and presence of mcr genes.

J Microbiol Methods 2019 Apr 8;159:174-178. Epub 2019 Mar 8.

ARSIA (Association Régionale de Santé et d'Identification Animale), Ciney B5590, Belgium.

The identification of colistin-resistant enterobacteria in veterinary medicine is impaired by the absence of first-line reliable phenotypic assay. The purpose of this study was to assess two selective agar media for the detection of colistin-resistant bovine pathogenic Escherichia coli. A total of 158 E. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.004DOI Listing

A duplex quantitative real-time PCR assay for the detection and quantification of Xanthomonas phaseoli pv. dieffenbachiae from diseased and latently infected anthurium tissue.

J Microbiol Methods 2019 Mar 8. Epub 2019 Mar 8.

UMR PVBMT, CIRAD, F-97410 St Pierre, Reunion island, France,. Electronic address:

Anthurium bacterial blight caused by Xanthomonas phaseoli pv. dieffenbachiae (formerly Xanthomonas axonopodis pv. dieffenbachiae) is the major phytosanitary threat in many anthurium growing areas worldwide. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.003DOI Listing
March 2019
2.026 Impact Factor

MALDI-TOF MS based procedure to detect KPC-2 directly from positive blood culture bottles and colonies.

J Microbiol Methods 2019 Apr 5;159:120-127. Epub 2019 Mar 5.

Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Argentina; CONICET, Argentina. Electronic address:

In this study, we identified specific carbapenemase-producing isolates applying an easy and rapid protocol for the detection of mature KPC-2 β-lactamase by MALDI-TOF MS from colony and positive blood culture bottles. In addition, we evaluated the correlation of the ~11,109 Da signal as a biomarker associated with KPC-2 production. A collection of 126 well-characterized clinical isolates were evaluated (including 60 KPC-2-producing strains). Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.02.020DOI Listing
April 2019
2 Reads

Nanopore ultra-long read sequencing technology for antimicrobial resistance detection in Mannheimia haemolytica.

J Microbiol Methods 2019 Apr 5;159:138-147. Epub 2019 Mar 5.

Oklahoma Animal Disease Diagnostic Laboratory, Center for Veterinary Health Sciences, 1950 W. Farm Road, Stillwater, OK 74078, United States. Electronic address:

Disruptive innovations in long-range, cost-effective direct template nucleic acid sequencing are transforming clinical and diagnostic medicine. A multidrug resistant strain and a pan-susceptible strain of Mannheimia haemolytica, isolated from pneumonic bovine lung samples, were sequenced at 146× and 111× coverage, respectively with Oxford Nanopore Technologies MinION. De novo assembly produced a complete genome for the non-resistant strain and a nearly complete assembly for the drug resistant strain. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.03.001DOI Listing
April 2019
1 Read

Enhanced inulinase production by Fusarium solani JALPK from invasive weed using response surface methodology.

J Microbiol Methods 2019 Apr 2;159:99-111. Epub 2019 Mar 2.

Department of Microbiology, Rajaram College Kolhapur, 416004, India. Electronic address:

The present study is the first report of utilizing Tithonia rotundifolia weed as a substrate for inulinase production from Fusarium solani JALPK. It also deals with the statistical optimization of culture conditions to enhance the enzyme yield. Amongst the 11 variables screened by Plackett- Burman design, Inulin in combination with Agave sisalana extract, Tithonia rotundifolia extract and NaNO had a significant influence on inulinase production and their concentrations were further optimized employing Box Behnken design. Read More

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S01677012193004
Publisher Site
http://dx.doi.org/10.1016/j.mimet.2019.02.021DOI Listing
April 2019
5 Reads

Reactive mechanism and the applications of bioactive prebiotics for human health: Review.

J Microbiol Methods 2019 Apr 28;159:128-137. Epub 2019 Feb 28.

Department of Basic Sciences, School of Engineering & Technology, JAIN Deemed-to-be University, 562112, Karnataka, India; Food Technology, Centre for Emerging Technology, JAIN Deemed-to-be University, 562112, Karnataka, India. Electronic address:

Prebiotics plays an important role in improving the growth of gut bacteria and it majorly found in various natural food sources such as fruits and vegetables. Nowadays, the prebiotic sources are added as a supplement in various food products such as dairy products, beverages, health drinks, infant formulae, and meat products. The presence of prebiotics provides various health benefits such as improveing calcium and magnesium absorption, increases bone density, reduces cancer risk, decreases cardiovascular diseases and also improves the immune system. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.02.019DOI Listing

Robust biofilm assay for quantification and high throughput screening applications.

J Microbiol Methods 2019 Apr 28;159:179-185. Epub 2019 Feb 28.

US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Ft. Detrick, Frederick, MD 21702, USA. Electronic address:

Bacterial biofilms are populations of bacteria within a self-produced adherent extracellular matrix that are notoriously resistant to treatment. Existing methods for biofilm quantification are often limited in their dynamic range of detection (signal-to-background), throughput, and require modifications to the protocol depending on the bacterial species. To address these limitations, a broad utility, high-throughput (HTP) method was required. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.02.018DOI Listing
April 2019
4 Reads

Staphylococcus aureus and methicillin resistance detection directly from pediatric samples using PCR assays with differential cycle threshold values for corroboration of methicillin resistance.

J Microbiol Methods 2019 Apr 28;159:167-173. Epub 2019 Feb 28.

Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital and The Ohio State University, Columbus, OH, United States of America. Electronic address:

Staphylococcus aureus is a major human pathogen, causing a variety of nosocomial and community-acquired infections. While S. aureus usually grows well, there are situations where it cannot be isolated in culture, such as patients who have received prior antimicrobial therapy. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.01.009DOI Listing
April 2019
1 Read

Protective effects of oral immunization with formalin-inactivated whole-cell Citrobacter rodentium on Citrobacter rodentium infection in mice.

J Microbiol Methods 2019 Apr 25;159:62-68. Epub 2019 Feb 25.

Department of Pharmacy, Laboratory of Microbiology and Immunology, Gifu Pharmaceutical University, Gifu 501-1196, Japan. Electronic address:

Evaluation of the efficacy of vaccine candidates that prevent enteropathogenic and enterohemorrhagic Escherichia coli (EPEC/EHEC) infection in mouse models is difficult due to their limited pathogenicity in mice. Citrobacter rodentium, a murine pathogenic bacterium that shares its infection strategy and virulence genes with EPEC/EHEC, has been used as a model pathogen to develop novel vaccine strategies or platforms for these bacteria. However, there are few reports on the comparative effectiveness of novel vaccine platforms as no C. Read More

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S01677012193002
Publisher Site
http://dx.doi.org/10.1016/j.mimet.2019.02.016DOI Listing
April 2019
10 Reads
2.026 Impact Factor

Rapid and sensitive detection of Mycoplasma hyopneumoniae by recombinase polymerase amplification assay.

J Microbiol Methods 2019 Apr 23;159:56-61. Epub 2019 Feb 23.

College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China. Electronic address:

Mycoplasma hyopneumoniae is the etiological agent of swine enzootic pneumonia, which is associated with high economic losses in swine production worldwide. In this study, recombinase polymerase amplification assays using real-time fluorescence detection (real-time RPA) and lateral flow strip detection (LFS RPA) were developed to detect M. hyopneumoniae based on the conserved region of the mhp165 gene. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.02.015DOI Listing
April 2019
1 Read

Settling velocity and size distribution measurement of anaerobic granular sludge using microscopic image analysis.

J Microbiol Methods 2019 Apr 22;159:81-90. Epub 2019 Feb 22.

Department of Process, Energy and Environmental Technology, University of South-Eastern Norway, Kjølnes ring 56, NO 3918 Porsgrunn, Norway.

Settling velocity and size distribution of anaerobic granular sludge samples were studied using microscopic image analysis and settling column experiments. Five granule samples were considered in this study. Three samples were collected at the Top, Middle and Bottom sections of a lab scale upflow anaerobic sludge bed reactor (UASB). Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.02.013DOI Listing
April 2019
1 Read

Hydroxyapatite powder cake filtration reduces false positives associated with halophilic bacteria when evaluating Escherichia coli in seawater using Colilert-18.

J Microbiol Methods 2019 Apr 22;159:69-74. Epub 2019 Feb 22.

Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima, Japan. Electronic address:

Escherichia coli is an important fecal indicator bacterium that is used to evaluate the microbiological quality of water. The Colilert-18 (Quanti-Tray/2000) is a widely used, rapid, and simple quantitative method for detecting E. coli in drinking water, bathing water, and wastewater. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.02.012DOI Listing

Bio-functionalization of phytogenic Ag and ZnO nanobactericides onto cellulose films for bactericidal activity against multiple drug resistant pathogens.

J Microbiol Methods 2019 Apr 20;159:42-50. Epub 2019 Feb 20.

School of Petroleum and Natural Gas Engineering, Siberian Federal University, Russia.

The present study describes the synthesis of silver and zinc oxide nanobactericides from the phytogenic source Bupleurum aureum. The synthesized nanobactericides were characterized and evaluated for bio-functionalization onto bacterial cellulose membrane which was synthesized by Komagataeibacterxylinus B-12068 culture strain. The synthesis of nanobacterides were initially confirmed using UV-Visible spectroscopy which indicated localized surface resonance (LSPR) peaks at 415 nm for silver nanobactericides and 280 nm for zinc nanobactericides. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.mimet.2019.02.009DOI Listing
April 2019
4 Reads