نشریه زیست شناسی میکروبی
پیاپی 52 (Winter 2025)

The rising demand for non-dairy probiotic products is driven by factors such as vegetarian diets, concerns about high cholesterol in milk and lactose intolerance. This research investigated the presence of Lactobacillus plantarum in apple, pear, and quince vinegar using molecular and biochemical methods. Isolated microorganisms were evaluated for probiotic potential based on their ability to grow at different bile salt concentrations and pH levels. Biochemical characterization included sugar fermentation profile, presence of extracellular enzymes and antibiotic susceptibility testing. Molecular identification of strains employed specific L. plantarum recA (Recombinase A) primer targeting the recA gene, which encodes a multifunctional protein essential for bacterial cells. Among the 24 microorganisms isolated from apple, pear, and quince vinegar, nine strains displayed a specific band with the L. plantarum recA primers, confirming their identity. These Gram-positive bacteria were positive for lipase and protease activity but negative for catalase, amylase, gelatinase, and oxidase. The L. plantarum strains fermented all tested sugars except xylose and demonstrated tolerance to acidic and bile-containing environments, high temperatures, and salt concentrations.  While resistant to eight of the 15 antibiotics tested, the bacteria showed relative sensitivity to three. Furthermore, they exhibited anti-proliferative effects on human HT-29 cancer cells, suggesting potential as anticancer agents. This study successfully isolated L. plantarum strains from apple, pear, and quince vinegar with promising probiotic and anticancer properties.

Gold mine operations release toxic arsenic and other heavy metals into the environment, which can be accumulated in water resources and the food chain. As microbial bioremediation has been a promising method for pollutant removal from contaminated sites, the identification of bacterial communities in arsenic-contaminated resources has recently been in focus. The bacterial communities of tailings dam effluent (TDE) of a gold mine in Iran were analyzed. The bacterial communities were examined using the next-generation sequencing method (Illumina platform) targeting the V3-V4 region of 16S rRNA genes. The 16S rRNA dataset from this study was compared with three arsenic-contaminated groundwater (GW) microbiomes from SRA databases, using the bioinformatics tool QIIME 2. Our findings revealed that the prevalent taxonomic groups observed in all of the samples belonged to Proteobacteria (8.06-45.49%), Bacteroidetes (1.85-50.32%), Firmicutes (1.00-6.2%) and Actinobacteria (0.86-5.09%). Metagenomic analyses showed that Algoriphagus, Rhodobacter, Anaerospora, Limnobacter, Halomonas and Yonghaparkia are the main bacterial genera in TDE. Despite the limited similarities in the prokaryotic community of the samples, the most of the retrieved genera of the TDE are unique and the native bacteria of Iran. Conclusions Long-term exposure to arsenic causes changes in bacterial abundance and richness. This resulted in natural selection and expression of the most compatible genes in existing condition. Although there are similarities in some microbial communities of ground waters, but it can be found some native microorganisms, which was adapted to the harsh environment of TDE.

Resistant Klebsiella pneumoniae to the latest solution (carbapenem antibiotics) distributed worldwide. The proliferation of carbapenemase genes among Klebsiella pneumoniae strains has led to their resistance to the carbapenem group. The aim of this study is to estimate antibiotic resistancepatterns and distribution of carbapenemase genes  of Klebsiella pneumoniea in Iran. PubMed, Scholar ,SID, and Iran civilica  databases were searched for the related articles that were published between 1999 and 2019. A total  of 225 articles were found, out of which 70 relevant articles were selected for complete evaluation. According to the results, the highest rates of drug resistance in Klebsiella pneumoniae were observed against aztreonam (58%), cephalosporins family (54%), and then SXT (52%). The incidence rate of resistance was 19% for carbapenems family (IMP, MER), 37% for aminoglycosides family (GM, AN) and 41% for quinolones family (FM, CIP). Among the genes encoding CRE during 2014–2019, OXA, KPC, NDM, VIM, IMP, and GES were found with a prevalence of 39%, 35%, 18%, 13%, 11%, and 3%, respectively. Conclusion Carbapenem resistance and the production of the metallo-beta-lactamase enzyme in K. pneumoniae are increasing. Due to the presence of carbapenemase-producing genes and the possibility of horizontal transfer of these genes to other bacteria, combined with changing the patterns of antibiotic use, more attention should be paid to the predisposing criteria for controlling nosocomial infections.

The alarming rate of Acinetobacter baumannii infections necessitates immediate attention to tackle this issue. The emergence of multidrug-resistant strains has greatly complicated the treatment, making it a challenging endeavour. This problem has been exacerbated by the COVID-19 pandemic, with higher mortality rates observed among COVID-19 patients infected with multidrug-resistant A. baumannii during treatment. Infections caused by A. baumannii result in a range of health complications, such as urinary tract infections, wound infections, bacteraemia, pneumonia, meningitis, heightened morbidity, and in severe cases, even mortality. The virulence factors and mechanisms of pathogenesis of A. baumannii are complex and still encompassing areas of ongoing investigation. Therefore, this review aims to provide a comprehensive overview of the current knowledge regarding key virulence factors, including the secretion of proteases, lipases, catalase, and motility, which contribute to the pathogenesis of A. baumannii infection. Additionally, the review explores the organism’s resistance and persistence strategy, primarily attributed to its remarkable ability to form biofilms on various surfaces, rendering complete eradication from medical devices an arduous task. Overall, this review emphasizes the importance of A. baumannii as a significant pathogen in healthcare settings and underscores the need for continued research to develop more effective strategies for the prevention and treatment of A. baumannii infections.

Due to the emergence of antibiotic-resistant clinical strains of Pseudomonas aeruginosa, there is an urgent need for a suitable and affordable alternative that is a non-antibiotic antimicrobial agent and creates a new generation of infectious disease treatment. In this regard, this study aims to investigate the antimicrobial potential of ellagic acid against clinical strains of P. aeruginosa under physiological growth conditions and oxidative stress. P. aeruginosa isolates from clinical samples were identified by biochemical tests and their antibiotic susceptibility was tested by disc diffusion method. The inhibitory effect of ellagic acid against multiple drug resistance isolates was investigated by disc diffusion and broth microdilution methods and its effect on bacterial survival under physiological conditions and oxidative stress was investigated by Time-Kill assay. The effect of ellagic acid on rpoS gene expression was also investigated by the Real time-PCR method. In this study, ellagic acid showed an inhibitory effect on the growth of all MDR isolates of P. aeruginosa tested. The minimum inhibitory concentration (MIC) of ellagic acid in 5 isolates varied between 250 and 2000 µg/ml. Treatment with ellagic acid rendered drug-resistant clinical strains of P. aeruginosa sensitive to oxidative stress. It reduced the survival of P. aeruginosa, while treatment with 1/4MIC concentration of ellagic acid resulted in a 4.7-fold decrease in log10 CFU/mL compared to the control. In the present study, treatment with a sub-inhibitory concentration of ellagic acid also caused a significant decrease in rpoS gene expression (P˂0.05). The results of this study indicate that ellagic acid inhibits the growth of P. aeruginosa and increases its sensitivity to oxidative stress conditions. Conducting in vivo studies may clarify the possibility of its clinical application in the control of infections caused by resistant isolates of P. aeruginosa.

Although Zataria multiflora essential oil (ZEO) has good antimicrobial properties like other EOs, it cannot be used in food systems and commercial products due to its high volatility and low water solubility, and its bioactive compounds can be easily degraded under the influence of environmental factors. In this case, their nanoemulsification may be an efficient and practical approach to overcome this problem. In addition, such delivery systems can improve the stability, bioactivity and quality properties of antimicrobial EOs in food systems. The optimized formulation, prepared using a low energy production method, containing 4% w/w ZEO and 12% w/w mixed surfactant (SDS+Tween 80), produced a transparent and stable nanoemulsion for 90 days with a mean particle diameter of 120.1 nm. The antibacterial activity of pure ZEO (PZEO) and its nanoemulsions (ZEON) against the tested strain was evaluated using solid diffusion, vapour phase and broth assays. Minimum inhibitory concentration (MIC) and bacteriostatic concentration (MBC), dynamic time-kill, anti-biofilm activity and morphological changes in Salmonella were determined. The strong antibacterial activity of PZEO and ZEON was demonstrated with MIC values of 2000 ppm and 4000 ppm, respectively. The killing kinetics study showed that there was a rapid and widespread decrease in CFU during the first 15 min of exposure to ZEON at MIC concentration. In addition, ZEON had significant anti-biofilm activity , reducing  82% of the one-day-old biofilm of S. typhimurium at the MIC concentration. The SEM micrographs taken at MIC showed significant morphological damage in the ZEON treated bacterial cells and no viability. The data presented, taking into account the optimal performance of antimicrobials against foodborne pathogens, can help in the rational design of delivery systems based on nanoemulsion of essential oils in the food industry.

The antibacterial and anticancer potential of silver nanoparticles (Ag-NPs) is promising for cancer treatment and fighting multidrug-resistant bacteria. This study introduces the first eco-friendly synthesis of Ag-NPs using a cell-free extract (CFE) of Chaetomium olivaceum strain B422 isolated from grapevine. In this study, ten fungal strains collected from grapevine trunks and twigs were purified and cultured on potato dextrose agar (PDA) at 25 °C (pH 5) under dark conditions for 7 to 14 days. Ag-NPs were synthesized using CFEs of the fungal strains and silver nitrate as precursor. The biosynthesis process was optimized by varying factors such as silver nitrate concentration, pH, temperature, agitation speed and incubation time using a one-factor-at-a-time approach. The synthesized Ag-NPs were characterized for various properties such as size, structure and stability using UV-Vis spectroscopy, field emission scanning electron microscopy (FESEM), dynamic light scattering (DLS), Raman spectroscopy and X-ray diffraction (XRD). Of the ten fungal strains studied, only strain B422, identified as C. olivaceum by phylogenetic analysis of DNA sequence data, successfully synthesized Ag-NPs by reduction of silver nitrate. This was confirmed by a color change to dark brown and a distinct UV-Vis absorption peak at 425 nm. Optimal conditions for biosynthesis were found to be 5 mM silver nitrate, pH 7, 35 °C, no shaking and an incubation period of 96-120 h. FE-SEM analysis revealed nanoparticles ranging in size from 2 to 92 nm, with an average size of 32 to 42 nm, while DLS analysis revealed a hydrodynamic size of 46.3 nm. Zeta potential measurements showed high stability (-23.5 mV). Raman spectroscopy identified functional groups associated with the Ag-NPs and XRD confirmed their crystalline structure. The sustainable synthesis of Ag-NPs using fungal CFE allows precise control of nanoparticle size and morphology, making it highly relevant for biomedical applications and a significant advancement in green nanotechnology for healthcare.