Eurasian Journal of Applied Biotechnology

Metagenomic Analysis of the Sputum Microbial Community in Pneumonia Patients Using Targeted NGS Sequencing

2024-12-31T09:57:21+05:00

This study presents the results of analyzing the sputum microbiome of 46 patients diagnosed with pneumonia using targeted NGS sequencing of the 16S rRNA gene.

As a result of the study, 114 species of bacteria belonging to 47 genera and 29 families were identified. Based on the obtained data, potential pathogens associated with the development of pneumonia were identified, and a quantitative analysis of their prevalence among patients was conducted. At the species level, Streptococcus pneumoniae was detected in 26 samples (56.5%). Acinetobacter baumannii was found in 10 samples (21.7%). Klebsiella pneumoniae was detected in 9 samples (19.5%), and Pseudomonas aeruginosa was found in 17.4% of samples. Other species that may be involved in the development of pneumonia included Escherichia coli, Haemophilus influenzae, and Staphylococcus aureus in 15.2%, 10.87%, and 8.7% of samples, respectively. Additionally, Neisseria meningitidis was detected in 5 samples (10.8%), and Stenotrophomonas maltophilia was found in two samples.

The obtained results can contribute to a deeper understanding of microbiome communities associated with pneumonia and enrich knowledge about the microbiome of the upper respiratory tract. These data may be useful for developing new strategies for the diagnosis and treatment of pneumonia, as well as for optimizing preventive measures.

STUDY OF GENE EXPRESSION IN RESPONSE TO SERIAL EXPOSURE TO MEROPENEM IN BACTEROIDES FRAGILIS

2025-01-28T10:52:16+05:00

Antibiotic resistance is a major global health concern, and inappropriate antibiotic use contributes significantly to the development of resistance in pathogens. Bacteroides fragilis, an anaerobic bacterium, is commonly treated with β-lactam antibiotics like meropenem. B. fragilis possesses various antibiotic resistance mechanisms, including enzymatic modification of antibiotics, efflux systems, and reduction of cell membrane permeability. The primary mechanism of carbapenem resistance in B. fragilis is linked to the production of a metallo-β-lactamase encoded by the cfiA gene. However, this gene is frequently inactive and requires activation by insertion elements.

The study aimed to explore the expression of specific genes in B. fragilis associated with different metabolic pathways in response to exposure to sub-inhibitory concentrations of meropenem. The study used B. fragilis strain BFR KZ01, obtained from a patient with appendicitis and peritonitis. Serial exposure to meropenem was conducted, and gene expression was analyzed using quantitative RT-PCR. Significant and long-lasting alterations in gene expression patterns were observed in B. fragilis following exposure to meropenem, even after removal of the antibiotic. Genes such as cfiA, oxyR, and Ddl showed heightened expression levels even after discontinuation of meropenem.

The study discussed the implications of gene expression changes induced by meropenem exposure, highlighting the role of oxidative stress response (oxyR), D-Ala-D-Ala ligase (Ddl), and carbapenemase (cfiA) genes in antibiotic resistance mechanisms. The study concluded that exposure to meropenem induced lasting alterations in gene expression in B. fragilis, contributing to antibiotic resistance. Understanding these mechanisms is crucial for developing strategies to combat antibiotic resistance.

MULTIOMICS TECHNOLOGIES IN THE STUDY OF THE PATHOGENESIS OF BRAIN ARTERIOVENOUS MALFORMATIONS

2025-02-18T12:16:39+05:00

Brain arteriovenous malformations (bAVMs) are abnormal vascular structures in which arteries directly connect to veins, bypassing the capillary network. Studying the pathogenesis of bAVMs is important for understanding the mechanisms of their occurrence and development, allowing the development of more effective diagnosis, treatment, and prevention methods. This review aims to collect and analyze data about genes, proteins, and metabolites that affect the pathogenesis of brain AVMs obtained using multi-omics technologies. The use of whole-exome sequencing, RNA-sequencing, TMT-MS, iTRAQ, UHPLC-MS allowed us to identify key genetic mutations, signaling pathways and mechanisms associated with the development of bAVMs. They include the KRAS gene in endothelial cells and the MAPK, Wnt and TGF-β pathways. The discovery of differentially expressed proteins and metabolites such as hydroxyproline, dihydrojasmonic acid, L-2-amino-4-methylenepentanedioic acid, piperettine, 20-hydroxy-PGF2a, 2,2,4,4-tetramethyl-6-(1-oxobutyl)-1,3,5-cyclohexanetrione, DL-tryptophan, 9-oxoODE, alpha-linolenic acid also offers new biomarkers for diagnosis and treatment. The data obtained through multi-omics approaches are critical for developing personalized treatment strategies and improving clinical management, with the ultimate goal of reducing morbidity and mortality associated with brain AVMs.

POLLEN VIABILITY AND GERMINATION RESPONSES OF CASHEW (ANACARDIUM OCCIDENTALE L.) UNDER IN VITRO CONDITIONS

2025-04-01T11:37:06+05:00

Cashew (Anacardium occidentale L.) is a vital cash crop in tropical and subtropical regions, valued for its economic significance and nutritional benefits. Pollen is crucial in plant reproduction, with viability and germination determining fertilization success. However, variations in pollen viability among cashew accessions remain understudied. Understanding genetic variability in pollen fertility will aid in selecting superior pollen donors, enhance cross-breeding efficiency, and supports the development of improved cashew cultivars for sustainable production. This study investigated pollen viability and optimized in vitro germination conditions for 18 cashew clones. The research aimed to determine the efficacy of pollen from different clones and establish optimal protocols for successful in vitro pollen germination. The findings are expected to contribute to improved cashew breeding strategies and enhanced genetic resource management. At the Cocoa Research Institute of Nigeria (CRIN), Ibadan, pollen viability was evaluated via aniline blue-lactophenol staining. In vitro pollen germination was assessed using modified Brewbaker and Kwack's (1964) media, with observations recorded after a 24-hour incubation. Pollen tube lengths were subsequently measured using ImageJ, and the resultant data were subjected to ANOVA analysis, followed by Duncan's Multiple Range Test for mean separation. Pollen viability analysis revealed significant inter-accession variation, from 56.3% to 97.2%. Accessions EU202 (97.2%) and CR102 (96.1%) demonstrated superior viability, while Brazilian Medium (56.3%) and India Madras (59.5%) exhibited comparatively poor performance. Germination rates also varied considerably, with select clones achieving complete germination in Media 2. Statistical analysis confirmed genotype-specific influences on pollen germination in response to differing media conditions.

MOLECULAR PHYLOGENETIC ANALYSIS OF THE RANUNCULACEAE FAMILY PLANTS BASED ON DNA BARCODING IN THE KARAGANDA REGION FLORA

2025-04-01T11:41:09+05:00

The Ranunculaceae family is one of the most diverse groups of angiosperms, including species of high ecological and pharmacological significance. In this work, a molecular phylogenetic analysis of 19 Ranunculaceae species from the flora of the Karaganda region, including the rare and protected species Anemone patens, Adonis volgensis and Adonis vernalis, was carried out. The rbcL, matK, trnH-psbA, and ITS markers were used for the study, and phylogenetic trees were constructed using the maximum likelihood (ML) method with bootstrap support.

The results showed that the ITS marker had the highest discriminatory ability at the species level (17.64%), while rbcL, matK, and trnH-psbA provided reliable classification at the tribe and genus level. Phylogenetic analysis confirmed a clear separation of the subfamilies Thalictroideae and Ranunculoideae with high bootstrap support (0.87 and 0.90, respectively). Within the Ranunculoideae, the tribes Ranunculeae, Anemoneae, Delphinieae, and Adonideae formed stable clades (>0.84). Anemone patens was clearly distinguished at the species level (0.97).

The data obtained clarify the taxonomic relationships of Ranunculaceae in the region and emphasize the need for the combined use of multiple DNA markers. For the first time, this study provides molecular data on rare species of Ranunculaceae in Kazakhstan, which is important for their monitoring and conservation.

BIOTECHNOLOGICAL WASTEWATER TREATMENT USING STRAINS OF MICROORGANISMS

2025-03-26T09:39:42+05:00

The article presents the results of biotechnological wastewater treatment using strains of fat-destructive microorganisms. The urgency of the work is the shortage of fresh water and pollution of reservoirs with sewage, which are global problems. The purpose of the research is to study and use microbial strains for biotechnological wastewater treatment. The use of biological methods of modern biotechnology is typical for combating environmental pollution. Biological wastewater treatment using microorganisms is a promising direction in solving these problems. This contributes to solving the following application issues: using anaerobic digestion, disposal of solid household waste and the solid phase of wastewater; biological purification of wastewater and natural waters from organic and inorganic compounds; microbial restoration of contaminated soils capable of neutralizing heavy metals in wastewater sediments; composting, biological oxidation of plant waste (leaf litter, straw, etc.); for the purification of polluted air, the study of biologically active sorbent material. The following methods were applied: sampling of water from the stabilization pond of Astana sewage treatment plants, microbiological analysis; determination of COD, BOD₅, chromaticity, pH, turbidity, suspended solids, ammonium and phosphates, study of the conditions of cultivation of strains of microorganisms in order to increase lipase yield, conducting pilot tests of biological products on the basis of sewage facilities in Astana. Based on the results of the studies, strains of microorganisms with high lipolytic activity were selected, and a biological product based on these strains was also studied.