journal
https://read.qxmd.com/read/39009285/microbial-dna-sample-preservation-and-possible-artifacts-for-field-based-research-in-remote-tropical-peatlands
#1
JOURNAL ARTICLE
Mark C Reynolds, Hinsby Cadillo-Quiroz
Surveying bacterial and archaeal microbial communities in host and environmental studies requires the collection and storage of samples. Many studies are conducted in distant locations challenging these prerequisites. The use of preserving buffers is an important alternative when lacking access to cryopreservation, however, its effectivity for samples with challenging chemistry or samples that provide opportunities for fast bacterial or archaeal growth upon exposure to an aerobic environment, like peat samples, requires methodological assessment...
July 13, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/39004285/escherichia-coli-grown-in-inexpensive-conical-flat-bottom-polypropylene-tubes-produce-a-high-level-of-puc-vector
#2
JOURNAL ARTICLE
Mayra Marquez, Qian Chen, Silvia Cachaco, Jun Yang, Hongyan Sui, Tomozumi Imamichi
The pUC-derived plasmid yield from E. coli using polypropylene tubes (PP) was compared among round and conical tubes. The yield from cells grown in a cheaper conical-PP with flat-bottom was 1.5-fold higher (p < 0.001) than other PP. The use of the conical-PP can save research budgets in the current inflationary environment.
July 12, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38996925/gene-function-characterization-in-aspergillus-niger-using-a-dual-resistance-marker-transformation-system-mediated-by-agrobacterium-tumefaciens
#3
JOURNAL ARTICLE
Hanh-Dung Thai, Minh Thi Trinh, Loc Thi Binh Xuan Do, Thu-Hang Le, Duc-Thanh Nguyen, Que Thi Tran, Van-Khanh Tong Tran, Linh Thi Dam Mai, Duc-Ngoc Pham, Diep Hong Le, Tao Xuan Vu, Van-Tuan Tran
Aspergillus niger is a well-known workhorse for the industrial production of enzymes and organic acids. This fungus can also cause postharvest diseases in fruits. Although Agrobacterium tumefaciens-mediated transformation (ATMT) based on antibiotic resistance markers has been effectively exploited for inspecting functions of target genes in wild-type fungi, it still needs to be further improved in A. niger. In the present study, we re-examined the ATMT in the wild-type A. niger strains using the hygromycin resistance marker and introduced the nourseothricin resistance gene as a new selection marker for this fungus...
July 10, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38977080/comparison-of-the-diversity-of-anaerobic-cultured-gut-bacterial-communities-on-different-culture-media-using-16s-rdna-sequencing
#4
JOURNAL ARTICLE
Anne Sophie Lichtenegger, Sara Posadas-Cantera, Mohamed Tarek Badr, Georg Häcker
The gut microbiome is a dense and diverse community of different microorganisms that deeply influence human physiology and that have important interactions with pathogens. For the correct antibiotic treatment of infections, with its twin goals of effective inhibition of the pathogen and limitation of collateral damage to the microbiome, the identification of infectious organisms is key. Microbiological culturing is still the mainstay of pathogen identification, and anaerobic species are among the most demanding bacterial communities to culture...
July 6, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38969181/inhibitors-of-lamp-used-to-detect-tenacibaculum-sp-strain-pbs-1-associated-with-black-spot-shell-disease-in-akoya-pearl-oysters-and-additives-to-reduce-the-effect-of-the-inhibitors
#5
JOURNAL ARTICLE
Akihiro Sakatoku, Takaya Suzuki, Kaito Hatano, Makoto Seki, Daisuke Tanaka, Shogo Nakamura, Nobuo Suzuki, Tadashi Isshiki
Black-spot shell disease is an unresolved disease that decreases pearl quality and threatens pearl oyster survival. In previous studies, the bacterium Tenacibaculum sp. strain Pbs-1 was isolated from diseased Akoya pearl oysters Pinctada fucata, and a rapid, specific, and sensitive loop-mediated isothermal amplification (LAMP) assay for detecting this pathogen was established. This technology has considerable potential for routine diagnosis of strain Pbs-1 in oyster hatcheries and/or pearl farms; therefore, it is vital to identify substances in environmental samples that might inhibit LAMP and to find additives that can reduce the inhibition...
July 3, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38960329/interrelationship-among-substrate-utilization-metabolic-productions-and-housekeeping-related-gene-expression-levels-in-mortierella-alpine-cbs-754-68
#6
JOURNAL ARTICLE
Hamid Reza Samadlouie, Shahrokh Gharanjik, Abdolah Vatandost, Side Maryam Ghasemi Tarvigi
The impacts of Magnesium oxide nanoparticles (MgONPs) on the expression of 10 potential housekeeping genes of Mortierella alpine were assayed. Actin emerged as the good candidate when Mortierella alpine entered the death phase subsequent to the growth phase while Dihydropteridine reductase and 28 s were identified as suitable candidates when Mortierella alpine remained in the growth phase.
July 1, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38960328/long-term-storage-stability-of-pgl-i-coated-elisa-plates-for-anti-mycobacterium-leprae-igm-detection
#7
JOURNAL ARTICLE
Matheus Bernardes Torres Fogaça, Djairo Pastor Saavedra, Maria Beatris de Jesus Sousa, Nicolle Kathlen Alves Belém de Oliveira, Mariane Martins de Araújo Stefani, Samira Buhrer-Sékula
The assessment of ELISA plates coated with phenolic glycolipid-I/PGL-I revealed excellent stability during eight years of storage at room temperature, promoting consistent IgM antibody detection in multibacillary leprosy patients. These stable, standardized plates can significantly contribute to efficient leprosy serology research and support its widespread distribution and use in endemic countries.
July 1, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38955305/alternative-protocol-leading-to-rapid-identification-of-actinomycetes-isolated-from-algerian-desertic-soil-by-maldi-tof-mass-spectrometry
#8
JOURNAL ARTICLE
Sarra Benhasna, Allaoueddine Boudemagh
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is the first-line method for the rapid identification of most cultured microorganisms. As for Streptomyces strains, MALDI-TOF MS identification is complicated by the characteristic incrustation of colonies in agar and the strong cell wall of Actinomycetes cells requiring the use of alternative protein extraction protocols. In this study, we developed a specific protocol to overcome these difficulties for the MALDI-TOF MS identification of Actinomycetes made on solid medium...
June 30, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38945305/colorimetric-strategies-applicable-for-loop-mediated-isothermal-amplification
#9
REVIEW
Syaidatul Akmal Saifuddin, Roslina Rashid, Nurin Jazlina Nor Azmi, Suharni Mohamad
In recent years, loop-mediated isothermal amplification (LAMP) has gained popularity for detecting various pathogen-specific genes due to its superior sensitivity and specificity compared to conventional polymerase chain reaction (PCR). The simplicity and flexibility of naked-eye detection of the amplicon make LAMP an ideal rapid and straightforward diagnostic tool, especially in resource-limited laboratories. Colorimetric detection is one of the simplest and most straightforward among all detection methods...
June 28, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38945304/applicability-of-non-invasive-and-live-cell-holotomographic-imaging-on-fungi
#10
JOURNAL ARTICLE
Susanne Fritsche, Felix Fronek, Robert L Mach, Matthias G Steiger
The ability to acquire three-dimensional (3D) information of cellular structures without the need for fluorescent tags or staining makes holotomographic imaging a powerful tool in cellular biology. It provides valuable insights by measuring the refractive index (RI), an optical parameter describing the phase delay of light that passes through the living cell. Here, we demonstrate holotomographic imaging on industrial relevant ascomycete fungi and study their development and morphogenesis. This includes conidial germination, subcellular dynamics, and cytoplasmic flow during hyphal growth in Aspergillus niger...
June 28, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38944284/quantification-of-early-biofilm-growth-in-microtiter-plates-through-a-novel-image-analysis-software
#11
JOURNAL ARTICLE
Anderson J Castilla-Sedano, José Zapana-García, Erika Valdivia-Del Águila, Pierre G Padilla-Huamantinco, Daniel G Guerra
Given the significant impact of biofilms on human health and material corrosion, research in this field urgently needs more accessible techniques to facilitate the testing of new control agents and general understanding of biofilm biology. Microtiter plates offer a convenient format for standardized evaluations, including high-throughput assays of alternative treatments and molecular modulators. This study introduces a novel Biofilm Analysis Software (BAS) for quantifying biofilms from microtiter plate images...
June 27, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38942122/identification-of-sepsis-causing-bacteria-from-whole-blood-without-culture-using-primers-with-no-cross-reactivity-to-human-dna
#12
JOURNAL ARTICLE
Yasuyuki Kawai, Akifumi Nakayama, Hidetada Fukushima
Sepsis is a major health concern globally, and identification of the causative organism usually takes several days. Furthermore, molecular amplification using whole blood from patients with sepsis remains challenging because of primer cross-reactivity with human DNA, which can delay appropriate clinical intervention. To address these concerns, we designed primers that could reduce cross-reactivity. By evaluating these primers against human DNA, we confirmed that the cross-reactivity observed with conventional primers was notably absent...
June 26, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38936432/comparison-of-plate-counting-with-flow-cytometry-using-four-different-fluorescent-dye-techniques-for-the-enumeration-of-bacillus-cereus-in-milk
#13
JOURNAL ARTICLE
Ben T Somerton, Brooke L Morgan
This study aimed to compare the performance of flow cytometry methods with plate counting for the enumeration of bacteria, using Bacillus cereus as a model organism. It was found that the cFDA-propidium iodide, CellROX™ Green-propidium iodide, and DiOC2 dye techniques had similar accuracy to plate counting, while the SYTO 24-propidium iodide dye technique was not as accurate. The four dye techniques had comparable precision to plate counting, with the CellROX™ Green-propidium iodide dye having the greatest precision...
June 25, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38936431/identification-of-genus-deinococcus-strains-by-pcr-detection-using-the-gyrb-gene-and-its-extension-to-bacteria-domain
#14
JOURNAL ARTICLE
Hyeonsik Yoon, Hyun Hee Lee, Hee Seong Noh, Sung-Jae Lee
In radiation-resistant bacteria belonging to the genus Deinococcus, transposition events of insertion sequences (IS elements) leading to phenotypic changes from a reddish color to white were detected following exposure to gamma irradiation and hydrogen peroxide treatment. This change resulted from the integration of IS elements into the phytoene desaturase gene, a key enzyme in the carotenoid biosynthesis pathway. To facilitate species identification and distinguish among Deinococcus strains, the gyrB gene encoding the B subunit of DNA gyrase was utilized...
June 25, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38936430/mica-legionella-an-innovative-and-rapid-method-for-enumeration-of-legionella-pneumophila-in-french-sanitary-water
#15
JOURNAL ARTICLE
M Passot Fanny, Peslier Sabine, Dukan Sam, Dumont Audrey
A new innovative method, MICA Legionella, allows for the automatic enumeration of Legionella pneumophila in domestic water samples in 2 days, with a detection limit of 2 CFU per test portion. Here we show that it gives equivalent results to those obtained by the French standard method NF T90-431 in 7 to 15 days.
June 25, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38925440/improved-productivity-and-dye-removal-performance-of-trametes-versicolor-pellets-using-rice-husk-as-a-co-substrate
#16
JOURNAL ARTICLE
Juan Antonio Gutiérrez-Quirós, Alonso Coronado-Marchena, Diego Villegas-Solano, Sebastián Rodríguez-Saravia, Víctor Castro-Gutiérrez, Carlos E Rodríguez-Rodríguez
Pellet production represents a critical step for several processes requiring fungal biomass, nevertheless, its optimization is seldom reported. The use of finely ground rice husk as a microcarrier and co-substrate permitted a marked increase (≈ 2.7×) in the productivity of fungal pellet production using Trametes versicolor compared to traditional production systems. The pellets show similar structure and smaller size compared to typical sole-mycelium pellets, as well as comparable laccase activity...
June 24, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38889842/lc-hrms-based-metabolomics-and-lipidomics-analyses-of-a-novel-probiotic-akkermansia-muciniphila-in-response-to-different-nutritional-stimulations
#17
JOURNAL ARTICLE
Huan Zhang, Shiqi Zhang, Li Chen, Rui Xu, Jiangjiang Zhu
The mucin-degrading gut commensal Akkermansia muciniphila (A. muciniphila) negatively correlates with various diseases, including metabolic disorders, neurodegenerative disorders, and cancers, through interaction with host receptors by versatile molecules. Still, their exact metabolic capability within the nutrient-rich environment (such as in the human gut) is not fully characterized. Therefore, in the present study, we investigated the comprehensive metabolome and lipidome of A. muciniphila after supplementation of four major gut microbial nutrients known to be present in the gut environment: mucin, inorganic salts, bile salts, and short-chain fatty acids (SCFAs)...
June 16, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38880389/adaptation-and-validation-of-a-light-microscope-for-use-in-energy-insecure-settings-a-proof-of-concept-study
#18
JOURNAL ARTICLE
Nina Bühler, Diana Velten, Philipp Jung, Sophie E Müller, Sören L Becker, Sakib Burza, Sophie Schneitler
Microscopy as a basic diagnostic method cannot be used everywhere globally. Validity of slide reading was tested on torch-modified microscopes. Experienced microscopists handled the modification without prior standard-adaptation. In contrast, microscopist-trainees required more detailed instructions to get acquainted with this new technique. The overall results encourage further, setting-specific validation.
June 14, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38880388/integrated-decentralized-blood-culture-incubation-a-step-towards-a-24-7-microbiology-service
#19
JOURNAL ARTICLE
Frieder Schaumburg, Franziska Schuler, Manfred Fobker, Jutta Esser
To have an impact on the mortality of bloodstream infections, microbiological diagnostics of blood cultures (BC) should provide first results within 12 h. Here, we show how a decentralized BC incubation connected to the central BC incubators via a browser-based application significantly reduces turnaround times.
June 14, 2024: Journal of Microbiological Methods
https://read.qxmd.com/read/38871227/comparison-of-available-methods-to-evaluate-cefiderocol-susceptibility-in-acinetobacter-spp
#20
JOURNAL ARTICLE
Fernando Pasteran, Olivia Wong, Vyanka Mezcord, Christina Lopez, Nardin Georgeos, Venjaminne Fua, Alonzo Ozuna, Dema Ramlaoui, Cristian Sánchez, Paulina Marchetti, Alejandra Corso, Marcelo E Tolmasky, Robert A Bonomo, María Soledad Ramirez
Recently, considerable uncertainty has arisen concerning the appropriate susceptibility testing for cefiderocol in gram-negative bacilli, particularly in the context of its application to Acinetobacter spp. The optimal method for assessing the susceptibility levels of Acinetobacter spp. to cefiderocol remains a subject of debate due to substantial disparities observed in the values obtained through various testing procedures. This study employed four minimum inhibitory concentration (MIC) methodologies and the disk diffusion to assess the susceptibility of twenty-seven carbapenem resistant (CR)-Acinetobacter strains to cefiderocol...
June 11, 2024: Journal of Microbiological Methods
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