Search Results (1,285)

Studying marine Actinobacteria across ecological niches is essential for discovering novel natural products and understanding microbial interactions. In this study, we investigated the diversity of Actinobacteria associated with five Arctic marine invertebrates using both selective culture-based techniques and culture-independent methods. Additionally, we investigated bacteria–bacteria interactions in an advanced high-throughput co-cultivation assay. We isolated 25 Actinobacteria and classified them into 15 genera, with 53% of the isolates recovered from the sponge Halichondria panicea. In contrast, metabarcoding revealed a high diversity of Actinobacteria, with Chlamys islandica exhibiting the highest uniqueness of Amplicon Sequence Variants (ASVs), as 21.76% of its ASVs were found exclusively in this species. Similarly, not only did Dendrobeania sp. and Tricellaria ternata display notable levels of unique ASVs at 19.91% and 18.06%, respectively, they also shared 17.74% of ASVs, demonstrating a greater similarity in their microbial communities than between more distantly related hosts. A variety of microbial interactions were observed on solid medium, including both cooperative and antagonistic relationships, using the co-cultivation assay. These included inter- and intra-Actinobacteria interactions, as well as interactions with human pathogenic bacteria. The duration of co-cultivation and the physical proximity of bacterial partners influenced the extent of these interactions. Full article

Cyclic di-GMP (c-di-GMP), a universal second messenger in bacteria, orchestrates a wide array of essential life processes. Its intracellular dynamics are meticulously regulated by diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), ensuring precise spatiotemporal control. The functional output of c-di-GMP signaling hinges on effector proteins—molecular decoders that translate c-di-GMP signals into specific cellular responses. This review systematically examines diverse classes of c-di-GMP effectors, using several representative bacterial species as model systems, to dissect their structural and mechanistic diversity. Particular emphasis is placed on their pivotal roles in bacterial pathogenicity, antibiotic tolerance, and host–pathogen interactions, offering fresh insights into the regulatory mechanisms underlying c-di-GMP signaling. Full article

Periodontitis is a globally prevalent oral disease and is closely associated with various systemic diseases. Periodontitis arises from dynamic and complex interactions between polymicrobial communities and host immune responses. Extracellular vesicles (EVs) are circulating subcellular particles carrying multiple signaling molecules. EVs play a key role in intercellular communication, and hold promise for diagnostic and therapeutic purposes. Bacterial extracellular vesicles (BEVs), released from oral pathogens, have been implicated in delivering virulence factors to host cells. In contrast, host cell-derived EVs (CEVs), secreted by periodontal cells, contain molecular cargo that reflect disease status. Both BEVs and CEVs contribute to periodontitis progression by exacerbating inflammation and tissue destruction, and they may also influence related systemic diseases. Moreover, the molecular components of EVs derived from saliva and gingival crevicular fluid (GCF) show potential as diagnostic biomarkers for periodontitis. In addition, mesenchymal stem cell-derived EVs (MSC-EVs) exhibit therapeutic potential in periodontitis, and engineering approaches have been developed to enhance their therapeutic efficacy and accelerate clinical translation. This review summarizes recent advances in understanding the pathogenic, diagnostic, and therapeutic roles of EVs in periodontitis and discusses current challenges and future directions toward their clinical application. Full article

Wound healing is a dynamic process involving distinct phases that are regulated by cellular and molecular interactions. This review explores the fundamental mechanisms involved in wound healing, including the roles of cytokines and growth factors within the local microenvironment, with a particular focus on antimicrobial peptides (AMPs) as immune modulators and therapeutic agents in chronic wounds. Notably, AMPs such as LL-37 have been shown to reduce biofilm density by up to 60%, highlighting their dual role in both modulating host immune responses and combating persistent bacterial infections. It further examines emerging technologies that are transforming the field, extending beyond traditional biological mechanisms to innovations such as smart dressings, 3D bioprinting, AI-driven therapies, regenerative medicine, gene therapy, and organoid models. Additionally, the review addresses strategies to overcome bacterial biofilms and highlights promising approaches including biomaterials, nanomedicine, gene therapy, peptide-loaded nanoparticles, and the application of organoids as advanced platforms for studying and enhancing wound repair. Full article

Defensins are a class of small cysteine-rich cationic antimicrobial peptides (AMPs) that play vital roles in immune-regulating insect–microbe interaction, offering great potential for developing pest control approaches using RNA interference (RNAi) and insect pathogens. However, the biocontrol potential of defensins from the destructive rice pest Nilaparvata lugens (brown planthopper, BPH) remains largely unexplored. Here, we identified and functionally characterized a defensin-encoding gene NldefB in BPH. The open reading frame (ORF) of NldefB is 315 bp in length, encoding 104 amino acids with a conserved Knot1 domain. The qRT-PCR results showed that the transcription level of NldefB went upward with the increasing developmental stages, with the highest expressions in the female adults and their fat body. The expression of NldefB was continuously induced by bacterial pathogens but exhibited a pattern of initial increase followed by a decrease when challenged by a fungal pathogen Metarhizium anisopliae. RNAi-mediated silencing of NldefB significantly decreased the host survival rate, egg production and hatchability, as well as the capability to resist fungal infection. Additionally, NldefB suppression resulted in a significant increase in microbial loads. Our findings underscored that NldefB plays essential roles in regulating host development, pathogen defense, and microbial maintenance, providing a potential target for RNAi- and microbe-mediated BPH biocontrol. Full article

Background: Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options and poor clinical outcomes. Emerging evidence suggests that the tumor-associated microbiome may influence disease progression and therapy response. Methods: We investigated how the Gram-negative bacterium Pseudomonas aeruginosa and Gram-positive bacterium Staphylococcus aureus, together with their cell wall components lipopolysaccharide (LPS) and lipoteichoic acid (LTA), modulate doxorubicin (DOX) efficacy in TNBC cells. Using gentamicin protection combined with flow cytometry of eFluor 450-labeled bacteria and CFU quantification, we assessed bacterial uptake, persistence, and effects on drug response in MDA-MB-468, MDA-MB-231, and MDA-MB-453 cells. Results: Both bacteria entered TNBC cells and survived for several days in a cell line-dependent manner. Notably, bacterial infection and purified cell wall ligands (LPS and LTA) significantly increased DOX accumulation and enhanced cytotoxicity in MDA-MB-468 and MDA-MB-231, but not in MDA-MB-453. The similar effects of LPS and LTA implicate Toll-like receptor signaling (TLR2 and TLR4) in modulating drug uptake. Conclusions: These findings demonstrate that bacterial infection and associated ligands can enhance doxorubicin uptake and cytotoxicity in TNBC cells, implicating TLR signaling as a potential contributor. Our results highlight the importance of host–microbe interactions in shaping chemotherapy response and warrant further investigation into their therapeutic relevance. Full article

Antimicrobial peptides (AMPs), also referred to as host defense peptides, are promising molecules in the development of the next generation of antibiotics against drug-resistant bacterial pathogens. Thanatin comprises a family of naturally occurring cationic AMPs derived from several species of insects. The first thanatin, 21 residues long, was identified from the spined soldier bug, and more thanatin peptides have been discovered in recent studies. The 16-residue thanatin from Anasa tristis, or Ana-thanatin, represents the shortest sequence in the family. However, the antimicrobial activity and mechanistic process underpinning bacterial cell killing have yet to be reported for Ana-thanatin peptide. In this work, we examined the antibacterial activity, structures, and target interactions of Ana-thanatin. Our results demonstrated that Ana-thanatin exerts potent antibiotic activity against strains of Gram-negative and Gram-positive bacteria. Biophysical studies demonstrated that Ana-thanatin interacts with LPS outer membrane and can permeabilize the OM barrier in the process. Atomic-resolution structures of the peptide in free solution and in complex with lipopolysaccharide (LPS) micelle were solved by NMR, determining canonical β-sheet structures. Notably, in complex with LPS, the β-sheet structure of the peptide was better defined in terms of the packing of amino acid residues. Further, MD simulations demonstrated rapid binding of the Ana-thanatin peptide with the LPS molecules within the lipid bilayers. These studies have revealed structural features which could be responsible for LPS-OM disruption of the Gram-negative bacteria. In addition, NMR heteronuclear single quantum coherence (HSQC) studies have demonstrated that Ana-thanatin can strongly interact with the LPS transport periplasmic protein LptA_m, potentially inhibiting OM biogenesis. Taken together, we surmise that the Ana-thanatin peptide could serve as a template for the further development of novel antibiotics. Full article

Postpartum uterine diseases such as metritis and endometritis impair reproductive performance and cause substantial economic losses in dairy cows worldwide. The multifactorial etiology, involving polymicrobial infections and complex host immune responses, poses diagnostic and therapeutic challenges. Traditional treatments rely on antibiotics, e.g., cephalosporins like ceftiofur and cephapirin, with broad-spectrum efficacy. However, emerging antimicrobial resistance, biofilm formation by pathogens such as Trueperella pyogenes, Fusobacterium necrophorum, and Escherichia coli, and bacterial virulence factors have reduced effectiveness of conventional therapies. Advances in systems biology, particularly proteomics, metabolomics, and microRNA (miRNA) profiling, have provided unprecedented insights into the molecular mechanisms underpinning uterine disease pathophysiology. Proteomic analyses reveal dynamic changes in inflammatory proteins and immune pathways, whereas metabolomics highlight shifts in energy metabolism and bacterial–host interactions. Furthermore, miRNAs have critical roles in post-transcriptional gene regulation affecting immune modulation, inflammation, and tissue repair, and also in modulating neutrophil function and inflammatory signaling. Uterine inflammation not only disrupts local tissue homeostasis but also compromises early embryo development by altering endometrial receptivity, cytokine milieu, and oocyte quality. Integration of multi-omics approaches, combined with improved diagnostics and adjunct therapies—including micronutrient supplementation and immunomodulators—offers promising avenues for enhancing disease management and fertility in dairy herds. This review synthesizes current knowledge on proteomics, metabolomics, and miRNAs in postpartum uterine diseases and highlights future directions for research and clinical applications. Full article

Ochratoxin A (OTA) is a widespread foodborne mycotoxin that poses significant risks to both human and animal health. Upon ingestion, the gastrointestinal tract (GIT) becomes the main site of exposure, where OTA interacts directly with the intestinal epithelium and resident microbiota. Research indicates that OTA disrupts the integrity of the intestinal barrier and alters its permeability. Moreover, OTA undergoes transport and partial metabolism within the intestine before being excreted. Detoxification pathways for OTA include enzymatic degradation and adsorption by microorganisms. Notably, OTA has profound toxic effects on the gut ecosystem; it can alter the relative abundance of bacterial taxa by reducing beneficial populations and promoting opportunistic or pathogenic strains. These changes contribute to an imbalance in the microbiota, impairing host metabolic and immune functions. This dysbiosis is characterized by disrupted microbial homeostasis and impaired communication between the host and its gut microbiome. This review highlights the dual role of the intestine as both a target and a modulator of OTA toxicity. It emphasizes the importance of gut microbiota in mediating the toxicological outcomes of OTA and explores microbiome-based strategies as potential avenues for detoxification. Full article

Age-related impaired wounds often become infected with bacteria, leading to substantial mortality and morbidity in the elderly. The decline in androgen levels with increasing age is believed to exacerbate inflammation during wound infections. Despite its well-documented anti-inflammatory activities in wound repair, little is known about the effect of age-related androgen deprivation on bacterial phagocytosis in impaired chronic wounds. The aim of this study was to investigate the effect of age-related testosterone deprivation on the phagocytic functions of THP-1 monocyte-derived macrophages to eliminate Gram-positive and Gram-negative bacteria in vitro. Host–pathogen interaction experiments were conducted to quantify the macrophage-mediated clearance of two common wound-associated bacteria, methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa, under in vitro environments that model testosterone levels representative of those found in elderly males, healthy young adults and testosterone replacement therapy (TRT). Testosterone and its metabolite 5α-dihydrotestosterone (DHT) significantly dampened the macrophage-mediated phagocytosis of both MRSA and P. aeruginosa in a dose-dependent manner (p < 0.05). Blockade of the androgen receptor (AR) using enzalutamide confirmed that testosterone mediates bacterial clearance through binding to the AR. Blocking the conversion of testosterone to DHT through stimulation of macrophages with the 5-α-reductase inhibitor finasteride reversed the testosterone-mediated effects on bacterial clearance, which confirmed that testosterone could potentially dampen the innate phagocytic responses in macrophages through conversion to DHT. Novel findings in this study suggest that the selective manipulation of the AR and/or blockade of testosterone–DHT conversion may provide effective therapeutic treatments to combat wound infections in the elderly. Full article

Background: Porcine reproductive and respiratory syndrome virus (PRRSV) causes significant economic losses for the global swine industry. Gilt immunization using modified live virus (MLV) vaccines is crucial for herd stability, but it is complicated by frequent mixed infections of PRRSV strains on farm. This study monitored the administration of tylvalosin during a PRRSV-2 MLV (TJM) immunization program, focusing on viral dynamics and immune responses in gilts naturally exposed to co-circulating classical (GD240101) and highly pathogenic like (HP-PRRSV-like, GD240102) PRRSV strains. Methods: The animal study was approved by the Laboratory Animal Ethical Committee of China Agricultural University. One hundred gilts were randomized into control and tylvalosin groups (n = 50/group). All received the TJM MLV vaccination. The tylvalosin group received tylvalosin tartrate premix cyclically in-feed for three cycles. Serum and saliva samples were collected periodically. PRRSV RNA (RT-qPCR) and specific antibodies (ELISA) were assessed. Viral population dynamics (relative abundance, mutation, recombination of TJM, GD240101, and GD240102) were monitored via next-generation sequencing (NGS) on a pooled PRRSV-positive sample. Results: In this field trial where tylvalosin was used, a shorter duration of PRRSV viremia and saliva shedding was observed to compare with controls. NGS analysis showed accelerated vaccine strain (TJM) clearance in the tylvalosin group (by week 3 vs. week 9 in control). Field strain dynamics were also altered, showing a faster decline in the tylvalosin group. Antibody response uniformity was altered, with lower coefficient of variation (CV) for PRRSV and CSFV observed following tylvalosin usage. Conclusions: In gilts receiving tylvalosin for the management of bacterial pathogens during a PRRSV MLV immunization program, it was associated with accelerated viral clearance and enhanced systemic immune response uniformity under mixed-infection field conditions. NGS provides invaluable data for dissecting these complex viral dynamics. Crucially, these findings describe a biological drug–host–virus interaction and should not be interpreted as an endorsement for the prophylactic use of antimicrobials. In alignment with global antimicrobial stewardship principles, tylvalosin should be reserved for the therapeutic treatment of diagnosed bacterial diseases to mitigate the risk of promoting resistance. Full article

The growing threat of Antimicrobial Resistance (AMR) demands innovative drug discovery, yet conventional 2D cell cultures fail to accurately mimic in vivo conditions, leading to high failure rates in preclinical studies. This review addresses the critical need for more physiologically relevant platforms by exploring recent advancements in bioengineered 3D tissue models for studying bacterial pathogenesis and antimicrobial drug discovery. We conducted a systematic search of peer-reviewed articles from 2015 to 2025 across PubMed, Scopus, and Web of Science, focusing on studies that used 3D models to investigate host–pathogen interactions or antimicrobial screening. Data on model types, biomaterials, fabrication techniques, and key findings were systematically charted to provide a comprehensive overview. Our findings reveal that a diverse range of biomaterials, including biopolymers and synthetic polymers, combined with advanced techniques like 3D bioprinting, are effectively used to create sophisticated tissue scaffolds. While these 3D models demonstrate clear superiority in mimicking biofilm properties and complex host–pathogen dynamics, our analysis identified a significant research gap: very few studies directly integrate these advanced bioengineered 3D models for high-throughput antimicrobial drug discovery. In conclusion, this review highlights the urgent need to bridge this disparity through increased research, standardization, and scalability in this critical interdisciplinary field, with the ultimate goal of accelerating the development of new therapeutics to combat AMR. Full article

Forest ecosystems undergo seasonal shifts in bacterial and fungal communities, but little is known about the specific microbiota associated with Quercus robur–Boletus edulis systems. This study represents the first examination of seasonal changes in soil microbiota in pedunculate oak habitats in Galicia (NW Spain) and their relationship with Boletus edulis and Boletus reticulatus mycelium prevalence and concentration. Soil microbiota richness, diversity, and composition, as well as seasonal variation in Boletus mycelium, were assessed using DNA metabarcoding and qPCR, respectively. Sampling was conducted in autumn at two 30–40-year-old Q. robur stands. Bacterial communities were dominated by Acidobacteria (34%) and Proteobacteria (33%), with Acidobacterium (12%), Paludibaculum (9%), and Edaphobacter (7%) identified as most abundant. Fungal communities were primarily Basidiomycota (93%), led by Russula (46%). For both bacteria and fungi, the highest OTU richness was observed in September, followed by a significant decrease in October and a partial recovery in November. Boletus species were found to exhibit positive correlations with specific bacteria (e.g., Massilia, Rhizobium) and fungi (e.g., Amanita, Clavaria, Inocybe, Scleroderma, Suillus and Mortierella), suggesting a potential influence of these microbes on mycelium development. This study provides novel insights into the seasonal dynamics of soil microbiota and their potential role in Boletus ecology, thereby advancing understanding of host–microbe interactions in temperate forests. Full article

Bacteriophages, or phages, are sophisticated nanomachines that efficiently infect bacteria. Their infection of lactic acid bacteria (LAB) used in fermentation can lead to significant industrial losses. Among phages that infect monoderm bacteria, those with siphovirion morphology characterized by a long, non-contractile tail are predominant. The initial stage of phage infection involves precise host recognition and binding. To achieve this, phages feature host adhesion devices (HADs) located at the distal end of their tails, which have evolved to recognize specific proteinaceous or saccharidic receptors on the host cell wall. Ceduovirus represents a group of unique lytic siphophages that specifically infect the LAB Lactococcus lactis by targeting proteinaceous receptors. Despite having compact genomes, most of their structural genes are poorly annotated and the architecture and function of their HADs remain unknown. Here we used AlphaFold3 to explore the Ceduovirus HADs and their interaction with the host. We show that Ceduovirus HADs exhibit unprecedented features among bacteriophages infecting Gram⁺, share structural similarities with bacterial secretion system VI, and combine both saccharide and protein-binding modules. Moreover, we could annotate the majority of Ceduovirus genes encoding structural proteins by leveraging their predicted structures, highlighting AlphaFold’s significant contribution to phage genome annotation. Full article

Population stratification based on gut microbiota composition has revealed several enterotypes in humans and animals, providing valuable tools for studying the gut microbiota landscape, which is crucial for animal health and production. However, knowledge about rumen enterotype identification in sheep, its influencing factors, and its association with growth performance and host genetics remains limited. Here, we investigated host genetic effects and phenotypic landscapes of rumen bacterial enterotypes in a large sheep population. Ruminal contents from 1150 healthy sheep were analyzed using 16S rRNA gene sequencing and genus-level clustering, complemented by extensive phenotypic data covering 47 traits spanning growth, feed efficiency, meat yield, and ruminal fermentation, along with whole-genome resequencing data. We identified two distinct enterotypes: Enterotype 1 (E1), a mixture of multiple genera, and Enterotype 2 (E2), dominated by Prevotella. E2 sheep exhibit superior growth and meat production performance, but lower feed efficiency and increased fat deposition. Two-part beta-regression models and co-occurrence network analyses revealed the extensive impact of enterotypes on microbial community structure, with E1 displaying a higher frequency of unique bacterial interactions. The estimated heritability of the enterotype was 0.47, and a GWAS identified five key genetic markers associated with rumen enterotype, localized to two candidate genes: CHODL and ENPP6. These markers significantly influence 58 ruminal bacterial genera, including key taxa and driving genus. Overall, our data provide new insights into sheep rumen-enterotype characteristics, contributing to a better understanding of microbial interactions that are crucial for improving ruminant growth performance. Full article