Journal of microbiological methods最新文献

The identification of key genes responsible for the colonization and infection of E. coli strains associated with diarrhea (DEC) has made significant progress. Unfortunately, for uropathogenic E. coli (UPEC) strains, there are currently no defined genes that contribute to the identification of strains associated with urinary tract infections. This paper presents data regarding genes associated with the virulence and adaptability of UPEC strains isolated from urinary tract infections (UTI), aiming to evaluate the possibility of identifying a molecular marker for this pathotype. We analyzed 166 E. coli strains (90 recovered from urine and 76 isolated from feces) characterized by serotyping, phylogenetic analysis, and PCR detection of fimH, iutA, fyuA, feoB, ompT, kguS and kguR, genes associated with the virulence and metabolism of UPEC. Herein, results showed a higher prevalence of kguS/kguR combination in strains isolated from persistent UTI (peUTI), which correlated with strains of classic UPEC serogroups, a higher virulence gene load, and inclusion in pathogenic phylogroups (B2 and D). The presence of the genes in strains isolated from feces showed that the kguS/kguR presence was minimal (14%), while the presence of kguR was almost inexistent (1%), contrary to kguS (39%). The results obtained suggest that the presence of the kguS/kguR pair encoding the homonymous two-component system (TCS) plays an important role in the adaptation and colonization of the urinary tract by E. coli strains that cause UTI. In conclusion, the combination of kguS/kguR could be used as a molecular marker to identify pathogenic strains with a high capacity for adaptation to the urinary environment.

In this study, we have reported production of a semi-dry fruit wine using Cape Gooseberry for the first time using very high gravity conditions at laboratory scale. Employing industrial strain Saccharomyces cerevisiae, the batch fermentation was carried out at room temperature in 1-l flasks in triplicates. The moisture content of fruit was calculated to be 80% after 24 days. The °Bx of raw fruit juice was found to be 4.9 and was raised to 25°Bx on addition of sucrose, the yeast assimilable nitrogen content of cape goose berry juice was calculated to be 280 mg N/L. Average fermentation time calculated based on cessation of bubbling and attainment of final °Bx of 3.8 ± 0.3 was found to be 21 days. The initial pH of raw juice was observed to be 4.51 ± 0.04 before fermentation, while post fermentation it was calculated to be 3.63 ± 0.03. The ethanol estimated using HPLC, GC-FID and refractometric analysis showed concentration of 13.29 ± 0.26, 13.15 ± 0.03 and 13.63 ± 0.374% respectively. The antioxidant activity of raw juice vs processed cape gooseberry wine was calculated to be 65.06% and 39.64% respectively, while it was estimated to be 53.86% in one-year-old preserved cape gooseberry wine sample. The titratable acidity and volatile acidity of wine was determined to be 6 g/L and 0.15 g/L respectively and was found to be well within the desired range. Our results provide a clear demonstration of feasibility of very high gravity fermentation for producing semi-dry Cape Gooseberry wine with moderate antioxidant preservation.

Phytophthora stem blight (PSB), caused by Phytophthora cajani, is a destructive disease of pigeonpea (Cajanus cajan L.) that can lead to complete crop loss under favorable conditions. Effective resistance breeding is constrained by the lack of reliable and reproducible screening methods. The present study aimed to standardize and compare artificial inoculation techniques for consistent induction of Phytophthora blight under controlled conditions. Ten inoculation methods targeting different infection pathways were evaluated in greenhouse pot experiments over two consecutive seasons (2023-24 and 2024-25) using susceptible (UPAS-120, ICP-7119, ICP-2376) and moderately resistant (KPBR-80-2-1, IPAC-79, IPAB-7-2-1-7) pigeonpea cultivars. Disease incidence was recorded to assess the efficiency and reproducibility of each technique. All methods successfully established infection; however, disease severity varied significantly among techniques and genotypes. The leaf-lamina inoculation method consistently produced the highest and most uniform disease incidence, recording 97.7% and 96.6% in the susceptible cultivar UPAS-120 and 83.3% and 86.6% in the moderately resistant cultivar KPBR-80-2-1 across the two seasons. Node inoculation emerged as the second most reliable method. The study identifies most efficient and quick, reproducible inoculation techniques that enable rapid and high-throughput resistance screening, providing a robust methodological framework to support pigeonpea breeding and Phytophthora blight management.

Pharmaceutical water is a crucial component in drug manufacturing, as its quality directly affects drug safety and efficacy. This study focuses on membrane biofouling in pharmaceutical water systems during downtime, revealing its unique formation mechanisms: abrupt decreases in flow rate, reduced dissolved oxygen, and nutrient accumulation collectively create favourable conditions for microbial colonization. Biofilm formation not only causes a decline in membrane flux and an increase in transmembrane pressure but may also release harmful substances, such as endotoxins, posing a severe threat to water quality. The study systematically reviews existing control technologies, encompassing conventional methods such as chemical cleaning and backflushing, as well as innovative approaches including electrochemical treatment and cold atmospheric pressure plasma (CAP) technology. Furthermore, this paper prospectively explores future research directions, such as the development of green antifouling agents and the application of intelligent monitoring technologies, providing a scientific basis and technical support for achieving water safety and sustainable development in the pharmaceutical industry.

In this study, we modified the Zymo Research Quick-RNA™ Fungal/Bacterial Miniprep Kit for P. aeruginosa biofilms by incorporating a lysozyme pre-treatment step. The modified protocol markedly increased RNA yield with consistent purity compared to the manufacturer's protocols, meeting commonly accepted quality criteria for downstream molecular analyses. This modification offers a simple, reproducible improvement.

This article completes the preliminary work published in the Journal of Fluorescence (PMID: 38109032) that demonstrated both external surface and seemingly internal binding of DNA aptamers to Cyclospora cayetanensis oocysts by disclosing the actual aptamer DNA sequences for public scrutiny and use in experimentation. These aptamer DNA sequences were previously held as trade secrets due to their perceived potential commercial value, but given the inability to generate much commercial interest in the aptamers for diagnostics applications, the author has decided to reveal the sequences so that other researchers may further study aptamer binding to the oocysts especially with regard to the unexpected internal binding. The author also shows that these aptamers appear useful in binding magnetic microbeads to the oocysts in buffer. Thus, perhaps the aptamers can be validated for magnetic separation of oocysts in more complex natural water or sewage samples as well. And finally, the public disclosure of these sequences could be applied to lateral flow test strip, Western blots and ELISA-like or other diagnostic assays. Both the refined and vetted list of highest affinity and most specific aptamer sequences against known Cyclospora cayetanensis proteins and whole oocysts as well as the comprehensive lists of thousands of aptamer sequences from next generation Illumina-based sequencing are disclosed.

Synthetic dyes are traditionally used for staining arbuscular mycorrhizal fungi (AMF) yet their toxicity, environmental persistence raise health and ecological concerns. Herein, we report turmeric and pomegranate derived natural dyes for visualizing AMF which offer user-safe, low-cost, environmentally benign alternatives to synthetic stains, while promoting sustainable research practices.

A novel method is described for the short to medium term storage of environmental bacteria up to six months. Fifty environmental bacteria were employed in this study, which had been previously isolated from green spaces. These organisms comprised of 14 genera (10 Gram negative and 4 Gram positive) [Arthrobacter, Bacillus, Buttiauxella, Carnobacterium, Citrobacter, Enterobacter, Lelliottia, Pectobacterium, Pseudomonas, Rahnella, Serratia, Sporosarcina, Stenotrophomonas, Yersinia] and 16 identified species. Organisms were inoculated onto fresh plates of Standard Plate Count (SPC) agar and incubated aerobically at 30 °C for 72 h. Following this, plates with growth were stacked in metal plate racks and wrapped in plastic with a large autoclave bag and sealed with a cable tie. Plates were stored at 5 °C in the dark for six months, after which they were removed and the colonies checked for viability. All isolates were able to be recovered through passaging onto fresh SPC plates. This method is simple, inexpensive, versatile and widely adaptable and requires minimum preparation/handling/processing, utilising a small laboratory footprint for refrigerator space. Adoption and employment of this simple storage system encourages the routine archiving of environmental isolates for future research purposes.

FastqOrienter is a Python tool that corrects inconsistent read orientations in Illumina paired-end metabarcoding reads using a primer-aware logic and IUPAC-compliant matching. In addition, it provides detailed diagnostics and actionable insights for discarded reads. It ensures data integrity for downstream pipelines like DADA2 and QIIME 2.