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Journal of Microbiological Methods

Kwabena O Duedu, Christopher E French
Monitoring bacteria growth is an important technique required for many applications such as testing bacteria against compounds (e.g. drugs), evaluating bacteria composition in the environment (e.g. sewage and wastewater or food suspensions) and testing engineered bacteria for various functions (e.g. cellulose degradation). Traditionally, rapid estimation of bacterial growth is performed using spectrophotometric measurement at 600nm (OD600) but this estimation does not differentiate live and dead cells or other debris...
February 16, 2017: Journal of Microbiological Methods
Yuan-Shan Wang, Qi-Wei Hu, Xing-Chang Zheng, Jian-Fen Zhang, Yu-Guo Zheng
A spectrophotometric screening method for avermectin oxidizing microbes by determination of 4″-oxo-avermectin was established based on the reaction between 4″-oxo-avermectin and 2,4-dinitrophenylhydrazine (DNPH). Combined with a gradient HPLC assay, microorganisms capable of regioselectively oxidizing avermectin to 4″-oxo-avermectin were successfully obtained by this method.
February 16, 2017: Journal of Microbiological Methods
Annette Blaich, Reno Frei, Carine Castellano, Christine Kiessling, Angelika Geschke, Katharina M Rentsch, Adrian Egli
A novel immunoassay for Clostridium difficile glutamate dehydrogenase (GDH) and toxin A&B (LIAISON, DiaSorin) was compared to another GDH assay (Alere), PCR and toxigenic culture. The GDH-DiaSorin is slightly more sensitive than the GDH-Alere. Sensitivity of the Toxin-Diasorin test is in accordance to the sensitivity of other immunoassays in literature.
February 10, 2017: Journal of Microbiological Methods
João Carlos Gomes-Neto, Sara Mantz, Kyler Held, Rohita Sinha, Rafael R Segura Munoz, Robert Schmaltz, Andrew K Benson, Jens Walter, Amanda E Ramer-Tait
Changes in the gastrointestinal microbial community are frequently associated with chronic diseases such as Inflammatory Bowel Diseases. However, understanding the relationship of any individual taxon within the community to host physiology is made complex due to the diversity and individuality of the gut microbiota. Defined microbial communities such as the Altered Schaedler Flora (ASF) help alleviate the challenges of a diverse microbiota by allowing one to interrogate the relationship between individual bacterial species and host responses...
February 9, 2017: Journal of Microbiological Methods
Jing-Zhuang Zhao, Li-Ming Xu, Miao Liu, Yong-Sheng Cao, Scott E LaPatra, Jia-Sheng Yin, Hong-Bai Liu, Tong-Yan Lu
BACKGROUND: The development of oral vaccines using yeast surface display technology is an area of intensive study in vaccine development, but the protein level displayed on yeast surfaces is not currently high enough to obtain a robust immune response. METHODS: To address this issue, we established an efficient and simple method of increasing the level of displayed protein on the yeast cell surface. We used the single chain variable fragment (scFv) of an antibody against the infectious hematopoietic necrosis virus isolate Sn1203 as a target display protein...
February 7, 2017: Journal of Microbiological Methods
Jun Ren, Haram Lee, Seung Min Yoo, Myeong-Sang Yu, Hansoo Park, Dokyun Na
DNA transformation that delivers plasmid DNAs into bacterial cells is fundamental in genetic manipulation to engineer and study bacteria. Developed transformation methods to date are optimized to specific bacterial species for high efficiency. Thus, there is always a demand for simple and species-independent transformation methods. We herein describe the development of a chemico-physical transformation method that combines a rubidium chloride (RbCl)-based chemical method and sepiolite-based physical method, and report its use for the simple and efficient delivery of DNA into various bacterial species...
February 7, 2017: Journal of Microbiological Methods
Hyunmin Koo, Joseph A Hakim, Mickie L Powell, Ranjit Kumar, Peter G Eipers, Casey D Morrow, Michael Crowley, Elliot J Lefkowitz, Stephen A Watts, Asim K Bej
In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine...
February 3, 2017: Journal of Microbiological Methods
Macarena Varas, Alonso Fariña, Francisco Díaz-Pascual, Javiera Ortíz-Severín, Andrés E Marcoleta, Miguel L Allende, Carlos A Santiviago, Francisco P Chávez
The zebrafish model has been used to determine the role of vertebrate innate immunity during bacterial infections. Here, we compare the in vivo immune response induced by GFP-tagged Salmonella Typhimurium inoculated by immersion and microinjection in transgenic zebrafish larvae. Our novel infection protocols in zebrafish allow live-cell imaging of Salmonella colonization.
February 1, 2017: Journal of Microbiological Methods
Owen W Duckworth, Dawn S Markarian, Dorothy L Parker, James M Harrington
Our knowledge of the biological and environmental reactivity of siderophores is limited by the difficulty and cost of obtaining reasonable quantities by purification or synthesis. In this note, we describe a modified procedure for the low-cost, mg-scale purification of pyoverdin-type siderophores using a dual-flash chromatography (reverse-phase absorption and size exclusion) approach.
February 1, 2017: Journal of Microbiological Methods
Bethan M Jones, Adam B Kustka
Advances in sequencing technologies continue to provide unprecedented opportunities to characterize microbial communities. For example, the Pacific Biosciences Single Molecule Real-Time (SMRT) platform has emerged as a unique approach harnessing DNA polymerase activity to sequence template molecules, enabling long reads at low costs. With the aim to simultaneously classify and enumerate in situ microbial populations, we developed a quantitative SMRT (qSMRT) approach that involves the addition of exogenous standards to quantify ribosomal amplicons derived from environmental samples...
February 1, 2017: Journal of Microbiological Methods
István Weyda, Lei Yang, Jesper Vang, Birgitte K Ahring, Mette Lübeck, Peter S Lübeck
In recent years, versatile genetic tools have been developed and applied to a number of filamentous fungi of industrial importance. However, the existing techniques have limitations when it comes to achieve the desired genetic modifications, especially for efficient gene targeting. In this study, we used Aspergillus carbonarius as a host strain due to its potential as a cell factory, and compared three gene targeting techniques by disrupting the ayg1 gene involved in the biosynthesis of conidial pigment in A...
February 1, 2017: Journal of Microbiological Methods
Christina Ferrato, Linda Chui, Robin King, Marie Louie
Salmonella is one of the most common enteric pathogens related to foodborne illness. Alberta's Provincial Laboratory for Public Health (ProvLab) provides Outbreak and Surveillance support by performing serotyping. The Check&Trace Salmonella™ (CTS) assay (Check-Points, Netherlands), a commercial DNA microarray system, can determine the serotype designation of a Salmonella isolate with automated interpretation. Here we evaluate 1028 Salmonella isolates of human clinical or environmental sources in Alberta, Canada with the CTS assay...
February 1, 2017: Journal of Microbiological Methods
Mark Fisher, Tania Dolby, Shireen Surtie, Gaironesa Omar, Nchimunya Hapeela, Debby Basu, Abby DeWalt, David Kelso, Mark Nicol, Sally McFall
The quality and quantity of sputum collected has an important impact on the laboratory diagnosis of pulmonary TB. We conducted a pilot study to assess a new collection cups for the collection of sputum for the diagnosis of pulmonary tuberculosis. The pilot study utilized the standard collection cup in South Africa demonstrating a mean collection volume of 2.86±2.36SDml for 198 samples; 19% of the specimens contained <1ml and 12% contained >5ml. We designed and tested two novel sputum cups with a narrow bottom section and clear minimum and maximum markings to allow patients and clinicians to know whether sufficient sputum volume has been produced...
January 31, 2017: Journal of Microbiological Methods
Elisabeth Eschlbeck, Ulrich Kulozik
Contact angle measurement of microorganisms is often described in literature, either to investigate their hydrophobic characteristic or the adhesion behavior of cells. However, in some key aspects the preparation methods differ. Thus, it is difficult to compare results and to choose a procedure for repetition of measurements. The aim of this paper is to point out some critical points during microorganism film preparation that can alter the resulting contact angles. Depending on the moisturizing medium and equilibration time, contact angles differ significantly...
January 27, 2017: Journal of Microbiological Methods
Vladimira Hinić, Ivo Amrein, Sabrina Stammler, Judith Heckendorn, Dominik Meinel, Reno Frei, Adrian Egli
We evaluated RAPIDEC® CARBA NP, Neo-Rapid CARB, chromID® CARBA SMART (CARB/OXA), Brilliance™ CRE/ESBL, ChromArt CRE and BBL™ CHROMagar™ CPE for the detection of carbapenemase-producing bacteria. The analytical sensitivity of RAPIDEC® CARBA NP was better than that of Neo-Rapid CARB. A combination of carbapenemase and ESBL screening plates could be advantageous.
January 25, 2017: Journal of Microbiological Methods
Shizuo Kayama, Hiroki Ohge, Motoyuki Sugai
Stealth-type carbapenem-resistant Enterobacteriaceae that are resistant to almost all β-lactams except imipenem is emerging in Japan. This resistance is mediated by specific variants of the metallo-β-lactamases (blaIMP-6 or blaIMP-34) that differs by one amino acid from the common variant blaIMP-1. We developed an amplification refractory mutation system (ARMS) PCR assay enabling rapid, sequence independent, identification of these variants.
January 24, 2017: Journal of Microbiological Methods
Natalie Lorenz, Jacelyn M S Loh, Nicole J Moreland, Thomas Proft
The lack of standardised protocols for the assessment of functional antibodies has hindered Streptococcus pyogenes research and the development of vaccines. A robust, high throughput opsonophagocytic bactericidal assay to determine protective antibodies in human and rabbit serum has been developed that utilises bioluminescence as a rapid read out.
January 21, 2017: Journal of Microbiological Methods
Dobryan M Tracz, Andrea D Tyler, Ian Cunningham, Kym S Antonation, Cindi R Corbett
A high-quality custom database of MALDI-TOF mass spectral profiles was developed with the goal of improving clinical diagnostic identification of high-consequence bacterial pathogens. A biomarker discovery method is presented for identifying and evaluating MALDI-TOF MS spectra to potentially differentiate biothreat bacteria from less-pathogenic near-neighbour species.
January 18, 2017: Journal of Microbiological Methods
Eloy Gonzales-Gustavson, Yexenia Cárdenas-Youngs, Miquel Calvo, Marcelle Figueira Marques da Silva, Ayalkibet Hundesa, Inmaculada Amorós, Yolanda Moreno, Laura Moreno-Mesonero, Rosa Rosell, Llilianne Ganges, Rosa Araujo, Rosina Girones
In this study, the use of skimmed milk flocculation (SMF) to simultaneously concentrate viruses, bacteria and protozoa was evaluated. We selected strains of faecal indicator bacteria and pathogens, such as Escherichia coli and Helicobacter pylori. The viruses selected were adenovirus (HAdV 35), rotavirus (RoV SA-11), the bacteriophage MS2 and bovine viral diarrhoea virus (BVDV). The protozoa tested were Acanthamoeba, Giardia and Cryptosporidium. The mean recoveries with q(RT)PCR were 66% (HAdV 35), 24% (MS2), 28% (RoV SA-11), 15% (BVDV), 60% (E...
January 16, 2017: Journal of Microbiological Methods
C Dard, S Bailly, T Drouet, H Fricker-Hidalgo, M P Brenier-Pinchart, H Pelloux
BACKGROUND: Serological investigation of Toxoplasma gondii can answer many questions about toxoplasmosis in human pathology. Along these lines, studies on serum storage in biobanks need to be performed especially in terms of determining the impact of storage on relevance of sera analysis after freezing. This study assessed the impact of long-term sera storage on the stability of anti-Toxoplasma immunoglobulins. MATERIAL AND METHODS: The stability of anti-Toxoplasma IgG and IgM was studied in 244 and 242 sera respectively, stored at -20°C from one month to ten years...
January 16, 2017: Journal of Microbiological Methods
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