Vietnam Journal of Biotechnology

Plant endophytes are an interesting group of microorganisms that colonize the internal tissues of living plants and do not cause any disease symptoms in the host plant. It exists in different parts of plants, such as roots, leaves, and stems, and significantly affects the formation of metabolic products in plants by promoting the accumulation of important secondary metabolites. The present study focused on analyzing the diversity and distribution of endophytic fungi related to different tissues from samples of the medicinal plant Dysosma difformis (Hemsl & E.H. Wilson) T.H. Wang collected in Ha Giang and Lai Chau, in which the isolates from roots were 27 strains (50.94%), 12 strains from stems (22.64%), and 14 strains from leaves (26.42%). Based on the isolates, we analyzed the fungal diversity through seven different diversity indices. The results showed that isolates’ diversity was similar to the endophytic fungal population in tissues of D. difformis distributed in different vegetation in Vietnam. Specifically, Shannon's index showed the highest diversity in roots (H′ = 2.673), followed by stems (H′ = 2.162) and leaves (H′ = 2,054). Similarly, species richness was highest in roots (Dmg = 4,551; Dmn = 3,079) and stem (Dmg = 4,024; Dmn = 3,175) and lowest in leaves (Dmg = 3.41; Dmn = 2,405). However, the Simpson diversity index showed that the endophytic fungal community was most abundance in leaves (1-D = 0.911), followed by stems (1-D = 0.897) and roots (1-D = 0.867). In addition, the Sorensen index of 0.615 shows the average similarity in species composition between the two sites, Ha Giang and Lai Chau. This is the first report on the diversity of endophytic fungi isolated from D. difformis, paving a potential way for screening endogenous fungal strains capable of producing important secondary compounds.

Salmonella infections, or salmonellosis, represent a significant threat to poultry health and the global poultry industry, leading to considerable economic losses and serving as a major source of foodborne illnesses in humans and animals. Identifying the specific strains present in local poultry farms is crucial for implementing targeted interventions, including the development of effective biosecurity measures, vaccination strategies, and treatment protocols to mitigate outbreaks. This study focuses on isolating and characterizing Salmonella strains associated with diarrhea in chickens and ducks in Hai Duong province, Vietnam. The Salmonella strains were initially isolated using a culture-based method, followed by identification and characterization through Matrix-Assisted Laser Desorption Ionization/Time of Flight (MALDI-TOF), PCR amplification of the invA gene, and 16S rRNA gene sequencing. As a result, 18 Salmonella isolates were obtained, all of which contained the invA gene, indicating its potential significance in Salmonella pathogenesis. Analysis of the 16S rRNA gene sequences confirmed that all isolates belonged to the species Salmonella enterica, a well-known causative agent of intestinal diseases in humans and animals. Furthermore, phylogenetic analysis revealed that all 18 isolates grouped with Salmonella enterica subsp. enterica strains from China and Korea, suggesting a close relationship with strains circulating in the broader Southeast Asian region. This regional similarity may be attributed to the movement of poultry and poultry products, facilitating the cross-border spread of Salmonella. Our findings underscore the importance of implementing robust biosafety measures throughout the poultry production chain to control the spread of Salmonella, thereby enhancing both animal and food safety.

Marek’s disease is a contagious avian viral disease that is caused by a Marek’s disease virus serotype 1 (MDV-1) or gallid herpesvirus 2 (GaHV-2), a member of the genus Alphaherpesvirus, family Herpesviridae. Up to now, the disease has caused significant losses to the chicken farming industry in many provinces and cities across the country. In this study, four MDV-1 (GaHV-2) strains causing the disease in Bac Ninh province during the 2019–2022 period were identified by multiplex Polymerase Chain Reaction (PCR). Subsequently, the segments of 1020 bp encoding 339 amino acids of Meq gene (Marek’s disease virus EcoRI fragment Q) from four samples were collected and sequenced. The rate of identity and homology between the four Vietnamese strains and other global strains ranged from 89.4% to 100% and 87.6% to 100%, respectively. These rates were higher between the four Vietnamese strains and MDV-1 Chinese strains, ranging from 99.2% to 100% and 98.2% to 100%, respectively. The molecular characterization of the Meq gene revealed that all four of the GaHV-2 strains infecting chickens in the Bac Ninh province belonged to the highly virulent group, with a low proline ratio in Meq protein (ranging from 20.59–21.18%), consisting of three PPPP motifs and three interrupted motifs that contain mutations at the second position of the proline rich region (PRR): PPPP>P (Q/A/R)PP. Overall, this study provides valuable information on molecular characteristics of MDV-1 strains in Bac Ninh province during the 2019–2022 period.

Carbapenem-resistant Pseudomonas aeruginosa belongs to the critical species of global priority pathogens, nevertheless, molecular mechanisms of such resistance in low- and middle-income countries are limited. In this context, we conducted a comparative genomic analysis between two clinical carbapenem-resistant P. aeruginosa strains VD641 and XP646 isolated from hospitals in Hanoi, Vietnam. The phenotypic-resistant profile revealed that both strains were resistant to at least 26 drugs belonging to 6 different antibiotic classes, and therefore they were identified as extensively drug-resistant bacteria. The chromosomal genome of strain VD641 was 7.1 Mb with GC a content of 65%, while the genome of XP646 consisted of an approximately 7.3 Mb with a GC content of 64.8%.  The two strains belong to sequence type 3151 (ST3151). Genomic comparative analysis revealed that VD641 possessed higher numbers of antimicrobial resistance genes compared to XP646 (35 and 26 genes, respectively). This data was in accordance with their antibiotic-susceptibility profiles. Notably, the strain VD641 acquired a multidrug-resistant gene region with 223 kb in length carrying 11 antibiotic-resistant genes. Strains VD641 and XP646 acquired a blaIMP-15 and blaKPC-2 carbapenem-resistant gene, respectively. Analysis of virulent protein-protein interaction networks revealed six gene clusters involving the pathogenicity of the ST3151. Finally, four plasmids found in P. aeruginosa XP646 (n=1) and VD641 (n=3) carried different ARGs genes. The draft genomes and plasmid sequences of P. aeruginosa VD641 and XP646 were submitted to GenBank under BioSample accessions SAMN39268202 and SAMN39268203, respectively. The findings in our study underline that genomic surveillance is essential for management of carbapenem resistance emergence in healthcare setting in Vietnam.

This study aimed to develop a raw material blending process and evaluate the sensory characteristics of an herbal tea mixture containing Cordyceps militaris in combination with pineapple (Ananas comosus), ginger (Zingiber officinale(Willd.)), lemongrass (Cymbopogon citratus), and chrysanthemum (Chrysanthemum indicum). The research showed no presence (negative) of harmful microorganisms and quantities that could affect consumers in two consecutive tests. The sterilization and raw material blending process met the food safety standards (TCVN). The sensory evaluation results from consumers identified two mixed herbal (NT2 and NT5) tea formulations that received the highest ratings (7.730 and 8.040 points, respectively) and they were significantly higher than the remaining formulations while being not significantly different from each other, indicated that researchers can select suitable raw materials and blending ratios for large-scale production.

Acute diarrhea is a common disease in children under 5 years old and can develop into persistent diarrhea, greatly affecting the children's health. Although advanced techniques had been used to diagnose and detect common pathogens in hospitals, however, 40% of cases are negative for the pathogens. In this study, to investigate dominant bacteria in stool samples of three persistent-diarrheal children with unidentified pathogenic agents, the V3 and V68 regions of the 16S rRNA gene were amplified from fecal bacterial metagenomic DNA, separated on DGGE gel, and the dominant DNA bands were sequenced. As a result, the V3 and V68 regions of bacteria in persistent diarrheal children were less diverse and different from the corresponding DNA bands of the indicator strains. Sequence analysis and similarity comparison of six DNA bands of V3 regions and seven DNA bands of V68 regions showed that two V3 sequences (of 160 bp) derived from two samples were novel and did not match any genes from the non-redundant database, but they shared 93.75% similarity to each other. The four V3 sequences left derived from all three samples were the most similar (94.53-100%) with the corresponding genes of Brevibacterium. Six of the seven V68 sequences derived from dominant DNA bands of all three samples were the most similar (from 99.4% to 100%) to the corresponding genes of referent strains belonging to the genus Enterococcus. In sample D3, a sequence of the V68 region possessed 100% identity to the E. faecalis ATCC 19433 strain. This is the first study report that Brevibacterium was the dominant bacteria in the gastrointestinal microflora of children with persistent diarrhea although the bacterial genus has been reported to cause dangerous diseases in humans with immunodeficiency. 

Gut bacteria comprise a complex bacterial community related to many functions in a host. The stability of gut bacteria plays important models in the health and immunology of a host. Many studies on intestine bacteria constructed via cultivation and Denaturation Gradient Gel Electrophoresis (DDGE) methods have proved a limited efficiency. In order to tackle these drawbacks, the next generation sequencing method was developed on 16S-rRNA-based sequences (Metabarcoding). The composition of bacterial communities was revealed based on the analysis of 16S rRNA sequences of intestine bacteria in Litopenaeus vannamei ponds in comparison with microbial communities in a Penaeus monodon pond and a muscle of shrimp. These results showed that the dominant phyla of intestine bacteria in Litopenaeus vannamei were Proteobacteria (49.3–57.4%), Firmicutes (15.6–34.4%) and Bacteroidetes (0.1–16.9%). Rhizobium(0.4%-26.1%), Vibrio(0–23.9%) and Spongiimonas(0–16,7%) were dominant genera in Litopenaeus vannamei gut. A higher proportion of Fusobacterium (10%), a shrimp pathogen group, was found in a disease shrimp pond (ST4) in comparison with a low growth shrimp pond (ST3) (0%) and a healthy shrimp pond (ST1) (0.6%). Vibrio was marked as shrimp pathogen genus accounted for 22.3% of total genera in ST4 in comparison with 2.4% in ST3 and 3.5% in ST1. Interestingly, a higher percentage of Vibrio rotiferianus (7.98%) was found in ST4 compared to ST3 (1%) and ST1 (0%). Fusobacterium and Vibrio will be the objects for the next experiments to discover shrimp pathogens specifically.

The group of proteins containing the VQ motif (named VQ proteins) is a family of plant-specific proteins with a FxxhVQxhTG conservative VQ-motif region. VQ proteins regulate many developmental processes, including responses to biotic and abiotic stresses, and seed development. The VQ9 protein has an interaction with the WRKY8 factor, when this interaction occurs, it causes a decrease in the DNA binding ability of WRKY8 to DNA, which plays a role in the regulation function of the plant to stress. Some mutations in the VQ9 gene increase salt tolerance in plants, suggesting that VQ9 acts antagonistically to regulate responses to salt conditions. This antagonism is consistent with an increase or decrease in the Na+/K+ ratio. Ipomoea aquatica is commonly grown and used as a vegetable in Southeast Asia. The research involved RNA extraction from I. aquatica leaves, followed by PCR sequencing to confirm the presence of the IaVQ9 gene. Subsequently, a specific guide RNA (gRNA) was designed using CRISPR-P ver.2.0 and inserted into the pRGEB31 vector, optimized for CRISPR/Cas9 applications. The gRNA-inserted vector was successfully transformed into E. coli DH10B and then into Agrobacterium tumefaciens EHA105, verified through colony PCR and restriction enzyme analysis. This process created a delivery system capable of editing the VQ9 gene in I. aquatica. This research represents a significant step towards improving crop resilience to salinity, addressing a critical challenge for agriculture in salt-affected regions. Future studies will focus on transferring the construct back into I. aquatica plants to assess its impact on enhancing salt tolerance, potentially contributing to sustainable crop production in adverse environmental conditions.

Biosurfactants are amphiphilic molecules with effective surface-active and biological properties applicable to replace synthetic surfactant in petroleum industry. Interest in microbial surfactants has been steadily increasing in recent years, as they have numerous advantages compared to chemical surfactants including a lower toxicity, better environmental compatibility and effective properties at extreme temperature, pH levels and salinity. A crude oil-degrading yeast strain (C. 1214-BK14) was selected among the isolated strains as a potential biosurfactant-producer from producing oil wells at White Tiger oilfield because of its ability to produce biosurfactant using crude oil as a sole carbon source. An emulsification index (E24%) of 57% was obtained initially by Candida tropicalis 1214-BK14 in previous study. Therefore, the optimization of biosurfactant production of this strain for enhanced crude oil degradation was carried out based on central composite design and analyzed using response surface methodology (RSM). The biosurfactant production process was investigated as function of three independent variables: crude oil (2.5-5 % w/v), (NH4)2SO4 (0.35-0.45% w/v), and solution pH (5-8). RSM analysis showed that the optimum condition for the biosurfactant production by C. tropicalis 1214-BK14 were 6.1, 3.97% (w/v) and 0.37% (w/v) for pH, concentration of carbon (crude oil) and nitrogen substrate ((NH4)2SO4), respectively, with the emulsification index measured in the conditions was 80.2%. The total crude oil and C10-C43 alkanes degradation efficiency by this strain estimated using GC/MS were 89.8% and 80.47-98.58%, respectively. These results revealed that the strain Candida tropicalis 1214-BK14 exhibited a tremendous potential for contaminated-crude oil degradation and microbial enhanced oil recovery (MEOR).

Mesenchymal stem cells (MSCs) have become an effective tool for treating immune-related diseases due to their multilineage potential and immunomodulatory capabilities. However, a high cell dose is frequently essential for stem cell infusion in clinical practice. Therefore, it is necessary to produce sufficient quantities of MSCs while ensuring cell quality for clinical application in humans. To be able to use stem cells in patients requires a more rigorous captive procedure than using a xeno-free medium that does not contain substances derived from the hypothetical allergenic regime. Therefore, current cell culture procedures substitute xeno-free culture media with added supplement serum for the traditional DMEM media with bovine fetal serum (FBS). This switch increased the production cost immensely and made it difficult to produce MSCs on an industrial scale. In this study, we optimized the condition of MSCs’ cultures by adjusting the amount of the supplement serum usage to reduce production costs for industrial manufacturing. This is the first study to claim that reducing the amount of xeno-free supplement serum had no effect on the quality of hUC-MSCs isolated from Vietnamese children’s umbilical cords.