https://bjm.ui.ac.ir/ Journal of Microbial Biology en daily 1 Sat, 21 Mar 2026 00:00:00 +0330 Sat, 21 Mar 2026 00:00:00 +0330 https://bjm.ui.ac.ir/article_30546.html https://bjm.ui.ac.ir/article_29921.html The cultivation of flowers and ornamental plants in greenhouses plays a significant role in the country’s economy through income generation and exportation. Bacterial pathogens, particularly leaf spot-causing species, can lead to severe damage, resulting in complete yield loss. Plants of the Araceae family are highly susceptible to these pathogens, yet research on this issue remains limited. Sampling was carried out on Araceae plants exhibiting leaf spot symptoms in various commercial greenhouses. Infected samples were cultured on nutrient agar medium, and 20 bacterial strains were isolated, purified, and preserved for pathogenicity and identification assays. Pathogenicity tests were performed on susceptible hosts, such as Epipremnum aureum (Pothos), Aglaonema treubii, and Syngonium podophyllum, which confirmed the virulence of selected strains. For identification, phenotypic characterizations such as fluorescent pigment production on King's B medium, LOPAT tests (Levan production, Oxidase activity, Potato soft rot, Arginine dihydrolase activity, and Tobacco hypersensitivity), carbon and energy utilization patterns, and sequencing of the 16S rRNA gene and housekeeping genes rpoD and recA were examined. Phenotypic and molecular data showed that the tested strains belonged to Pseudomonas aeruginosa. Based on the available literature, this is the first report of P. aeruginosa pathogenicity on plants from the Araceae family in Iran. https://bjm.ui.ac.ir/article_30214.html Anaerobic digestion is a microbial process that is widely used for the treatment of organic waste. Anaerobic digesters are considered an efficient method for waste management and renewable energy production. In this study, the communities of bacteria and archaea in the anaerobic digester of the Isfahan municipal solid waste treatment facility were investigated using the 16S rRNA gene next-generation sequencing technique. The main objective of this study was to identify and evaluate the most significant bacteria that play a key role in biogas production. The results of this study demonstrated that the microbial community in the anaerobic digester of the Isfahan region was mainly composed of two phyla: Bacteroidota (44.7%) and Firmicutes (30.5%), which together accounted for 75.2% of the total microbial population. Furthermore, the phyla Proteobacteria (9%), Cloacimonadota (5.6%), Patescibacteria (5.6%), and Actinobacteriota (4.5%) were present in significant proportions. At the genus level, uncharacterized genera, such as DMER64 and LNR_A2-18, were identified as dominant groups. In contrast, the presence of key functional genera, including syntrophic bacteria such as Syntrophomonas and Pelotomaculum, which play a crucial role in degrading long-chain fatty acids, along with hydrogenotrophic methanogens such as Methanobrevibacter, indicated the existence of an efficient metabolic network within this system. By identifying the microbial community and key functional groups, this study provides insights into the metabolic capacity of the digester. These findings can serve as a foundation for future studies investigating the direct relationship between these microbial communities and digester performance indicators, such as the methane production rate, and for proposing practical strategies for process optimization. https://bjm.ui.ac.ir/article_30316.html Mycoplasma agalactiae is the primary etiological agent of contagious agalactia in small ruminants, a disease that has been reported in several countries, including Iran. The microorganism's ability to persist in chronic infections within herds results in substantial economic losses in the dairy industry. Recent advances in bioinformatics tools for macromolecular analysis, combined with the availability of the complete genome sequence of M. agalactiae, have enabled the systematic evaluation of diagnostically relevant epitopes and the rational design of novel constructs for diagnostic applications. The objective of the present study was to identify and evaluate epitopes with diagnostic potential and to design a multi-epitope protein suitable for use in diagnostic assays. The open reading frames (ORFs) of M. agalactiae were extracted using bioinformatics approaches. These ORFs were subsequently screened based on cellular localization, species specificity, toxicity, allergenicity, immunogenicity, and membrane-associated features to select appropriate candidate proteins for B-cell epitope prediction. The most promising epitopes were then employed in the design of a diagnostic multi-epitope protein. In silico analyses were performed to evaluate its structural and physicochemical properties, solubility, and interaction with the host MHC class II receptor. The results demonstrated that the bioinformatics screening process led to the selection of 5 ORFs and, ultimately, 7 B-cell epitopes exhibiting high immunogenicity, non-toxic and non-allergenic, and suitable specificity for M. agalactiae. Furthermore, the designed multi-epitope protein exhibited favorable structural stability, adequate solubility, and strong predicted interactions with the MHC class II receptor of goat immune cells. Overall, these findings suggest that the epitopes have significant potential for use in diagnostic assays and represent promising candidates for subsequent experimental validation of M. agalactiae infection. https://bjm.ui.ac.ir/article_30373.html Introduction: At present, antibiotic resistance is recognized as one of the major global threats to human health. The clinical importance of Acinetobacter baumannii is due to its ability to acquire and transmit antibiotic resistance factors. Resistance genes, such as class D β-lactamases (oxacillinases), enable A. baumannii to resist the effects of several antibiotic families. The aim of this study was to investigate the antibiotic resistance pattern and estimate the prevalence of the resistance genes blaOXA-23 and blaOXA-51 in A. baumannii isolates obtained from hospitalized patients in a hospital in Tehran Province. Materials and Methods: In this study, 60 A. baumannii isolates were collected from hospitalized patients in a teaching hospital in Tehran Province in 2024. Following biochemical tests for final bacterial identification, the antibiotic susceptibility of isolates against 12 antibiotics was determined using the agar disk diffusion method. Colistin susceptibility was also evaluated using the disk diffusion method. Then, the prevalence of antibiotic resistance genes blaOXA-23 and blaOXA-51 was assessed by PCR. Results: In this study, among 60 isolates, the highest observed susceptibility was to colistin with 3.3% resistance, while the highest resistance (100%) was to imipenem, cefepime, cefotaxime, piperacillin–tazobactam, and ciprofloxacin. The prevalence of blaOXA-23 and blaOXA-51 was 81.6% and 100%, respectively. Conclusion: The increase in antibiotic resistance and widespread prevalence of resistance genes have caused serious concerns. Effective infection control and prevention of the spread of drug-resistant bacteria require precise drug prescription management and timely identification of resistant isolates. https://bjm.ui.ac.ir/article_30361.html Nowadays, the development of new antimicrobial agents to replace antibiotics, especially biological compounds, is of great interest. In this study, the synthesis of nanoliposomes loaded with clove essential oil and their use as antibacterial and antifungal agent were investigated. For this purpose, liposomes were synthesized using the ethanol injection method with lecithin as a precursor in the presence of clove essential oil. Their physicochemical properties were characterized using transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), dynamic light scattering (DLS) and zetasizer analysis. Then, their antimicrobial effects were evaluated against Escherichia coli and Staphylococcus aureus bacteria, as well as Aspergillus niger, Aspergillus terreus and Aspergillus flavus fungi. Nanoliposomes loaded with clove essential oil showed high colloidal stability, with a zeta potential of -58.5 and no sedimentation was observed even after 6 months. TEM imaging showed that the nanoparticles had a hemispherical and homogeneous shape with a size range of 100-200 nm. Nanoliposomes showed high biocompatibility, with 73.8% and 81.3% of human fibroblast cells remaining viable after incubation with 200 μg/mL of the initial and clove essential oil-loaded nanoliposomes, respectively. Although nanoliposomes loaded with clove essential oil showed limited antibacterial effect against S. aureus and E. coli strains, they showed a potent antifungal effect on A. niger, A. terreus and A. flavus, with complete growth inhibition of fungal mycelia at concentrations of 2, 2, and 1 mg/mL, respectively. Based on the results, clove essential oil-loaded nanoliposomes can be a suitable antifungal agent for food and pharmaceutical applications. https://bjm.ui.ac.ir/article_30438.html Biodeterioration is irreversible damage caused by microorganisms or their metabolites to historical monuments, and fungi are considered important factors in this deterioration. In this regard, the use of new, effective, and low-risk antifungal agents, such as biosynthesized nanoparticles and plant essential oils, is of interest. The aim of this study was to investigate and compare the antifungal activity of silver nanoparticles synthesized using an aqueous extract of green walnut shells and lavender essential oil against six species of biodeteriorative fungi isolated from Iran cultural heritage. The antifungal activity was evaluated using two methods: diffusion in agar and determination of minimum inhibitory concentration and minimum lethal concentration. The results showed that silver nanoparticles at a concentration of 1 mg/mL were effective against a wide range of fungi, whereas lavender essential oil had favorable activity at high concentrations (50 and 100%). Based on the microtiter plate method, nanoparticles with MIC values ​​between 0.125 and 1 mg/mL and strong bactericidal properties against fungi such as Aspergillus niger, Aspergillus flavus, and Penicillium polonicum showed their superiority. In contrast, the essential oil exhibited no measurable fungicidal properties against the three fungi. According to the results, the biosynthesized silver nanoparticles are very efficient and promising option, and lavender essential oil can be considered an alternative or complementary natural agent for controlling the biodeterioration of cultural heritage, depending on the conservation conditions and the concentration used. Furthermore, determining the final decision for the application of these compounds requires additional studies on the materials used in historical monuments. https://bjm.ui.ac.ir/article_30363.html Astaxanthin is a xanthophyll carotenoid with potent antioxidant activity that has attracted substantial attention due to its wide pharmaceutical, nutritional, and industrial applications. It is also utilized as a natural and safe pigment in food product and aquaculture feed. In the cosmetic industry, astaxanthin is recognized for its anti-aging and photoprotective properties. Recently, marine thraustochytrids have emerged as promising cell factories for eco-efficient and large-scale biosynthesis of astaxanthin and total carotenoids, providing a sustainable alternative to traditional chemical synthesis. In this study, the cultivation conditions of Thraustochytrium sp. 3F, a marine protist isolated from mangrove leaf litter along the southern coast of Iran, were optimized to enhance carotenoid biosynthesis, particularly astaxanthin. A Taguchi L9 orthogonal array design was applied to evaluate the effects of glucose and yeast extract concentration, seawater proportion, and agitation speed on biomass growth and carotenoid accumulation. Cultivation conditions significantly influenced both biomass formation and carotenoid yields. Based on Taguchi analysis, an optimal set of cultivation parameters, comprising 10 g/L glucose, 3 g/L yeast extract, 20 % (v/v) seawater, and 170 rpm was predicted and experimentally validated, resulting in balanced biomass production and substantial carotenoid accumulation. Time-course analysis indicated that carotenoid and astaxanthin biosynthesis primarily occurred during the stationary phase of biomass growth, accompanied by depletion of glucose and nitrogen sources. These findings highlight the importance of fine-tuning carbon, nitrogen, and salinity inputs to optimize biomass growth and secondary metabolite production that demonstrates the potential of Thraustochytrium sp. 3F as a sustainable natural source of carotenoids. https://bjm.ui.ac.ir/article_30362.html OprD purine serve as a specific entry channel for drugs such as carbapenems in the outer membrane of Pseudomonas aeruginosa. Probiotics can play a role in inhibiting carbapenems resistance through efflux pumps by regulating the expression of OprD. This study aimed to investigate the effect of Lactobacillus casei on the expression of the oprD gene in clinical isolates of carbapenem-resistant P. aeruginosa. Bacteria were isolated and identified biochemically from clinical samples in Isfahan, and the carbapenem-resistant pattern was studied. The effect of L. casei and its cell-free culture supernatant (CFS) in De Man, Rogosa, and Sharpe (MRS) culture medium was investigated on oprD gene expression in the strains (one-way analysis of variance). A total of 37 P. aeruginosa strains were isolated, of which 54% were obtained from female patients and 46% from male patients. The highest number of strains (29.8%) was isolated from the age group of 21 to 30 years, and the lowest number (5.4%) was isolated from the age group of 51 to 60 years. The majority of strains were isolated from wounds (32.4%), and the lowest number was isolated from blood (19%). All strains produced biofilms, of which 10 (27%), 12 (32.4%), and 12 strains (32.4%) formed weak, moderate, and strong biofilms, respectively. The highest resistance was to the antibiotic imipenem (43.2%). All strains carrying the oprD gene exhibited resistance to the antimicrobial effects of the probiotic L. casei and its supernatant. However, the expression of the oprD gene was 67% and 36% of control after treatment with the probiotic and its CSF, respectively. Given the key role of the OprD porin in antibiotic-resistant strains of P. aeruginosa, inhibition of OprD production by L. casei and its supernatant is of particular preventive and therapeutic importance by controlling resistance to antibiotics in these strains. https://bjm.ui.ac.ir/article_30514.html Along with the growth in industrial activity, particularly due to the exploitation of easily processable metal resources, there comes a concern about a gradual decrease in these metal deposits. Consequently, the development of environmentally friendly technologies capable of extracting metals from complex and refractory sources has gained significant importance. Biohydrometallurgy is recognized as a green and sustainable technology that relies on iron-oxidizing microorganisms to facilitate metal dissolution. These microorganisms contribute to the leaching process through the production of ferric iron, which act as an effective and low-cost oxidizing agent. In this study, the individual and interactive effects of the operational parameters, pulp density, time, and bacterial inoculum, on ferric iron production in the copper bioleaching from the Kal-e-Kafi ore using uranium-resistant Acidithiobacillus ferrooxidans strain THA3 were investigated. The experiments were designed using a central composite design within the framework of response surface methodology. The results indicated that increasing the time from 2 to 21 days led to a decrease in ferric concentration from 1695.86mg/L to 135.36mg/L. Similarly, an increase in pulp density from 5% to 15% resulted in a reduction of ferric production from 1590.86mg/L to 838.34mg/L. On the other hand, when the bacterial inoculum was increased from 5% to 14.7%, there were increases in ferric production from 520.89mg/L to 1269mg/L. The proposed statistical model demonstrated satisfactory predictive performance, with a P-value=0.0022 and R²=0.93. The key innovation of this work is the combination of efficient bacterial strains with a central composite design to model and simultaneously analyze the influences of the most important operational factors for ferric iron production. The statistically efficient method of this work has been effective in reducing trial and error to a considerable extent for optimizing operational factors to move forward with innovations in the aspect of native bacterial strains for bioleaching on a larger scale. https://bjm.ui.ac.ir/article_30561.html Endophytic fungi are diverse microorganisms that colonize plant tissues symbiotically without causing visible disease symptoms. To identify and evaluate endophytic fungi associated with corn(Zea mays L.), samples were collected from different plant organs during 2023 and 2024 in maize fields of Nahavand County, Iran. Following surface sterilization, endophytic fungi were isolated and identified based on morphological characteristics and molecular markers, including ITS and TEF1-α gene regions.Morphological and molecular analyses revealed that the maize endophytic fungi comprised seven species: Acremonium sclerotigenum, Alternaria tellustris, Aspergillus fumigatus, Aspergillus terreus, Fusarium equiseti, Fusarium verticillioides, and Chaetomium globosum. Greenhouse experiments evaluating plant growth–promoting potential showed that most isolates had a significant positive effect (P < 0.05) on maize growth parameters. The strongest growth-promoting effects were observed for Chaetomium globosum and Fusarium equiseti. In contrast, Fusarium verticillioides significantly reduced growth indices and exhibited pathogenic behavior.A review of the available literature indicated that A. sclerotigenum, A. tellustris, A. fumigatus, A. terreus, F. equiseti, and C. globosum are reported here for the first time as endophytes of maize in Iran. Moreover, to the best of our knowledge, there are no previous reports of A. tellustris and A. terreus as endophytic fungi associated with maize worldwide. Therefore, the present study may represent the first report of these two species as maize endophytes. Overall, the findings demonstrate the considerable functional diversity of maize endophytic fungi and highlight the potential of selected isolates for application in sustainable agriculture as plant growth-promoting microorganisms. https://bjm.ui.ac.ir/article_30613.html Fortified foods are developed for public health purposes and as carriers for functional bioactive compounds. This study investigated the activity of anticancer lipopeptides (LP) in homogenized milk and evaluated the properties of LP-fortified milk powder. Our results showed that LP activity decreased with increasing milk fat content. The addition of LP to homogenized milk resulted in only minor or non-significant changes in protein content, moisture content, bulk density, tapped density, Carr index (CI), Hausner ratio (HR) of milk powders as well as pH, and particle size of the rehydrated milk powders. However, a significant color difference and reduced solubility were observed in fortified samples compared with the non-fortified controls. Despite the reduced activity of LP in milk—particularly in fat-containing milk—measurable bioactivity was retained. Importantly, since the only negative effect of LP was on solubility, LP can be added to milk powder without major loss of quality. Although the activity of bacterial LP has previously been studied in non-homogenized milk, this is the first report evaluating LP activity in homogenized milk. https://bjm.ui.ac.ir/article_30627.html Pseudomonas aeruginosa is an opportunistic pathogen with a remarkable capacity to adapt to environmental stresses and antibiotic exposure. The combined effects of osmotic stress and fluoroquinolones on the reorganization of oxidative stress responses, particularly in multidrug resistant strains, remain incompletely understood. The present study aimed to investigate phenotypic, enzymatic, protein-level alterations in the antioxidant defense system of P. aeruginosa under combined osmotic and fluoroquinolone stress conditions. Three clinical MDR strains and one reference strain were exposed to ciprofloxacin, norfloxacin, and ofloxacin. Fluoroquinolones were applied at sub-inhibitory concentrations corresponding to one-quarter and one-half of the minimum inhibitory concentration , while osmotic stress was induced using 0.3 M and 0.5 M sodium chloride. Changes in MIC, phenotypic antibiotic susceptibility, bacterial growth, antioxidant enzyme activities including superoxide dismutase , catalase and glutathione peroxidase as well as the expression levels of OxyR, KatA, and SodB proteins, were evaluated. The results demonstrated that the combination of osmotic stress and sub-inhibitory concentrations of fluoroquinolones led to increased minimum inhibitory concentrations, reduced phenotypic susceptibility, and the induction of responses associated with adaptive antibiotic tolerance in multidrug-resistant strains.These conditions were accompanied by a relative reduction in bacterial growth and significant increases in antioxidant enzyme activities and the levels of the investigated proteins. The most pronounced changes were observed in MDR strains exposed to 0.5 M osmotic stress, whereas the reference strain exhibited more limited responses. The findings indicate that osmotic stress enhances antibiotic tolerance in P. aeruginosa through the upregulation of OxyR-associated oxidative defense components and the strengthening of the cellular antioxidant system. These findings are more appropriately interpreted within the framework of stress adaptive tolerance and do not provide direct evidence for the development of stable genetic antibiotic resistance. Such adaptive responses may contribute to the survival, persistence, and ecological fitness of multidrug-resistant strains in clinical environments https://bjm.ui.ac.ir/article_30636.html Introduction: The gradual decline in T-CD4+ cell counts following HIV infection leads to impaired immune function and serves as a primary determinant of the clinical course in HIV-infected patients. Antiretroviral therapy increases CD4+ lymphocyte levels, thereby enhancing immunity and reducing opportunistic infections and mortality. This study aimed to investigate the effect of three-drug antiretroviral regimens on CD4+ cell counts in HIV-infected patients in Khorramabad city. Materials and Methods: In this observational cohort study, data from 242 HIV-infected patients receiving either NNRTI-based (n=181) or INSTI-based (n=61) regimens were analyzed. CD4+ cell counts were measured at baseline and at 6 months, 1, 2, 3, and 4 years post-treatment initiation. Generalized Estimating Equations (GEE) models were used to evaluate longitudinal changes in absolute CD4+ counts, and an independent t-test was performed to compare the mean change from baseline between groups. Results: The INSTI-based group had a significantly lower baseline CD4+ count compared to the NNRTI-based group (331 vs. 452 cells/μL). The mean increase in CD4+ count from baseline was significantly greater in the INSTI-based group (406 cells/μL) compared to the NNRTI-based group (299 cells/μL) (P=0.002). However, GEE analysis demonstrated that patients on the NNRTI-based regimen maintained significantly higher absolute CD4+ counts throughout follow-up compared to the INSTI-based regimen (P<0.001), which likely reflects their higher baseline values. Conclusion: Both regimens were associated with improvements in CD4+ cell counts. The INSTI-based regimen showed a greater mean increase from baseline, while the NNRTI-based regimen maintained higher absolute CD4+ levels over time. Due to the observational design, substantial baseline imbalances between groups, and small sample size in the INSTI group during long-term follow-up, no causal claims of superiority can be made for either regimen. These hypothesis-generating findings require confirmation through randomized controlled trials with balanced baseline characteristics.