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_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 Introduction: Mycoplasma agalactiae is the primary etiological agent of contagious agalactia in small ruminants, a disease that has been reported in numerous countries, including Iran, and due to its ability to persist in chronic form of infection within herds, is responsible for substantial economic losses in the dairy industry. Recent advances in bioinformatics tools for macromolecular analysis, coupled 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. Material and method: For this purpose, 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. Results: The results demonstrated that the bioinformatics screening process led to the selection of 5 ORFs and, ultimately, 7 B-cell epitopes exhibiting high immunogenicity, lack of toxicity and allergenicity, and suitable specificity for M. agalactiae. Furthermore, the designed multi-epitope protein showed favorable structural stability, adequate solubility, and strong predicted interactions with the MHC class II receptor of goat immune cells. Discussion and conclusion: Overall, these findings suggest that the proposed epitopes possess significant potential for use in diagnostic assays and represent promising candidates for subsequent experimental validation aimed at the detection of M. agalactiae infection. https://bjm.ui.ac.ir/article_30361.html Nowadays, 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 an antibacterial and antifungal agent in MHA and PDA media,respectively were investigated. For this purpose, liposomes were synthesized by the ethanol injection method using lecithin as a precursor in the presence of clove essential oil, and their physicochemical properties were investigated by transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), dynamic light scattering (DLS) and zetasizer. Then, their antimicrobial effects were investigated on Escherichia coli and Staphylococcus aureus bacteria, and 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 as 73.8 and 81.3% of human fibroblast cells remained viable after incubation with 200 μg mL-1 of the initial and clove essential oil-loaded nanoliposomes, respectively. Although nanoliposomes loaded with clove essential oil showed limited antibacterial effect against Staphylococcus aureus and Escherichia coli strains, they showed a potent antifungal effect on A. niger, A. terreus and A. flavus, with the complete growth inhibition of fungal mycelia at concentrations of 2, 2, and 1 mg mL-1 (m/v), 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_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. The present study was aimed to investigate the effect of Lactobacillus casei on the expression of the oprD gene in clinical isolates of carbapenem-resistant Pseudomonas aeruginosa. Bacteria were isolated and identified biochemically from clinical samples in Isfahan, and the carbapenem-resistant pattern was studied. The effect of Lactobacillus casei and its cell-free culture supernatant (CSF) 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 Pseudomonas aeruginosa strains were isolated, of which 54% were obtained from female 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 highest number of strains was 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 of oprD gene carrying strains showed resistance to the antimicrobial effects of the probiotic Lactobacillus 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 purine in antibiotic-resistant strains of Pseudomonas aeruginosa, inhibition of OprD production by Lactobacillus 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_30363.html آستاگزانتین یک کاروتنوئید گزانتوفیل با فعالیت آنتی‌اکسیدانی قوی است که به دلیل کاربردهای گسترده دارویی، تغذیه‌ای و صنعتی، توجه زیادی را به خود جلب کرده است. این ترکیب همچنین به‌عنوان رنگدانه‌ای طبیعی و ایمن در صنایع غذایی و خوراک آبزیان استفاده می‌شود و در صنایع آرایشی به خاطر خواص ضدپیری و محافظت‌کننده در برابر نور شناخته شده است. اخیراً، ترائوستوکیتریدهای دریایی به‌عنوان کارخانه‌های سلولی امیدبخش برای سنتز اکولوژیکی و در مقیاس بزرگ آستاگزانتین و مجموع کاروتنوئیدها معرفی شده‌اند و جایگزینی پایدار برای سنتز شیمیایی سنتی فراهم می‌کنند. در این مطالعه، شرایط کشت Thraustochytrium sp. 3F، یک پروتیست دریایی جداسازی‌شده از برگ‌های مانگرو در سواحل جنوبی ایران، به منظور بهینه‌سازی بیوسنتز کاروتنوئیدها به‌ویژه آستاگزانتین، مورد بررسی قرار گرفت. از طراحی آرایه‌ی متعامد Taguchi L9 برای ارزیابی تأثیرات غلظت گلوکز و عصاره مخمر، نسبت آب دریا و سرعت هم‌زدن بر رشد زیست توده و تجمع کاروتنوئیدها استفاده شد. شرایط کشت تأثیر قابل‌توجهی بر هر دو پارامتر تولید زیست توده و عملکرد کاروتنوئیدها داشت. بر اساس تحلیل Taguchi، شرایط بهینه شامل ۱۰ گرم بر لیتر گلوکز، ۳ گرم بر لیتر عصاره مخمر، ۲۰٪ (v/v) آب دریا و سرعت هم‌زدن ۱۷۰ دور در دقیقه پیش‌بینی و به‌صورت تجربی تأیید شد، که منجر به تعادل در تولید زیست توده و تجمع قابل‌توجه کاروتنوئیدها گردید. تحلیل زمان‌محور نشان داد که بیوسنتز کاروتنوئیدها و آستاگزانتین عمدتاً در فاز سکون رشد زیست توده رخ می‌دهد و با کاهش منابع گلوکز و نیتروژن همراه است. این یافته‌ها اهمیت تنظیم دقیق ورودی‌های کربن، نیتروژن و شوری را برای بهینه‌سازی رشد بیوماس و تولید متابولیت‌های ثانویه نشان می‌دهند و پتانسیل Thraustochytrium sp. 3F را به‌عنوان منبع طبیعی پایدار کاروتنوئیدها برجسته می‌سازند.