Search Results (637)

Interactions between bacteria and bacteriophages are important for the maintenance of soil communities. In this study, we characterized the giant bacteriophages found within diverse soil bacteria and 14 additional phages isolated directly from soil samples. Based on their genome sizes and genetic composition, we concluded that these phages belong to the Dolichocephalovirinae subfamily. In addition, we used pulsed-field gel electrophoresis to show that the genomes of these phages were present as episomal pseudolysogens in the cytoplasm of their host cells. These findings suggest that episomal phages are important components of soil microbial ecosystems. Understanding the interactions between bacteriophages and bacteria is essential for microbial ecology, as they influence nutrient cycling, community composition, and host evolution. Furthermore, these phage-bacteria dynamics offer potential applications in plant disease control, as bacteriophages could serve as biocontrol agents against soilborne pathogens, promoting sustainable agricultural practices. Full article

Biofilm formation is important for microbial survival, adaptation, and persistence within mutualistic and pathogenic systems in the Vibironaceae. Biofilms offer protection against environmental stressors, immune responses, and antimicrobial treatments by increasing host colonization and resilience. This review examines the mechanisms of biofilm formation in Vibrio species, focusing on quorum sensing, cyclic-di-GMP signaling, and host-specific adaptations that influence biofilm structure and function. We discuss how biofilms differ between mutualistic and pathogenic species based on environmental and host signals. Recent advances in omics technologies such as transcriptomics and metabolomics have enhanced research in biofilm regulation under different conditions. Horizontal gene transfer and phase variation promote the greater fitness of bacterial biofilms due to the diversity of environmental isolates that utilize biofilms to colonize host species. Despite progress, questions remain regarding the long-term effects of biofilm formation and persistence on host physiology and biofilm community dynamics. Research integrating multidisciplinary approaches will help advance our understanding of biofilms and their implications for influencing microbial adaptation, symbiosis, and disease. These findings have applications in biotechnology and medicine, where the genetic manipulation of biofilm regulation can enhance or disrupt microbiome stability and pathogen resistance, eventually leading to targeted therapeutic strategies. Full article

Extracellular vesicles (EVs) are nanometer-sized lipid structures actively secreted by Gram-negative and Gram-positive bacteria, representing a sophisticated microbial adaptation and communication strategy. These structures are involved in biomolecular transport, the regulation of biological processes, the modulation of host–pathogen interactions, and adaptation to hostile environmental conditions. EVs also play a crucial role in virulence, antibiotic resistance, and biofilm formation. This review will explore the biogenesis, composition, and biological mechanisms of outer membrane vesicles (OMVs) secreted by Gram-negative bacteria and membrane vesicles (MVs) generated by Gram-positive bacteria. In detail, the modulation of EVs in response to antibiotic exposure will be addressed. The role of EV morpho-functional adaptations will be studied in antimicrobial resistance, the gene determinant spread, and survival in adverse environments. This study aims to provide a comprehensive overview of the EV role in bacterial physiology, highlighting their ecological, evolutionary, and biotechnological implications. An overview of the enzymes and proteins mainly involved in OMV-mediated resistance mechanisms will also be provided. These insights could open new perspectives for developing therapeutic strategies that counteract EV secretion and biotechnological applications, such as vaccines and drug delivery systems. Full article

Microbial transplantation represents a sustainable strategy to address productivity gaps in agricultural soils by transferring microbiomes that enhance nutrient cycling, pathogen suppression, and stress tolerance. This study evaluates whether probiotic consortia from high-yield soybean soils (donor soil) could improve crop performance in less productive fields (recipient soil). We developed a host-adapted inoculant from soybean rhizospheres grown in donor soil and applied it to seeds at five concentrations (0.25–10 g/kg seed) in recipient soil, with untreated controls for comparison. To assess crop-specific microbial recruitment, we prepared a parallel bean-derived inoculant under identical conditions. Through 16S rRNA sequencing and growth/yield analysis, we found the following: (1) Distinct bacteriome assemblies between soybean- and bean-derived inoculants, confirming host specificity; (2) Successful enrichment of beneficial taxa (Enterobacteriaceae increased by 15–22%, Rhizobiaceae by 7–12%) despite native community resilience; and (3) Consistent yield improvement trends (4.8–6.2%), demonstrating potential to bridge productivity gaps. These results show that transplanted microbiomes can effectively modulate rhizosphere communities while maintaining ecological balance. This work establishes a scalable approach to address soil productivity limitations through microbiome transplantation. Future research should optimize (a) inoculant composition for specific productivity gaps; (b) delivery systems; and (c) compatibility with resident microbiomes, particularly in systems where niche-specific processes govern microbial establishment. Full article

Plant-associated bacteria play a crucial role in protecting plants from pathogens, yet the diversity and antagonistic potential of these bacteria across different plant species remain underexplored, especially in central Asia. To investigate the competitive dynamics between phytopathogenic fungi and plant-associated bacteria, we collected stem and root samples from 50 plant species across nine regions of Uzbekistan. A total of 3355 bacterial isolates were obtained (1896 from roots and 1459 from shoots) and screened for antifungal activity against six fungal pathogens, resulting in 432 antagonistic isolates. These were identified through 16S rDNA sequencing, revealing 65 bacterial species across three phyla: Firmicutes, Proteobacteria, and Actinobacteria, predominantly in the respective families Bacillaceae, Pseudomonadaceae, and Caryophanaceae. The plant Salsola vvedenskii hosted the highest diversity of antagonists (26 species), while other species harbored fewer. Plant species showed strong associations with specific bacterial communities, with 14 plant species each hosting unique antagonists. Enzymatic profiling revealed functional diversity, with Bacillus species producing protease, cellulase, and lipase activities, while Pseudomonas species excelled in xylanase, glucanase, and cellobiase production. B. mojavensis 9r-29 stood out by producing all six enzymes. These findings underscore the ecological diversity and biocontrol potential of plant-associated bacteria in natural ecosystems, offering promising candidates for sustainable plant protection strategies. Full article

In ex situ conservation, gut bacteria and fungi play a crucial role in maintaining the intestinal microecological balance of the gut, and disruptions in this system may negatively impact host health. The South China tiger (Panthera tigris amoyensis) is a critically endangered tiger subspecies currently surviving under human-managed care and captive breeding programs, with only a small number of individuals remaining. Disruption in the gut microbiota, particularly the proliferation of pathogenic bacteria, can be fatal for cubs. This study analyzed the composition and seasonal changes of the gut bacterial and fungal communities of South China tigers in captive and semi-released environments during the winter of 2023 and the summer of 2024, using 16S rRNA and ITS high-throughput sequencing. The results showed that the dominant gut bacteria were Bacillota, Actinomycetota, Fusobacteriota, Pseudomonadota, and Bacteroidota. The abundance of Bacillota decreased in summer and was slightly lower in captive tigers than in semi-released tigers. Fungal communities were dominated by Ascomycota, with a negative correlation observed between Ascomycota and Basidiomycota. The abundance of Ascomycetes was lower in summer but significantly higher in semi-released tigers than in captive ones. Diversity analysis revealed no significant effects of the season or the environment on bacterial α-diversity, and fungal α-diversity was also not significantly affected by seasonal variation. However, microbial diversity increased under semi-free-range conditions, with fungal richness significantly higher than in captive environments (p < 0.01). Principal coordinate analysis (PCoA) based on Bray–Curtis distances revealed significant differences in the community structures of both bacterial (Adonis, R² = 0.2364, p = 0.001) and fungal (Adonis, R² = 0.1542, p = 0.001) communities across different seasons and environments. These findings provide valuable insights into the health management strategies and ecological adaptation of South China tigers. Full article

Infectious spleen and kidney necrosis virus (ISKNV) is an emerging viral pathogen with an expanding host range, posing a significant threat to economically important fish species. In this study, we isolated the ISKNV strain responsible for disease outbreaks in Asian seabass (Lates calcarifer) and analyzed the transcriptomic profile of spleen tissues from experimentally infected fish. The phylogenetic analysis confirmed that the virus belongs to clade I of ISKNV. Next-generation sequencing identified differentially expressed genes, providing a comprehensive overview of the transcriptional landscape in the spleen of ISKNV-infected fish. The pathway analysis revealed complex host–virus interactions, impacting immune regulation, endocytosis, cell communication, cell cycle arrest, and programmed cell death. To further investigate these interactions, we analyzed relevant pathways in the Reactome database for Asian seabass, humans, and zebrafish, constructed a protein–protein interaction (PPI) network using STRING database, and identified hub genes using six different algorithms. This analysis revealed 69 key genes, including 41 hub genes and 28 key genes that connect different pathways or clusters within the PPI network. These findings provide new insights into the molecular mechanisms driving ISKNV infection in Asian seabass. Future research should focus on elucidating the regulatory functions of these key genes and their roles in ISKNV pathogenesis. Full article

Endocytosis is a specialized transport mechanism in which the cell membrane folds inward to enclose large molecules, fluids, or particles, forming vesicles that are transported within the cell. It plays a crucial role in nutrient uptake, immune responses, and cellular communication. However, many pathogens exploit the endocytic pathway to invade and survive within host cells, allowing them to evade the immune system and establish infection. Endocytosis can be classified as clathrin-mediated (CME) or clathrin-independent (CIE), based on the mechanism of vesicle formation. Unlike CME, which involves the formation of clathrin-coated vesicles that bud from the plasma membrane, CIE does not rely on clathrin-coated vesicles. Instead, other mechanisms facilitate membrane invagination and vesicle formation. CIE encompasses a variety of pathways, including caveolin-mediated, Arf6-dependent, and flotillin-dependent pathways. In this review, we discuss key features of CIE pathways, including cargo selection, vesicle formation, routes taken by internalized cargo, and the regulatory mechanisms governing CIE. Many viruses and bacteria hijack host cell CIE mechanisms to facilitate intracellular trafficking and persistence. We also revisit the exploitation of CIE by bacterial and viral pathogens, highlighting recent discoveries in entry mechanisms, intracellular fate, and host-pathogen interactions. Understanding how pathogens manipulate CIE in host cells can inform the development of novel antimicrobial and immunomodulatory interventions, offering new avenues for disease prevention and treatment. Full article

The intestinal health and functionality of animals play pivotal roles in nutrient digestion and absorption, as well as in maintaining defense against pathogenic invasions. These biological processes are modulated by various determinants, including husbandry conditions, dietary composition, and gut microbial ecology. The excessive use of anthropogenic antibiotics may disrupt intestinal microbiota composition, potentially leading to dysbiosis that directly compromises host homeostasis. While Lactobacillus species are recognized for their immunomodulatory properties, their precise mechanisms in regulating host anti-inflammatory gene expression and influencing mucosal layer maturation, particularly regarding E. coli colonization resistance, require further elucidation. To investigate the regulatory mechanisms of Lactobacillus in relation to intestinal architecture and function during E. coli infection, we established a colonic infection model using Bal b/c mice, conducting systematic analyses of intestinal morphology, inflammatory mediator profiles, and microbial community dynamics. Our results demonstrate that Lactobacillus supplementation (Pediococcus acidilactici) effectively mitigated E. coli O78-induced enteritis, with co-administration during infection facilitating the restoration of physiological parameters, including body mass, intestinal histoarchitecture, and microbial metabolic functions. Microbiome profiling revealed that the Lactobacillus intervention significantly elevated Lactococcus abundance while reducing Weissella populations (p < 0.05), concurrently enhancing metabolic pathways related to nutrient assimilation and environmental signal processing (including translation mechanisms, ribosomal biogenesis, amino acid transport metabolism, and energy transduction systems; p < 0.05). Mechanistically, Lactobacillus administration attenuated E. coli-induced intestinal pathology through multiple pathways: downregulating pro-inflammatory cytokine expression (IL-1β, IL-1α, and TNF-α), upregulating epithelial junctional complexes (Occludin, Claudin-1, and ZO-1), and stimulating mucin biosynthesis (MUC1 and MUC2; p < 0.05). These modifications collectively enhanced mucosal barrier integrity and promoted epithelial maturation. This investigation advances our comprehension of microbiota–host crosstalk during enteropathogenic infections under probiotic intervention, offering valuable insights for developing novel nutritional strategies and microbial management protocols in animal husbandry. Full article

Community-acquired infections caused by Klebsiella pneumoniae (K. pneumoniae) have become a significant global health concern, particularly with the emergence of hypervirulent strains (hvKP). These strains are associated with severe infections, such as pyogenic liver abscesses, even in otherwise healthy individuals. Initially reported in Taiwan in the 1980s, hvKP has now spread worldwide. The pathogenicity of hvKP is attributed to an array of virulence factors that enhance its ability to colonize and evade host immune defenses. Additionally, the convergence of hypervirulence with antibiotic resistance has further complicated treatment strategies. As a member of the ESKAPE group of pathogens, K. pneumoniae exhibits high resistance to multiple antibiotics, posing a challenge for healthcare settings. This review provides a comprehensive overview of hvKP, highlighting its structural and pathogenic differences from classical K. pneumoniae strains, key virulence factors, mechanisms of antibiotic resistance, and the increasing threat of multidrug-resistant hvKP. Lastly, we discuss current treatment guidelines and emerging therapeutic strategies to combat this formidable pathogen. Full article

Objectives: The oral cavity hosts one of the most complex microbial communities in the body. A disruption of the balance favors the growth of pathogenic species, contributing to oral diseases. The rise in microbial resistance has limited the effectiveness of conventional treatments, shifting the interest to natural product-based alternatives. Given its superior bioavailability and bioactivity in other models, this study investigates the antifungal potential of a novel curcumin derivative, PAC (3,5-bis(4-hydroxy-3-methoxybenzylidene)-N-methyl-4-piperidone), and studies its impact on host–pathogen dynamics and host defense mechanisms. Methods: Candida albicans was used as the model organism. Viability, growth kinetics, and colony formation were evaluated using optical density, agar culture, and MTT assay. Biofilm formation was assessed through electron microscopy and total sugar quantification. The morphological transition from hyphae to the less virulent blastospore was monitored using an optical microscope. The gene expression of adhesion factors and host defense markers was analyzed using RT-PCR. Results: PAC impairs C. albicans viability and reduces virulence by compromising biofilm formation and ensuring phenotypic transition to a blastospore form. Also, PAC controls C. albicans growth via necrosis/ROS pathways. As a result, PAC appears to repress host–pathogen interaction by downregulating SAPs, EAP1, and HWP1 adhesion genes, thus relieving the need to activate gingival epithelial cell defense mechanisms. This is highlighted by recording baseline levels of IL-6, IL-8, and IL-1β cytokines and antimicrobial β-defensin peptides in the presence of less virulent candida forms. Conclusions: PAC effectively reduces C. albicans virulence by limiting biofilm formation and adhesion while minimizing inflammatory responses. These findings support its potential as a promising therapeutic agent for infectious disease control. Full article

Bacterial pathogens have evolved diverse strategies to infect hosts, evade immune responses, and establish successful infections. While the role of transcription factors in bacterial virulence is well documented, emerging evidence highlights the significant contribution of small regulatory RNAs (sRNAs) in bacterial pathogenesis. These sRNAs function as posttranscriptional regulators that fine-tune gene expression, enabling bacteria to adapt rapidly to challenging environments. This review explores the multifaceted roles of bacterial sRNAs in host–pathogen interactions. Firstly, it examines how sRNAs regulate pathogenicity by modulating the expression of key virulence factors, including fimbriae, toxins, and secretion systems, followed by discussing the role of sRNAs in bacterial stress response mechanisms that counteract host immune defenses, such as oxidative and envelope stress. Additionally, this review investigates the involvement of sRNAs in antibiotic resistance by regulating efflux pumps, biofilm formation, and membrane modifications, which contribute to multi-drug resistance phenotypes. Lastly, this review highlights how sRNAs contribute to intra- and interspecies communication through quorum sensing, thereby coordinating bacterial behavior in response to environmental cues. Understanding these regulatory networks governed by sRNAs is essential for the development of innovative antimicrobial strategies. This review highlights the growing significance of sRNAs in bacterial pathogenicity and explores their potential as therapeutic targets for the treatment of bacterial infections. Full article

The breeding of large animals in the family Cervidae in China contributes to achieving two tasks: restoring the provenance of wild populations and providing raw materials for traditional Chinese medicine. Currently, red deer (Cervus elaphus), sika deer (C. nippon), and white-lipped deer (C. albirostris) maintain a large number of breeding populations. Some studies on the relationship between the intestinal microbiota and the feed of these deer have been conducted; however, owing to differences in feeding conditions between studies, it has been impossible to compare the intestinal microecology and related adaptability between species. Therefore, the present study is aiming to investigate whether the differences in intestinal microbiota of the three deer species are related to the distance of phylogenetic relationships under the same feeding environment. On this basis, we discuss whether there are differences in the adaptability of the intestinal microbiota of the three deer species to feed nutrients, deepen the understanding of the relationship between the three deer intestinal microbiota and feed nutrition, and provide basic data for improving the scientific feeding of the three deer species. In this study, 16S rRNA high-throughput sequencing technology was utilized to analyze the intestinal microbiota in feces of the abovementioned healthy deer species. The results of this study indicated that the intestinal microbiota diversity and relative abundance in female white-lipped deer (FWLD) were significantly lower than those in female sika deer (FSD) and female red deer (FRD; p < 0.05); however, there was no significant difference between the latter two groups (p > 0.05). The community compositions of the intestinal microbiota in FSD and FRD were more similar, whereas that of FWLD was significantly different from those of the first two groups. Firmicutes and Bacteroidetes were the most abundant phyla in the intestinal microbiota of all three deer species, and Ruminococcceae_UCG-005 was the most abundant genus. No known obligatory pathogenic bacteria were observed in any sample. The relative abundance of the operational taxonomic units Christensenellaceae_R-7_group, Treponema_2, and Akkermansia exhibited significant differences among FSD, FRD, and FWLD, respectively. Therefore, the phylogenetic relatedness of the three deer species appears to play a major role in their intestinal microecology under the same feeding conditions—the greater the phylogenetic relatedness between hosts, the more similar is their intestinal microbiota. In addition, the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) function prediction results indicated that FSD were less capable than FRD and FWLD in the functional category of nutrient metabolism, and FWLD were less capable than FSD and FRD in the functional category of intestinal absorption. These results indicated that there may be differences in the nutritional adaptation abilities of the three deer species under different feeding conditions. In summary, these results revealed the differences in intestinal microbiota among the three deer species under the same food conditions, indicating that the intestinal microbiota of the three deer species had significant differences in food adaptation. Based on this, the nutritional supply of feed for the three deer should consider the species differences. Full article

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a foodborne pathogen that causes a variety of diseases, ranging from self-limiting gastroenteritis to life-threatening extra-intestinal diseases such as hemolytic uremic syndrome. EspF, an effector protein secreted by the type III secretion system of EHEC, is primarily responsible for the development of inflammatory colitis. Our previous study revealed that EspF interacts with the host Annexin A6 (ANXA6) protein and targets the endoplasmic reticulum (ER). Given the critical effects of ER stress on the host responses of gastroenteritis, we explored the role of EspF–ANXA6 interaction in ER stress. Caco-2 cells were infected with different strains of EHEC and transfected with modified plasmids to establish in vitro research models. Our results revealed that infection with espF-deletion EHEC strains significantly exacerbated ER stress. Specifically, the phosphorylation of eIF2α was elevated, and the expression levels of BiP, ATF4, and CHOP were increased by more than 15% compared to those in cells infected with wild-type EHEC strains. Further experiments showed that EspF co-localizes with BiP and down-regulates the PERK pathway. Meanwhile, the EspF–ANXA6 interaction could aggravate the inhibition of the PERK pathway and stimulate calcium influx to disturb ER homeostasis, eventually leading to apoptosis. Our findings suggest that the EspF–ANXA6 interaction could inhibit ER stress through the PERK pathway, which may limit cell-to-cell communication and block the clearance of bacteria in host cells. Full article

Fusarium graminearum is one of the most important pathogenic fungi with a wide range of plant and animal hosts. This study investigated the effects of F. graminearum infection on the rhizosphere microbiota and growth of two barley (Hordeum vulgare L.) cultivars, Baudin and Kenpi 7, and explored microbiota transplantation as a strategy to enhance disease resistance. By exchanging surface microbiotas between varieties and analyzing rhizosphere bacterial communities using 16S rRNA sequencing, researchers observed that F. graminearum infection increased bacterial diversity and abundance, especially in Baudin barley. Growth indicators (root length, plant height, fresh/dry mass) also exhibited that Baudin barley showed stronger resistance. Functional analysis underscored that the microbial community composition of Baudin barley promoted metabolic pathways related to plant resilience and was associated with improved seedling health. In contrast, Kenpi 7 barley showed weaker resistance, emphasizing the role of seed-specific microbiotas in pathogen defense. An effective antagonistic strain, Bacillus amyloliquefaciens B1, was isolated from Baudin barley, and its inhibition rate against F. graminearum was 80%. The results showed that microbiota transplantation enhanced the disease resistance of low-diversity seeds, and identified B. amyloliquefaciens B1 as a promising biocontrol agent, providing a potential application for sustainable agriculture and reducing dependence on chemical fungicides. This study highlights the importance of seed-associated microbial communities in plant–pathogen interactions and provides a basis for the development of microbiota-based strategies to mitigate crop diseases. Full article